cdk-commits
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From: <noreply@gi...> - 2011-02-15 15:23:24
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Branch: refs/heads/13-unsorted-patches Home: https://github.com/cdk/cdk Commit: 96785a62f1e0c1bebdece5500b507666a925de38 https://github.com/cdk/cdk/commit/96785a62f1e0c1bebdece5500b507666a925de38 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderbasic.cdkdepends A src/META-INF/renderbasic.libdepends A src/META-INF/test-renderbasic.cdkdepends A src/META-INF/test-renderbasic.devellibdepends A src/META-INF/test-renderbasic.libdepends A src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java A src/main/org/openscience/cdk/renderer/elements/AtomSymbolElement.java A src/main/org/openscience/cdk/renderer/elements/ElementGroup.java A src/main/org/openscience/cdk/renderer/elements/LineElement.java A src/main/org/openscience/cdk/renderer/elements/OvalElement.java A src/main/org/openscience/cdk/renderer/elements/PathElement.java A src/main/org/openscience/cdk/renderer/elements/RectangleElement.java A src/main/org/openscience/cdk/renderer/elements/RingElement.java A src/main/org/openscience/cdk/renderer/elements/TextGroupElement.java A src/main/org/openscience/cdk/renderer/elements/WedgeLineElement.java A src/main/org/openscience/cdk/renderer/font/AWTFontManager.java A src/main/org/openscience/cdk/renderer/font/AbstractFontManager.java A src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicGenerator.java A src/main/org/openscience/cdk/renderer/generators/RingGenerator.java A src/main/org/openscience/cdk/renderer/selection/AbstractSelection.java A src/test/org/openscience/cdk/coverage/RenderbasicCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java Log Message: ----------- Setting up the new renderbasic module. * builds on the infrastructure defined in the render module * defines a basic renderer around an IAtomContainer data structure * new test framework including coverage testing Patches derived from: http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/branches/jchempaint-primary/ Commit: 40d743777761e97eeb9d0edc5393ff358cb47222 https://github.com/cdk/cdk/commit/40d743777761e97eeb9d0edc5393ff358cb47222 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/BoundsCalculator.java Log Message: ----------- Added the BoundsCalculator Commit: 82a77825b6c297c84de9efe91e42b212040729e5 https://github.com/cdk/cdk/commit/82a77825b6c297c84de9efe91e42b212040729e5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for IBond.Stereo Commit: 348a0c81c3648bac13f26ba47ca3e0fd040ccd6c https://github.com/cdk/cdk/commit/348a0c81c3648bac13f26ba47ca3e0fd040ccd6c Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/elements/GeneralPath.java A src/main/org/openscience/cdk/renderer/elements/path/Close.java A src/main/org/openscience/cdk/renderer/elements/path/CubicTo.java A src/main/org/openscience/cdk/renderer/elements/path/LineTo.java A src/main/org/openscience/cdk/renderer/elements/path/MoveTo.java A src/main/org/openscience/cdk/renderer/elements/path/PathBuilder.java A src/main/org/openscience/cdk/renderer/elements/path/PathElement.java A src/main/org/openscience/cdk/renderer/elements/path/QuadTo.java A src/main/org/openscience/cdk/renderer/elements/path/Type.java Log Message: ----------- Added new path element to describe more general paths see java.awt.geom.GeneralPath or org.eclipse.swt.graphics.Path Commit: c6c49f45698af4d977a5bfd511347f0b6610bbde https://github.com/cdk/cdk/commit/c6c49f45698af4d977a5bfd511347f0b6610bbde Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/renderbasic.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c009eba9f1a7d42ad76439fb8d598391f81e80f5 https://github.com/cdk/cdk/commit/c009eba9f1a7d42ad76439fb8d598391f81e80f5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the new IGeneratorParameter interfaces Commit: fd6dbf047f17942cbf8e8a4e438ec1d139f1d3fe https://github.com/cdk/cdk/commit/fd6dbf047f17942cbf8e8a4e438ec1d139f1d3fe Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: dcb922853c907e191e5311ad8adc6db4a0586d7e https://github.com/cdk/cdk/commit/dcb922853c907e191e5311ad8adc6db4a0586d7e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 0e3fb77f3bf6cf6360d116277a85d3401235ec62 https://github.com/cdk/cdk/commit/0e3fb77f3bf6cf6360d116277a85d3401235ec62 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- BasicBondGenerator should generate bonds in consistent order Commit: d7f0fa2ac16ce26e7283bff2fb53be6bf077f12b https://github.com/cdk/cdk/commit/d7f0fa2ac16ce26e7283bff2fb53be6bf077f12b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator Commit: 04a52c43df549ea79481161babc0f412a683827b https://github.com/cdk/cdk/commit/04a52c43df549ea79481161babc0f412a683827b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Moved rendering parameters for atom draw colors to the new IGeneratorParameter API Commit: 43d60d474fb594c22d464cbd925043bbf1b741bd https://github.com/cdk/cdk/commit/43d60d474fb594c22d464cbd925043bbf1b741bd Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Moved the atom radius into the new rendering parameter API (renderbasic module) Commit: b492a0396016806e1c1de97026642883856f92ec https://github.com/cdk/cdk/commit/b492a0396016806e1c1de97026642883856f92ec Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Set up a API to retrieve a IRenderingParameter from the RenderModel Commit: 4b09852a913bdea3839147c97b28dfc4fbf5959f https://github.com/cdk/cdk/commit/4b09852a913bdea3839147c97b28dfc4fbf5959f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Fixed returning of parameters Commit: fc44e2ea0ec2d255a52059dbe5af97934c4ac692 https://github.com/cdk/cdk/commit/fc44e2ea0ec2d255a52059dbe5af97934c4ac692 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- some double bonds were rendered as wedge Signed-off-by: Arvid Berg <goglepox@...> Commit: 99fc5de1e836a7c0bc342dcb28803c2bf18ccd26 https://github.com/cdk/cdk/commit/99fc5de1e836a7c0bc342dcb28803c2bf18ccd26 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Removed last four rendering parameters from BasicAtomGenerator: isCompact, compactShape, isKekule, and showEndCarbons Commit: 0250c9a116802f260bd92ca65d299841de3f03d2 https://github.com/cdk/cdk/commit/0250c9a116802f260bd92ca65d299841de3f03d2 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Converted bondWidth and defaultBondColor into IGeneratorParameter's Commit: f0d26f61e57e13070858da7a9d37b7abecda5506 https://github.com/cdk/cdk/commit/f0d26f61e57e13070858da7a9d37b7abecda5506 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RingGenerator.java Log Message: ----------- Converted showAromaticity and cdkStyleAromaticity to IGeneratorParameter variants Commit: 16dc479b7eb705c913408af54955ba5e33b034c8 https://github.com/cdk/cdk/commit/16dc479b7eb705c913408af54955ba5e33b034c8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Added missing parameter from returned list Commit: 969069f81ef1b7ef4e076ae39f0b5bdc28786367 https://github.com/cdk/cdk/commit/969069f81ef1b7ef4e076ae39f0b5bdc28786367 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RingGenerator.java Log Message: ----------- Converted ringProportion to IGeneratorParameter variants Commit: a02222e6d5bf4a7df75ad406ed044659c1f0a5d1 https://github.com/cdk/cdk/commit/a02222e6d5bf4a7df75ad406ed044659c1f0a5d1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted margin into the RenderingParameter variant Commit: ac593945f6129c3b2441ec2d018b62d0b5d5115f https://github.com/cdk/cdk/commit/ac593945f6129c3b2441ec2d018b62d0b5d5115f Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/test/org/openscience/cdk/renderer/ElementUtility.java A src/test/org/openscience/cdk/renderer/RendererTest.java A src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java A src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java A src/test/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java Log Message: ----------- A few test classes for the renderer package Commit: d17253afb597bf10140ddbcca9b8b03573778208 https://github.com/cdk/cdk/commit/d17253afb597bf10140ddbcca9b8b03573778208 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/RendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Copyright headers Commit: 2a86908fc73006e8972de92ef8c01210aead6662 https://github.com/cdk/cdk/commit/2a86908fc73006e8972de92ef8c01210aead6662 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/RendererTest.java Log Message: ----------- Cleaned up unit test a bit: * added missing assertion * removed uncommented ugly hacks * use AtomContainerRenderer from this module, not Renderer from renderextra Commit: dc0b6855c3447a6fc6380ed3c88fdff1e61ee882 https://github.com/cdk/cdk/commit/dc0b6855c3447a6fc6380ed3c88fdff1e61ee882 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java R src/test/org/openscience/cdk/renderer/RendererTest.java Log Message: ----------- Renamed into AtomContainerRendererTest, following common naming patterns Commit: 4eab24a2fbf509711425dc51be95850f9f8ea54e https://github.com/cdk/cdk/commit/4eab24a2fbf509711425dc51be95850f9f8ea54e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java Log Message: ----------- Added new tests to the module test suite Commit: 19ff7448b57f24647f9d98803dd9498371e89ef9 https://github.com/cdk/cdk/commit/19ff7448b57f24647f9d98803dd9498371e89ef9 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java Log Message: ----------- Placed in the appropriate test modules Commit: 9b700e9d974c438b28f83bff7d1b0a16ad634822 https://github.com/cdk/cdk/commit/9b700e9d974c438b28f83bff7d1b0a16ad634822 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/test-renderbasic.cdkdepends Log Message: ----------- Added missing dependencies Commit: 8ce2474495121d41640cc809c20c69157f2222c8 https://github.com/cdk/cdk/commit/8ce2474495121d41640cc809c20c69157f2222c8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted useAntiAliasing into a IGeneratorParameter Commit: 16276749009c6b4b29943eb90b16efb5373027ad https://github.com/cdk/cdk/commit/16276749009c6b4b29943eb90b16efb5373027ad Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted FontName and FontStyle into IGeneratorParameters Commit: c4f720fba40253536e628b162ea718be2411d339 https://github.com/cdk/cdk/commit/c4f720fba40253536e628b162ea718be2411d339 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Converted BondDistance into an IGeneratorParameter Commit: fd3b6cf0e4a1d6dbaf6a057e9b394cae7aa29549 https://github.com/cdk/cdk/commit/fd3b6cf0e4a1d6dbaf6a057e9b394cae7aa29549 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Factored out a ColorHash IRenderingParamater Commit: 2fa3d30b2540a25f586a40accadd3b628e281db3 https://github.com/cdk/cdk/commit/2fa3d30b2540a25f586a40accadd3b628e281db3 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: 078f65e47391abb28ac7995eb620aa50f1a01851 https://github.com/cdk/cdk/commit/078f65e47391abb28ac7995eb620aa50f1a01851 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Refactored foreground color into a IGeneratorParameter Commit: 61d079216d7b4c28cb537866743e2df34ff57717 https://github.com/cdk/cdk/commit/61d079216d7b4c28cb537866743e2df34ff57717 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java A src/main/org/openscience/cdk/renderer/generators/IAtomContainerGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Split up the old IGenerator interface into IGenerator and IAtomContainerGenerator, the first now only containing the method for getting the parameters Commit: be75022adf7cf805c74a66ef2e3a64b544593f41 https://github.com/cdk/cdk/commit/be75022adf7cf805c74a66ef2e3a64b544593f41 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 25dd8ea140f8d2cb6eb37b9b916d0a415fb3a820 https://github.com/cdk/cdk/commit/25dd8ea140f8d2cb6eb37b9b916d0a415fb3a820 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 523a84b6be8895e6a5ed841b8e8757e5a8a94012 https://github.com/cdk/cdk/commit/523a84b6be8895e6a5ed841b8e8757e5a8a94012 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 135a308337fe0c3164028688446e6d243b20f6ec https://github.com/cdk/cdk/commit/135a308337fe0c3164028688446e6d243b20f6ec Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java R src/main/org/openscience/cdk/renderer/generators/IAtomContainerGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (renderbasic). Commit: ac55656a378694c45340c93f874bb96a5909ffb4 https://github.com/cdk/cdk/commit/ac55656a378694c45340c93f874bb96a5909ffb4 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 587e7be570302db50f50469095643df4fa1cd279 https://github.com/cdk/cdk/commit/587e7be570302db50f50469095643df4fa1cd279 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (renderbasic). Commit: f9574b55406c0cb2f5057f8c76519ca4a5d16ee8 https://github.com/cdk/cdk/commit/f9574b55406c0cb2f5057f8c76519ca4a5d16ee8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Return two missing parameters Commit: 9811ce941f98684c3b3ed1dd2065c47645b59b8c https://github.com/cdk/cdk/commit/9811ce941f98684c3b3ed1dd2065c47645b59b8c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Fixed a generics warning: strong typed the field Commit: 7d9b9eb92cd3a6944673bf1584ad2bfba94b74be https://github.com/cdk/cdk/commit/7d9b9eb92cd3a6944673bf1584ad2bfba94b74be Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Removed scale and zoom form renderer and replaced with values form the generator parameters Commit: 2dca77d7c51374562bf91a0bf334552ed7b6505a https://github.com/cdk/cdk/commit/2dca77d7c51374562bf91a0bf334552ed7b6505a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderbasic). Commit: e577ea911115878f5e409ee3d6d1a693fef40d0e https://github.com/cdk/cdk/commit/e577ea911115878f5e409ee3d6d1a693fef40d0e Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Compact shape tests Commit: a1abb8e8ad20407c8c3291e99f8fa36b5eaf3a1d https://github.com/cdk/cdk/commit/a1abb8e8ad20407c8c3291e99f8fa36b5eaf3a1d Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Atom color tests Commit: 40d52b8511653a5bda39c95b0b44656c1c5c5796 https://github.com/cdk/cdk/commit/40d52b8511653a5bda39c95b0b44656c1c5c5796 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Color by type test Commit: e2b6a102369bf3c15521849a491ea78a6d4f5a50 https://github.com/cdk/cdk/commit/e2b6a102369bf3c15521849a491ea78a6d4f5a50 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Explicit hydrogens test Commit: 8b2feb49574012eb98d672d3f2496d9240cbe15e https://github.com/cdk/cdk/commit/8b2feb49574012eb98d672d3f2496d9240cbe15e Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Kekule test Commit: e6eefdce160cd65af8eeae991d7c21c7bb545203 https://github.com/cdk/cdk/commit/e6eefdce160cd65af8eeae991d7c21c7bb545203 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Show end carbons test Commit: 351a1a2332ca9e81036456f1acc2c3df381f8298 https://github.com/cdk/cdk/commit/351a1a2332ca9e81036456f1acc2c3df381f8298 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/test-renderbasic.cdkdepends M src/META-INF/test-renderbasic.libdepends Log Message: ----------- Added missing new dependencies for the test-renderbasic module Commit: a25c24521580bdbbd49a4e004e39f2565f389683 https://github.com/cdk/cdk/commit/a25c24521580bdbbd49a4e004e39f2565f389683 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Use the basic scene generator in the abstract base class Commit: 4c0d6818dc931ee3fe7b6ada5e7a626250198cf8 https://github.com/cdk/cdk/commit/4c0d6818dc931ee3fe7b6ada5e7a626250198cf8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/elements/PathElement.java M src/main/org/openscience/cdk/renderer/elements/WedgeLineElement.java M src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java A src/test/org/openscience/cdk/renderer/elements/AbstractElementTest.java A src/test/org/openscience/cdk/renderer/elements/PathElementTest.java A src/test/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java Log Message: ----------- Added two missing test classes, for PathElement and WedgeLineElement Commit: 9f7b74ef729992fe314e46c79540f44664443cba https://github.com/cdk/cdk/commit/9f7b74ef729992fe314e46c79540f44664443cba Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/elements/AbstractElementTest.java M src/test/org/openscience/cdk/renderer/elements/PathElementTest.java M src/test/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java Log Message: ----------- Fixed compiliation: corrected cdk module annotation. Commit: 621168f2ac9764ff930d013ef4934dccea169cb3 https://github.com/cdk/cdk/commit/621168f2ac9764ff930d013ef4934dccea169cb3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Mirror structures on Y-axis to compensate for different coordinate systems. Fixes bc-bug #1654 cdk-bug #2855247 Commit: 45cf451ebda7e4e834f1af8851212c169fcc0713 https://github.com/cdk/cdk/commit/45cf451ebda7e4e834f1af8851212c169fcc0713 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Fixed the AtomContainerRender to implement IRenderer; updated the toModelCoordinates() to match this interface Commit: 00147d507eec3b0849844b525835a0fd2ab88947 https://github.com/cdk/cdk/commit/00147d507eec3b0849844b525835a0fd2ab88947 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java A src/main/org/openscience/cdk/renderer/AverageBondLengthCalculator.java Log Message: ----------- Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (renderbasic). Commit: d9e33c1cc7ab143696e358f44712884280f32b80 https://github.com/cdk/cdk/commit/d9e33c1cc7ab143696e358f44712884280f32b80 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- More types in renderers, and associations between renderers Commit: 4e523290aeac1f5f58a531586873e09fc9ce8b48 https://github.com/cdk/cdk/commit/4e523290aeac1f5f58a531586873e09fc9ce8b48 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Using IRenderer<T> interface instead of implementation Commit: b7084c196ee14cabb333f104b410b25fd5789275 https://github.com/cdk/cdk/commit/b7084c196ee14cabb333f104b410b25fd5789275 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Made the aromatic ring property 'proportion to move in towards the ring center' customizable (implements #3047009) Commit: 07173b917c67bbfc8f806645b5d440d3872ff2b6 https://github.com/cdk/cdk/commit/07173b917c67bbfc8f806645b5d440d3872ff2b6 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Updated for API changes in CDK 1.3.6 Commit: 624649a4dc3feab73c7303452a6f31c0299ab233 https://github.com/cdk/cdk/commit/624649a4dc3feab73c7303452a6f31c0299ab233 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/rendercontrol.cdkdepends A src/META-INF/rendercontrol.libdepends A src/META-INF/test-rendercontrol.cdkdepends A src/META-INF/test-rendercontrol.devellibdepends A src/META-INF/test-rendercontrol.libdepends A src/main/org/openscience/cdk/renderer/generators/ControllerFeedbackGenerator.java A src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java A src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java A src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java A src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java A src/main/org/openscience/cdk/renderer/selection/IncrementalSelection.java A src/main/org/openscience/cdk/renderer/selection/LassoSelection.java A src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java A src/main/org/openscience/cdk/renderer/selection/MultiSelection.java A src/main/org/openscience/cdk/renderer/selection/RectangleSelection.java A src/main/org/openscience/cdk/renderer/selection/ShapeSelection.java A src/main/org/openscience/cdk/renderer/selection/SingleSelection.java A src/test/org/openscience/cdk/coverage/RendercontrolCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrendercontrolTests.java Log Message: ----------- Set up of the rendercontrol module, containing the rendering of controller feedback. * rendercontrol module * enabled DocCheck and PMD testing Commit: b6592d04c7e43f18586d1af948f12af0adac10bb https://github.com/cdk/cdk/commit/b6592d04c7e43f18586d1af948f12af0adac10bb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Updated for the new IGenerator.getParameters() interface method Commit: 278ec4ce119b4559411b5b461de3ee2469ae659d https://github.com/cdk/cdk/commit/278ec4ce119b4559411b5b461de3ee2469ae659d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Changed rendering of merge candidates to indicate what pairs will merge Uses new GeneralPath element Commit: e52a292c3f1b5e453a19c4a95d6d31c460edc142 https://github.com/cdk/cdk/commit/e52a292c3f1b5e453a19c4a95d6d31c460edc142 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/rendercontrol.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: b7ec937aa09bc147f7478df4a8672c6efda41d3e https://github.com/cdk/cdk/commit/b7ec937aa09bc147f7478df4a8672c6efda41d3e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 08fd5542a3903f2f228d4a5a164ed81b7f39e351 https://github.com/cdk/cdk/commit/08fd5542a3903f2f228d4a5a164ed81b7f39e351 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/selection/LinkedSelection.java M src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java Log Message: ----------- Added LinkedSelection A selection for selecting a connected part of a model Commit: 9287a5fd8b635b9da8f89f20ab412a8fbe5b8524 https://github.com/cdk/cdk/commit/9287a5fd8b635b9da8f89f20ab412a8fbe5b8524 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Updated for more IGeneratorParameter changes in BasicAtomGenerator Commit: 07dff754c7a06cb09a2881880264fbe9e2dcaa84 https://github.com/cdk/cdk/commit/07dff754c7a06cb09a2881880264fbe9e2dcaa84 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: 871f7477cda6e25154e1bbff62d108071820299e https://github.com/cdk/cdk/commit/871f7477cda6e25154e1bbff62d108071820299e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Updated for BondWidth now being a IGeneratorParameter Commit: 5b7e29c3bf184c00e34eda1621c0ea17ce19464a https://github.com/cdk/cdk/commit/5b7e29c3bf184c00e34eda1621c0ea17ce19464a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/selection/LinkedSelection.java M src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java M src/main/org/openscience/cdk/renderer/selection/MultiSelection.java M src/main/org/openscience/cdk/renderer/selection/ShapeSelection.java M src/main/org/openscience/cdk/renderer/selection/SingleSelection.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: e21bbe85de1fdc5357e884df1e1748e03b49aee1 https://github.com/cdk/cdk/commit/e21bbe85de1fdc5357e884df1e1748e03b49aee1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 6494ec3518b0021c5b97abe0e68927994382c212 https://github.com/cdk/cdk/commit/6494ec3518b0021c5b97abe0e68927994382c212 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Converted externalHighlightColor to the new rendering parameter API Commit: 84026a24aedda324ecb4fb39da73ade0e70a76fa https://github.com/cdk/cdk/commit/84026a24aedda324ecb4fb39da73ade0e70a76fa Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Converted hoverOverColor to the new rendering parameter API Commit: 9b0f8659fd9f2a8f3cffde27d016303d1a5a17bb https://github.com/cdk/cdk/commit/9b0f8659fd9f2a8f3cffde27d016303d1a5a17bb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Moved ExternalHighlightColor into RendererModel for now, to solve a compile dependency Commit: d060e06546fce74dad846093cea6dffcc573ca65 https://github.com/cdk/cdk/commit/d060e06546fce74dad846093cea6dffcc573ca65 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (rendercontrol). Commit: ea7a8bfd0c3ee5c4f26ad039e8688dfb880a85d7 https://github.com/cdk/cdk/commit/ea7a8bfd0c3ee5c4f26ad039e8688dfb880a85d7 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: ba15d73a35e4211622b8a74cd929eb15017a07a0 https://github.com/cdk/cdk/commit/ba15d73a35e4211622b8a74cd929eb15017a07a0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (rendercontrol). Commit: 2b20d3ee13a2f71f3ef29e3fb7178a6cbc4a72a2 https://github.com/cdk/cdk/commit/2b20d3ee13a2f71f3ef29e3fb7178a6cbc4a72a2 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (rendercontrol). Commit: 5475408f8c9ebf57cc5e65d189e416ab5480b615 https://github.com/cdk/cdk/commit/5475408f8c9ebf57cc5e65d189e416ab5480b615 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Also return the parameters of the super class -a (rendercontrol). Commit: 1708bfb2fe757c9647923938a7ea3763641ca68d https://github.com/cdk/cdk/commit/1708bfb2fe757c9647923938a7ea3763641ca68d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml M src/META-INF/control.cdkdepends A src/META-INF/test-control.cdkdepends A src/META-INF/test-control.devellibdepends A src/META-INF/test-control.libdepends A src/main/org/openscience/cdk/controller/Changed.java A src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java A src/main/org/openscience/cdk/controller/IChemModelEventRelayHandler.java A src/main/org/openscience/cdk/controller/IChemModelRelay.java A src/main/org/openscience/cdk/controller/IControllerModel.java A src/main/org/openscience/cdk/controller/IControllerModule.java M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java A src/main/org/openscience/cdk/controller/edit/IEdit.java A src/main/org/openscience/cdk/controller/undoredo/IUndoListener.java A src/main/org/openscience/cdk/controller/undoredo/IUndoRedoFactory.java A src/main/org/openscience/cdk/controller/undoredo/IUndoRedoable.java A src/main/org/openscience/cdk/controller/undoredo/UndoRedoHandler.java M src/test/org/openscience/cdk/coverage/ControlCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolTests.java Log Message: ----------- Set up of the new controller infrastructure. * new content of the 'control' module * new test suite with coverage testing * enabled DocCheck and PMD testing Commit: 37031a5c4e6ae6f11a37a8a686c7592d9ff67ee7 https://github.com/cdk/cdk/commit/37031a5c4e6ae6f11a37a8a686c7592d9ff67ee7 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: d41ef733c24dfa6290f8aefd46eb69707d964d19 https://github.com/cdk/cdk/commit/d41ef733c24dfa6290f8aefd46eb69707d964d19 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/controller/IAtomBondEdits.java M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Re-factored out methods for atom and bonds edit These methods are candidates for being replaced with IEdit With copyright Commit: 57cecf8e8d4b8cee0ea74ee1febfec528e9dadf7 https://github.com/cdk/cdk/commit/57cecf8e8d4b8cee0ea74ee1febfec528e9dadf7 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/IEdit.java Log Message: ----------- Added new edits for replacing modify methods in ControllerHub The edits handles the modifying of the model and the undo/redo stuff. Commit: f1c0ca878cc4fb4d9a72b6f26966634c7af15355 https://github.com/cdk/cdk/commit/f1c0ca878cc4fb4d9a72b6f26966634c7af15355 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/control.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c23c3d4a219e46465aee90f0208e175b428b58ba https://github.com/cdk/cdk/commit/c23c3d4a219e46465aee90f0208e175b428b58ba Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Defines two new stereo types. Commit: 641a96bc366029277d5ef82a05ffd45c66d60969 https://github.com/cdk/cdk/commit/641a96bc366029277d5ef82a05ffd45c66d60969 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Rewrote selection check to avoid NPE Commit: 19d8cfa381569b81ab02ecc3256b15cf19ca13af https://github.com/cdk/cdk/commit/19d8cfa381569b81ab02ecc3256b15cf19ca13af Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: c68c3f18710d7beef920806fb64694bd342ed9e7 https://github.com/cdk/cdk/commit/c68c3f18710d7beef920806fb64694bd342ed9e7 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Changed wedge width to rendering parameter Commit: cf88296b23767e49ec5d1ea32462b8061da48dc0 https://github.com/cdk/cdk/commit/cf88296b23767e49ec5d1ea32462b8061da48dc0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (control). Commit: 966b90e92968cf3fe20a8978073ea6df236a8cef https://github.com/cdk/cdk/commit/966b90e92968cf3fe20a8978073ea6df236a8cef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml Log Message: ----------- Added compiling of the test-control module Commit: 1a1a01738c6aabba8edd596347c243a4d52812c4 https://github.com/cdk/cdk/commit/1a1a01738c6aabba8edd596347c243a4d52812c4 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IAtomBondEdits.java M src/main/org/openscience/cdk/controller/IChemModelRelay.java A src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Moved all methods except the most important from IChemModelRelay to IOldChemModelRelay Commit: d2a2e174554c12867f7c909fd7bc2dd8290a1c4e https://github.com/cdk/cdk/commit/d2a2e174554c12867f7c909fd7bc2dd8290a1c4e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java M src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module control Commit: 625a595e3b2a8b1e0e5f90a76180b728c1d49f6f https://github.com/cdk/cdk/commit/625a595e3b2a8b1e0e5f90a76180b728c1d49f6f Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module controlbasic Commit: f4d24333f3e7e450e21a883bb10ca5963976e287 https://github.com/cdk/cdk/commit/f4d24333f3e7e450e21a883bb10ca5963976e287 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Changed select(IncrementalSelection) to select(IChemObjectSelection) The select method uses method that exists on IChemObjectSelection interface Commit: 3e233f9330a0875294fd05161708badb3b3470ef https://github.com/cdk/cdk/commit/3e233f9330a0875294fd05161708badb3b3470ef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Added dependency on IOldChemModelRelay which is needed at this level Commit: 40ecbc7e75e27b30fb128177bf4a44725343f571 https://github.com/cdk/cdk/commit/40ecbc7e75e27b30fb128177bf4a44725343f571 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IMouseEventRelay.java Log Message: ----------- Added two missing methods for scroll event handling Commit: 26c93a67eb06b0f59a27052faa46533b2a933a5f https://github.com/cdk/cdk/commit/26c93a67eb06b0f59a27052faa46533b2a933a5f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlbasic.cdkdepends A src/META-INF/controlbasic.libdepends A src/META-INF/test-controlbasic.cdkdepends A src/META-INF/test-controlbasic.devellibdepends A src/META-INF/test-controlbasic.libdepends A src/main/org/openscience/cdk/controller/AddAtomModule.java A src/main/org/openscience/cdk/controller/AddBondDragModule.java A src/main/org/openscience/cdk/controller/AddBondModule.java A src/main/org/openscience/cdk/controller/AddRingModule.java A src/main/org/openscience/cdk/controller/AlterBondStereoModule.java A src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java A src/main/org/openscience/cdk/controller/ControllerHub.java A src/main/org/openscience/cdk/controller/ControllerModel.java A src/main/org/openscience/cdk/controller/ControllerParameters.java A src/main/org/openscience/cdk/controller/CycleSymbolModule.java A src/main/org/openscience/cdk/controller/DrawBondModule.java A src/main/org/openscience/cdk/controller/HighlightModule.java A src/main/org/openscience/cdk/controller/MoveModule.java A src/main/org/openscience/cdk/controller/PhantomBondGenerator.java A src/main/org/openscience/cdk/controller/RemoveModule.java A src/main/org/openscience/cdk/controller/RotateModule.java A src/main/org/openscience/cdk/controller/SelectLassoModule.java A src/main/org/openscience/cdk/controller/SelectSquareModule.java A src/main/org/openscience/cdk/controller/ZoomModule.java A src/main/org/openscience/cdk/controller/edit/AbstractEdit.java A src/main/org/openscience/cdk/controller/edit/AddAtom.java A src/main/org/openscience/cdk/controller/edit/AddBond.java A src/main/org/openscience/cdk/controller/edit/AppendAtom.java A src/main/org/openscience/cdk/controller/edit/CreateBond.java A src/main/org/openscience/cdk/controller/edit/RemoveAtom.java A src/main/org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.java A src/main/org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeAtomSymbolEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeChargeEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeCoordsEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeHydrogenCountEdit.java A src/main/org/openscience/cdk/controller/undoredo/ClearAllEdit.java A src/main/org/openscience/cdk/controller/undoredo/MoveAtomEdit.java A src/main/org/openscience/cdk/controller/undoredo/RemoveAtomsAndBondsEdit.java A src/main/org/openscience/cdk/controller/undoredo/ReplaceAtomEdit.java A src/test/org/openscience/cdk/coverage/ControlbasicCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolbasicTests.java Log Message: ----------- Set up a controlbasic module, with basic editing functionality, like adding and moving atoms, and changing basic atom and bond properties. * includes javadoc and pmd testing * includes coverage testing framework Commit: c81e97c0a83d65bbc8baf9904b4625e147baca33 https://github.com/cdk/cdk/commit/c81e97c0a83d65bbc8baf9904b4625e147baca33 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/RotateModule.java Log Message: ----------- implemented RotateModule Commit: 8e8dddeb592ccc0a11da836e52cbf22b1b2e2b2d https://github.com/cdk/cdk/commit/8e8dddeb592ccc0a11da836e52cbf22b1b2e2b2d Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Moving bugs fixed Commit: 753143383dfcc03c615eee06655d941c5a35fc70 https://github.com/cdk/cdk/commit/753143383dfcc03c615eee06655d941c5a35fc70 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- bugfixed mergeMolecules methods Commit: 150fcf8256329be2835f1dbeb8be494dc67cbdde https://github.com/cdk/cdk/commit/150fcf8256329be2835f1dbeb8be494dc67cbdde Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/DrawBondModule.java M src/main/org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.java M src/main/org/openscience/cdk/controller/undoredo/IUndoRedoFactory.java Log Message: ----------- Updated for IBond.Stereo API change Commit: 136cf08dfa13555439c3ce500db1d02ee5654ec6 https://github.com/cdk/cdk/commit/136cf08dfa13555439c3ce500db1d02ee5654ec6 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Using add operation in Point2d Commit: 7bfa9e0c76b186a26949b19fd3b8acc554afe774 https://github.com/cdk/cdk/commit/7bfa9e0c76b186a26949b19fd3b8acc554afe774 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- mergeMap reference model.getMerge() using the former for clarity Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: b98b021f455e3b6265187cfb9c33458550203f5b https://github.com/cdk/cdk/commit/b98b021f455e3b6265187cfb9c33458550203f5b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java M src/main/org/openscience/cdk/controller/HighlightModule.java M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: d5d18831e90d435ecaa8d04ade72c77e44f5c9c9 https://github.com/cdk/cdk/commit/d5d18831e90d435ecaa8d04ade72c77e44f5c9c9 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/edit/AbstractEdit.java M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java A src/main/org/openscience/cdk/controller/edit/CompositEdit.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java A src/main/org/openscience/cdk/controller/edit/Merge.java A src/main/org/openscience/cdk/controller/edit/Move.java A src/main/org/openscience/cdk/controller/edit/MoveOptionalUndo.java M src/main/org/openscience/cdk/controller/edit/RemoveAtom.java A src/main/org/openscience/cdk/controller/edit/RemoveBond.java A src/main/org/openscience/cdk/controller/edit/SetBondOrder.java A src/main/org/openscience/cdk/controller/edit/SetCharge.java A src/main/org/openscience/cdk/controller/edit/SetStereo.java A src/main/org/openscience/cdk/controller/edit/SetSymbol.java Log Message: ----------- Added new edits for replacing modify methods in ControllerHub The edits handles the modifying of the model and the undo/redo stuff. Commit: 49d9884d84aa63dcedfd9d6459ac2789ce96d057 https://github.com/cdk/cdk/commit/49d9884d84aa63dcedfd9d6459ac2789ce96d057 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Added hack to filter out none final MoveOptionalUndo edits Commit: e6e6d22f632b13d35f77d310f2f8c2f7c4501622 https://github.com/cdk/cdk/commit/e6e6d22f632b13d35f77d310f2f8c2f7c4501622 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/AddBondModule.java M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java R src/main/org/openscience/cdk/controller/DrawBondModule.java M src/main/org/openscience/cdk/controller/MoveModule.java M src/main/org/openscience/cdk/controller/RemoveModule.java Log Message: ----------- Re-factored modules to use new edit operations instead of methods in IChemModelRelay Commit: c6763eee70b565170b8ce4e5e7023eb3280ed12a https://github.com/cdk/cdk/commit/c6763eee70b565170b8ce4e5e7023eb3280ed12a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/controlbasic.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: b5357b0eb378f2c701d1aad233cfd17426192a13 https://github.com/cdk/cdk/commit/b5357b0eb378f2c701d1aad233cfd17426192a13 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java M src/main/org/openscience/cdk/controller/RotateModule.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: 012ae44007516467b3bb10df925d8e2c2165ee8b https://github.com/cdk/cdk/commit/012ae44007516467b3bb10df925d8e2c2165ee8b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/PhantomBondGenerator.java Log Message: ----------- Changed PhantomBondGenerator to use override color in BasicBondRenderer This simplifies this generator and allows it to draw aromatic rings Commit: e2ba6c60ed38b945582d30306d74a984d63d996d https://github.com/cdk/cdk/commit/e2ba6c60ed38b945582d30306d74a984d63d996d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Moved code handling merge to static methods This so that they can be reused in other modules like AddRingModuel Commit: c7078ba8fc2dceabccea8cd252ba13dacbcb09db https://github.com/cdk/cdk/commit/c7078ba8fc2dceabccea8cd252ba13dacbcb09db Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java A src/main/org/openscience/cdk/controller/edit/CreateRing.java Log Message: ----------- Added CreateRing edit and re-factored AddRingModule to use it The handling of aromaticity is slightly different from the old way, and it should be handled by the Merge edit to get the same behavior when merging a aromatic ring with move. Commit: cc0b47cd4350817cacd0ec1568c2421fe70a2659 https://github.com/cdk/cdk/commit/cc0b47cd4350817cacd0ec1568c2421fe70a2659 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/MoveModule.java R src/main/org/openscience/cdk/controller/edit/MoveOptionalUndo.java A src/main/org/openscience/cdk/controller/edit/OptionalUndoEdit.java Log Message: ----------- Replaced MoveOptionalUndo with OptionalUndoEdit wrapper. The wrapper allows for adding optional undo to any edit. This is a workaround for allowing small incremental edits that is not pushed to the undo stack and then push a edit that is not executed but are pushed to the undo stack representing the operations done by all smaller incremental edits. Commit: c6102883c9eb65f9664735888f9fd3167ded7d60 https://github.com/cdk/cdk/commit/c6102883c9eb65f9664735888f9fd3167ded7d60 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/RotateModule.java A src/main/org/openscience/cdk/controller/edit/Rotate.java Log Message: ----------- Moved RotateModule to new edit model Commit: 4932e066c8da79a092f4dfc53bf7a8c9e59c5c64 https://github.com/cdk/cdk/commit/4932e066c8da79a092f4dfc53bf7a8c9e59c5c64 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/CycleSymbolModule.java Log Message: ----------- Fixed bug where the last element would not be part of cycle Also moved execute(...) to end of method Commit: a177b105620107a769d4b3eb8bccbce5db3c3866 https://github.com/cdk/cdk/commit/a177b105620107a769d4b3eb8bccbce5db3c3866 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/CompositEdit.java M src/main/org/openscience/cdk/controller/edit/RemoveAtom.java Log Message: ----------- Changed add/remove explicit hydrogens to use IEdits Solves bug #1249 Commit: 193776bff21902f3234635e9c882cecaa272b06f https://github.com/cdk/cdk/commit/193776bff21902f3234635e9c882cecaa272b06f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/ZoomModule.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 2a0ddacdfe2f418889e261590e8c07603bdf466f https://github.com/cdk/cdk/commit/2a0ddacdfe2f418889e261590e8c07603bdf466f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/PhantomBondGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (controlbasic). Commit: 529338fcd21901d46f13bcef7ce002531dfc9e43 https://github.com/cdk/cdk/commit/529338fcd21901d46f13bcef7ce002531dfc9e43 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 16f976730d2ac29979f525bbd45846810f83b42d https://github.com/cdk/cdk/commit/16f976730d2ac29979f525bbd45846810f83b42d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/ZoomModule.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (controlbasic). Commit: b1eb74fa3ddc4b501bd9b7e17b647716c97b66e5 https://github.com/cdk/cdk/commit/b1eb74fa3ddc4b501bd9b7e17b647716c97b66e5 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java Log Message: ----------- Enables AlterBondStereoModule to cycle between different stereo modes UP->UP_INVERTED->NONE->UP... DOWN->DOWN_INVERTED->NONE->DOWN... Commit: 276eb4a21f8a3974263c1cb66c84e0222a374e5a https://github.com/cdk/cdk/commit/276eb4a21f8a3974263c1cb66c84e0222a374e5a Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Removed structure changed event when changing model Commit: 4f3026296ffe3adf5dea3dd14025d5178daaed18 https://github.com/cdk/cdk/commit/4f3026296ffe3adf5dea3dd14025d5178daaed18 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddBondModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module controlbasic Commit: c1295219f50048c542c49b96ba485f488f5f46e0 https://github.com/cdk/cdk/commit/c1295219f50048c542c49b96ba485f488f5f46e0 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Calculate average bond for atomcontainer instead of chemModel Commit: d8b3e6ffa3e4cd01241640ee8599b66afd3563ac https://github.com/cdk/cdk/commit/d8b3e6ffa3e4cd01241640ee8599b66afd3563ac Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java Log Message: ----------- Only create atoms and bonds the first time redo is called. Solves cdk-bug #2886402 Commit: 67565e82394103c47be5229ed16b7570ef2c0675 https://github.com/cdk/cdk/commit/67565e82394103c47be5229ed16b7570ef2c0675 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/edit/AbstractEdit.java M src/main/org/openscience/cdk/controller/edit/CompositEdit.java Log Message: ----------- Added update of hydrogens after edit. Commit: 556819612dc7093e26c2bce8c3b21ba10202dd7c https://github.com/cdk/cdk/commit/556819612dc7093e26c2bce8c3b21ba10202dd7c Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Changed select(IncrementalSelection) to select(IChemObjectSelection) The select method uses method that exists on IChemObjectSelection interface Commit: 3370bb08992a07e0fc8e649ecc087e9444c47acb https://github.com/cdk/cdk/commit/3370bb08992a07e0fc8e649ecc087e9444c47acb Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- MergeEdit is passed a copy of the merge-map. The merge-map is reused and could have been changed when it is time to undo. It is also transient and doesn't need to be restored with an undo. Commit: 617f8a9c24efb98687f4806631b9dd0acd87f72d https://github.com/cdk/cdk/commit/617f8a9c24efb98687f4806631b9dd0acd87f72d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- Sets a default bondLength when it is 0 or NaN This makes sure rings are rendered when placing on empyt canvas. Commit: 235f8bb1f9dfe9447a14c66f2040b199a66c225e https://github.com/cdk/cdk/commit/235f8bb1f9dfe9447a14c66f2040b199a66c225e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/AddAtom.java Log Message: ----------- Makes AddAtom-edit actualy add the atom. Commit: 2d29307efd9eb85363644e07544417e23b89db5d https://github.com/cdk/cdk/commit/2d29307efd9eb85363644e07544417e23b89db5d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Use atom- instead of mouse-coordinates when drawing bonds Also change snap angle to 15 This commit does exactly the same as ae28a16ff2cf2eab44748db75b40701f4e6f6241, dragging bonds in regular angles using atom 2d point from ebi_patches but adapter for the IEdit refactoring Commit: fe06e58b5d8081443e036a8ec9f576419958c8b2 https://github.com/cdk/cdk/commit/fe06e58b5d8081443e036a8ec9f576419958c8b2 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/SetSymbol.java Log Message: ----------- SetSymbol converts from pseudo atom Dose the same thing as: 936ba7885e8c7b8cd6eb363e7f012a6d20a9ff6d, the setsymbol converts to a normal atom in case it was a pseudo atom. from ebi_patches Commit: 853eb763a0e3d44c5a2e7c2651eb73ad42d3dbe3 https://github.com/cdk/cdk/commit/853eb763a0e3d44c5a2e7c2651eb73ad42d3dbe3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Added check for 0 or Double.NaN bond length Commit: f887290c47f67a62bf0d60b168bb9cb2ac5e826e https://github.com/cdk/cdk/commit/f887290c47f67a62bf0d60b168bb9cb2ac5e826e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Added checks for NaN coordinates for general path. SWT doesn't like NaN when drawing thees Commit: b5cbb738d13ac6091b2b89a47d7f1fe9c2a20fe4 https://github.com/cdk/cdk/commit/b5cbb738d13ac6091b2b89a47d7f1fe9c2a20fe4 Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- the cleanup no longer collapses fragments Signed-off-by: Arvid Berg <goglepox@...> Commit: 5e12cf075adf87f07be5657983170dbcc6cb3ecf https://github.com/cdk/cdk/commit/5e12cf075adf87f07be5657983170dbcc6cb3ecf Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- Made ring fit to atom/bond when hovered Fixes bug #1738 Commit: 3b5972d0f6c5a1d502293856be6518bde82a3066 https://github.com/cdk/cdk/commit/3b5972d0f6c5a1d502293856be6518bde82a3066 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Fix for generating a merge ring when two atoms are at the same positions Commit: 6d277707416096ca720f9d4dd96409ea0cf68cd1 https://github.com/cdk/cdk/commit/6d277707416096ca720f9d4dd96409ea0cf68cd1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java M src/main/org/openscience/cdk/controller/edit/CreateRing.java M src/main/org/openscience/cdk/controller/edit/SetSymbol.java M src/main/org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.java M src/main/org/openscience/cdk/controller/undoredo/RemoveAtomsAndBondsEdit.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 1722c4d1646338ed485bb64ee019167eea90e856 https://github.com/cdk/cdk/commit/1722c4d1646338ed485bb64ee019167eea90e856 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/undoredo/ChangeHydrogenCountEdit.java Log Message: ----------- Updated for API changes in CDK 1.3.6 (controlbasic). Commit: 2e5cdbbf99d013a14506794ca620f220e8cdb940 https://github.com/cdk/cdk/commit/2e5cdbbf99d013a14506794ca620f220e8cdb940 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderextra.cdkdepends A src/META-INF/renderextra.libdepends A src/META-INF/test-renderextra.cdkdepends A src/META-INF/test-renderextra.devellibdepends A src/META-INF/test-renderextra.libdepends A src/main/org/openscience/cdk/renderer/Renderer.java A src/main/org/openscience/cdk/renderer/elements/ArrowElement.java A src/main/org/openscience/cdk/renderer/elements/AtomMassSymbolElement.java A src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java A src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java A src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java A src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java A src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java A src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java A src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java A src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java A src/main/org/openscience/cdk/renderer/visitor/DistanceSearchVisitor.java A src/main/org/openscience/cdk/renderer/visitor/PrintVisitor.java A src/test/org/openscience/cdk/coverage/RenderextraCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderextraTests.java Log Message: ----------- Render extra module with rendering functionality beyond IAtomContainers. * adds rendering of reactions * added javadoc and PMD testing * added module test suite * new modules: renderextra and test-renderextra Commit: 5c15d57847151a0d98b8db6d0908ca7dfb65f084 https://github.com/cdk/cdk/commit/5c15d57847151a0d98b8db6d0908ca7dfb65f084 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Updated for the new IGenerator.getParameters() interface method Commit: f1cc78742417f46585dae45e3db9916f70a0551a https://github.com/cdk/cdk/commit/f1cc78742417f46585dae45e3db9916f70a0551a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/renderextra.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c94b9d2880fb782bde512737c72055e8d71a3fd5 https://github.com/cdk/cdk/commit/c94b9d2880fb782bde512737c72055e8d71a3fd5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: 58bc885196c56bb3c43f73e41eb3f500b636277c https://github.com/cdk/cdk/commit/58bc885196c56bb3c43f73e41eb3f500b636277c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Fixed the Renderer to implement IRenderer Commit: c07fbe8bc233d9d38a021b422391c7dac8155f74 https://github.com/cdk/cdk/commit/c07fbe8bc233d9d38a021b422391c7dac8155f74 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 2102064189f1e761e42920e28da909ec1c71ee8d https://github.com/cdk/cdk/commit/2102064189f1e761e42920e28da909ec1c71ee8d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for the move of the rendering parameters for atom draw colors to the new IGeneratorParameter API Commit: 1d7f8de1d27850e8355bbfc3c0cf8ed50e4d2af8 https://github.com/cdk/cdk/commit/1d7f8de1d27850e8355bbfc3c0cf8ed50e4d2af8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Set up a API to retrieve a IRenderingParameter from the RenderModel Commit: 2364703d3c3e63b9d2d352c3f14932cbe2e279b6 https://github.com/cdk/cdk/commit/2364703d3c3e63b9d2d352c3f14932cbe2e279b6 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Moved the atom radius into the new rendering parameter API (renderextra module) Commit: e3809c9cf54f47094b177294b9cf7faff3ff99a3 https://github.com/cdk/cdk/commit/e3809c9cf54f47094b177294b9cf7faff3ff99a3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Added ability to generate atom number at an offset. This is a naive solution but allows for better looking rendering that the numbers rendered on top of the atom. Commit: c40560d1535022120307b2e7b01d7ba5ab737cef https://github.com/cdk/cdk/commit/c40560d1535022120307b2e7b01d7ba5ab737cef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for more IGeneratorParameter changes in BasicAtomGenerator Commit: 4dfd81bf9198e4620a86e562d4d30cf402b47c56 https://github.com/cdk/cdk/commit/4dfd81bf9198e4620a86e562d4d30cf402b47c56 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Converted margin into the RenderingParameter variant Commit: 7ef24a4bd02bc1f6a8053fe3d48302083ff89b32 https://github.com/cdk/cdk/commit/7ef24a4bd02bc1f6a8053fe3d48302083ff89b32 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Converted FontName and FontStyle into IGeneratorParameters Commit: 705ecf24620ec1d1d42c560f02bae881bfde9975 https://github.com/cdk/cdk/commit/705ecf24620ec1d1d42c560f02bae881bfde9975 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: a7b343abbbd53d24a24bca8afcdc4ae1a2f34587 https://github.com/cdk/cdk/commit/a7b343abbbd53d24a24bca8afcdc4ae1a2f34587 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Refactored foreground color into a IGeneratorParameter Commit: 5b3feef2971a22df5a3a118617a6967f035bf4ed https://github.com/cdk/cdk/commit/5b3feef2971a22df5a3a118617a6967f035bf4ed Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- IReactionGenerator now has parameters too Commit: 6aa558741c0d54a08413f2f0852e1b7ca6f9e519 https://github.com/cdk/cdk/commit/6aa558741c0d54a08413f2f0852e1b7ca6f9e519 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Refactored reaction boxes into a IGeneratorParameter Commit: edda0f3b2a96562d8c17f518c49a0ec1c7c3a160 https://github.com/cdk/cdk/commit/edda0f3b2a96562d8c17f518c49a0ec1c7c3a160 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Updated for the IGenerator/IAtomContainerGenerator refactoring Commit: 789f5cb25a58920ed44efb0468518d8e882038c5 https://github.com/cdk/cdk/commit/789f5cb25a58920ed44efb0468518d8e882038c5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java Log Message: ----------- Extend IGenerator which now provides getParameters() Commit: a6d89bbdeca6ddaeea872ad11b7dd2b33d47fccd https://github.com/cdk/cdk/commit/a6d89bbdeca6ddaeea872ad11b7dd2b33d47fccd Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- the RadicalGenerator can render atoms with more than one single electron. Signed-off-by: Arvid Berg <goglepox@...> Added rendering of more than one for vertical alignment too. And reverse direction on vertical alignment. Commit: e047e81cb577a8959656ae9960536fa38a6d8e66 https://github.com/cdk/cdk/commit/e047e81cb577a8959656ae9960536fa38a6d8e66 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: a24a7cd3af59e03b647104ea02a5551a91758366 https://github.com/cdk/cdk/commit/a24a7cd3af59e03b647104ea02a5551a91758366 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java Log Message: ----------- Converted boundsColor to the new rendering parameter API Commit: 7ba56125ff53b0dd08ff400c0440c87bd7bd052d https://github.com/cdk/cdk/commit/7ba56125ff53b0dd08ff400c0440c87bd7bd052d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java Log Message: ----------- Converted mappingColor and mappingLineWidth to the new rendering parameter API Commit: ccc0cb3436450c2814bf0ce3e9947ae22899ba93 https://github.com/cdk/cdk/commit/ccc0cb3436450c2814bf0ce3e9947ae22899ba93 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java R src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (renderextra). Commit: c4aac69310e8bc88b829dbc2cf31b57997c65ceb https://github.com/cdk/cdk/commit/c4aac69310e8bc88b829dbc2cf31b57997c65ceb Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 89b696123f7f65258462f8c0472040c76aef04f5 https://github.com/cdk/cdk/commit/89b696123f7f65258462f8c0472040c76aef04f5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (renderextra). Commit: b4944dee9b86ac710b4876dfff7e493d5097801b https://github.com/cdk/cdk/commit/b4944dee9b86ac710b4876dfff7e493d5097801b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Removed scale and zoom form renderer and replaced with values form the generator parameters Commit: 6ef75e26728b5b06bb8d5062c8043b1cbc1cd3bf https://github.com/cdk/cdk/commit/6ef75e26728b5b06bb8d5062c8043b1cbc1cd3bf Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderextra). Commit: 97011f50361deb126b0851492ef37278e0b95457 https://github.com/cdk/cdk/commit/97011f50361deb126b0851492ef37278e0b95457 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Also return the parameters of the super class -a (renderextra). Commit: 70224c99853f80009257fb652e8bedda543f4b79 https://github.com/cdk/cdk/commit/70224c99853f80009257fb652e8bedda543f4b79 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Converted the offset from a constructor parameter into a proper IRenderingParamater (renderextra). Commit: 8556391577cb22a4fe5cae262ff2bd493a879597 https://github.com/cdk/cdk/commit/8556391577cb22a4fe5cae262ff2bd493a879597 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Added rendering parameters for coloring the atom numbers by some scheme, e.g. by element type Commit: 06246f14e10b705b39806852a519023de7849ebb https://github.com/cdk/cdk/commit/06246f14e10b705b39806852a519023de7849ebb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/DistanceSearchVisitor.java Log Message: ----------- Fixed some PMD warnings: longer variable names (renderextra). Commit: 431ceeda7bc346b439fed3ec6ab30163a0aeaa0e https://github.com/cdk/cdk/commit/431ceeda7bc346b439fed3ec6ab30163a0aeaa0e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Mirror structures on Y-axis to compensate for different coordinate systems. Fixes bc-bug #1654 cdk-bug #2855247 Commit: 2381b3a6cf2614bd30be073efe20ef512f97fc2f https://github.com/cdk/cdk/commit/2381b3a6cf2614bd30be073efe20ef512f97fc2f Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Added null check to avoid NPE when no model is present Commit: 829a057f3d0c1d0cd15520b95d3b6abcebe83758 https://github.com/cdk/cdk/commit/829a057f3d0c1d0cd15520b95d3b6abcebe83758 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java A src/main/org/openscience/cdk/renderer/ReactionRenderer.java A src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (renderextra). Commit: eaead5212198cc8ac99b2bd0b73dca43e929f0ae https://github.com/cdk/cdk/commit/eaead5212198cc8ac99b2bd0b73dca43e929f0ae Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/ChemModelRenderer.java R src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Renamed the Renderer to ChemModelRenderer, following the naming pattern for the other IRenderer implementations Commit: 6284f815f6fe917750aec14d8ee52103e9b2c894 https://github.com/cdk/cdk/commit/6284f815f6fe917750aec14d8ee52103e9b2c894 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java M src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java Log Message: ----------- More types in renderers, and associations between renderers Commit: 259e9db19adc68bc207c92f013f2b71c111a405b https://github.com/cdk/cdk/commit/259e9db19adc68bc207c92f013f2b71c111a405b Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java M src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java Log Message: ----------- Using IRenderer<T> interface instead of implementation Commit: 46e7bb37526ce411ee1844a2ed77ce385dab4fab https://github.com/cdk/cdk/commit/46e7bb37526ce411ee1844a2ed77ce385dab4fab Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for API changes in CDK 1.3.6 (renderextra). Commit: 2e6a60284f068990be14026b43308a1f720473de https://github.com/cdk/cdk/commit/2e6a60284f068990be14026b43308a1f720473de Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Fixed registering of rendering parameters (renderextra). Commit: 7e11e24f8126bdd19787edbec4100c5393d5befb https://github.com/cdk/cdk/commit/7e11e24f8126bdd19787edbec4100c5393d5befb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java Log Message: ----------- Fixed NullPointerException by creating an empty list of generators, and return a list too, rather than a null Commit: e7e7b80b0fee596ae4a1fcea0306ed1da6875d82 https://github.com/cdk/cdk/commit/e7e7b80b0fee596ae4a1fcea0306ed1da6875d82 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Because the renderers are now typed itself, we can use this.generators instead, fixign a NullPointerException while rendering reactions Commit: 9ce50cb884aa852d520f2a27fa9c3c916ae2072b https://github.com/cdk/cdk/commit/9ce50cb884aa852d520f2a27fa9c3c916ae2072b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java Log Message: ----------- Implemented the generateDiagram and use that in the paint methods, which fixes reaction rendering as the ReactionRenderer.generateDiagram() uses MoleculeSetRenderer.generateDiagram() Commit: 344b6e7677787d40d5b59396add115b2b1198cf5 https://github.com/cdk/cdk/commit/344b6e7677787d40d5b59396add115b2b1198cf5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlextra.cdkdepends A src/META-INF/controlextra.libdepends A src/META-INF/test-controlextra.cdkdepends A src/META-INF/test-controlextra.devellibdepends A src/META-INF/test-controlextra.libdepends A src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java A src/main/org/openscience/cdk/controller/undoredo/ChangeIsotopeEdit.java A src/main/org/openscience/cdk/controller/undoredo/ConvertToRadicalEdit.java A src/main/org/openscience/cdk/controller/undoredo/LoadNewModelEdit.java A src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInExistingReactionEdit.java A src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInNewReactionEdit.java A src/main/org/openscience/cdk/controller/undoredo/MergeMoleculesEdit.java A src/test/org/openscience/cdk/coverage/ControlextraCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolextraTests.java Log Message: ----------- Set up the controlextra module for editing functionality for things beyond the IAtomContainer, such as drawing reactions. * includes javadoc and pmd checking * includes coverage test infrastructure Commit: 18afb0882db2ca17cdca74797da66ff81cb4b0de https://github.com/cdk/cdk/commit/18afb0882db2ca17cdca74797da66ff81cb4b0de Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: 0306361bd24144abb3453e34a843c4ba20e1ac93 https://github.com/cdk/cdk/commit/0306361bd24144abb3453e34a843c4ba20e1ac93 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/META-INF/controlextra.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: 252cf81e859900f519fa0e4c44760bf82c81145a https://github.com/cdk/cdk/commit/252cf81e859900f519fa0e4c44760bf82c81145a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/META-INF/controlextra.cdkdepends Log Message: ----------- The module controlextra can depend on controlbasic Commit: dbb5fb0a8789137ec5958937b67e748e40676a66 https://github.com/cdk/cdk/commit/dbb5fb0a8789137ec5958937b67e748e40676a66 Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: A src/main/org/openscience/cdk/controller/ChangeSingleElectronModule.java A src/main/org/openscience/cdk/controller/edit/AddSingleElectron.java A src/main/org/openscience/cdk/controller/edit/RemoveSingleElectron.java Log Message: ----------- Added modules and edits for radical support Commit: ec086581511b46038f7965bb9f787be37ab356fb https://github.com/cdk/cdk/commit/ec086581511b46038f7965bb9f787be37ab356fb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Set up the controlextra module for editing functionality for things beyond the IAtomContainer, such as drawing reactions. * includes javadoc and pmd checking * includes coverage test infrastructure Commit: 357361ded7c965c12f229f17787ba131a76922d0 https://github.com/cdk/cdk/commit/357361ded7c965c12f229f17787ba131a76922d0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 2f97bb599daec6547f3b0c1f37ef0057f88bce69 https://github.com/cdk/cdk/commit/2f97bb599daec6547f3b0c1f37ef0057f88bce69 Author: maclean <gilleain.torrance@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 96748b410e37f090a50b3b8f4446f82203569a36 https://github.com/cdk/cdk/commit/96748b410e37f090a50b3b8f4446f82203569a36 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (controlextra). Commit: a3c1e2e339079960978525035d552bc76caf58d7 https://github.com/cdk/cdk/commit/a3c1e2e339079960978525035d552bc76caf58d7 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java M src/main/org/openscience/cdk/controller/edit/AddSingleElectron.java M src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInExistingReactionEdit.java M src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInNewReactionEdit.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 5e50def60508b96039704ea4c325fe81f3c4fe57 https://github.com/cdk/cdk/commit/5e50def60508b96039704ea4c325fe81f3c4fe57 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderawt.cdkdepends A src/META-INF/renderawt.libdepends A src/META-INF/test-renderawt.cdkdepends A src/META-INF/test-renderawt.devellibdepends A src/META-INF/test-renderawt.libdepends A src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java A src/main/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java A src/test/org/openscience/cdk/coverage/RenderawtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderawtTests.java Log Message: ----------- Render AWT module which allows rendering of the abstract rendering elements onto an AWT widget (or Swing). * added javadoc and PMD testing * added module test suite * new modules: renderawt and test-renderawt Commit: b0c2a588bde250338800a52522e281cc6563aeed https://github.com/cdk/cdk/commit/b0c2a588bde250338800a52522e281cc6563aeed Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java M src/main/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java Log Message: ----------- Added support for GeneralPath to AWTDrawVisitor also made transform in AbstractAWTDrawVisitor protected Commit: 5606c9a7b871db928e9040c8c3497fe8135e617c https://github.com/cdk/cdk/commit/5606c9a7b871db928e9040c8c3497fe8135e617c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator Commit: 8c9b23bbad40fff01b927afcc3650e1905515757 https://github.com/cdk/cdk/commit/8c9b23bbad40fff01b927afcc3650e1905515757 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 41dac46b375c3f97215efd9906110c70a15af12c https://github.com/cdk/cdk/commit/41dac46b375c3f97215efd9906110c70a15af12c Author: maclean <gilleain.torrance@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 48b1707b5105b3035e24dba8ea39e63a38625529 https://github.com/cdk/cdk/commit/48b1707b5105b3035e24dba8ea39e63a38625529 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderawt). Commit: 17ec87bc05805ef8184491366592bdaad9b13ff7 https://github.com/cdk/cdk/commit/17ec87bc05805ef8184491366592bdaad9b13ff7 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Fixed some PMD warnings: longer variable names (renderawt). Commit: 176c7266c053560d47fc5706f44dd4e626a75b1d https://github.com/cdk/cdk/commit/176c7266c053560d47fc5706f44dd4e626a75b1d Author: Peter Odéus <peter.odeus@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Made buggy method visit(OvalElement..) render an oval correctly (position and size) by adding SWTRenderer's code from http://github.com/egonw/bioclipse.cheminformatics/blob/2.2.x/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/SWTRenderer.java Commit: 7715469854d903d2bcefaf4915702f0cc1e9742d https://github.com/cdk/cdk/commit/7715469854d903d2bcefaf4915702f0cc1e9742d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/rendersvg.cdkdepends A src/META-INF/rendersvg.libdepends A src/META-INF/test-rendersvg.cdkdepends A src/META-INF/test-rendersvg.devellibdepends A src/META-INF/test-rendersvg.libdepends A src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java A src/test/org/openscience/cdk/coverage/RendersvgCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrendersvgTests.java Log Message: ----------- Render SVG module allowing translation of the rendering elements to be converted into SVG statements. * added javadoc and PMD testing * added module test suite * new modules: rendersvg and test-rendersvg Commit: e9bf552befd85652dc01d7823eee632287679383 https://github.com/cdk/cdk/commit/e9bf552befd85652dc01d7823eee632287679383 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 4e0c84dcede7013ce711353e052427ebb68bd497 https://github.com/cdk/cdk/commit/4e0c84dcede7013ce711353e052427ebb68bd497 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (rendersvg). Commit: 63c03c982e000203a2e9b5e18882e1487f767922 https://github.com/cdk/cdk/commit/63c03c982e000203a2e9b5e18882e1487f767922 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Fixed some PMD warnings: longer variable names (rendersvg). Commit: 82e1ca7035e34f1994a70a1db0e468f6c8ec4111 https://github.com/cdk/cdk/commit/82e1ca7035e34f1994a70a1db0e468f6c8ec4111 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Compile fixes caused by rebasing artefacts as some modules still change bits in order modules Commit: af23b966222402b89930af6e8ff35361b96f4b1e https://github.com/cdk/cdk/commit/af23b966222402b89930af6e8ff35361b96f4b1e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlawt.cdkdepends A src/META-INF/controlawt.libdepends A src/META-INF/test-controlawt.cdkdepends A src/META-INF/test-controlawt.devellibdepends A src/META-INF/test-controlawt.libdepends M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java A src/test/org/openscience/cdk/coverage/ControlawtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolawtTests.java Log Message: ----------- Setting up the controlawt module. * including test module with coverage testgin * enabled PMD and JavaDoc testing Commit: a02bfb78b01efc8ede9a5879c7851776c286501c https://github.com/cdk/cdk/commit/a02bfb78b01efc8ede9a5879c7851776c286501c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Converted useAntiAliasing into a IGeneratorParameter Commit: 361accfbe6ab59e135c25fcfa9fa6d0adf5a9459 https://github.com/cdk/cdk/commit/361accfbe6ab59e135c25fcfa9fa6d0adf5a9459 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M .classpath M build.xml A jar/swt-gtk-3.4.2.jar A jar/swt-gtk-3.4.2.jar.meta A src/META-INF/renderswt.cdkdepends A src/META-INF/renderswt.libdepends A src/META-INF/test-renderswt.cdkdepends A src/META-INF/test-renderswt.devellibdepends A src/META-INF/test-renderswt.libdepends A src/main/org/openscience/cdk/renderer/font/SWTFontManager.java A src/test/org/openscience/cdk/coverage/RenderswtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderswtTests.java Log Message: ----------- Created a renderswt module, prepopulated with a SWTFontManager Commit: a0e4f10899bb634d3d1824d4ad6946a1505df2fc https://github.com/cdk/cdk/commit/a0e4f10899bb634d3d1824d4ad6946a1505df2fc Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M META-INF/MANIFEST.MF Log Message: ----------- Added all other CDK java package to be exported, solving access restriction issues in JChemPaint Commit: ddf86e4a2e4308a0efbfef7622b0e1a36752fa10 https://github.com/cdk/cdk/commit/ddf86e4a2e4308a0efbfef7622b0e1a36752fa10 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml Log Message: ----------- Added new control and renderer jars to dist-large and test-dist-large Commit: 95567738601700dcfafb89f0afcf338517c4fb35 https://github.com/cdk/cdk/commit/95567738601700dcfafb89f0afcf338517c4fb35 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M .gitignore Log Message: ----------- Ignore patch folders Commit: 9db6623e48c52cd05c80d7cce9e6e4030ad7d8e0 https://github.com/cdk/cdk/commit/9db6623e48c52cd05c80d7cce9e6e4030ad7d8e0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props M build.xml Log Message: ----------- Added a build.xml target to make a cdk-jchempaint add-on jar for the cdk.jar Commit: e13772509104710031aae10978aa0b34019c3a57 https://github.com/cdk/cdk/commit/e13772509104710031aae10978aa0b34019c3a57 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml Log Message: ----------- Only run the CDK-JChemPaint specific tests Commit: 73fa063af35d7f936a10339cdcac9cd83ec7a113 https://github.com/cdk/cdk/commit/73fa063af35d7f936a10339cdcac9cd83ec7a113 Author: Egon Willighagen <egonw@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M javadoc.xml Log Message: ----------- Removed use of the proprietary DocCheck utility Commit: 1d2a3ed701dc082cdaae66d36efbbadec888197c https://github.com/cdk/cdk/commit/1d2a3ed701dc082cdaae66d36efbbadec888197c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 15 Commit: f466cb4fa337ca56e9f772fa33b0cdcedbbc71a0 https://github.com/cdk/cdk/commit/f466cb4fa337ca56e9f772fa33b0cdcedbbc71a0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java Log Message: ----------- Uncommented method which seem to have gone lost. (controlawt). Commit: 314da4e2370d7a079eded982aff1d9d5ccc79d46 https://github.com/cdk/cdk/commit/314da4e2370d7a079eded982aff1d9d5ccc79d46 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 16 Commit: 0f0567d379b0096830b0d5d90810b8471ac23231 https://github.com/cdk/cdk/commit/0f0567d379b0096830b0d5d90810b8471ac23231 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 17 (rebased on CDK 1.3.8) Commit: d163bb2d36aeb31830813e1cf66facf16d787435 https://github.com/cdk/cdk/commit/d163bb2d36aeb31830813e1cf66facf16d787435 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-02-15 (Tue, 15 Feb 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Proper initialization at the primary renderer too. (renderextra). |
|
From: <noreply@gi...> - 2011-07-03 08:44:08
|
Branch: refs/tags/cdk-jchempaint-17 Home: https://github.com/cdk/cdk Commit: 96785a62f1e0c1bebdece5500b507666a925de38 https://github.com/cdk/cdk/commit/96785a62f1e0c1bebdece5500b507666a925de38 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderbasic.cdkdepends A src/META-INF/renderbasic.libdepends A src/META-INF/test-renderbasic.cdkdepends A src/META-INF/test-renderbasic.devellibdepends A src/META-INF/test-renderbasic.libdepends A src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java A src/main/org/openscience/cdk/renderer/elements/AtomSymbolElement.java A src/main/org/openscience/cdk/renderer/elements/ElementGroup.java A src/main/org/openscience/cdk/renderer/elements/LineElement.java A src/main/org/openscience/cdk/renderer/elements/OvalElement.java A src/main/org/openscience/cdk/renderer/elements/PathElement.java A src/main/org/openscience/cdk/renderer/elements/RectangleElement.java A src/main/org/openscience/cdk/renderer/elements/RingElement.java A src/main/org/openscience/cdk/renderer/elements/TextGroupElement.java A src/main/org/openscience/cdk/renderer/elements/WedgeLineElement.java A src/main/org/openscience/cdk/renderer/font/AWTFontManager.java A src/main/org/openscience/cdk/renderer/font/AbstractFontManager.java A src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicGenerator.java A src/main/org/openscience/cdk/renderer/generators/RingGenerator.java A src/main/org/openscience/cdk/renderer/selection/AbstractSelection.java A src/test/org/openscience/cdk/coverage/RenderbasicCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java Log Message: ----------- Setting up the new renderbasic module. * builds on the infrastructure defined in the render module * defines a basic renderer around an IAtomContainer data structure * new test framework including coverage testing Patches derived from: http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/branches/jchempaint-primary/ Commit: 40d743777761e97eeb9d0edc5393ff358cb47222 https://github.com/cdk/cdk/commit/40d743777761e97eeb9d0edc5393ff358cb47222 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/BoundsCalculator.java Log Message: ----------- Added the BoundsCalculator Commit: 82a77825b6c297c84de9efe91e42b212040729e5 https://github.com/cdk/cdk/commit/82a77825b6c297c84de9efe91e42b212040729e5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for IBond.Stereo Commit: 348a0c81c3648bac13f26ba47ca3e0fd040ccd6c https://github.com/cdk/cdk/commit/348a0c81c3648bac13f26ba47ca3e0fd040ccd6c Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/elements/GeneralPath.java A src/main/org/openscience/cdk/renderer/elements/path/Close.java A src/main/org/openscience/cdk/renderer/elements/path/CubicTo.java A src/main/org/openscience/cdk/renderer/elements/path/LineTo.java A src/main/org/openscience/cdk/renderer/elements/path/MoveTo.java A src/main/org/openscience/cdk/renderer/elements/path/PathBuilder.java A src/main/org/openscience/cdk/renderer/elements/path/PathElement.java A src/main/org/openscience/cdk/renderer/elements/path/QuadTo.java A src/main/org/openscience/cdk/renderer/elements/path/Type.java Log Message: ----------- Added new path element to describe more general paths see java.awt.geom.GeneralPath or org.eclipse.swt.graphics.Path Commit: c6c49f45698af4d977a5bfd511347f0b6610bbde https://github.com/cdk/cdk/commit/c6c49f45698af4d977a5bfd511347f0b6610bbde Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/renderbasic.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c009eba9f1a7d42ad76439fb8d598391f81e80f5 https://github.com/cdk/cdk/commit/c009eba9f1a7d42ad76439fb8d598391f81e80f5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the new IGeneratorParameter interfaces Commit: fd6dbf047f17942cbf8e8a4e438ec1d139f1d3fe https://github.com/cdk/cdk/commit/fd6dbf047f17942cbf8e8a4e438ec1d139f1d3fe Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: dcb922853c907e191e5311ad8adc6db4a0586d7e https://github.com/cdk/cdk/commit/dcb922853c907e191e5311ad8adc6db4a0586d7e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 0e3fb77f3bf6cf6360d116277a85d3401235ec62 https://github.com/cdk/cdk/commit/0e3fb77f3bf6cf6360d116277a85d3401235ec62 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- BasicBondGenerator should generate bonds in consistent order Commit: d7f0fa2ac16ce26e7283bff2fb53be6bf077f12b https://github.com/cdk/cdk/commit/d7f0fa2ac16ce26e7283bff2fb53be6bf077f12b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator Commit: 04a52c43df549ea79481161babc0f412a683827b https://github.com/cdk/cdk/commit/04a52c43df549ea79481161babc0f412a683827b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Moved rendering parameters for atom draw colors to the new IGeneratorParameter API Commit: 43d60d474fb594c22d464cbd925043bbf1b741bd https://github.com/cdk/cdk/commit/43d60d474fb594c22d464cbd925043bbf1b741bd Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Moved the atom radius into the new rendering parameter API (renderbasic module) Commit: b492a0396016806e1c1de97026642883856f92ec https://github.com/cdk/cdk/commit/b492a0396016806e1c1de97026642883856f92ec Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Set up a API to retrieve a IRenderingParameter from the RenderModel Commit: 4b09852a913bdea3839147c97b28dfc4fbf5959f https://github.com/cdk/cdk/commit/4b09852a913bdea3839147c97b28dfc4fbf5959f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Fixed returning of parameters Commit: fc44e2ea0ec2d255a52059dbe5af97934c4ac692 https://github.com/cdk/cdk/commit/fc44e2ea0ec2d255a52059dbe5af97934c4ac692 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- some double bonds were rendered as wedge Signed-off-by: Arvid Berg <goglepox@...> Commit: 99fc5de1e836a7c0bc342dcb28803c2bf18ccd26 https://github.com/cdk/cdk/commit/99fc5de1e836a7c0bc342dcb28803c2bf18ccd26 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Removed last four rendering parameters from BasicAtomGenerator: isCompact, compactShape, isKekule, and showEndCarbons Commit: 0250c9a116802f260bd92ca65d299841de3f03d2 https://github.com/cdk/cdk/commit/0250c9a116802f260bd92ca65d299841de3f03d2 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Converted bondWidth and defaultBondColor into IGeneratorParameter's Commit: f0d26f61e57e13070858da7a9d37b7abecda5506 https://github.com/cdk/cdk/commit/f0d26f61e57e13070858da7a9d37b7abecda5506 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RingGenerator.java Log Message: ----------- Converted showAromaticity and cdkStyleAromaticity to IGeneratorParameter variants Commit: 16dc479b7eb705c913408af54955ba5e33b034c8 https://github.com/cdk/cdk/commit/16dc479b7eb705c913408af54955ba5e33b034c8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Added missing parameter from returned list Commit: 969069f81ef1b7ef4e076ae39f0b5bdc28786367 https://github.com/cdk/cdk/commit/969069f81ef1b7ef4e076ae39f0b5bdc28786367 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RingGenerator.java Log Message: ----------- Converted ringProportion to IGeneratorParameter variants Commit: a02222e6d5bf4a7df75ad406ed044659c1f0a5d1 https://github.com/cdk/cdk/commit/a02222e6d5bf4a7df75ad406ed044659c1f0a5d1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted margin into the RenderingParameter variant Commit: ac593945f6129c3b2441ec2d018b62d0b5d5115f https://github.com/cdk/cdk/commit/ac593945f6129c3b2441ec2d018b62d0b5d5115f Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/test/org/openscience/cdk/renderer/ElementUtility.java A src/test/org/openscience/cdk/renderer/RendererTest.java A src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java A src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java A src/test/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java Log Message: ----------- A few test classes for the renderer package Commit: d17253afb597bf10140ddbcca9b8b03573778208 https://github.com/cdk/cdk/commit/d17253afb597bf10140ddbcca9b8b03573778208 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/RendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Copyright headers Commit: 2a86908fc73006e8972de92ef8c01210aead6662 https://github.com/cdk/cdk/commit/2a86908fc73006e8972de92ef8c01210aead6662 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/RendererTest.java Log Message: ----------- Cleaned up unit test a bit: * added missing assertion * removed uncommented ugly hacks * use AtomContainerRenderer from this module, not Renderer from renderextra Commit: dc0b6855c3447a6fc6380ed3c88fdff1e61ee882 https://github.com/cdk/cdk/commit/dc0b6855c3447a6fc6380ed3c88fdff1e61ee882 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java R src/test/org/openscience/cdk/renderer/RendererTest.java Log Message: ----------- Renamed into AtomContainerRendererTest, following common naming patterns Commit: 4eab24a2fbf509711425dc51be95850f9f8ea54e https://github.com/cdk/cdk/commit/4eab24a2fbf509711425dc51be95850f9f8ea54e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java Log Message: ----------- Added new tests to the module test suite Commit: 19ff7448b57f24647f9d98803dd9498371e89ef9 https://github.com/cdk/cdk/commit/19ff7448b57f24647f9d98803dd9498371e89ef9 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java Log Message: ----------- Placed in the appropriate test modules Commit: 9b700e9d974c438b28f83bff7d1b0a16ad634822 https://github.com/cdk/cdk/commit/9b700e9d974c438b28f83bff7d1b0a16ad634822 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/test-renderbasic.cdkdepends Log Message: ----------- Added missing dependencies Commit: 8ce2474495121d41640cc809c20c69157f2222c8 https://github.com/cdk/cdk/commit/8ce2474495121d41640cc809c20c69157f2222c8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted useAntiAliasing into a IGeneratorParameter Commit: 16276749009c6b4b29943eb90b16efb5373027ad https://github.com/cdk/cdk/commit/16276749009c6b4b29943eb90b16efb5373027ad Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted FontName and FontStyle into IGeneratorParameters Commit: c4f720fba40253536e628b162ea718be2411d339 https://github.com/cdk/cdk/commit/c4f720fba40253536e628b162ea718be2411d339 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Converted BondDistance into an IGeneratorParameter Commit: fd3b6cf0e4a1d6dbaf6a057e9b394cae7aa29549 https://github.com/cdk/cdk/commit/fd3b6cf0e4a1d6dbaf6a057e9b394cae7aa29549 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Factored out a ColorHash IRenderingParamater Commit: 2fa3d30b2540a25f586a40accadd3b628e281db3 https://github.com/cdk/cdk/commit/2fa3d30b2540a25f586a40accadd3b628e281db3 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: 078f65e47391abb28ac7995eb620aa50f1a01851 https://github.com/cdk/cdk/commit/078f65e47391abb28ac7995eb620aa50f1a01851 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Refactored foreground color into a IGeneratorParameter Commit: 61d079216d7b4c28cb537866743e2df34ff57717 https://github.com/cdk/cdk/commit/61d079216d7b4c28cb537866743e2df34ff57717 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java A src/main/org/openscience/cdk/renderer/generators/IAtomContainerGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Split up the old IGenerator interface into IGenerator and IAtomContainerGenerator, the first now only containing the method for getting the parameters Commit: be75022adf7cf805c74a66ef2e3a64b544593f41 https://github.com/cdk/cdk/commit/be75022adf7cf805c74a66ef2e3a64b544593f41 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 25dd8ea140f8d2cb6eb37b9b916d0a415fb3a820 https://github.com/cdk/cdk/commit/25dd8ea140f8d2cb6eb37b9b916d0a415fb3a820 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 523a84b6be8895e6a5ed841b8e8757e5a8a94012 https://github.com/cdk/cdk/commit/523a84b6be8895e6a5ed841b8e8757e5a8a94012 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 135a308337fe0c3164028688446e6d243b20f6ec https://github.com/cdk/cdk/commit/135a308337fe0c3164028688446e6d243b20f6ec Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java R src/main/org/openscience/cdk/renderer/generators/IAtomContainerGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (renderbasic). Commit: ac55656a378694c45340c93f874bb96a5909ffb4 https://github.com/cdk/cdk/commit/ac55656a378694c45340c93f874bb96a5909ffb4 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 587e7be570302db50f50469095643df4fa1cd279 https://github.com/cdk/cdk/commit/587e7be570302db50f50469095643df4fa1cd279 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (renderbasic). Commit: f9574b55406c0cb2f5057f8c76519ca4a5d16ee8 https://github.com/cdk/cdk/commit/f9574b55406c0cb2f5057f8c76519ca4a5d16ee8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Return two missing parameters Commit: 9811ce941f98684c3b3ed1dd2065c47645b59b8c https://github.com/cdk/cdk/commit/9811ce941f98684c3b3ed1dd2065c47645b59b8c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Fixed a generics warning: strong typed the field Commit: 7d9b9eb92cd3a6944673bf1584ad2bfba94b74be https://github.com/cdk/cdk/commit/7d9b9eb92cd3a6944673bf1584ad2bfba94b74be Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Removed scale and zoom form renderer and replaced with values form the generator parameters Commit: 2dca77d7c51374562bf91a0bf334552ed7b6505a https://github.com/cdk/cdk/commit/2dca77d7c51374562bf91a0bf334552ed7b6505a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderbasic). Commit: e577ea911115878f5e409ee3d6d1a693fef40d0e https://github.com/cdk/cdk/commit/e577ea911115878f5e409ee3d6d1a693fef40d0e Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Compact shape tests Commit: a1abb8e8ad20407c8c3291e99f8fa36b5eaf3a1d https://github.com/cdk/cdk/commit/a1abb8e8ad20407c8c3291e99f8fa36b5eaf3a1d Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Atom color tests Commit: 40d52b8511653a5bda39c95b0b44656c1c5c5796 https://github.com/cdk/cdk/commit/40d52b8511653a5bda39c95b0b44656c1c5c5796 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Color by type test Commit: e2b6a102369bf3c15521849a491ea78a6d4f5a50 https://github.com/cdk/cdk/commit/e2b6a102369bf3c15521849a491ea78a6d4f5a50 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Explicit hydrogens test Commit: 8b2feb49574012eb98d672d3f2496d9240cbe15e https://github.com/cdk/cdk/commit/8b2feb49574012eb98d672d3f2496d9240cbe15e Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Kekule test Commit: e6eefdce160cd65af8eeae991d7c21c7bb545203 https://github.com/cdk/cdk/commit/e6eefdce160cd65af8eeae991d7c21c7bb545203 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Show end carbons test Commit: 351a1a2332ca9e81036456f1acc2c3df381f8298 https://github.com/cdk/cdk/commit/351a1a2332ca9e81036456f1acc2c3df381f8298 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/test-renderbasic.cdkdepends M src/META-INF/test-renderbasic.libdepends Log Message: ----------- Added missing new dependencies for the test-renderbasic module Commit: a25c24521580bdbbd49a4e004e39f2565f389683 https://github.com/cdk/cdk/commit/a25c24521580bdbbd49a4e004e39f2565f389683 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Use the basic scene generator in the abstract base class Commit: 4c0d6818dc931ee3fe7b6ada5e7a626250198cf8 https://github.com/cdk/cdk/commit/4c0d6818dc931ee3fe7b6ada5e7a626250198cf8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/elements/PathElement.java M src/main/org/openscience/cdk/renderer/elements/WedgeLineElement.java M src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java A src/test/org/openscience/cdk/renderer/elements/AbstractElementTest.java A src/test/org/openscience/cdk/renderer/elements/PathElementTest.java A src/test/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java Log Message: ----------- Added two missing test classes, for PathElement and WedgeLineElement Commit: 9f7b74ef729992fe314e46c79540f44664443cba https://github.com/cdk/cdk/commit/9f7b74ef729992fe314e46c79540f44664443cba Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/elements/AbstractElementTest.java M src/test/org/openscience/cdk/renderer/elements/PathElementTest.java M src/test/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java Log Message: ----------- Fixed compiliation: corrected cdk module annotation. Commit: 621168f2ac9764ff930d013ef4934dccea169cb3 https://github.com/cdk/cdk/commit/621168f2ac9764ff930d013ef4934dccea169cb3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Mirror structures on Y-axis to compensate for different coordinate systems. Fixes bc-bug #1654 cdk-bug #2855247 Commit: 45cf451ebda7e4e834f1af8851212c169fcc0713 https://github.com/cdk/cdk/commit/45cf451ebda7e4e834f1af8851212c169fcc0713 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Fixed the AtomContainerRender to implement IRenderer; updated the toModelCoordinates() to match this interface Commit: 00147d507eec3b0849844b525835a0fd2ab88947 https://github.com/cdk/cdk/commit/00147d507eec3b0849844b525835a0fd2ab88947 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java A src/main/org/openscience/cdk/renderer/AverageBondLengthCalculator.java Log Message: ----------- Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (renderbasic). Commit: d9e33c1cc7ab143696e358f44712884280f32b80 https://github.com/cdk/cdk/commit/d9e33c1cc7ab143696e358f44712884280f32b80 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- More types in renderers, and associations between renderers Commit: 4e523290aeac1f5f58a531586873e09fc9ce8b48 https://github.com/cdk/cdk/commit/4e523290aeac1f5f58a531586873e09fc9ce8b48 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Using IRenderer<T> interface instead of implementation Commit: b7084c196ee14cabb333f104b410b25fd5789275 https://github.com/cdk/cdk/commit/b7084c196ee14cabb333f104b410b25fd5789275 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Made the aromatic ring property 'proportion to move in towards the ring center' customizable (implements #3047009) Commit: 07173b917c67bbfc8f806645b5d440d3872ff2b6 https://github.com/cdk/cdk/commit/07173b917c67bbfc8f806645b5d440d3872ff2b6 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Updated for API changes in CDK 1.3.6 Commit: 624649a4dc3feab73c7303452a6f31c0299ab233 https://github.com/cdk/cdk/commit/624649a4dc3feab73c7303452a6f31c0299ab233 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/rendercontrol.cdkdepends A src/META-INF/rendercontrol.libdepends A src/META-INF/test-rendercontrol.cdkdepends A src/META-INF/test-rendercontrol.devellibdepends A src/META-INF/test-rendercontrol.libdepends A src/main/org/openscience/cdk/renderer/generators/ControllerFeedbackGenerator.java A src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java A src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java A src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java A src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java A src/main/org/openscience/cdk/renderer/selection/IncrementalSelection.java A src/main/org/openscience/cdk/renderer/selection/LassoSelection.java A src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java A src/main/org/openscience/cdk/renderer/selection/MultiSelection.java A src/main/org/openscience/cdk/renderer/selection/RectangleSelection.java A src/main/org/openscience/cdk/renderer/selection/ShapeSelection.java A src/main/org/openscience/cdk/renderer/selection/SingleSelection.java A src/test/org/openscience/cdk/coverage/RendercontrolCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrendercontrolTests.java Log Message: ----------- Set up of the rendercontrol module, containing the rendering of controller feedback. * rendercontrol module * enabled DocCheck and PMD testing Commit: b6592d04c7e43f18586d1af948f12af0adac10bb https://github.com/cdk/cdk/commit/b6592d04c7e43f18586d1af948f12af0adac10bb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Updated for the new IGenerator.getParameters() interface method Commit: 278ec4ce119b4559411b5b461de3ee2469ae659d https://github.com/cdk/cdk/commit/278ec4ce119b4559411b5b461de3ee2469ae659d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Changed rendering of merge candidates to indicate what pairs will merge Uses new GeneralPath element Commit: e52a292c3f1b5e453a19c4a95d6d31c460edc142 https://github.com/cdk/cdk/commit/e52a292c3f1b5e453a19c4a95d6d31c460edc142 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/rendercontrol.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: b7ec937aa09bc147f7478df4a8672c6efda41d3e https://github.com/cdk/cdk/commit/b7ec937aa09bc147f7478df4a8672c6efda41d3e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 08fd5542a3903f2f228d4a5a164ed81b7f39e351 https://github.com/cdk/cdk/commit/08fd5542a3903f2f228d4a5a164ed81b7f39e351 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/selection/LinkedSelection.java M src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java Log Message: ----------- Added LinkedSelection A selection for selecting a connected part of a model Commit: 9287a5fd8b635b9da8f89f20ab412a8fbe5b8524 https://github.com/cdk/cdk/commit/9287a5fd8b635b9da8f89f20ab412a8fbe5b8524 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Updated for more IGeneratorParameter changes in BasicAtomGenerator Commit: 07dff754c7a06cb09a2881880264fbe9e2dcaa84 https://github.com/cdk/cdk/commit/07dff754c7a06cb09a2881880264fbe9e2dcaa84 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: 871f7477cda6e25154e1bbff62d108071820299e https://github.com/cdk/cdk/commit/871f7477cda6e25154e1bbff62d108071820299e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Updated for BondWidth now being a IGeneratorParameter Commit: 5b7e29c3bf184c00e34eda1621c0ea17ce19464a https://github.com/cdk/cdk/commit/5b7e29c3bf184c00e34eda1621c0ea17ce19464a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/selection/LinkedSelection.java M src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java M src/main/org/openscience/cdk/renderer/selection/MultiSelection.java M src/main/org/openscience/cdk/renderer/selection/ShapeSelection.java M src/main/org/openscience/cdk/renderer/selection/SingleSelection.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: e21bbe85de1fdc5357e884df1e1748e03b49aee1 https://github.com/cdk/cdk/commit/e21bbe85de1fdc5357e884df1e1748e03b49aee1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 6494ec3518b0021c5b97abe0e68927994382c212 https://github.com/cdk/cdk/commit/6494ec3518b0021c5b97abe0e68927994382c212 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Converted externalHighlightColor to the new rendering parameter API Commit: 84026a24aedda324ecb4fb39da73ade0e70a76fa https://github.com/cdk/cdk/commit/84026a24aedda324ecb4fb39da73ade0e70a76fa Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Converted hoverOverColor to the new rendering parameter API Commit: 9b0f8659fd9f2a8f3cffde27d016303d1a5a17bb https://github.com/cdk/cdk/commit/9b0f8659fd9f2a8f3cffde27d016303d1a5a17bb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Moved ExternalHighlightColor into RendererModel for now, to solve a compile dependency Commit: d060e06546fce74dad846093cea6dffcc573ca65 https://github.com/cdk/cdk/commit/d060e06546fce74dad846093cea6dffcc573ca65 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (rendercontrol). Commit: ea7a8bfd0c3ee5c4f26ad039e8688dfb880a85d7 https://github.com/cdk/cdk/commit/ea7a8bfd0c3ee5c4f26ad039e8688dfb880a85d7 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: ba15d73a35e4211622b8a74cd929eb15017a07a0 https://github.com/cdk/cdk/commit/ba15d73a35e4211622b8a74cd929eb15017a07a0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (rendercontrol). Commit: 2b20d3ee13a2f71f3ef29e3fb7178a6cbc4a72a2 https://github.com/cdk/cdk/commit/2b20d3ee13a2f71f3ef29e3fb7178a6cbc4a72a2 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (rendercontrol). Commit: 5475408f8c9ebf57cc5e65d189e416ab5480b615 https://github.com/cdk/cdk/commit/5475408f8c9ebf57cc5e65d189e416ab5480b615 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Also return the parameters of the super class -a (rendercontrol). Commit: 1708bfb2fe757c9647923938a7ea3763641ca68d https://github.com/cdk/cdk/commit/1708bfb2fe757c9647923938a7ea3763641ca68d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml M src/META-INF/control.cdkdepends A src/META-INF/test-control.cdkdepends A src/META-INF/test-control.devellibdepends A src/META-INF/test-control.libdepends A src/main/org/openscience/cdk/controller/Changed.java A src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java A src/main/org/openscience/cdk/controller/IChemModelEventRelayHandler.java A src/main/org/openscience/cdk/controller/IChemModelRelay.java A src/main/org/openscience/cdk/controller/IControllerModel.java A src/main/org/openscience/cdk/controller/IControllerModule.java M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java A src/main/org/openscience/cdk/controller/edit/IEdit.java A src/main/org/openscience/cdk/controller/undoredo/IUndoListener.java A src/main/org/openscience/cdk/controller/undoredo/IUndoRedoFactory.java A src/main/org/openscience/cdk/controller/undoredo/IUndoRedoable.java A src/main/org/openscience/cdk/controller/undoredo/UndoRedoHandler.java M src/test/org/openscience/cdk/coverage/ControlCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolTests.java Log Message: ----------- Set up of the new controller infrastructure. * new content of the 'control' module * new test suite with coverage testing * enabled DocCheck and PMD testing Commit: 37031a5c4e6ae6f11a37a8a686c7592d9ff67ee7 https://github.com/cdk/cdk/commit/37031a5c4e6ae6f11a37a8a686c7592d9ff67ee7 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: d41ef733c24dfa6290f8aefd46eb69707d964d19 https://github.com/cdk/cdk/commit/d41ef733c24dfa6290f8aefd46eb69707d964d19 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/controller/IAtomBondEdits.java M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Re-factored out methods for atom and bonds edit These methods are candidates for being replaced with IEdit With copyright Commit: 57cecf8e8d4b8cee0ea74ee1febfec528e9dadf7 https://github.com/cdk/cdk/commit/57cecf8e8d4b8cee0ea74ee1febfec528e9dadf7 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/IEdit.java Log Message: ----------- Added new edits for replacing modify methods in ControllerHub The edits handles the modifying of the model and the undo/redo stuff. Commit: f1c0ca878cc4fb4d9a72b6f26966634c7af15355 https://github.com/cdk/cdk/commit/f1c0ca878cc4fb4d9a72b6f26966634c7af15355 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/control.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c23c3d4a219e46465aee90f0208e175b428b58ba https://github.com/cdk/cdk/commit/c23c3d4a219e46465aee90f0208e175b428b58ba Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Defines two new stereo types. Commit: 641a96bc366029277d5ef82a05ffd45c66d60969 https://github.com/cdk/cdk/commit/641a96bc366029277d5ef82a05ffd45c66d60969 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Rewrote selection check to avoid NPE Commit: 19d8cfa381569b81ab02ecc3256b15cf19ca13af https://github.com/cdk/cdk/commit/19d8cfa381569b81ab02ecc3256b15cf19ca13af Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: c68c3f18710d7beef920806fb64694bd342ed9e7 https://github.com/cdk/cdk/commit/c68c3f18710d7beef920806fb64694bd342ed9e7 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Changed wedge width to rendering parameter Commit: cf88296b23767e49ec5d1ea32462b8061da48dc0 https://github.com/cdk/cdk/commit/cf88296b23767e49ec5d1ea32462b8061da48dc0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (control). Commit: 966b90e92968cf3fe20a8978073ea6df236a8cef https://github.com/cdk/cdk/commit/966b90e92968cf3fe20a8978073ea6df236a8cef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml Log Message: ----------- Added compiling of the test-control module Commit: 1a1a01738c6aabba8edd596347c243a4d52812c4 https://github.com/cdk/cdk/commit/1a1a01738c6aabba8edd596347c243a4d52812c4 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IAtomBondEdits.java M src/main/org/openscience/cdk/controller/IChemModelRelay.java A src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Moved all methods except the most important from IChemModelRelay to IOldChemModelRelay Commit: d2a2e174554c12867f7c909fd7bc2dd8290a1c4e https://github.com/cdk/cdk/commit/d2a2e174554c12867f7c909fd7bc2dd8290a1c4e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java M src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module control Commit: 625a595e3b2a8b1e0e5f90a76180b728c1d49f6f https://github.com/cdk/cdk/commit/625a595e3b2a8b1e0e5f90a76180b728c1d49f6f Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module controlbasic Commit: f4d24333f3e7e450e21a883bb10ca5963976e287 https://github.com/cdk/cdk/commit/f4d24333f3e7e450e21a883bb10ca5963976e287 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Changed select(IncrementalSelection) to select(IChemObjectSelection) The select method uses method that exists on IChemObjectSelection interface Commit: 3e233f9330a0875294fd05161708badb3b3470ef https://github.com/cdk/cdk/commit/3e233f9330a0875294fd05161708badb3b3470ef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Added dependency on IOldChemModelRelay which is needed at this level Commit: 40ecbc7e75e27b30fb128177bf4a44725343f571 https://github.com/cdk/cdk/commit/40ecbc7e75e27b30fb128177bf4a44725343f571 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IMouseEventRelay.java Log Message: ----------- Added two missing methods for scroll event handling Commit: 26c93a67eb06b0f59a27052faa46533b2a933a5f https://github.com/cdk/cdk/commit/26c93a67eb06b0f59a27052faa46533b2a933a5f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlbasic.cdkdepends A src/META-INF/controlbasic.libdepends A src/META-INF/test-controlbasic.cdkdepends A src/META-INF/test-controlbasic.devellibdepends A src/META-INF/test-controlbasic.libdepends A src/main/org/openscience/cdk/controller/AddAtomModule.java A src/main/org/openscience/cdk/controller/AddBondDragModule.java A src/main/org/openscience/cdk/controller/AddBondModule.java A src/main/org/openscience/cdk/controller/AddRingModule.java A src/main/org/openscience/cdk/controller/AlterBondStereoModule.java A src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java A src/main/org/openscience/cdk/controller/ControllerHub.java A src/main/org/openscience/cdk/controller/ControllerModel.java A src/main/org/openscience/cdk/controller/ControllerParameters.java A src/main/org/openscience/cdk/controller/CycleSymbolModule.java A src/main/org/openscience/cdk/controller/DrawBondModule.java A src/main/org/openscience/cdk/controller/HighlightModule.java A src/main/org/openscience/cdk/controller/MoveModule.java A src/main/org/openscience/cdk/controller/PhantomBondGenerator.java A src/main/org/openscience/cdk/controller/RemoveModule.java A src/main/org/openscience/cdk/controller/RotateModule.java A src/main/org/openscience/cdk/controller/SelectLassoModule.java A src/main/org/openscience/cdk/controller/SelectSquareModule.java A src/main/org/openscience/cdk/controller/ZoomModule.java A src/main/org/openscience/cdk/controller/edit/AbstractEdit.java A src/main/org/openscience/cdk/controller/edit/AddAtom.java A src/main/org/openscience/cdk/controller/edit/AddBond.java A src/main/org/openscience/cdk/controller/edit/AppendAtom.java A src/main/org/openscience/cdk/controller/edit/CreateBond.java A src/main/org/openscience/cdk/controller/edit/RemoveAtom.java A src/main/org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.java A src/main/org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeAtomSymbolEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeChargeEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeCoordsEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeHydrogenCountEdit.java A src/main/org/openscience/cdk/controller/undoredo/ClearAllEdit.java A src/main/org/openscience/cdk/controller/undoredo/MoveAtomEdit.java A src/main/org/openscience/cdk/controller/undoredo/RemoveAtomsAndBondsEdit.java A src/main/org/openscience/cdk/controller/undoredo/ReplaceAtomEdit.java A src/test/org/openscience/cdk/coverage/ControlbasicCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolbasicTests.java Log Message: ----------- Set up a controlbasic module, with basic editing functionality, like adding and moving atoms, and changing basic atom and bond properties. * includes javadoc and pmd testing * includes coverage testing framework Commit: c81e97c0a83d65bbc8baf9904b4625e147baca33 https://github.com/cdk/cdk/commit/c81e97c0a83d65bbc8baf9904b4625e147baca33 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/RotateModule.java Log Message: ----------- implemented RotateModule Commit: 8e8dddeb592ccc0a11da836e52cbf22b1b2e2b2d https://github.com/cdk/cdk/commit/8e8dddeb592ccc0a11da836e52cbf22b1b2e2b2d Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Moving bugs fixed Commit: 753143383dfcc03c615eee06655d941c5a35fc70 https://github.com/cdk/cdk/commit/753143383dfcc03c615eee06655d941c5a35fc70 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- bugfixed mergeMolecules methods Commit: 150fcf8256329be2835f1dbeb8be494dc67cbdde https://github.com/cdk/cdk/commit/150fcf8256329be2835f1dbeb8be494dc67cbdde Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/DrawBondModule.java M src/main/org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.java M src/main/org/openscience/cdk/controller/undoredo/IUndoRedoFactory.java Log Message: ----------- Updated for IBond.Stereo API change Commit: 136cf08dfa13555439c3ce500db1d02ee5654ec6 https://github.com/cdk/cdk/commit/136cf08dfa13555439c3ce500db1d02ee5654ec6 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Using add operation in Point2d Commit: 7bfa9e0c76b186a26949b19fd3b8acc554afe774 https://github.com/cdk/cdk/commit/7bfa9e0c76b186a26949b19fd3b8acc554afe774 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- mergeMap reference model.getMerge() using the former for clarity Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: b98b021f455e3b6265187cfb9c33458550203f5b https://github.com/cdk/cdk/commit/b98b021f455e3b6265187cfb9c33458550203f5b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java M src/main/org/openscience/cdk/controller/HighlightModule.java M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: d5d18831e90d435ecaa8d04ade72c77e44f5c9c9 https://github.com/cdk/cdk/commit/d5d18831e90d435ecaa8d04ade72c77e44f5c9c9 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/edit/AbstractEdit.java M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java A src/main/org/openscience/cdk/controller/edit/CompositEdit.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java A src/main/org/openscience/cdk/controller/edit/Merge.java A src/main/org/openscience/cdk/controller/edit/Move.java A src/main/org/openscience/cdk/controller/edit/MoveOptionalUndo.java M src/main/org/openscience/cdk/controller/edit/RemoveAtom.java A src/main/org/openscience/cdk/controller/edit/RemoveBond.java A src/main/org/openscience/cdk/controller/edit/SetBondOrder.java A src/main/org/openscience/cdk/controller/edit/SetCharge.java A src/main/org/openscience/cdk/controller/edit/SetStereo.java A src/main/org/openscience/cdk/controller/edit/SetSymbol.java Log Message: ----------- Added new edits for replacing modify methods in ControllerHub The edits handles the modifying of the model and the undo/redo stuff. Commit: 49d9884d84aa63dcedfd9d6459ac2789ce96d057 https://github.com/cdk/cdk/commit/49d9884d84aa63dcedfd9d6459ac2789ce96d057 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Added hack to filter out none final MoveOptionalUndo edits Commit: e6e6d22f632b13d35f77d310f2f8c2f7c4501622 https://github.com/cdk/cdk/commit/e6e6d22f632b13d35f77d310f2f8c2f7c4501622 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/AddBondModule.java M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java R src/main/org/openscience/cdk/controller/DrawBondModule.java M src/main/org/openscience/cdk/controller/MoveModule.java M src/main/org/openscience/cdk/controller/RemoveModule.java Log Message: ----------- Re-factored modules to use new edit operations instead of methods in IChemModelRelay Commit: c6763eee70b565170b8ce4e5e7023eb3280ed12a https://github.com/cdk/cdk/commit/c6763eee70b565170b8ce4e5e7023eb3280ed12a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/controlbasic.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: b5357b0eb378f2c701d1aad233cfd17426192a13 https://github.com/cdk/cdk/commit/b5357b0eb378f2c701d1aad233cfd17426192a13 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java M src/main/org/openscience/cdk/controller/RotateModule.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: 012ae44007516467b3bb10df925d8e2c2165ee8b https://github.com/cdk/cdk/commit/012ae44007516467b3bb10df925d8e2c2165ee8b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/PhantomBondGenerator.java Log Message: ----------- Changed PhantomBondGenerator to use override color in BasicBondRenderer This simplifies this generator and allows it to draw aromatic rings Commit: e2ba6c60ed38b945582d30306d74a984d63d996d https://github.com/cdk/cdk/commit/e2ba6c60ed38b945582d30306d74a984d63d996d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Moved code handling merge to static methods This so that they can be reused in other modules like AddRingModuel Commit: c7078ba8fc2dceabccea8cd252ba13dacbcb09db https://github.com/cdk/cdk/commit/c7078ba8fc2dceabccea8cd252ba13dacbcb09db Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java A src/main/org/openscience/cdk/controller/edit/CreateRing.java Log Message: ----------- Added CreateRing edit and re-factored AddRingModule to use it The handling of aromaticity is slightly different from the old way, and it should be handled by the Merge edit to get the same behavior when merging a aromatic ring with move. Commit: cc0b47cd4350817cacd0ec1568c2421fe70a2659 https://github.com/cdk/cdk/commit/cc0b47cd4350817cacd0ec1568c2421fe70a2659 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/MoveModule.java R src/main/org/openscience/cdk/controller/edit/MoveOptionalUndo.java A src/main/org/openscience/cdk/controller/edit/OptionalUndoEdit.java Log Message: ----------- Replaced MoveOptionalUndo with OptionalUndoEdit wrapper. The wrapper allows for adding optional undo to any edit. This is a workaround for allowing small incremental edits that is not pushed to the undo stack and then push a edit that is not executed but are pushed to the undo stack representing the operations done by all smaller incremental edits. Commit: c6102883c9eb65f9664735888f9fd3167ded7d60 https://github.com/cdk/cdk/commit/c6102883c9eb65f9664735888f9fd3167ded7d60 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/RotateModule.java A src/main/org/openscience/cdk/controller/edit/Rotate.java Log Message: ----------- Moved RotateModule to new edit model Commit: 4932e066c8da79a092f4dfc53bf7a8c9e59c5c64 https://github.com/cdk/cdk/commit/4932e066c8da79a092f4dfc53bf7a8c9e59c5c64 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/CycleSymbolModule.java Log Message: ----------- Fixed bug where the last element would not be part of cycle Also moved execute(...) to end of method Commit: a177b105620107a769d4b3eb8bccbce5db3c3866 https://github.com/cdk/cdk/commit/a177b105620107a769d4b3eb8bccbce5db3c3866 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/CompositEdit.java M src/main/org/openscience/cdk/controller/edit/RemoveAtom.java Log Message: ----------- Changed add/remove explicit hydrogens to use IEdits Solves bug #1249 Commit: 193776bff21902f3234635e9c882cecaa272b06f https://github.com/cdk/cdk/commit/193776bff21902f3234635e9c882cecaa272b06f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/ZoomModule.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 2a0ddacdfe2f418889e261590e8c07603bdf466f https://github.com/cdk/cdk/commit/2a0ddacdfe2f418889e261590e8c07603bdf466f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/PhantomBondGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (controlbasic). Commit: 529338fcd21901d46f13bcef7ce002531dfc9e43 https://github.com/cdk/cdk/commit/529338fcd21901d46f13bcef7ce002531dfc9e43 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 16f976730d2ac29979f525bbd45846810f83b42d https://github.com/cdk/cdk/commit/16f976730d2ac29979f525bbd45846810f83b42d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/ZoomModule.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (controlbasic). Commit: b1eb74fa3ddc4b501bd9b7e17b647716c97b66e5 https://github.com/cdk/cdk/commit/b1eb74fa3ddc4b501bd9b7e17b647716c97b66e5 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java Log Message: ----------- Enables AlterBondStereoModule to cycle between different stereo modes UP->UP_INVERTED->NONE->UP... DOWN->DOWN_INVERTED->NONE->DOWN... Commit: 276eb4a21f8a3974263c1cb66c84e0222a374e5a https://github.com/cdk/cdk/commit/276eb4a21f8a3974263c1cb66c84e0222a374e5a Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Removed structure changed event when changing model Commit: 4f3026296ffe3adf5dea3dd14025d5178daaed18 https://github.com/cdk/cdk/commit/4f3026296ffe3adf5dea3dd14025d5178daaed18 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddBondModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module controlbasic Commit: c1295219f50048c542c49b96ba485f488f5f46e0 https://github.com/cdk/cdk/commit/c1295219f50048c542c49b96ba485f488f5f46e0 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Calculate average bond for atomcontainer instead of chemModel Commit: d8b3e6ffa3e4cd01241640ee8599b66afd3563ac https://github.com/cdk/cdk/commit/d8b3e6ffa3e4cd01241640ee8599b66afd3563ac Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java Log Message: ----------- Only create atoms and bonds the first time redo is called. Solves cdk-bug #2886402 Commit: 67565e82394103c47be5229ed16b7570ef2c0675 https://github.com/cdk/cdk/commit/67565e82394103c47be5229ed16b7570ef2c0675 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/edit/AbstractEdit.java M src/main/org/openscience/cdk/controller/edit/CompositEdit.java Log Message: ----------- Added update of hydrogens after edit. Commit: 556819612dc7093e26c2bce8c3b21ba10202dd7c https://github.com/cdk/cdk/commit/556819612dc7093e26c2bce8c3b21ba10202dd7c Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Changed select(IncrementalSelection) to select(IChemObjectSelection) The select method uses method that exists on IChemObjectSelection interface Commit: 3370bb08992a07e0fc8e649ecc087e9444c47acb https://github.com/cdk/cdk/commit/3370bb08992a07e0fc8e649ecc087e9444c47acb Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- MergeEdit is passed a copy of the merge-map. The merge-map is reused and could have been changed when it is time to undo. It is also transient and doesn't need to be restored with an undo. Commit: 617f8a9c24efb98687f4806631b9dd0acd87f72d https://github.com/cdk/cdk/commit/617f8a9c24efb98687f4806631b9dd0acd87f72d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- Sets a default bondLength when it is 0 or NaN This makes sure rings are rendered when placing on empyt canvas. Commit: 235f8bb1f9dfe9447a14c66f2040b199a66c225e https://github.com/cdk/cdk/commit/235f8bb1f9dfe9447a14c66f2040b199a66c225e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/AddAtom.java Log Message: ----------- Makes AddAtom-edit actualy add the atom. Commit: 2d29307efd9eb85363644e07544417e23b89db5d https://github.com/cdk/cdk/commit/2d29307efd9eb85363644e07544417e23b89db5d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Use atom- instead of mouse-coordinates when drawing bonds Also change snap angle to 15 This commit does exactly the same as ae28a16ff2cf2eab44748db75b40701f4e6f6241, dragging bonds in regular angles using atom 2d point from ebi_patches but adapter for the IEdit refactoring Commit: fe06e58b5d8081443e036a8ec9f576419958c8b2 https://github.com/cdk/cdk/commit/fe06e58b5d8081443e036a8ec9f576419958c8b2 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/SetSymbol.java Log Message: ----------- SetSymbol converts from pseudo atom Dose the same thing as: 936ba7885e8c7b8cd6eb363e7f012a6d20a9ff6d, the setsymbol converts to a normal atom in case it was a pseudo atom. from ebi_patches Commit: 853eb763a0e3d44c5a2e7c2651eb73ad42d3dbe3 https://github.com/cdk/cdk/commit/853eb763a0e3d44c5a2e7c2651eb73ad42d3dbe3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Added check for 0 or Double.NaN bond length Commit: f887290c47f67a62bf0d60b168bb9cb2ac5e826e https://github.com/cdk/cdk/commit/f887290c47f67a62bf0d60b168bb9cb2ac5e826e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Added checks for NaN coordinates for general path. SWT doesn't like NaN when drawing thees Commit: b5cbb738d13ac6091b2b89a47d7f1fe9c2a20fe4 https://github.com/cdk/cdk/commit/b5cbb738d13ac6091b2b89a47d7f1fe9c2a20fe4 Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- the cleanup no longer collapses fragments Signed-off-by: Arvid Berg <goglepox@...> Commit: 5e12cf075adf87f07be5657983170dbcc6cb3ecf https://github.com/cdk/cdk/commit/5e12cf075adf87f07be5657983170dbcc6cb3ecf Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- Made ring fit to atom/bond when hovered Fixes bug #1738 Commit: 3b5972d0f6c5a1d502293856be6518bde82a3066 https://github.com/cdk/cdk/commit/3b5972d0f6c5a1d502293856be6518bde82a3066 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Fix for generating a merge ring when two atoms are at the same positions Commit: 6d277707416096ca720f9d4dd96409ea0cf68cd1 https://github.com/cdk/cdk/commit/6d277707416096ca720f9d4dd96409ea0cf68cd1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java M src/main/org/openscience/cdk/controller/edit/CreateRing.java M src/main/org/openscience/cdk/controller/edit/SetSymbol.java M src/main/org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.java M src/main/org/openscience/cdk/controller/undoredo/RemoveAtomsAndBondsEdit.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 1722c4d1646338ed485bb64ee019167eea90e856 https://github.com/cdk/cdk/commit/1722c4d1646338ed485bb64ee019167eea90e856 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/undoredo/ChangeHydrogenCountEdit.java Log Message: ----------- Updated for API changes in CDK 1.3.6 (controlbasic). Commit: 2e5cdbbf99d013a14506794ca620f220e8cdb940 https://github.com/cdk/cdk/commit/2e5cdbbf99d013a14506794ca620f220e8cdb940 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderextra.cdkdepends A src/META-INF/renderextra.libdepends A src/META-INF/test-renderextra.cdkdepends A src/META-INF/test-renderextra.devellibdepends A src/META-INF/test-renderextra.libdepends A src/main/org/openscience/cdk/renderer/Renderer.java A src/main/org/openscience/cdk/renderer/elements/ArrowElement.java A src/main/org/openscience/cdk/renderer/elements/AtomMassSymbolElement.java A src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java A src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java A src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java A src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java A src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java A src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java A src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java A src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java A src/main/org/openscience/cdk/renderer/visitor/DistanceSearchVisitor.java A src/main/org/openscience/cdk/renderer/visitor/PrintVisitor.java A src/test/org/openscience/cdk/coverage/RenderextraCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderextraTests.java Log Message: ----------- Render extra module with rendering functionality beyond IAtomContainers. * adds rendering of reactions * added javadoc and PMD testing * added module test suite * new modules: renderextra and test-renderextra Commit: 5c15d57847151a0d98b8db6d0908ca7dfb65f084 https://github.com/cdk/cdk/commit/5c15d57847151a0d98b8db6d0908ca7dfb65f084 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Updated for the new IGenerator.getParameters() interface method Commit: f1cc78742417f46585dae45e3db9916f70a0551a https://github.com/cdk/cdk/commit/f1cc78742417f46585dae45e3db9916f70a0551a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/renderextra.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c94b9d2880fb782bde512737c72055e8d71a3fd5 https://github.com/cdk/cdk/commit/c94b9d2880fb782bde512737c72055e8d71a3fd5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: 58bc885196c56bb3c43f73e41eb3f500b636277c https://github.com/cdk/cdk/commit/58bc885196c56bb3c43f73e41eb3f500b636277c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Fixed the Renderer to implement IRenderer Commit: c07fbe8bc233d9d38a021b422391c7dac8155f74 https://github.com/cdk/cdk/commit/c07fbe8bc233d9d38a021b422391c7dac8155f74 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 2102064189f1e761e42920e28da909ec1c71ee8d https://github.com/cdk/cdk/commit/2102064189f1e761e42920e28da909ec1c71ee8d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for the move of the rendering parameters for atom draw colors to the new IGeneratorParameter API Commit: 1d7f8de1d27850e8355bbfc3c0cf8ed50e4d2af8 https://github.com/cdk/cdk/commit/1d7f8de1d27850e8355bbfc3c0cf8ed50e4d2af8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Set up a API to retrieve a IRenderingParameter from the RenderModel Commit: 2364703d3c3e63b9d2d352c3f14932cbe2e279b6 https://github.com/cdk/cdk/commit/2364703d3c3e63b9d2d352c3f14932cbe2e279b6 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Moved the atom radius into the new rendering parameter API (renderextra module) Commit: e3809c9cf54f47094b177294b9cf7faff3ff99a3 https://github.com/cdk/cdk/commit/e3809c9cf54f47094b177294b9cf7faff3ff99a3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Added ability to generate atom number at an offset. This is a naive solution but allows for better looking rendering that the numbers rendered on top of the atom. Commit: c40560d1535022120307b2e7b01d7ba5ab737cef https://github.com/cdk/cdk/commit/c40560d1535022120307b2e7b01d7ba5ab737cef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for more IGeneratorParameter changes in BasicAtomGenerator Commit: 4dfd81bf9198e4620a86e562d4d30cf402b47c56 https://github.com/cdk/cdk/commit/4dfd81bf9198e4620a86e562d4d30cf402b47c56 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Converted margin into the RenderingParameter variant Commit: 7ef24a4bd02bc1f6a8053fe3d48302083ff89b32 https://github.com/cdk/cdk/commit/7ef24a4bd02bc1f6a8053fe3d48302083ff89b32 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Converted FontName and FontStyle into IGeneratorParameters Commit: 705ecf24620ec1d1d42c560f02bae881bfde9975 https://github.com/cdk/cdk/commit/705ecf24620ec1d1d42c560f02bae881bfde9975 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: a7b343abbbd53d24a24bca8afcdc4ae1a2f34587 https://github.com/cdk/cdk/commit/a7b343abbbd53d24a24bca8afcdc4ae1a2f34587 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Refactored foreground color into a IGeneratorParameter Commit: 5b3feef2971a22df5a3a118617a6967f035bf4ed https://github.com/cdk/cdk/commit/5b3feef2971a22df5a3a118617a6967f035bf4ed Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- IReactionGenerator now has parameters too Commit: 6aa558741c0d54a08413f2f0852e1b7ca6f9e519 https://github.com/cdk/cdk/commit/6aa558741c0d54a08413f2f0852e1b7ca6f9e519 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Refactored reaction boxes into a IGeneratorParameter Commit: edda0f3b2a96562d8c17f518c49a0ec1c7c3a160 https://github.com/cdk/cdk/commit/edda0f3b2a96562d8c17f518c49a0ec1c7c3a160 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Updated for the IGenerator/IAtomContainerGenerator refactoring Commit: 789f5cb25a58920ed44efb0468518d8e882038c5 https://github.com/cdk/cdk/commit/789f5cb25a58920ed44efb0468518d8e882038c5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java Log Message: ----------- Extend IGenerator which now provides getParameters() Commit: a6d89bbdeca6ddaeea872ad11b7dd2b33d47fccd https://github.com/cdk/cdk/commit/a6d89bbdeca6ddaeea872ad11b7dd2b33d47fccd Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- the RadicalGenerator can render atoms with more than one single electron. Signed-off-by: Arvid Berg <goglepox@...> Added rendering of more than one for vertical alignment too. And reverse direction on vertical alignment. Commit: e047e81cb577a8959656ae9960536fa38a6d8e66 https://github.com/cdk/cdk/commit/e047e81cb577a8959656ae9960536fa38a6d8e66 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: a24a7cd3af59e03b647104ea02a5551a91758366 https://github.com/cdk/cdk/commit/a24a7cd3af59e03b647104ea02a5551a91758366 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java Log Message: ----------- Converted boundsColor to the new rendering parameter API Commit: 7ba56125ff53b0dd08ff400c0440c87bd7bd052d https://github.com/cdk/cdk/commit/7ba56125ff53b0dd08ff400c0440c87bd7bd052d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java Log Message: ----------- Converted mappingColor and mappingLineWidth to the new rendering parameter API Commit: ccc0cb3436450c2814bf0ce3e9947ae22899ba93 https://github.com/cdk/cdk/commit/ccc0cb3436450c2814bf0ce3e9947ae22899ba93 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java R src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (renderextra). Commit: c4aac69310e8bc88b829dbc2cf31b57997c65ceb https://github.com/cdk/cdk/commit/c4aac69310e8bc88b829dbc2cf31b57997c65ceb Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 89b696123f7f65258462f8c0472040c76aef04f5 https://github.com/cdk/cdk/commit/89b696123f7f65258462f8c0472040c76aef04f5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (renderextra). Commit: b4944dee9b86ac710b4876dfff7e493d5097801b https://github.com/cdk/cdk/commit/b4944dee9b86ac710b4876dfff7e493d5097801b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Removed scale and zoom form renderer and replaced with values form the generator parameters Commit: 6ef75e26728b5b06bb8d5062c8043b1cbc1cd3bf https://github.com/cdk/cdk/commit/6ef75e26728b5b06bb8d5062c8043b1cbc1cd3bf Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderextra). Commit: 97011f50361deb126b0851492ef37278e0b95457 https://github.com/cdk/cdk/commit/97011f50361deb126b0851492ef37278e0b95457 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Also return the parameters of the super class -a (renderextra). Commit: 70224c99853f80009257fb652e8bedda543f4b79 https://github.com/cdk/cdk/commit/70224c99853f80009257fb652e8bedda543f4b79 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Converted the offset from a constructor parameter into a proper IRenderingParamater (renderextra). Commit: 8556391577cb22a4fe5cae262ff2bd493a879597 https://github.com/cdk/cdk/commit/8556391577cb22a4fe5cae262ff2bd493a879597 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Added rendering parameters for coloring the atom numbers by some scheme, e.g. by element type Commit: 06246f14e10b705b39806852a519023de7849ebb https://github.com/cdk/cdk/commit/06246f14e10b705b39806852a519023de7849ebb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/DistanceSearchVisitor.java Log Message: ----------- Fixed some PMD warnings: longer variable names (renderextra). Commit: 431ceeda7bc346b439fed3ec6ab30163a0aeaa0e https://github.com/cdk/cdk/commit/431ceeda7bc346b439fed3ec6ab30163a0aeaa0e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Mirror structures on Y-axis to compensate for different coordinate systems. Fixes bc-bug #1654 cdk-bug #2855247 Commit: 2381b3a6cf2614bd30be073efe20ef512f97fc2f https://github.com/cdk/cdk/commit/2381b3a6cf2614bd30be073efe20ef512f97fc2f Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Added null check to avoid NPE when no model is present Commit: 829a057f3d0c1d0cd15520b95d3b6abcebe83758 https://github.com/cdk/cdk/commit/829a057f3d0c1d0cd15520b95d3b6abcebe83758 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java A src/main/org/openscience/cdk/renderer/ReactionRenderer.java A src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (renderextra). Commit: eaead5212198cc8ac99b2bd0b73dca43e929f0ae https://github.com/cdk/cdk/commit/eaead5212198cc8ac99b2bd0b73dca43e929f0ae Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/ChemModelRenderer.java R src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Renamed the Renderer to ChemModelRenderer, following the naming pattern for the other IRenderer implementations Commit: 6284f815f6fe917750aec14d8ee52103e9b2c894 https://github.com/cdk/cdk/commit/6284f815f6fe917750aec14d8ee52103e9b2c894 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java M src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java Log Message: ----------- More types in renderers, and associations between renderers Commit: 259e9db19adc68bc207c92f013f2b71c111a405b https://github.com/cdk/cdk/commit/259e9db19adc68bc207c92f013f2b71c111a405b Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java M src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java Log Message: ----------- Using IRenderer<T> interface instead of implementation Commit: 46e7bb37526ce411ee1844a2ed77ce385dab4fab https://github.com/cdk/cdk/commit/46e7bb37526ce411ee1844a2ed77ce385dab4fab Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for API changes in CDK 1.3.6 (renderextra). Commit: 2e6a60284f068990be14026b43308a1f720473de https://github.com/cdk/cdk/commit/2e6a60284f068990be14026b43308a1f720473de Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Fixed registering of rendering parameters (renderextra). Commit: 7e11e24f8126bdd19787edbec4100c5393d5befb https://github.com/cdk/cdk/commit/7e11e24f8126bdd19787edbec4100c5393d5befb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java Log Message: ----------- Fixed NullPointerException by creating an empty list of generators, and return a list too, rather than a null Commit: e7e7b80b0fee596ae4a1fcea0306ed1da6875d82 https://github.com/cdk/cdk/commit/e7e7b80b0fee596ae4a1fcea0306ed1da6875d82 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Because the renderers are now typed itself, we can use this.generators instead, fixign a NullPointerException while rendering reactions Commit: 9ce50cb884aa852d520f2a27fa9c3c916ae2072b https://github.com/cdk/cdk/commit/9ce50cb884aa852d520f2a27fa9c3c916ae2072b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java Log Message: ----------- Implemented the generateDiagram and use that in the paint methods, which fixes reaction rendering as the ReactionRenderer.generateDiagram() uses MoleculeSetRenderer.generateDiagram() Commit: 344b6e7677787d40d5b59396add115b2b1198cf5 https://github.com/cdk/cdk/commit/344b6e7677787d40d5b59396add115b2b1198cf5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlextra.cdkdepends A src/META-INF/controlextra.libdepends A src/META-INF/test-controlextra.cdkdepends A src/META-INF/test-controlextra.devellibdepends A src/META-INF/test-controlextra.libdepends A src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java A src/main/org/openscience/cdk/controller/undoredo/ChangeIsotopeEdit.java A src/main/org/openscience/cdk/controller/undoredo/ConvertToRadicalEdit.java A src/main/org/openscience/cdk/controller/undoredo/LoadNewModelEdit.java A src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInExistingReactionEdit.java A src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInNewReactionEdit.java A src/main/org/openscience/cdk/controller/undoredo/MergeMoleculesEdit.java A src/test/org/openscience/cdk/coverage/ControlextraCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolextraTests.java Log Message: ----------- Set up the controlextra module for editing functionality for things beyond the IAtomContainer, such as drawing reactions. * includes javadoc and pmd checking * includes coverage test infrastructure Commit: 18afb0882db2ca17cdca74797da66ff81cb4b0de https://github.com/cdk/cdk/commit/18afb0882db2ca17cdca74797da66ff81cb4b0de Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: 0306361bd24144abb3453e34a843c4ba20e1ac93 https://github.com/cdk/cdk/commit/0306361bd24144abb3453e34a843c4ba20e1ac93 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/META-INF/controlextra.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: 252cf81e859900f519fa0e4c44760bf82c81145a https://github.com/cdk/cdk/commit/252cf81e859900f519fa0e4c44760bf82c81145a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/META-INF/controlextra.cdkdepends Log Message: ----------- The module controlextra can depend on controlbasic Commit: dbb5fb0a8789137ec5958937b67e748e40676a66 https://github.com/cdk/cdk/commit/dbb5fb0a8789137ec5958937b67e748e40676a66 Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: A src/main/org/openscience/cdk/controller/ChangeSingleElectronModule.java A src/main/org/openscience/cdk/controller/edit/AddSingleElectron.java A src/main/org/openscience/cdk/controller/edit/RemoveSingleElectron.java Log Message: ----------- Added modules and edits for radical support Commit: ec086581511b46038f7965bb9f787be37ab356fb https://github.com/cdk/cdk/commit/ec086581511b46038f7965bb9f787be37ab356fb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Set up the controlextra module for editing functionality for things beyond the IAtomContainer, such as drawing reactions. * includes javadoc and pmd checking * includes coverage test infrastructure Commit: 357361ded7c965c12f229f17787ba131a76922d0 https://github.com/cdk/cdk/commit/357361ded7c965c12f229f17787ba131a76922d0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 2f97bb599daec6547f3b0c1f37ef0057f88bce69 https://github.com/cdk/cdk/commit/2f97bb599daec6547f3b0c1f37ef0057f88bce69 Author: maclean <gilleain.torrance@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 96748b410e37f090a50b3b8f4446f82203569a36 https://github.com/cdk/cdk/commit/96748b410e37f090a50b3b8f4446f82203569a36 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (controlextra). Commit: a3c1e2e339079960978525035d552bc76caf58d7 https://github.com/cdk/cdk/commit/a3c1e2e339079960978525035d552bc76caf58d7 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java M src/main/org/openscience/cdk/controller/edit/AddSingleElectron.java M src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInExistingReactionEdit.java M src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInNewReactionEdit.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 5e50def60508b96039704ea4c325fe81f3c4fe57 https://github.com/cdk/cdk/commit/5e50def60508b96039704ea4c325fe81f3c4fe57 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderawt.cdkdepends A src/META-INF/renderawt.libdepends A src/META-INF/test-renderawt.cdkdepends A src/META-INF/test-renderawt.devellibdepends A src/META-INF/test-renderawt.libdepends A src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java A src/main/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java A src/test/org/openscience/cdk/coverage/RenderawtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderawtTests.java Log Message: ----------- Render AWT module which allows rendering of the abstract rendering elements onto an AWT widget (or Swing). * added javadoc and PMD testing * added module test suite * new modules: renderawt and test-renderawt Commit: b0c2a588bde250338800a52522e281cc6563aeed https://github.com/cdk/cdk/commit/b0c2a588bde250338800a52522e281cc6563aeed Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java M src/main/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java Log Message: ----------- Added support for GeneralPath to AWTDrawVisitor also made transform in AbstractAWTDrawVisitor protected Commit: 5606c9a7b871db928e9040c8c3497fe8135e617c https://github.com/cdk/cdk/commit/5606c9a7b871db928e9040c8c3497fe8135e617c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator Commit: 8c9b23bbad40fff01b927afcc3650e1905515757 https://github.com/cdk/cdk/commit/8c9b23bbad40fff01b927afcc3650e1905515757 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 41dac46b375c3f97215efd9906110c70a15af12c https://github.com/cdk/cdk/commit/41dac46b375c3f97215efd9906110c70a15af12c Author: maclean <gilleain.torrance@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 48b1707b5105b3035e24dba8ea39e63a38625529 https://github.com/cdk/cdk/commit/48b1707b5105b3035e24dba8ea39e63a38625529 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderawt). Commit: 17ec87bc05805ef8184491366592bdaad9b13ff7 https://github.com/cdk/cdk/commit/17ec87bc05805ef8184491366592bdaad9b13ff7 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Fixed some PMD warnings: longer variable names (renderawt). Commit: 176c7266c053560d47fc5706f44dd4e626a75b1d https://github.com/cdk/cdk/commit/176c7266c053560d47fc5706f44dd4e626a75b1d Author: Peter Odéus <peter.odeus@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Made buggy method visit(OvalElement..) render an oval correctly (position and size) by adding SWTRenderer's code from http://github.com/egonw/bioclipse.cheminformatics/blob/2.2.x/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/SWTRenderer.java Commit: 7715469854d903d2bcefaf4915702f0cc1e9742d https://github.com/cdk/cdk/commit/7715469854d903d2bcefaf4915702f0cc1e9742d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/rendersvg.cdkdepends A src/META-INF/rendersvg.libdepends A src/META-INF/test-rendersvg.cdkdepends A src/META-INF/test-rendersvg.devellibdepends A src/META-INF/test-rendersvg.libdepends A src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java A src/test/org/openscience/cdk/coverage/RendersvgCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrendersvgTests.java Log Message: ----------- Render SVG module allowing translation of the rendering elements to be converted into SVG statements. * added javadoc and PMD testing * added module test suite * new modules: rendersvg and test-rendersvg Commit: e9bf552befd85652dc01d7823eee632287679383 https://github.com/cdk/cdk/commit/e9bf552befd85652dc01d7823eee632287679383 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 4e0c84dcede7013ce711353e052427ebb68bd497 https://github.com/cdk/cdk/commit/4e0c84dcede7013ce711353e052427ebb68bd497 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (rendersvg). Commit: 63c03c982e000203a2e9b5e18882e1487f767922 https://github.com/cdk/cdk/commit/63c03c982e000203a2e9b5e18882e1487f767922 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Fixed some PMD warnings: longer variable names (rendersvg). Commit: 82e1ca7035e34f1994a70a1db0e468f6c8ec4111 https://github.com/cdk/cdk/commit/82e1ca7035e34f1994a70a1db0e468f6c8ec4111 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Compile fixes caused by rebasing artefacts as some modules still change bits in order modules Commit: af23b966222402b89930af6e8ff35361b96f4b1e https://github.com/cdk/cdk/commit/af23b966222402b89930af6e8ff35361b96f4b1e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlawt.cdkdepends A src/META-INF/controlawt.libdepends A src/META-INF/test-controlawt.cdkdepends A src/META-INF/test-controlawt.devellibdepends A src/META-INF/test-controlawt.libdepends M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java A src/test/org/openscience/cdk/coverage/ControlawtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolawtTests.java Log Message: ----------- Setting up the controlawt module. * including test module with coverage testgin * enabled PMD and JavaDoc testing Commit: a02bfb78b01efc8ede9a5879c7851776c286501c https://github.com/cdk/cdk/commit/a02bfb78b01efc8ede9a5879c7851776c286501c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Converted useAntiAliasing into a IGeneratorParameter Commit: 361accfbe6ab59e135c25fcfa9fa6d0adf5a9459 https://github.com/cdk/cdk/commit/361accfbe6ab59e135c25fcfa9fa6d0adf5a9459 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M .classpath M build.xml A jar/swt-gtk-3.4.2.jar A jar/swt-gtk-3.4.2.jar.meta A src/META-INF/renderswt.cdkdepends A src/META-INF/renderswt.libdepends A src/META-INF/test-renderswt.cdkdepends A src/META-INF/test-renderswt.devellibdepends A src/META-INF/test-renderswt.libdepends A src/main/org/openscience/cdk/renderer/font/SWTFontManager.java A src/test/org/openscience/cdk/coverage/RenderswtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderswtTests.java Log Message: ----------- Created a renderswt module, prepopulated with a SWTFontManager Commit: a0e4f10899bb634d3d1824d4ad6946a1505df2fc https://github.com/cdk/cdk/commit/a0e4f10899bb634d3d1824d4ad6946a1505df2fc Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M META-INF/MANIFEST.MF Log Message: ----------- Added all other CDK java package to be exported, solving access restriction issues in JChemPaint Commit: ddf86e4a2e4308a0efbfef7622b0e1a36752fa10 https://github.com/cdk/cdk/commit/ddf86e4a2e4308a0efbfef7622b0e1a36752fa10 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml Log Message: ----------- Added new control and renderer jars to dist-large and test-dist-large Commit: 95567738601700dcfafb89f0afcf338517c4fb35 https://github.com/cdk/cdk/commit/95567738601700dcfafb89f0afcf338517c4fb35 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M .gitignore Log Message: ----------- Ignore patch folders Commit: 9db6623e48c52cd05c80d7cce9e6e4030ad7d8e0 https://github.com/cdk/cdk/commit/9db6623e48c52cd05c80d7cce9e6e4030ad7d8e0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props M build.xml Log Message: ----------- Added a build.xml target to make a cdk-jchempaint add-on jar for the cdk.jar Commit: e13772509104710031aae10978aa0b34019c3a57 https://github.com/cdk/cdk/commit/e13772509104710031aae10978aa0b34019c3a57 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml Log Message: ----------- Only run the CDK-JChemPaint specific tests Commit: 73fa063af35d7f936a10339cdcac9cd83ec7a113 https://github.com/cdk/cdk/commit/73fa063af35d7f936a10339cdcac9cd83ec7a113 Author: Egon Willighagen <egonw@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M javadoc.xml Log Message: ----------- Removed use of the proprietary DocCheck utility Commit: 1d2a3ed701dc082cdaae66d36efbbadec888197c https://github.com/cdk/cdk/commit/1d2a3ed701dc082cdaae66d36efbbadec888197c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 15 Commit: f466cb4fa337ca56e9f772fa33b0cdcedbbc71a0 https://github.com/cdk/cdk/commit/f466cb4fa337ca56e9f772fa33b0cdcedbbc71a0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java Log Message: ----------- Uncommented method which seem to have gone lost. (controlawt). Commit: 314da4e2370d7a079eded982aff1d9d5ccc79d46 https://github.com/cdk/cdk/commit/314da4e2370d7a079eded982aff1d9d5ccc79d46 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 16 Commit: 0f0567d379b0096830b0d5d90810b8471ac23231 https://github.com/cdk/cdk/commit/0f0567d379b0096830b0d5d90810b8471ac23231 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 17 (rebased on CDK 1.3.8) Compare: https://github.com/cdk/cdk/compare/96785a6^...0f0567d |
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From: GitHub <noreply@gi...> - 2013-04-19 13:02:21
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Branch: refs/tags/cdk-jchempaint-17 Home: https://github.com/cdk/cdk Commit: 96785a62f1e0c1bebdece5500b507666a925de38 https://github.com/cdk/cdk/commit/96785a62f1e0c1bebdece5500b507666a925de38 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderbasic.cdkdepends A src/META-INF/renderbasic.libdepends A src/META-INF/test-renderbasic.cdkdepends A src/META-INF/test-renderbasic.devellibdepends A src/META-INF/test-renderbasic.libdepends A src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java A src/main/org/openscience/cdk/renderer/elements/AtomSymbolElement.java A src/main/org/openscience/cdk/renderer/elements/ElementGroup.java A src/main/org/openscience/cdk/renderer/elements/LineElement.java A src/main/org/openscience/cdk/renderer/elements/OvalElement.java A src/main/org/openscience/cdk/renderer/elements/PathElement.java A src/main/org/openscience/cdk/renderer/elements/RectangleElement.java A src/main/org/openscience/cdk/renderer/elements/RingElement.java A src/main/org/openscience/cdk/renderer/elements/TextGroupElement.java A src/main/org/openscience/cdk/renderer/elements/WedgeLineElement.java A src/main/org/openscience/cdk/renderer/font/AWTFontManager.java A src/main/org/openscience/cdk/renderer/font/AbstractFontManager.java A src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicGenerator.java A src/main/org/openscience/cdk/renderer/generators/RingGenerator.java A src/main/org/openscience/cdk/renderer/selection/AbstractSelection.java A src/test/org/openscience/cdk/coverage/RenderbasicCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java Log Message: ----------- Setting up the new renderbasic module. * builds on the infrastructure defined in the render module * defines a basic renderer around an IAtomContainer data structure * new test framework including coverage testing Patches derived from: http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/branches/jchempaint-primary/ Commit: 40d743777761e97eeb9d0edc5393ff358cb47222 https://github.com/cdk/cdk/commit/40d743777761e97eeb9d0edc5393ff358cb47222 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/BoundsCalculator.java Log Message: ----------- Added the BoundsCalculator Commit: 82a77825b6c297c84de9efe91e42b212040729e5 https://github.com/cdk/cdk/commit/82a77825b6c297c84de9efe91e42b212040729e5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for IBond.Stereo Commit: 348a0c81c3648bac13f26ba47ca3e0fd040ccd6c https://github.com/cdk/cdk/commit/348a0c81c3648bac13f26ba47ca3e0fd040ccd6c Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/elements/GeneralPath.java A src/main/org/openscience/cdk/renderer/elements/path/Close.java A src/main/org/openscience/cdk/renderer/elements/path/CubicTo.java A src/main/org/openscience/cdk/renderer/elements/path/LineTo.java A src/main/org/openscience/cdk/renderer/elements/path/MoveTo.java A src/main/org/openscience/cdk/renderer/elements/path/PathBuilder.java A src/main/org/openscience/cdk/renderer/elements/path/PathElement.java A src/main/org/openscience/cdk/renderer/elements/path/QuadTo.java A src/main/org/openscience/cdk/renderer/elements/path/Type.java Log Message: ----------- Added new path element to describe more general paths see java.awt.geom.GeneralPath or org.eclipse.swt.graphics.Path Commit: c6c49f45698af4d977a5bfd511347f0b6610bbde https://github.com/cdk/cdk/commit/c6c49f45698af4d977a5bfd511347f0b6610bbde Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/renderbasic.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c009eba9f1a7d42ad76439fb8d598391f81e80f5 https://github.com/cdk/cdk/commit/c009eba9f1a7d42ad76439fb8d598391f81e80f5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the new IGeneratorParameter interfaces Commit: fd6dbf047f17942cbf8e8a4e438ec1d139f1d3fe https://github.com/cdk/cdk/commit/fd6dbf047f17942cbf8e8a4e438ec1d139f1d3fe Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: dcb922853c907e191e5311ad8adc6db4a0586d7e https://github.com/cdk/cdk/commit/dcb922853c907e191e5311ad8adc6db4a0586d7e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 0e3fb77f3bf6cf6360d116277a85d3401235ec62 https://github.com/cdk/cdk/commit/0e3fb77f3bf6cf6360d116277a85d3401235ec62 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- BasicBondGenerator should generate bonds in consistent order Commit: d7f0fa2ac16ce26e7283bff2fb53be6bf077f12b https://github.com/cdk/cdk/commit/d7f0fa2ac16ce26e7283bff2fb53be6bf077f12b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicGenerator.java A src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator Commit: 04a52c43df549ea79481161babc0f412a683827b https://github.com/cdk/cdk/commit/04a52c43df549ea79481161babc0f412a683827b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Moved rendering parameters for atom draw colors to the new IGeneratorParameter API Commit: 43d60d474fb594c22d464cbd925043bbf1b741bd https://github.com/cdk/cdk/commit/43d60d474fb594c22d464cbd925043bbf1b741bd Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Moved the atom radius into the new rendering parameter API (renderbasic module) Commit: b492a0396016806e1c1de97026642883856f92ec https://github.com/cdk/cdk/commit/b492a0396016806e1c1de97026642883856f92ec Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Set up a API to retrieve a IRenderingParameter from the RenderModel Commit: 4b09852a913bdea3839147c97b28dfc4fbf5959f https://github.com/cdk/cdk/commit/4b09852a913bdea3839147c97b28dfc4fbf5959f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Fixed returning of parameters Commit: fc44e2ea0ec2d255a52059dbe5af97934c4ac692 https://github.com/cdk/cdk/commit/fc44e2ea0ec2d255a52059dbe5af97934c4ac692 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- some double bonds were rendered as wedge Signed-off-by: Arvid Berg <goglepox@...> Commit: 99fc5de1e836a7c0bc342dcb28803c2bf18ccd26 https://github.com/cdk/cdk/commit/99fc5de1e836a7c0bc342dcb28803c2bf18ccd26 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Removed last four rendering parameters from BasicAtomGenerator: isCompact, compactShape, isKekule, and showEndCarbons Commit: 0250c9a116802f260bd92ca65d299841de3f03d2 https://github.com/cdk/cdk/commit/0250c9a116802f260bd92ca65d299841de3f03d2 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Converted bondWidth and defaultBondColor into IGeneratorParameter's Commit: f0d26f61e57e13070858da7a9d37b7abecda5506 https://github.com/cdk/cdk/commit/f0d26f61e57e13070858da7a9d37b7abecda5506 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RingGenerator.java Log Message: ----------- Converted showAromaticity and cdkStyleAromaticity to IGeneratorParameter variants Commit: 16dc479b7eb705c913408af54955ba5e33b034c8 https://github.com/cdk/cdk/commit/16dc479b7eb705c913408af54955ba5e33b034c8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Added missing parameter from returned list Commit: 969069f81ef1b7ef4e076ae39f0b5bdc28786367 https://github.com/cdk/cdk/commit/969069f81ef1b7ef4e076ae39f0b5bdc28786367 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RingGenerator.java Log Message: ----------- Converted ringProportion to IGeneratorParameter variants Commit: a02222e6d5bf4a7df75ad406ed044659c1f0a5d1 https://github.com/cdk/cdk/commit/a02222e6d5bf4a7df75ad406ed044659c1f0a5d1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted margin into the RenderingParameter variant Commit: ac593945f6129c3b2441ec2d018b62d0b5d5115f https://github.com/cdk/cdk/commit/ac593945f6129c3b2441ec2d018b62d0b5d5115f Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/test/org/openscience/cdk/renderer/ElementUtility.java A src/test/org/openscience/cdk/renderer/RendererTest.java A src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java A src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java A src/test/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java Log Message: ----------- A few test classes for the renderer package Commit: d17253afb597bf10140ddbcca9b8b03573778208 https://github.com/cdk/cdk/commit/d17253afb597bf10140ddbcca9b8b03573778208 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/RendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Copyright headers Commit: 2a86908fc73006e8972de92ef8c01210aead6662 https://github.com/cdk/cdk/commit/2a86908fc73006e8972de92ef8c01210aead6662 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/RendererTest.java Log Message: ----------- Cleaned up unit test a bit: * added missing assertion * removed uncommented ugly hacks * use AtomContainerRenderer from this module, not Renderer from renderextra Commit: dc0b6855c3447a6fc6380ed3c88fdff1e61ee882 https://github.com/cdk/cdk/commit/dc0b6855c3447a6fc6380ed3c88fdff1e61ee882 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java R src/test/org/openscience/cdk/renderer/RendererTest.java Log Message: ----------- Renamed into AtomContainerRendererTest, following common naming patterns Commit: 4eab24a2fbf509711425dc51be95850f9f8ea54e https://github.com/cdk/cdk/commit/4eab24a2fbf509711425dc51be95850f9f8ea54e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java Log Message: ----------- Added new tests to the module test suite Commit: 19ff7448b57f24647f9d98803dd9498371e89ef9 https://github.com/cdk/cdk/commit/19ff7448b57f24647f9d98803dd9498371e89ef9 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java Log Message: ----------- Placed in the appropriate test modules Commit: 9b700e9d974c438b28f83bff7d1b0a16ad634822 https://github.com/cdk/cdk/commit/9b700e9d974c438b28f83bff7d1b0a16ad634822 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/test-renderbasic.cdkdepends Log Message: ----------- Added missing dependencies Commit: 8ce2474495121d41640cc809c20c69157f2222c8 https://github.com/cdk/cdk/commit/8ce2474495121d41640cc809c20c69157f2222c8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted useAntiAliasing into a IGeneratorParameter Commit: 16276749009c6b4b29943eb90b16efb5373027ad https://github.com/cdk/cdk/commit/16276749009c6b4b29943eb90b16efb5373027ad Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted FontName and FontStyle into IGeneratorParameters Commit: c4f720fba40253536e628b162ea718be2411d339 https://github.com/cdk/cdk/commit/c4f720fba40253536e628b162ea718be2411d339 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Converted BondDistance into an IGeneratorParameter Commit: fd3b6cf0e4a1d6dbaf6a057e9b394cae7aa29549 https://github.com/cdk/cdk/commit/fd3b6cf0e4a1d6dbaf6a057e9b394cae7aa29549 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Factored out a ColorHash IRenderingParamater Commit: 2fa3d30b2540a25f586a40accadd3b628e281db3 https://github.com/cdk/cdk/commit/2fa3d30b2540a25f586a40accadd3b628e281db3 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: 078f65e47391abb28ac7995eb620aa50f1a01851 https://github.com/cdk/cdk/commit/078f65e47391abb28ac7995eb620aa50f1a01851 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Refactored foreground color into a IGeneratorParameter Commit: 61d079216d7b4c28cb537866743e2df34ff57717 https://github.com/cdk/cdk/commit/61d079216d7b4c28cb537866743e2df34ff57717 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java A src/main/org/openscience/cdk/renderer/generators/IAtomContainerGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Split up the old IGenerator interface into IGenerator and IAtomContainerGenerator, the first now only containing the method for getting the parameters Commit: be75022adf7cf805c74a66ef2e3a64b544593f41 https://github.com/cdk/cdk/commit/be75022adf7cf805c74a66ef2e3a64b544593f41 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 25dd8ea140f8d2cb6eb37b9b916d0a415fb3a820 https://github.com/cdk/cdk/commit/25dd8ea140f8d2cb6eb37b9b916d0a415fb3a820 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 523a84b6be8895e6a5ed841b8e8757e5a8a94012 https://github.com/cdk/cdk/commit/523a84b6be8895e6a5ed841b8e8757e5a8a94012 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 135a308337fe0c3164028688446e6d243b20f6ec https://github.com/cdk/cdk/commit/135a308337fe0c3164028688446e6d243b20f6ec Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java R src/main/org/openscience/cdk/renderer/generators/IAtomContainerGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (renderbasic). Commit: ac55656a378694c45340c93f874bb96a5909ffb4 https://github.com/cdk/cdk/commit/ac55656a378694c45340c93f874bb96a5909ffb4 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 587e7be570302db50f50469095643df4fa1cd279 https://github.com/cdk/cdk/commit/587e7be570302db50f50469095643df4fa1cd279 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (renderbasic). Commit: f9574b55406c0cb2f5057f8c76519ca4a5d16ee8 https://github.com/cdk/cdk/commit/f9574b55406c0cb2f5057f8c76519ca4a5d16ee8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Return two missing parameters Commit: 9811ce941f98684c3b3ed1dd2065c47645b59b8c https://github.com/cdk/cdk/commit/9811ce941f98684c3b3ed1dd2065c47645b59b8c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Fixed a generics warning: strong typed the field Commit: 7d9b9eb92cd3a6944673bf1584ad2bfba94b74be https://github.com/cdk/cdk/commit/7d9b9eb92cd3a6944673bf1584ad2bfba94b74be Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Removed scale and zoom form renderer and replaced with values form the generator parameters Commit: 2dca77d7c51374562bf91a0bf334552ed7b6505a https://github.com/cdk/cdk/commit/2dca77d7c51374562bf91a0bf334552ed7b6505a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java M src/test/org/openscience/cdk/renderer/AtomContainerRendererTest.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderbasic). Commit: e577ea911115878f5e409ee3d6d1a693fef40d0e https://github.com/cdk/cdk/commit/e577ea911115878f5e409ee3d6d1a693fef40d0e Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Compact shape tests Commit: a1abb8e8ad20407c8c3291e99f8fa36b5eaf3a1d https://github.com/cdk/cdk/commit/a1abb8e8ad20407c8c3291e99f8fa36b5eaf3a1d Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Atom color tests Commit: 40d52b8511653a5bda39c95b0b44656c1c5c5796 https://github.com/cdk/cdk/commit/40d52b8511653a5bda39c95b0b44656c1c5c5796 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Color by type test Commit: e2b6a102369bf3c15521849a491ea78a6d4f5a50 https://github.com/cdk/cdk/commit/e2b6a102369bf3c15521849a491ea78a6d4f5a50 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/ElementUtility.java M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Explicit hydrogens test Commit: 8b2feb49574012eb98d672d3f2496d9240cbe15e https://github.com/cdk/cdk/commit/8b2feb49574012eb98d672d3f2496d9240cbe15e Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Kekule test Commit: e6eefdce160cd65af8eeae991d7c21c7bb545203 https://github.com/cdk/cdk/commit/e6eefdce160cd65af8eeae991d7c21c7bb545203 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java M src/test/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java Log Message: ----------- Show end carbons test Commit: 351a1a2332ca9e81036456f1acc2c3df381f8298 https://github.com/cdk/cdk/commit/351a1a2332ca9e81036456f1acc2c3df381f8298 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/test-renderbasic.cdkdepends M src/META-INF/test-renderbasic.libdepends Log Message: ----------- Added missing new dependencies for the test-renderbasic module Commit: a25c24521580bdbbd49a4e004e39f2565f389683 https://github.com/cdk/cdk/commit/a25c24521580bdbbd49a4e004e39f2565f389683 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java Log Message: ----------- Use the basic scene generator in the abstract base class Commit: 4c0d6818dc931ee3fe7b6ada5e7a626250198cf8 https://github.com/cdk/cdk/commit/4c0d6818dc931ee3fe7b6ada5e7a626250198cf8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/elements/PathElement.java M src/main/org/openscience/cdk/renderer/elements/WedgeLineElement.java M src/test/org/openscience/cdk/modulesuites/MrenderbasicTests.java A src/test/org/openscience/cdk/renderer/elements/AbstractElementTest.java A src/test/org/openscience/cdk/renderer/elements/PathElementTest.java A src/test/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java Log Message: ----------- Added two missing test classes, for PathElement and WedgeLineElement Commit: 9f7b74ef729992fe314e46c79540f44664443cba https://github.com/cdk/cdk/commit/9f7b74ef729992fe314e46c79540f44664443cba Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/test/org/openscience/cdk/renderer/elements/AbstractElementTest.java M src/test/org/openscience/cdk/renderer/elements/PathElementTest.java M src/test/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java Log Message: ----------- Fixed compiliation: corrected cdk module annotation. Commit: 621168f2ac9764ff930d013ef4934dccea169cb3 https://github.com/cdk/cdk/commit/621168f2ac9764ff930d013ef4934dccea169cb3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Mirror structures on Y-axis to compensate for different coordinate systems. Fixes bc-bug #1654 cdk-bug #2855247 Commit: 45cf451ebda7e4e834f1af8851212c169fcc0713 https://github.com/cdk/cdk/commit/45cf451ebda7e4e834f1af8851212c169fcc0713 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Fixed the AtomContainerRender to implement IRenderer; updated the toModelCoordinates() to match this interface Commit: 00147d507eec3b0849844b525835a0fd2ab88947 https://github.com/cdk/cdk/commit/00147d507eec3b0849844b525835a0fd2ab88947 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java A src/main/org/openscience/cdk/renderer/AverageBondLengthCalculator.java Log Message: ----------- Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (renderbasic). Commit: d9e33c1cc7ab143696e358f44712884280f32b80 https://github.com/cdk/cdk/commit/d9e33c1cc7ab143696e358f44712884280f32b80 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- More types in renderers, and associations between renderers Commit: 4e523290aeac1f5f58a531586873e09fc9ce8b48 https://github.com/cdk/cdk/commit/4e523290aeac1f5f58a531586873e09fc9ce8b48 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/AbstractRenderer.java M src/main/org/openscience/cdk/renderer/AtomContainerRenderer.java Log Message: ----------- Using IRenderer<T> interface instead of implementation Commit: b7084c196ee14cabb333f104b410b25fd5789275 https://github.com/cdk/cdk/commit/b7084c196ee14cabb333f104b410b25fd5789275 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicBondGenerator.java Log Message: ----------- Made the aromatic ring property 'proportion to move in towards the ring center' customizable (implements #3047009) Commit: 07173b917c67bbfc8f806645b5d440d3872ff2b6 https://github.com/cdk/cdk/commit/07173b917c67bbfc8f806645b5d440d3872ff2b6 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java Log Message: ----------- Updated for API changes in CDK 1.3.6 Commit: 624649a4dc3feab73c7303452a6f31c0299ab233 https://github.com/cdk/cdk/commit/624649a4dc3feab73c7303452a6f31c0299ab233 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/rendercontrol.cdkdepends A src/META-INF/rendercontrol.libdepends A src/META-INF/test-rendercontrol.cdkdepends A src/META-INF/test-rendercontrol.devellibdepends A src/META-INF/test-rendercontrol.libdepends A src/main/org/openscience/cdk/renderer/generators/ControllerFeedbackGenerator.java A src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java A src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java A src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java A src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java A src/main/org/openscience/cdk/renderer/selection/IncrementalSelection.java A src/main/org/openscience/cdk/renderer/selection/LassoSelection.java A src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java A src/main/org/openscience/cdk/renderer/selection/MultiSelection.java A src/main/org/openscience/cdk/renderer/selection/RectangleSelection.java A src/main/org/openscience/cdk/renderer/selection/ShapeSelection.java A src/main/org/openscience/cdk/renderer/selection/SingleSelection.java A src/test/org/openscience/cdk/coverage/RendercontrolCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrendercontrolTests.java Log Message: ----------- Set up of the rendercontrol module, containing the rendering of controller feedback. * rendercontrol module * enabled DocCheck and PMD testing Commit: b6592d04c7e43f18586d1af948f12af0adac10bb https://github.com/cdk/cdk/commit/b6592d04c7e43f18586d1af948f12af0adac10bb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Updated for the new IGenerator.getParameters() interface method Commit: 278ec4ce119b4559411b5b461de3ee2469ae659d https://github.com/cdk/cdk/commit/278ec4ce119b4559411b5b461de3ee2469ae659d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Changed rendering of merge candidates to indicate what pairs will merge Uses new GeneralPath element Commit: e52a292c3f1b5e453a19c4a95d6d31c460edc142 https://github.com/cdk/cdk/commit/e52a292c3f1b5e453a19c4a95d6d31c460edc142 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/rendercontrol.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: b7ec937aa09bc147f7478df4a8672c6efda41d3e https://github.com/cdk/cdk/commit/b7ec937aa09bc147f7478df4a8672c6efda41d3e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 08fd5542a3903f2f228d4a5a164ed81b7f39e351 https://github.com/cdk/cdk/commit/08fd5542a3903f2f228d4a5a164ed81b7f39e351 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/selection/LinkedSelection.java M src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java Log Message: ----------- Added LinkedSelection A selection for selecting a connected part of a model Commit: 9287a5fd8b635b9da8f89f20ab412a8fbe5b8524 https://github.com/cdk/cdk/commit/9287a5fd8b635b9da8f89f20ab412a8fbe5b8524 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Updated for more IGeneratorParameter changes in BasicAtomGenerator Commit: 07dff754c7a06cb09a2881880264fbe9e2dcaa84 https://github.com/cdk/cdk/commit/07dff754c7a06cb09a2881880264fbe9e2dcaa84 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: 871f7477cda6e25154e1bbff62d108071820299e https://github.com/cdk/cdk/commit/871f7477cda6e25154e1bbff62d108071820299e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Updated for BondWidth now being a IGeneratorParameter Commit: 5b7e29c3bf184c00e34eda1621c0ea17ce19464a https://github.com/cdk/cdk/commit/5b7e29c3bf184c00e34eda1621c0ea17ce19464a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/selection/LinkedSelection.java M src/main/org/openscience/cdk/renderer/selection/LogicalSelection.java M src/main/org/openscience/cdk/renderer/selection/MultiSelection.java M src/main/org/openscience/cdk/renderer/selection/ShapeSelection.java M src/main/org/openscience/cdk/renderer/selection/SingleSelection.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: e21bbe85de1fdc5357e884df1e1748e03b49aee1 https://github.com/cdk/cdk/commit/e21bbe85de1fdc5357e884df1e1748e03b49aee1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 6494ec3518b0021c5b97abe0e68927994382c212 https://github.com/cdk/cdk/commit/6494ec3518b0021c5b97abe0e68927994382c212 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Converted externalHighlightColor to the new rendering parameter API Commit: 84026a24aedda324ecb4fb39da73ade0e70a76fa https://github.com/cdk/cdk/commit/84026a24aedda324ecb4fb39da73ade0e70a76fa Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Converted hoverOverColor to the new rendering parameter API Commit: 9b0f8659fd9f2a8f3cffde27d016303d1a5a17bb https://github.com/cdk/cdk/commit/9b0f8659fd9f2a8f3cffde27d016303d1a5a17bb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java Log Message: ----------- Moved ExternalHighlightColor into RendererModel for now, to solve a compile dependency Commit: d060e06546fce74dad846093cea6dffcc573ca65 https://github.com/cdk/cdk/commit/d060e06546fce74dad846093cea6dffcc573ca65 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (rendercontrol). Commit: ea7a8bfd0c3ee5c4f26ad039e8688dfb880a85d7 https://github.com/cdk/cdk/commit/ea7a8bfd0c3ee5c4f26ad039e8688dfb880a85d7 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: ba15d73a35e4211622b8a74cd929eb15017a07a0 https://github.com/cdk/cdk/commit/ba15d73a35e4211622b8a74cd929eb15017a07a0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (rendercontrol). Commit: 2b20d3ee13a2f71f3ef29e3fb7178a6cbc4a72a2 https://github.com/cdk/cdk/commit/2b20d3ee13a2f71f3ef29e3fb7178a6cbc4a72a2 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/SelectBondGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (rendercontrol). Commit: 5475408f8c9ebf57cc5e65d189e416ab5480b615 https://github.com/cdk/cdk/commit/5475408f8c9ebf57cc5e65d189e416ab5480b615 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/HighlightAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/HighlightBondGenerator.java Log Message: ----------- Also return the parameters of the super class -a (rendercontrol). Commit: 1708bfb2fe757c9647923938a7ea3763641ca68d https://github.com/cdk/cdk/commit/1708bfb2fe757c9647923938a7ea3763641ca68d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml M src/META-INF/control.cdkdepends A src/META-INF/test-control.cdkdepends A src/META-INF/test-control.devellibdepends A src/META-INF/test-control.libdepends A src/main/org/openscience/cdk/controller/Changed.java A src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java A src/main/org/openscience/cdk/controller/IChemModelEventRelayHandler.java A src/main/org/openscience/cdk/controller/IChemModelRelay.java A src/main/org/openscience/cdk/controller/IControllerModel.java A src/main/org/openscience/cdk/controller/IControllerModule.java M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java A src/main/org/openscience/cdk/controller/edit/IEdit.java A src/main/org/openscience/cdk/controller/undoredo/IUndoListener.java A src/main/org/openscience/cdk/controller/undoredo/IUndoRedoFactory.java A src/main/org/openscience/cdk/controller/undoredo/IUndoRedoable.java A src/main/org/openscience/cdk/controller/undoredo/UndoRedoHandler.java M src/test/org/openscience/cdk/coverage/ControlCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolTests.java Log Message: ----------- Set up of the new controller infrastructure. * new content of the 'control' module * new test suite with coverage testing * enabled DocCheck and PMD testing Commit: 37031a5c4e6ae6f11a37a8a686c7592d9ff67ee7 https://github.com/cdk/cdk/commit/37031a5c4e6ae6f11a37a8a686c7592d9ff67ee7 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: d41ef733c24dfa6290f8aefd46eb69707d964d19 https://github.com/cdk/cdk/commit/d41ef733c24dfa6290f8aefd46eb69707d964d19 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/controller/IAtomBondEdits.java M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Re-factored out methods for atom and bonds edit These methods are candidates for being replaced with IEdit With copyright Commit: 57cecf8e8d4b8cee0ea74ee1febfec528e9dadf7 https://github.com/cdk/cdk/commit/57cecf8e8d4b8cee0ea74ee1febfec528e9dadf7 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/IEdit.java Log Message: ----------- Added new edits for replacing modify methods in ControllerHub The edits handles the modifying of the model and the undo/redo stuff. Commit: f1c0ca878cc4fb4d9a72b6f26966634c7af15355 https://github.com/cdk/cdk/commit/f1c0ca878cc4fb4d9a72b6f26966634c7af15355 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/control.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c23c3d4a219e46465aee90f0208e175b428b58ba https://github.com/cdk/cdk/commit/c23c3d4a219e46465aee90f0208e175b428b58ba Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Defines two new stereo types. Commit: 641a96bc366029277d5ef82a05ffd45c66d60969 https://github.com/cdk/cdk/commit/641a96bc366029277d5ef82a05ffd45c66d60969 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Rewrote selection check to avoid NPE Commit: 19d8cfa381569b81ab02ecc3256b15cf19ca13af https://github.com/cdk/cdk/commit/19d8cfa381569b81ab02ecc3256b15cf19ca13af Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: c68c3f18710d7beef920806fb64694bd342ed9e7 https://github.com/cdk/cdk/commit/c68c3f18710d7beef920806fb64694bd342ed9e7 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Changed wedge width to rendering parameter Commit: cf88296b23767e49ec5d1ea32462b8061da48dc0 https://github.com/cdk/cdk/commit/cf88296b23767e49ec5d1ea32462b8061da48dc0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (control). Commit: 966b90e92968cf3fe20a8978073ea6df236a8cef https://github.com/cdk/cdk/commit/966b90e92968cf3fe20a8978073ea6df236a8cef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml Log Message: ----------- Added compiling of the test-control module Commit: 1a1a01738c6aabba8edd596347c243a4d52812c4 https://github.com/cdk/cdk/commit/1a1a01738c6aabba8edd596347c243a4d52812c4 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IAtomBondEdits.java M src/main/org/openscience/cdk/controller/IChemModelRelay.java A src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Moved all methods except the most important from IChemModelRelay to IOldChemModelRelay Commit: d2a2e174554c12867f7c909fd7bc2dd8290a1c4e https://github.com/cdk/cdk/commit/d2a2e174554c12867f7c909fd7bc2dd8290a1c4e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java M src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module control Commit: 625a595e3b2a8b1e0e5f90a76180b728c1d49f6f https://github.com/cdk/cdk/commit/625a595e3b2a8b1e0e5f90a76180b728c1d49f6f Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerModuleAdapter.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module controlbasic Commit: f4d24333f3e7e450e21a883bb10ca5963976e287 https://github.com/cdk/cdk/commit/f4d24333f3e7e450e21a883bb10ca5963976e287 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IOldChemModelRelay.java Log Message: ----------- Changed select(IncrementalSelection) to select(IChemObjectSelection) The select method uses method that exists on IChemObjectSelection interface Commit: 3e233f9330a0875294fd05161708badb3b3470ef https://github.com/cdk/cdk/commit/3e233f9330a0875294fd05161708badb3b3470ef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IChemModelRelay.java Log Message: ----------- Added dependency on IOldChemModelRelay which is needed at this level Commit: 40ecbc7e75e27b30fb128177bf4a44725343f571 https://github.com/cdk/cdk/commit/40ecbc7e75e27b30fb128177bf4a44725343f571 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/IMouseEventRelay.java Log Message: ----------- Added two missing methods for scroll event handling Commit: 26c93a67eb06b0f59a27052faa46533b2a933a5f https://github.com/cdk/cdk/commit/26c93a67eb06b0f59a27052faa46533b2a933a5f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlbasic.cdkdepends A src/META-INF/controlbasic.libdepends A src/META-INF/test-controlbasic.cdkdepends A src/META-INF/test-controlbasic.devellibdepends A src/META-INF/test-controlbasic.libdepends A src/main/org/openscience/cdk/controller/AddAtomModule.java A src/main/org/openscience/cdk/controller/AddBondDragModule.java A src/main/org/openscience/cdk/controller/AddBondModule.java A src/main/org/openscience/cdk/controller/AddRingModule.java A src/main/org/openscience/cdk/controller/AlterBondStereoModule.java A src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java A src/main/org/openscience/cdk/controller/ControllerHub.java A src/main/org/openscience/cdk/controller/ControllerModel.java A src/main/org/openscience/cdk/controller/ControllerParameters.java A src/main/org/openscience/cdk/controller/CycleSymbolModule.java A src/main/org/openscience/cdk/controller/DrawBondModule.java A src/main/org/openscience/cdk/controller/HighlightModule.java A src/main/org/openscience/cdk/controller/MoveModule.java A src/main/org/openscience/cdk/controller/PhantomBondGenerator.java A src/main/org/openscience/cdk/controller/RemoveModule.java A src/main/org/openscience/cdk/controller/RotateModule.java A src/main/org/openscience/cdk/controller/SelectLassoModule.java A src/main/org/openscience/cdk/controller/SelectSquareModule.java A src/main/org/openscience/cdk/controller/ZoomModule.java A src/main/org/openscience/cdk/controller/edit/AbstractEdit.java A src/main/org/openscience/cdk/controller/edit/AddAtom.java A src/main/org/openscience/cdk/controller/edit/AddBond.java A src/main/org/openscience/cdk/controller/edit/AppendAtom.java A src/main/org/openscience/cdk/controller/edit/CreateBond.java A src/main/org/openscience/cdk/controller/edit/RemoveAtom.java A src/main/org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.java A src/main/org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeAtomSymbolEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeChargeEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeCoordsEdit.java A src/main/org/openscience/cdk/controller/undoredo/ChangeHydrogenCountEdit.java A src/main/org/openscience/cdk/controller/undoredo/ClearAllEdit.java A src/main/org/openscience/cdk/controller/undoredo/MoveAtomEdit.java A src/main/org/openscience/cdk/controller/undoredo/RemoveAtomsAndBondsEdit.java A src/main/org/openscience/cdk/controller/undoredo/ReplaceAtomEdit.java A src/test/org/openscience/cdk/coverage/ControlbasicCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolbasicTests.java Log Message: ----------- Set up a controlbasic module, with basic editing functionality, like adding and moving atoms, and changing basic atom and bond properties. * includes javadoc and pmd testing * includes coverage testing framework Commit: c81e97c0a83d65bbc8baf9904b4625e147baca33 https://github.com/cdk/cdk/commit/c81e97c0a83d65bbc8baf9904b4625e147baca33 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/RotateModule.java Log Message: ----------- implemented RotateModule Commit: 8e8dddeb592ccc0a11da836e52cbf22b1b2e2b2d https://github.com/cdk/cdk/commit/8e8dddeb592ccc0a11da836e52cbf22b1b2e2b2d Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Moving bugs fixed Commit: 753143383dfcc03c615eee06655d941c5a35fc70 https://github.com/cdk/cdk/commit/753143383dfcc03c615eee06655d941c5a35fc70 Author: mark_rynbeek <markr@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- bugfixed mergeMolecules methods Commit: 150fcf8256329be2835f1dbeb8be494dc67cbdde https://github.com/cdk/cdk/commit/150fcf8256329be2835f1dbeb8be494dc67cbdde Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/DrawBondModule.java M src/main/org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.java M src/main/org/openscience/cdk/controller/undoredo/IUndoRedoFactory.java Log Message: ----------- Updated for IBond.Stereo API change Commit: 136cf08dfa13555439c3ce500db1d02ee5654ec6 https://github.com/cdk/cdk/commit/136cf08dfa13555439c3ce500db1d02ee5654ec6 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Using add operation in Point2d Commit: 7bfa9e0c76b186a26949b19fd3b8acc554afe774 https://github.com/cdk/cdk/commit/7bfa9e0c76b186a26949b19fd3b8acc554afe774 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- mergeMap reference model.getMerge() using the former for clarity Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: b98b021f455e3b6265187cfb9c33458550203f5b https://github.com/cdk/cdk/commit/b98b021f455e3b6265187cfb9c33458550203f5b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java M src/main/org/openscience/cdk/controller/HighlightModule.java M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: d5d18831e90d435ecaa8d04ade72c77e44f5c9c9 https://github.com/cdk/cdk/commit/d5d18831e90d435ecaa8d04ade72c77e44f5c9c9 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/edit/AbstractEdit.java M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java A src/main/org/openscience/cdk/controller/edit/CompositEdit.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java A src/main/org/openscience/cdk/controller/edit/Merge.java A src/main/org/openscience/cdk/controller/edit/Move.java A src/main/org/openscience/cdk/controller/edit/MoveOptionalUndo.java M src/main/org/openscience/cdk/controller/edit/RemoveAtom.java A src/main/org/openscience/cdk/controller/edit/RemoveBond.java A src/main/org/openscience/cdk/controller/edit/SetBondOrder.java A src/main/org/openscience/cdk/controller/edit/SetCharge.java A src/main/org/openscience/cdk/controller/edit/SetStereo.java A src/main/org/openscience/cdk/controller/edit/SetSymbol.java Log Message: ----------- Added new edits for replacing modify methods in ControllerHub The edits handles the modifying of the model and the undo/redo stuff. Commit: 49d9884d84aa63dcedfd9d6459ac2789ce96d057 https://github.com/cdk/cdk/commit/49d9884d84aa63dcedfd9d6459ac2789ce96d057 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Added hack to filter out none final MoveOptionalUndo edits Commit: e6e6d22f632b13d35f77d310f2f8c2f7c4501622 https://github.com/cdk/cdk/commit/e6e6d22f632b13d35f77d310f2f8c2f7c4501622 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/AddBondModule.java M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java R src/main/org/openscience/cdk/controller/DrawBondModule.java M src/main/org/openscience/cdk/controller/MoveModule.java M src/main/org/openscience/cdk/controller/RemoveModule.java Log Message: ----------- Re-factored modules to use new edit operations instead of methods in IChemModelRelay Commit: c6763eee70b565170b8ce4e5e7023eb3280ed12a https://github.com/cdk/cdk/commit/c6763eee70b565170b8ce4e5e7023eb3280ed12a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/controlbasic.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: b5357b0eb378f2c701d1aad233cfd17426192a13 https://github.com/cdk/cdk/commit/b5357b0eb378f2c701d1aad233cfd17426192a13 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java M src/main/org/openscience/cdk/controller/RotateModule.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: 012ae44007516467b3bb10df925d8e2c2165ee8b https://github.com/cdk/cdk/commit/012ae44007516467b3bb10df925d8e2c2165ee8b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/PhantomBondGenerator.java Log Message: ----------- Changed PhantomBondGenerator to use override color in BasicBondRenderer This simplifies this generator and allows it to draw aromatic rings Commit: e2ba6c60ed38b945582d30306d74a984d63d996d https://github.com/cdk/cdk/commit/e2ba6c60ed38b945582d30306d74a984d63d996d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Moved code handling merge to static methods This so that they can be reused in other modules like AddRingModuel Commit: c7078ba8fc2dceabccea8cd252ba13dacbcb09db https://github.com/cdk/cdk/commit/c7078ba8fc2dceabccea8cd252ba13dacbcb09db Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java A src/main/org/openscience/cdk/controller/edit/CreateRing.java Log Message: ----------- Added CreateRing edit and re-factored AddRingModule to use it The handling of aromaticity is slightly different from the old way, and it should be handled by the Merge edit to get the same behavior when merging a aromatic ring with move. Commit: cc0b47cd4350817cacd0ec1568c2421fe70a2659 https://github.com/cdk/cdk/commit/cc0b47cd4350817cacd0ec1568c2421fe70a2659 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/MoveModule.java R src/main/org/openscience/cdk/controller/edit/MoveOptionalUndo.java A src/main/org/openscience/cdk/controller/edit/OptionalUndoEdit.java Log Message: ----------- Replaced MoveOptionalUndo with OptionalUndoEdit wrapper. The wrapper allows for adding optional undo to any edit. This is a workaround for allowing small incremental edits that is not pushed to the undo stack and then push a edit that is not executed but are pushed to the undo stack representing the operations done by all smaller incremental edits. Commit: c6102883c9eb65f9664735888f9fd3167ded7d60 https://github.com/cdk/cdk/commit/c6102883c9eb65f9664735888f9fd3167ded7d60 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/RotateModule.java A src/main/org/openscience/cdk/controller/edit/Rotate.java Log Message: ----------- Moved RotateModule to new edit model Commit: 4932e066c8da79a092f4dfc53bf7a8c9e59c5c64 https://github.com/cdk/cdk/commit/4932e066c8da79a092f4dfc53bf7a8c9e59c5c64 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/CycleSymbolModule.java Log Message: ----------- Fixed bug where the last element would not be part of cycle Also moved execute(...) to end of method Commit: a177b105620107a769d4b3eb8bccbce5db3c3866 https://github.com/cdk/cdk/commit/a177b105620107a769d4b3eb8bccbce5db3c3866 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/CompositEdit.java M src/main/org/openscience/cdk/controller/edit/RemoveAtom.java Log Message: ----------- Changed add/remove explicit hydrogens to use IEdits Solves bug #1249 Commit: 193776bff21902f3234635e9c882cecaa272b06f https://github.com/cdk/cdk/commit/193776bff21902f3234635e9c882cecaa272b06f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/ZoomModule.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 2a0ddacdfe2f418889e261590e8c07603bdf466f https://github.com/cdk/cdk/commit/2a0ddacdfe2f418889e261590e8c07603bdf466f Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/PhantomBondGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (controlbasic). Commit: 529338fcd21901d46f13bcef7ce002531dfc9e43 https://github.com/cdk/cdk/commit/529338fcd21901d46f13bcef7ce002531dfc9e43 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 16f976730d2ac29979f525bbd45846810f83b42d https://github.com/cdk/cdk/commit/16f976730d2ac29979f525bbd45846810f83b42d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/ZoomModule.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (controlbasic). Commit: b1eb74fa3ddc4b501bd9b7e17b647716c97b66e5 https://github.com/cdk/cdk/commit/b1eb74fa3ddc4b501bd9b7e17b647716c97b66e5 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AlterBondStereoModule.java Log Message: ----------- Enables AlterBondStereoModule to cycle between different stereo modes UP->UP_INVERTED->NONE->UP... DOWN->DOWN_INVERTED->NONE->DOWN... Commit: 276eb4a21f8a3974263c1cb66c84e0222a374e5a https://github.com/cdk/cdk/commit/276eb4a21f8a3974263c1cb66c84e0222a374e5a Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Removed structure changed event when changing model Commit: 4f3026296ffe3adf5dea3dd14025d5178daaed18 https://github.com/cdk/cdk/commit/4f3026296ffe3adf5dea3dd14025d5178daaed18 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddAtomModule.java M src/main/org/openscience/cdk/controller/AddBondModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/ChangeFormalChargeModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/CycleSymbolModule.java M src/main/org/openscience/cdk/controller/MoveModule.java Log Message: ----------- Renamed accessors for getting render- and control-model @cdk.module controlbasic Commit: c1295219f50048c542c49b96ba485f488f5f46e0 https://github.com/cdk/cdk/commit/c1295219f50048c542c49b96ba485f488f5f46e0 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Calculate average bond for atomcontainer instead of chemModel Commit: d8b3e6ffa3e4cd01241640ee8599b66afd3563ac https://github.com/cdk/cdk/commit/d8b3e6ffa3e4cd01241640ee8599b66afd3563ac Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java Log Message: ----------- Only create atoms and bonds the first time redo is called. Solves cdk-bug #2886402 Commit: 67565e82394103c47be5229ed16b7570ef2c0675 https://github.com/cdk/cdk/commit/67565e82394103c47be5229ed16b7570ef2c0675 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/edit/AbstractEdit.java M src/main/org/openscience/cdk/controller/edit/CompositEdit.java Log Message: ----------- Added update of hydrogens after edit. Commit: 556819612dc7093e26c2bce8c3b21ba10202dd7c https://github.com/cdk/cdk/commit/556819612dc7093e26c2bce8c3b21ba10202dd7c Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- Changed select(IncrementalSelection) to select(IChemObjectSelection) The select method uses method that exists on IChemObjectSelection interface Commit: 3370bb08992a07e0fc8e649ecc087e9444c47acb https://github.com/cdk/cdk/commit/3370bb08992a07e0fc8e649ecc087e9444c47acb Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- MergeEdit is passed a copy of the merge-map. The merge-map is reused and could have been changed when it is time to undo. It is also transient and doesn't need to be restored with an undo. Commit: 617f8a9c24efb98687f4806631b9dd0acd87f72d https://github.com/cdk/cdk/commit/617f8a9c24efb98687f4806631b9dd0acd87f72d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- Sets a default bondLength when it is 0 or NaN This makes sure rings are rendered when placing on empyt canvas. Commit: 235f8bb1f9dfe9447a14c66f2040b199a66c225e https://github.com/cdk/cdk/commit/235f8bb1f9dfe9447a14c66f2040b199a66c225e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/AddAtom.java Log Message: ----------- Makes AddAtom-edit actualy add the atom. Commit: 2d29307efd9eb85363644e07544417e23b89db5d https://github.com/cdk/cdk/commit/2d29307efd9eb85363644e07544417e23b89db5d Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Use atom- instead of mouse-coordinates when drawing bonds Also change snap angle to 15 This commit does exactly the same as ae28a16ff2cf2eab44748db75b40701f4e6f6241, dragging bonds in regular angles using atom 2d point from ebi_patches but adapter for the IEdit refactoring Commit: fe06e58b5d8081443e036a8ec9f576419958c8b2 https://github.com/cdk/cdk/commit/fe06e58b5d8081443e036a8ec9f576419958c8b2 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/edit/SetSymbol.java Log Message: ----------- SetSymbol converts from pseudo atom Dose the same thing as: 936ba7885e8c7b8cd6eb363e7f012a6d20a9ff6d, the setsymbol converts to a normal atom in case it was a pseudo atom. from ebi_patches Commit: 853eb763a0e3d44c5a2e7c2651eb73ad42d3dbe3 https://github.com/cdk/cdk/commit/853eb763a0e3d44c5a2e7c2651eb73ad42d3dbe3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java Log Message: ----------- Added check for 0 or Double.NaN bond length Commit: f887290c47f67a62bf0d60b168bb9cb2ac5e826e https://github.com/cdk/cdk/commit/f887290c47f67a62bf0d60b168bb9cb2ac5e826e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Added checks for NaN coordinates for general path. SWT doesn't like NaN when drawing thees Commit: b5cbb738d13ac6091b2b89a47d7f1fe9c2a20fe4 https://github.com/cdk/cdk/commit/b5cbb738d13ac6091b2b89a47d7f1fe9c2a20fe4 Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java Log Message: ----------- the cleanup no longer collapses fragments Signed-off-by: Arvid Berg <goglepox@...> Commit: 5e12cf075adf87f07be5657983170dbcc6cb3ecf https://github.com/cdk/cdk/commit/5e12cf075adf87f07be5657983170dbcc6cb3ecf Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddRingModule.java Log Message: ----------- Made ring fit to atom/bond when hovered Fixes bug #1738 Commit: 3b5972d0f6c5a1d502293856be6518bde82a3066 https://github.com/cdk/cdk/commit/3b5972d0f6c5a1d502293856be6518bde82a3066 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MergeAtomsGenerator.java Log Message: ----------- Fix for generating a merge ring when two atoms are at the same positions Commit: 6d277707416096ca720f9d4dd96409ea0cf68cd1 https://github.com/cdk/cdk/commit/6d277707416096ca720f9d4dd96409ea0cf68cd1 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AddBondDragModule.java M src/main/org/openscience/cdk/controller/AddRingModule.java M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/edit/AddAtom.java M src/main/org/openscience/cdk/controller/edit/AddBond.java M src/main/org/openscience/cdk/controller/edit/AppendAtom.java M src/main/org/openscience/cdk/controller/edit/CreateBond.java M src/main/org/openscience/cdk/controller/edit/CreateRing.java M src/main/org/openscience/cdk/controller/edit/SetSymbol.java M src/main/org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.java M src/main/org/openscience/cdk/controller/undoredo/RemoveAtomsAndBondsEdit.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 1722c4d1646338ed485bb64ee019167eea90e856 https://github.com/cdk/cdk/commit/1722c4d1646338ed485bb64ee019167eea90e856 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/ControllerHub.java M src/main/org/openscience/cdk/controller/undoredo/ChangeHydrogenCountEdit.java Log Message: ----------- Updated for API changes in CDK 1.3.6 (controlbasic). Commit: 2e5cdbbf99d013a14506794ca620f220e8cdb940 https://github.com/cdk/cdk/commit/2e5cdbbf99d013a14506794ca620f220e8cdb940 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderextra.cdkdepends A src/META-INF/renderextra.libdepends A src/META-INF/test-renderextra.cdkdepends A src/META-INF/test-renderextra.devellibdepends A src/META-INF/test-renderextra.libdepends A src/main/org/openscience/cdk/renderer/Renderer.java A src/main/org/openscience/cdk/renderer/elements/ArrowElement.java A src/main/org/openscience/cdk/renderer/elements/AtomMassSymbolElement.java A src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java A src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java A src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java A src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java A src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java A src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java A src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java A src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java A src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java A src/main/org/openscience/cdk/renderer/visitor/DistanceSearchVisitor.java A src/main/org/openscience/cdk/renderer/visitor/PrintVisitor.java A src/test/org/openscience/cdk/coverage/RenderextraCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderextraTests.java Log Message: ----------- Render extra module with rendering functionality beyond IAtomContainers. * adds rendering of reactions * added javadoc and PMD testing * added module test suite * new modules: renderextra and test-renderextra Commit: 5c15d57847151a0d98b8db6d0908ca7dfb65f084 https://github.com/cdk/cdk/commit/5c15d57847151a0d98b8db6d0908ca7dfb65f084 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Updated for the new IGenerator.getParameters() interface method Commit: f1cc78742417f46585dae45e3db9916f70a0551a https://github.com/cdk/cdk/commit/f1cc78742417f46585dae45e3db9916f70a0551a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/META-INF/renderextra.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: c94b9d2880fb782bde512737c72055e8d71a3fd5 https://github.com/cdk/cdk/commit/c94b9d2880fb782bde512737c72055e8d71a3fd5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java Log Message: ----------- Updated for the ILoggingTool patch. Commit: 58bc885196c56bb3c43f73e41eb3f500b636277c https://github.com/cdk/cdk/commit/58bc885196c56bb3c43f73e41eb3f500b636277c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Fixed the Renderer to implement IRenderer Commit: c07fbe8bc233d9d38a021b422391c7dac8155f74 https://github.com/cdk/cdk/commit/c07fbe8bc233d9d38a021b422391c7dac8155f74 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Changed getParameters() to use IGeneratorParameter<?> so that any type of IGeneratorParamter can be contained in the list. Signed-off-by: Egon Willighagen <egon.willighagen@...> Commit: 2102064189f1e761e42920e28da909ec1c71ee8d https://github.com/cdk/cdk/commit/2102064189f1e761e42920e28da909ec1c71ee8d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for the move of the rendering parameters for atom draw colors to the new IGeneratorParameter API Commit: 1d7f8de1d27850e8355bbfc3c0cf8ed50e4d2af8 https://github.com/cdk/cdk/commit/1d7f8de1d27850e8355bbfc3c0cf8ed50e4d2af8 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Set up a API to retrieve a IRenderingParameter from the RenderModel Commit: 2364703d3c3e63b9d2d352c3f14932cbe2e279b6 https://github.com/cdk/cdk/commit/2364703d3c3e63b9d2d352c3f14932cbe2e279b6 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- Moved the atom radius into the new rendering parameter API (renderextra module) Commit: e3809c9cf54f47094b177294b9cf7faff3ff99a3 https://github.com/cdk/cdk/commit/e3809c9cf54f47094b177294b9cf7faff3ff99a3 Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Added ability to generate atom number at an offset. This is a naive solution but allows for better looking rendering that the numbers rendered on top of the atom. Commit: c40560d1535022120307b2e7b01d7ba5ab737cef https://github.com/cdk/cdk/commit/c40560d1535022120307b2e7b01d7ba5ab737cef Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for more IGeneratorParameter changes in BasicAtomGenerator Commit: 4dfd81bf9198e4620a86e562d4d30cf402b47c56 https://github.com/cdk/cdk/commit/4dfd81bf9198e4620a86e562d4d30cf402b47c56 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Converted margin into the RenderingParameter variant Commit: 7ef24a4bd02bc1f6a8053fe3d48302083ff89b32 https://github.com/cdk/cdk/commit/7ef24a4bd02bc1f6a8053fe3d48302083ff89b32 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Converted FontName and FontStyle into IGeneratorParameters Commit: 705ecf24620ec1d1d42c560f02bae881bfde9975 https://github.com/cdk/cdk/commit/705ecf24620ec1d1d42c560f02bae881bfde9975 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Refactored showIm/ExplicitHydrogens as IGeneratorParameter Commit: a7b343abbbd53d24a24bca8afcdc4ae1a2f34587 https://github.com/cdk/cdk/commit/a7b343abbbd53d24a24bca8afcdc4ae1a2f34587 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Refactored foreground color into a IGeneratorParameter Commit: 5b3feef2971a22df5a3a118617a6967f035bf4ed https://github.com/cdk/cdk/commit/5b3feef2971a22df5a3a118617a6967f035bf4ed Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- IReactionGenerator now has parameters too Commit: 6aa558741c0d54a08413f2f0852e1b7ca6f9e519 https://github.com/cdk/cdk/commit/6aa558741c0d54a08413f2f0852e1b7ca6f9e519 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java A src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Refactored reaction boxes into a IGeneratorParameter Commit: edda0f3b2a96562d8c17f518c49a0ec1c7c3a160 https://github.com/cdk/cdk/commit/edda0f3b2a96562d8c17f518c49a0ec1c7c3a160 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Updated for the IGenerator/IAtomContainerGenerator refactoring Commit: 789f5cb25a58920ed44efb0468518d8e882038c5 https://github.com/cdk/cdk/commit/789f5cb25a58920ed44efb0468518d8e882038c5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java Log Message: ----------- Extend IGenerator which now provides getParameters() Commit: a6d89bbdeca6ddaeea872ad11b7dd2b33d47fccd https://github.com/cdk/cdk/commit/a6d89bbdeca6ddaeea872ad11b7dd2b33d47fccd Author: Stefan Kuhn <Stefan.Kuhn@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java Log Message: ----------- the RadicalGenerator can render atoms with more than one single electron. Signed-off-by: Arvid Berg <goglepox@...> Added rendering of more than one for vertical alignment too. And reverse direction on vertical alignment. Commit: e047e81cb577a8959656ae9960536fa38a6d8e66 https://github.com/cdk/cdk/commit/e047e81cb577a8959656ae9960536fa38a6d8e66 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: a24a7cd3af59e03b647104ea02a5551a91758366 https://github.com/cdk/cdk/commit/a24a7cd3af59e03b647104ea02a5551a91758366 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java Log Message: ----------- Converted boundsColor to the new rendering parameter API Commit: 7ba56125ff53b0dd08ff400c0440c87bd7bd052d https://github.com/cdk/cdk/commit/7ba56125ff53b0dd08ff400c0440c87bd7bd052d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java Log Message: ----------- Converted mappingColor and mappingLineWidth to the new rendering parameter API Commit: ccc0cb3436450c2814bf0ce3e9947ae22899ba93 https://github.com/cdk/cdk/commit/ccc0cb3436450c2814bf0ce3e9947ae22899ba93 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java R src/main/org/openscience/cdk/renderer/generators/IReactionGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java Log Message: ----------- Removed IAtomContainerGenerator and IReactionGenerator in favor if using generics: IGenerator<T extends IChemObject> (renderextra). Commit: c4aac69310e8bc88b829dbc2cf31b57997c65ceb https://github.com/cdk/cdk/commit/c4aac69310e8bc88b829dbc2cf31b57997c65ceb Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 89b696123f7f65258462f8c0472040c76aef04f5 https://github.com/cdk/cdk/commit/89b696123f7f65258462f8c0472040c76aef04f5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Fixed instantiation of rendering parameter fields, which resulted in NullPointerException (renderextra). Commit: b4944dee9b86ac710b4876dfff7e493d5097801b https://github.com/cdk/cdk/commit/b4944dee9b86ac710b4876dfff7e493d5097801b Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Removed scale and zoom form renderer and replaced with values form the generator parameters Commit: 6ef75e26728b5b06bb8d5062c8043b1cbc1cd3bf https://github.com/cdk/cdk/commit/6ef75e26728b5b06bb8d5062c8043b1cbc1cd3bf Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java M src/main/org/openscience/cdk/renderer/generators/LonePairGenerator.java M src/main/org/openscience/cdk/renderer/generators/MappingGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/RadicalGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderextra). Commit: 97011f50361deb126b0851492ef37278e0b95457 https://github.com/cdk/cdk/commit/97011f50361deb126b0851492ef37278e0b95457 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Also return the parameters of the super class -a (renderextra). Commit: 70224c99853f80009257fb652e8bedda543f4b79 https://github.com/cdk/cdk/commit/70224c99853f80009257fb652e8bedda543f4b79 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Converted the offset from a constructor parameter into a proper IRenderingParamater (renderextra). Commit: 8556391577cb22a4fe5cae262ff2bd493a879597 https://github.com/cdk/cdk/commit/8556391577cb22a4fe5cae262ff2bd493a879597 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java Log Message: ----------- Added rendering parameters for coloring the atom numbers by some scheme, e.g. by element type Commit: 06246f14e10b705b39806852a519023de7849ebb https://github.com/cdk/cdk/commit/06246f14e10b705b39806852a519023de7849ebb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/DistanceSearchVisitor.java Log Message: ----------- Fixed some PMD warnings: longer variable names (renderextra). Commit: 431ceeda7bc346b439fed3ec6ab30163a0aeaa0e https://github.com/cdk/cdk/commit/431ceeda7bc346b439fed3ec6ab30163a0aeaa0e Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Mirror structures on Y-axis to compensate for different coordinate systems. Fixes bc-bug #1654 cdk-bug #2855247 Commit: 2381b3a6cf2614bd30be073efe20ef512f97fc2f https://github.com/cdk/cdk/commit/2381b3a6cf2614bd30be073efe20ef512f97fc2f Author: Arvid Berg <goglepox@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Added null check to avoid NPE when no model is present Commit: 829a057f3d0c1d0cd15520b95d3b6abcebe83758 https://github.com/cdk/cdk/commit/829a057f3d0c1d0cd15520b95d3b6abcebe83758 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java A src/main/org/openscience/cdk/renderer/ReactionRenderer.java A src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java M src/main/org/openscience/cdk/renderer/Renderer.java M src/main/org/openscience/cdk/renderer/generators/BoundsGenerator.java M src/main/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java M src/main/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java Log Message: ----------- Refactored into IRenderer<T extends IChemObject> with modules implementations for IAtomContainer (the existing AtomContainerRenderer), IMoleculeSet, IReaction, IReactionSet, and IChemModel (all for from the existing, overloaded Renderer) (renderextra). Commit: eaead5212198cc8ac99b2bd0b73dca43e929f0ae https://github.com/cdk/cdk/commit/eaead5212198cc8ac99b2bd0b73dca43e929f0ae Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: A src/main/org/openscience/cdk/renderer/ChemModelRenderer.java R src/main/org/openscience/cdk/renderer/Renderer.java Log Message: ----------- Renamed the Renderer to ChemModelRenderer, following the naming pattern for the other IRenderer implementations Commit: 6284f815f6fe917750aec14d8ee52103e9b2c894 https://github.com/cdk/cdk/commit/6284f815f6fe917750aec14d8ee52103e9b2c894 Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java M src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java Log Message: ----------- More types in renderers, and associations between renderers Commit: 259e9db19adc68bc207c92f013f2b71c111a405b https://github.com/cdk/cdk/commit/259e9db19adc68bc207c92f013f2b71c111a405b Author: maclean <gilleain.torrance@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ChemModelRenderer.java M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java M src/main/org/openscience/cdk/renderer/ReactionSetRenderer.java Log Message: ----------- Using IRenderer<T> interface instead of implementation Commit: 46e7bb37526ce411ee1844a2ed77ce385dab4fab https://github.com/cdk/cdk/commit/46e7bb37526ce411ee1844a2ed77ce385dab4fab Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-25 (Tue, 25 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/generators/AtomMassGenerator.java M src/main/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java Log Message: ----------- Updated for API changes in CDK 1.3.6 (renderextra). Commit: 2e6a60284f068990be14026b43308a1f720473de https://github.com/cdk/cdk/commit/2e6a60284f068990be14026b43308a1f720473de Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Fixed registering of rendering parameters (renderextra). Commit: 7e11e24f8126bdd19787edbec4100c5393d5befb https://github.com/cdk/cdk/commit/7e11e24f8126bdd19787edbec4100c5393d5befb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java Log Message: ----------- Fixed NullPointerException by creating an empty list of generators, and return a list too, rather than a null Commit: e7e7b80b0fee596ae4a1fcea0306ed1da6875d82 https://github.com/cdk/cdk/commit/e7e7b80b0fee596ae4a1fcea0306ed1da6875d82 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/ReactionRenderer.java Log Message: ----------- Because the renderers are now typed itself, we can use this.generators instead, fixign a NullPointerException while rendering reactions Commit: 9ce50cb884aa852d520f2a27fa9c3c916ae2072b https://github.com/cdk/cdk/commit/9ce50cb884aa852d520f2a27fa9c3c916ae2072b Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java Log Message: ----------- Implemented the generateDiagram and use that in the paint methods, which fixes reaction rendering as the ReactionRenderer.generateDiagram() uses MoleculeSetRenderer.generateDiagram() Commit: 344b6e7677787d40d5b59396add115b2b1198cf5 https://github.com/cdk/cdk/commit/344b6e7677787d40d5b59396add115b2b1198cf5 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlextra.cdkdepends A src/META-INF/controlextra.libdepends A src/META-INF/test-controlextra.cdkdepends A src/META-INF/test-controlextra.devellibdepends A src/META-INF/test-controlextra.libdepends A src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java A src/main/org/openscience/cdk/controller/undoredo/ChangeIsotopeEdit.java A src/main/org/openscience/cdk/controller/undoredo/ConvertToRadicalEdit.java A src/main/org/openscience/cdk/controller/undoredo/LoadNewModelEdit.java A src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInExistingReactionEdit.java A src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInNewReactionEdit.java A src/main/org/openscience/cdk/controller/undoredo/MergeMoleculesEdit.java A src/test/org/openscience/cdk/coverage/ControlextraCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolextraTests.java Log Message: ----------- Set up the controlextra module for editing functionality for things beyond the IAtomContainer, such as drawing reactions. * includes javadoc and pmd checking * includes coverage test infrastructure Commit: 18afb0882db2ca17cdca74797da66ff81cb4b0de https://github.com/cdk/cdk/commit/18afb0882db2ca17cdca74797da66ff81cb4b0de Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Implemented setChemModelRelay(...) in ControllerModuleAdapter and removed implementation from subclasses Moved implementation of method to superclass as all implementations was the same and the filed is define in this class Commit: 0306361bd24144abb3453e34a843c4ba20e1ac93 https://github.com/cdk/cdk/commit/0306361bd24144abb3453e34a843c4ba20e1ac93 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/META-INF/controlextra.cdkdepends Log Message: ----------- Added missing dependency on cdk-annotation, needed for TestClass Commit: 252cf81e859900f519fa0e4c44760bf82c81145a https://github.com/cdk/cdk/commit/252cf81e859900f519fa0e4c44760bf82c81145a Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/META-INF/controlextra.cdkdepends Log Message: ----------- The module controlextra can depend on controlbasic Commit: dbb5fb0a8789137ec5958937b67e748e40676a66 https://github.com/cdk/cdk/commit/dbb5fb0a8789137ec5958937b67e748e40676a66 Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: A src/main/org/openscience/cdk/controller/ChangeSingleElectronModule.java A src/main/org/openscience/cdk/controller/edit/AddSingleElectron.java A src/main/org/openscience/cdk/controller/edit/RemoveSingleElectron.java Log Message: ----------- Added modules and edits for radical support Commit: ec086581511b46038f7965bb9f787be37ab356fb https://github.com/cdk/cdk/commit/ec086581511b46038f7965bb9f787be37ab356fb Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Set up the controlextra module for editing functionality for things beyond the IAtomContainer, such as drawing reactions. * includes javadoc and pmd checking * includes coverage test infrastructure Commit: 357361ded7c965c12f229f17787ba131a76922d0 https://github.com/cdk/cdk/commit/357361ded7c965c12f229f17787ba131a76922d0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 2f97bb599daec6547f3b0c1f37ef0057f88bce69 https://github.com/cdk/cdk/commit/2f97bb599daec6547f3b0c1f37ef0057f88bce69 Author: maclean <gilleain.torrance@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 96748b410e37f090a50b3b8f4446f82203569a36 https://github.com/cdk/cdk/commit/96748b410e37f090a50b3b8f4446f82203569a36 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (controlextra). Commit: a3c1e2e339079960978525035d552bc76caf58d7 https://github.com/cdk/cdk/commit/a3c1e2e339079960978525035d552bc76caf58d7 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/AtomAtomMappingModule.java M src/main/org/openscience/cdk/controller/edit/AddSingleElectron.java M src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInExistingReactionEdit.java M src/main/org/openscience/cdk/controller/undoredo/MakeReactantOrProductInNewReactionEdit.java Log Message: ----------- Updated for the API changes in CDK 1.3.5 Commit: 5e50def60508b96039704ea4c325fe81f3c4fe57 https://github.com/cdk/cdk/commit/5e50def60508b96039704ea4c325fe81f3c4fe57 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/renderawt.cdkdepends A src/META-INF/renderawt.libdepends A src/META-INF/test-renderawt.cdkdepends A src/META-INF/test-renderawt.devellibdepends A src/META-INF/test-renderawt.libdepends A src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java A src/main/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java A src/test/org/openscience/cdk/coverage/RenderawtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderawtTests.java Log Message: ----------- Render AWT module which allows rendering of the abstract rendering elements onto an AWT widget (or Swing). * added javadoc and PMD testing * added module test suite * new modules: renderawt and test-renderawt Commit: b0c2a588bde250338800a52522e281cc6563aeed https://github.com/cdk/cdk/commit/b0c2a588bde250338800a52522e281cc6563aeed Author: Arvid Berg <goglepox@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java M src/main/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java Log Message: ----------- Added support for GeneralPath to AWTDrawVisitor also made transform in AbstractAWTDrawVisitor protected Commit: 5606c9a7b871db928e9040c8c3497fe8135e617c https://github.com/cdk/cdk/commit/5606c9a7b871db928e9040c8c3497fe8135e617c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Removed the background color from the RenderingModel and placed it in a new BasicSceneGenerator Commit: 8c9b23bbad40fff01b927afcc3650e1905515757 https://github.com/cdk/cdk/commit/8c9b23bbad40fff01b927afcc3650e1905515757 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 41dac46b375c3f97215efd9906110c70a15af12c https://github.com/cdk/cdk/commit/41dac46b375c3f97215efd9906110c70a15af12c Author: maclean <gilleain.torrance@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Changed wedge width to rendering parameter Commit: 48b1707b5105b3035e24dba8ea39e63a38625529 https://github.com/cdk/cdk/commit/48b1707b5105b3035e24dba8ea39e63a38625529 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (renderawt). Commit: 17ec87bc05805ef8184491366592bdaad9b13ff7 https://github.com/cdk/cdk/commit/17ec87bc05805ef8184491366592bdaad9b13ff7 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Fixed some PMD warnings: longer variable names (renderawt). Commit: 176c7266c053560d47fc5706f44dd4e626a75b1d https://github.com/cdk/cdk/commit/176c7266c053560d47fc5706f44dd4e626a75b1d Author: Peter Odéus <peter.odeus@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Made buggy method visit(OvalElement..) render an oval correctly (position and size) by adding SWTRenderer's code from http://github.com/egonw/bioclipse.cheminformatics/blob/2.2.x/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/SWTRenderer.java Commit: 7715469854d903d2bcefaf4915702f0cc1e9742d https://github.com/cdk/cdk/commit/7715469854d903d2bcefaf4915702f0cc1e9742d Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/rendersvg.cdkdepends A src/META-INF/rendersvg.libdepends A src/META-INF/test-rendersvg.cdkdepends A src/META-INF/test-rendersvg.devellibdepends A src/META-INF/test-rendersvg.libdepends A src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java A src/test/org/openscience/cdk/coverage/RendersvgCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrendersvgTests.java Log Message: ----------- Render SVG module allowing translation of the rendering elements to be converted into SVG statements. * added javadoc and PMD testing * added module test suite * new modules: rendersvg and test-rendersvg Commit: e9bf552befd85652dc01d7823eee632287679383 https://github.com/cdk/cdk/commit/e9bf552befd85652dc01d7823eee632287679383 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Converted zoomFactor, scale, bondLength, and arrowHeadWidth to the new rendering parameter API Commit: 4e0c84dcede7013ce711353e052427ebb68bd497 https://github.com/cdk/cdk/commit/4e0c84dcede7013ce711353e052427ebb68bd497 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Renamed get/setRenderingParameter methods to shorter names (rendersvg). Commit: 63c03c982e000203a2e9b5e18882e1487f767922 https://github.com/cdk/cdk/commit/63c03c982e000203a2e9b5e18882e1487f767922 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Fixed some PMD warnings: longer variable names (rendersvg). Commit: 82e1ca7035e34f1994a70a1db0e468f6c8ec4111 https://github.com/cdk/cdk/commit/82e1ca7035e34f1994a70a1db0e468f6c8ec4111 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/SVGGenerator.java Log Message: ----------- Compile fixes caused by rebasing artefacts as some modules still change bits in order modules Commit: af23b966222402b89930af6e8ff35361b96f4b1e https://github.com/cdk/cdk/commit/af23b966222402b89930af6e8ff35361b96f4b1e Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/controlawt.cdkdepends A src/META-INF/controlawt.libdepends A src/META-INF/test-controlawt.cdkdepends A src/META-INF/test-controlawt.devellibdepends A src/META-INF/test-controlawt.libdepends M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java A src/test/org/openscience/cdk/coverage/ControlawtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/McontrolawtTests.java Log Message: ----------- Setting up the controlawt module. * including test module with coverage testgin * enabled PMD and JavaDoc testing Commit: a02bfb78b01efc8ede9a5879c7851776c286501c https://github.com/cdk/cdk/commit/a02bfb78b01efc8ede9a5879c7851776c286501c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java Log Message: ----------- Converted useAntiAliasing into a IGeneratorParameter Commit: 361accfbe6ab59e135c25fcfa9fa6d0adf5a9459 https://github.com/cdk/cdk/commit/361accfbe6ab59e135c25fcfa9fa6d0adf5a9459 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M .classpath M build.xml A jar/swt-gtk-3.4.2.jar A jar/swt-gtk-3.4.2.jar.meta A src/META-INF/renderswt.cdkdepends A src/META-INF/renderswt.libdepends A src/META-INF/test-renderswt.cdkdepends A src/META-INF/test-renderswt.devellibdepends A src/META-INF/test-renderswt.libdepends A src/main/org/openscience/cdk/renderer/font/SWTFontManager.java A src/test/org/openscience/cdk/coverage/RenderswtCoverageTest.java A src/test/org/openscience/cdk/modulesuites/MrenderswtTests.java Log Message: ----------- Created a renderswt module, prepopulated with a SWTFontManager Commit: a0e4f10899bb634d3d1824d4ad6946a1505df2fc https://github.com/cdk/cdk/commit/a0e4f10899bb634d3d1824d4ad6946a1505df2fc Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M META-INF/MANIFEST.MF Log Message: ----------- Added all other CDK java package to be exported, solving access restriction issues in JChemPaint Commit: ddf86e4a2e4308a0efbfef7622b0e1a36752fa10 https://github.com/cdk/cdk/commit/ddf86e4a2e4308a0efbfef7622b0e1a36752fa10 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml Log Message: ----------- Added new control and renderer jars to dist-large and test-dist-large Commit: 95567738601700dcfafb89f0afcf338517c4fb35 https://github.com/cdk/cdk/commit/95567738601700dcfafb89f0afcf338517c4fb35 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M .gitignore Log Message: ----------- Ignore patch folders Commit: 9db6623e48c52cd05c80d7cce9e6e4030ad7d8e0 https://github.com/cdk/cdk/commit/9db6623e48c52cd05c80d7cce9e6e4030ad7d8e0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props M build.xml Log Message: ----------- Added a build.xml target to make a cdk-jchempaint add-on jar for the cdk.jar Commit: e13772509104710031aae10978aa0b34019c3a57 https://github.com/cdk/cdk/commit/e13772509104710031aae10978aa0b34019c3a57 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.xml M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml Log Message: ----------- Only run the CDK-JChemPaint specific tests Commit: 73fa063af35d7f936a10339cdcac9cd83ec7a113 https://github.com/cdk/cdk/commit/73fa063af35d7f936a10339cdcac9cd83ec7a113 Author: Egon Willighagen <egonw@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M javadoc.xml Log Message: ----------- Removed use of the proprietary DocCheck utility Commit: 1d2a3ed701dc082cdaae66d36efbbadec888197c https://github.com/cdk/cdk/commit/1d2a3ed701dc082cdaae66d36efbbadec888197c Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 15 Commit: f466cb4fa337ca56e9f772fa33b0cdcedbbc71a0 https://github.com/cdk/cdk/commit/f466cb4fa337ca56e9f772fa33b0cdcedbbc71a0 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M src/main/org/openscience/cdk/controller/SwingMouseEventRelay.java Log Message: ----------- Uncommented method which seem to have gone lost. (controlawt). Commit: 314da4e2370d7a079eded982aff1d9d5ccc79d46 https://github.com/cdk/cdk/commit/314da4e2370d7a079eded982aff1d9d5ccc79d46 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 16 Commit: 0f0567d379b0096830b0d5d90810b8471ac23231 https://github.com/cdk/cdk/commit/0f0567d379b0096830b0d5d90810b8471ac23231 Author: Egon Willighagen <egon.willighagen@...> Date: 2011-01-26 (Wed, 26 Jan 2011) Changed paths: M build.props Log Message: ----------- Release 17 (rebased on CDK 1.3.8) Compare: https://github.com/cdk/cdk/compare/96785a62f1e0^...0f0567d379b0 |