From: GitHub <no...@gi...> - 2013-03-24 07:12:20
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Branch: refs/heads/master Home: https://github.com/cdk/cdk Commit: f5b4be1c455836285bc30cb1cbff9b0b01710c3f https://github.com/cdk/cdk/commit/f5b4be1c455836285bc30cb1cbff9b0b01710c3f Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: A src/main/org/openscience/cdk/graph/AllShortestPaths.java M src/main/org/openscience/cdk/graph/PathTools.java A src/main/org/openscience/cdk/graph/ShortestPaths.java A src/test/org/openscience/cdk/graph/AllShortestPathsTest.java A src/test/org/openscience/cdk/graph/ShortestPathsTest.java M src/test/org/openscience/cdk/modulesuites/McoreTests.java Log Message: ----------- Introduced a new utility for computing the first shortest path and all shortest paths from a start to an end atom. This implementation replaces an existing static method in PathTools which has now been deprecated. Another helper class was added that simplifies the computation of all-vs-all shortest paths. Conflicts: src/test/org/openscience/cdk/modulesuites/McoreTests.java Change-Id: Ia6df8b06f3ac199be7ffe16c85c436da35656588 Commit: 43224b89372693720937152a0e9d40c3b503a881 https://github.com/cdk/cdk/commit/43224b89372693720937152a0e9d40c3b503a881 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/graph/AllShortestPaths.java M src/main/org/openscience/cdk/graph/ShortestPaths.java Log Message: ----------- Improved terminology in javadoc and added @cdk.githash to production classes. Commit: 2f9e10eba2f68ef9fce3bba4a6acd494455acc46 https://github.com/cdk/cdk/commit/2f9e10eba2f68ef9fce3bba4a6acd494455acc46 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/graph/ShortestPaths.java Log Message: ----------- Corrected constructor visibility Commit: ad96f243e7277d83b9cf7834a24e72d60c9b48c3 https://github.com/cdk/cdk/commit/ad96f243e7277d83b9cf7834a24e72d60c9b48c3 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Variable/method renaming and copyright update Commit: f43c72a2d0ccb4435ac59006a7650ec20106afe6 https://github.com/cdk/cdk/commit/f43c72a2d0ccb4435ac59006a7650ec20106afe6 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- replaced setAtom with a new method to encode a path of indexed vertices to a string. These changes cause no test regressions. Commit: 296d5392d5d2ca3f21c8a9bbb6151587a84a7866 https://github.com/cdk/cdk/commit/296d5392d5d2ca3f21c8a9bbb6151587a84a7866 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Commented out a line which could lead to a bug. This line was in the existing implementation but can cause issues when at molecule has multiple pseudo atoms with the same label. Also removed nPseudoAtoms, this is given by the size of the pseudoAtoms list. Commit: 10a245704b4f4542e7a60cd49cc3b5e71da44b4e https://github.com/cdk/cdk/commit/10a245704b4f4542e7a60cd49cc3b5e71da44b4e Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Replaced atom iteration with integer for loops - this causes no regressions. Commit: 83d68dd774c96eae93f5c7b584e7761ac83a577a https://github.com/cdk/cdk/commit/83d68dd774c96eae93f5c7b584e7761ac83a577a Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Replaced path tools shortest path implementation with the new AllShortestPaths. Removed redundant canonicalisation step. This patch cause a single regression due to multiple-shortests paths. Commit: 2cb509358314fe96776a7ad51e2160fb545a6f8a https://github.com/cdk/cdk/commit/2cb509358314fe96776a7ad51e2160fb545a6f8a Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Removed redundant allPaths set (no regressions) Commit: be69d813ee70cff0661fa5438db0ded224b6bfb2 https://github.com/cdk/cdk/commit/be69d813ee70cff0661fa5438db0ded224b6bfb2 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Removing temporary method Commit: e664a57dcdee99db2ff77c5daa209812fbd6a6c8 https://github.com/cdk/cdk/commit/e664a57dcdee99db2ff77c5daa209812fbd6a6c8 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Reduced number of iterations. This path also resolves the previous regression. Commit: ff0968c50a3090c7047458742bc17cc318946a12 https://github.com/cdk/cdk/commit/ff0968c50a3090c7047458742bc17cc318946a12 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Updated java doc and renamed getPaths() -> paths() Commit: 05400d440a165fc52aa4db3423cba55bc1cf7125 https://github.com/cdk/cdk/commit/05400d440a165fc52aa4db3423cba55bc1cf7125 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- Allowing traverse() to return the set of paths. Once the traversal is done the set is wrapped in an immutable decorator only once and stored for access. Commit: adce5735a67cabe553139c98b28adba61cdc30a4 https://github.com/cdk/cdk/commit/adce5735a67cabe553139c98b28adba61cdc30a4 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java M src/test/org/openscience/cdk/fingerprint/ShortestPathFingerprinterTest.java Log Message: ----------- Change shortest path implementation to encode multiple shortest paths. This causes two regressions in the unit tests as both these molecules had multiple shortest paths. Commit: c7f3a8b12a85454008a490956affb2830fbdc9f5 https://github.com/cdk/cdk/commit/c7f3a8b12a85454008a490956affb2830fbdc9f5 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java A src/main/org/openscience/cdk/graph/AllPairsShortestPaths.java R src/main/org/openscience/cdk/graph/AllShortestPaths.java M src/main/org/openscience/cdk/graph/PathTools.java M src/main/org/openscience/cdk/graph/ShortestPaths.java A src/test/org/openscience/cdk/graph/AllPairsShortestPathsTest.java R src/test/org/openscience/cdk/graph/AllShortestPathsTest.java M src/test/org/openscience/cdk/modulesuites/McoreTests.java Log Message: ----------- renamed AllShortestPaths to AllPairsShortestPaths as this is the correct name for the problem Commit: 43c282553fb96400bbce2534fd07938caa7818c6 https://github.com/cdk/cdk/commit/43c282553fb96400bbce2534fd07938caa7818c6 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M doc/refs/cheminf.bibx M src/main/org/openscience/cdk/graph/ShortestPaths.java M src/test/org/openscience/cdk/graph/ShortestPathsTest.java Log Message: ----------- including preceding path conditional required by Vismara's MCB Union, also included the reference for the article. Commit: fda085204bb7a899884c4c1622a345396304ae27 https://github.com/cdk/cdk/commit/fda085204bb7a899884c4c1622a345396304ae27 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/graph/ShortestPaths.java Log Message: ----------- Replacing array list with a linked list queue - quicker polling Commit: 460ba9d65a4092f9aa564e2285d5e028911f174f https://github.com/cdk/cdk/commit/460ba9d65a4092f9aa564e2285d5e028911f174f Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/test/org/openscience/cdk/graph/ShortestPathsTest.java Log Message: ----------- resolves failing unit tests Commit: a29c8d0afa59d7bf0cfbd3788cf9c4b85a989f3b https://github.com/cdk/cdk/commit/a29c8d0afa59d7bf0cfbd3788cf9c4b85a989f3b Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java Log Message: ----------- removed annotation to missing test method Commit: 63e085c99bbb44a6cae559d83ec8342affdf265f https://github.com/cdk/cdk/commit/63e085c99bbb44a6cae559d83ec8342affdf265f Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java Log Message: ----------- correct test method name Commit: f8b9d214e92bf2b226d4d5e05d387352172244ef https://github.com/cdk/cdk/commit/f8b9d214e92bf2b226d4d5e05d387352172244ef Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java Log Message: ----------- removed incorrect implementation, getRawFingerprint should return a map of path keys e.g. [CC:C] to the hash value, this implementation was returning a map of hashes (int) to hashes (int). Commit: 51106e5c3fdb11495e6c0b6f49fb04d19b0ec04f https://github.com/cdk/cdk/commit/51106e5c3fdb11495e6c0b6f49fb04d19b0ec04f Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- removed unused and redundant method, walker.paths().size() is equivalent Commit: 4d63442e2f259c179e061dc63209fe0b005d0bc4 https://github.com/cdk/cdk/commit/4d63442e2f259c179e061dc63209fe0b005d0bc4 Author: John May <joh...@gm...> Date: 2013-03-23 (Sat, 23 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java Log Message: ----------- toString tidy up, removed trailing join string '->' Commit: 99f3c7c047900ceba7927327a027f420289909ec https://github.com/cdk/cdk/commit/99f3c7c047900ceba7927327a027f420289909ec Author: John May <joh...@gm...> Date: 2013-03-24 (Sun, 24 Mar 2013) Changed paths: M src/main/org/openscience/cdk/fingerprint/ShortestPathWalker.java A src/test/org/openscience/cdk/fingerprint/ShortestPathWalkerTest.java M src/test/org/openscience/cdk/modulesuites/MfingerprintTests.java Log Message: ----------- tests for ShortestPathWalker Change-Id: Ie4d2d4e378519896cbc067b36c7a7392b682149b Signed-off-by: Egon Willighagen <eg...@us...> Compare: https://github.com/cdk/cdk/compare/a1bc45855bd9...99f3c7c04790 |