From: <tho...@us...> - 2008-03-27 10:47:52
|
Revision: 10539 http://cdk.svn.sourceforge.net/cdk/?rev=10539&view=rev Author: thomaskuhn Date: 2008-03-27 03:47:46 -0700 (Thu, 27 Mar 2008) Log Message: ----------- Some clean up and upgrade to Java 5 standards Modified Paths: -------------- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java 2008-03-27 10:46:52 UTC (rev 10538) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java 2008-03-27 10:47:46 UTC (rev 10539) @@ -28,14 +28,15 @@ import java.util.ArrayList; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; import org.embl.ebi.escience.baclava.DataThing; import org.openscience.cdk.applications.taverna.CMLChemFile; import org.openscience.cdk.applications.taverna.LocalWorkerCDK; +import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper; import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; +import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException; @@ -45,7 +46,7 @@ private String[] inputNames = new String[] { "inputStructures" }; private String[] outputNames = new String[] { "Comment" }; - // Region: input and outpout definition + // Region: input and output definition public String[] inputNames() { return inputNames; @@ -65,22 +66,21 @@ // Region: local worker execution - public Map execute(Map inputs) throws TaskExecutionException { + public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException { FileNameGenerator fileNameGenerator = new FileNameGenerator(); boolean tab = false; String ofor = "jpeg"; - List inputList = null; - List comment = new ArrayList(); + List<CMLChemFile> inputList = null; + List<String> comment = new ArrayList<String>(); if (inputs.get(inputNames[0]) != null) { - inputList = (List) ((DataThing) (inputs.get(inputNames[0]))).getDataObject(); + inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0])); } else { return null; } try { - for (Iterator iter = inputList.iterator(); iter.hasNext();) { - CMLChemFile file = (CMLChemFile) iter.next(); + for (CMLChemFile file : inputList) { String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); - List moleculeList = ChemFileManipulator.getAllAtomContainers(file); + List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); try { Draw2DStructure.draw(moleculeList, tab, ofor, fileName); comment.add("done"); @@ -91,7 +91,7 @@ } catch (Exception exception) { throw new TaskExecutionException(exception); } - Map outputs = new HashMap(); + Map<String, DataThing> outputs = new HashMap<String, DataThing>(); outputs.put(outputNames[0], new DataThing(comment)); return outputs; } Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java 2008-03-27 10:46:52 UTC (rev 10538) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java 2008-03-27 10:47:46 UTC (rev 10539) @@ -28,14 +28,15 @@ import java.util.ArrayList; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; import org.embl.ebi.escience.baclava.DataThing; import org.openscience.cdk.applications.taverna.CMLChemFile; import org.openscience.cdk.applications.taverna.LocalWorkerCDK; +import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper; import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; +import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException; @@ -45,7 +46,7 @@ private String[] inputNames = new String[] { "inputStructures" }; private String[] outputNames = new String[] { "Comment" }; - // Region: input and outpout definition + // Region: input and output definition public String[] inputNames() { return inputNames; @@ -65,33 +66,31 @@ // Region: local worker execution - public Map execute(Map inputs) throws TaskExecutionException { + public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException { FileNameGenerator fileNameGenerator = new FileNameGenerator(); boolean tab = true; /////// boolean first = true; String fileName = ""; - List giveList = new ArrayList(); + List<IAtomContainer> giveList = new ArrayList<IAtomContainer>(); /////////// String ofor = "pdf"; - List inputList = null; - List comment = new ArrayList(); + List<CMLChemFile> inputList = null; + List<String> comment = new ArrayList<String>(); if (inputs.get(inputNames[0]) != null) { - inputList = (List) ((DataThing) (inputs.get(inputNames[0]))).getDataObject(); + inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0])); } else { return null; } try { - for (Iterator iter = inputList.iterator(); iter.hasNext();) { - CMLChemFile file = (CMLChemFile) iter.next(); + for (CMLChemFile file : inputList) { if (first){ fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); first = false; } - List moleculeList = ChemFileManipulator.getAllAtomContainers(file); - for (Iterator iterator = moleculeList.iterator(); iterator - .hasNext();) { - giveList.add(iterator.next()); + List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); + for (IAtomContainer atomContainer : moleculeList) { + giveList.add(atomContainer); } } Draw2DStructure.setWidth(500); @@ -102,7 +101,7 @@ } catch (Exception exception) { throw new TaskExecutionException(exception); } - Map outputs = new HashMap(); + Map<String, DataThing> outputs = new HashMap<String, DataThing>(); outputs.put(outputNames[0], new DataThing(comment)); return outputs; } Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java 2008-03-27 10:46:52 UTC (rev 10538) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java 2008-03-27 10:47:46 UTC (rev 10539) @@ -28,17 +28,17 @@ import java.util.ArrayList; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; import org.embl.ebi.escience.baclava.DataThing; import org.openscience.cdk.applications.taverna.CMLChemFile; import org.openscience.cdk.applications.taverna.LocalWorkerCDK; +import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper; +import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; -import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException; public class CreatePNGWith2DStructures implements LocalWorkerCDK { @@ -46,7 +46,7 @@ private String[] inputNames = new String[] { "inputStructures" }; private String[] outputNames = new String[] { "Comment" }; - // Region: input and outpout definition + // Region: input and output definition public String[] inputNames() { return inputNames; @@ -66,22 +66,21 @@ // Region: local worker execution - public Map execute(Map inputs) throws TaskExecutionException { + public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException { FileNameGenerator fileNameGenerator = new FileNameGenerator(); boolean tab = false; String ofor = "PNG"; - List inputList = null; - List comment = new ArrayList(); + List<CMLChemFile> inputList = null; + List<String> comment = new ArrayList<String>(); if (inputs.get(inputNames[0]) != null) { - inputList = (List) ((DataThing) (inputs.get(inputNames[0]))).getDataObject(); + inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0])); } else { return null; } try { - for (Iterator iter = inputList.iterator(); iter.hasNext();) { - CMLChemFile file = (CMLChemFile) iter.next(); + for (CMLChemFile file : inputList) { String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); - List moleculeList = ChemFileManipulator.getAllAtomContainers(file); + List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); try { Draw2DStructure.draw(moleculeList, tab, ofor, fileName); comment.add("done"); @@ -92,7 +91,7 @@ } catch (Exception exception) { throw new TaskExecutionException(exception); } - Map outputs = new HashMap(); + Map<String, DataThing> outputs = new HashMap<String, DataThing>(); outputs.put(outputNames[0], new DataThing(comment)); return outputs; } Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java 2008-03-27 10:46:52 UTC (rev 10538) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java 2008-03-27 10:47:46 UTC (rev 10539) @@ -28,17 +28,17 @@ import java.util.ArrayList; import java.util.HashMap; -import java.util.Iterator; import java.util.List; import java.util.Map; import org.embl.ebi.escience.baclava.DataThing; import org.openscience.cdk.applications.taverna.CMLChemFile; import org.openscience.cdk.applications.taverna.LocalWorkerCDK; +import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper; +import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; -import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException; public class CreateSVGWith2DStructures implements LocalWorkerCDK { @@ -46,7 +46,7 @@ private String[] inputNames = new String[] { "inputStructures" }; private String[] outputNames = new String[] { "Comment" }; - // Region: input and outpout definition + // Region: input and output definition public String[] inputNames() { return inputNames; @@ -66,22 +66,21 @@ // Region: local worker execution - public Map execute(Map inputs) throws TaskExecutionException { + public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException { FileNameGenerator fileNameGenerator = new FileNameGenerator(); boolean tab = false; String ofor = "svg"; - List inputList = null; - List comment = new ArrayList(); + List<CMLChemFile> inputList = null; + List<String> comment = new ArrayList<String>(); if (inputs.get(inputNames[0]) != null) { - inputList = (List) ((DataThing) (inputs.get(inputNames[0]))).getDataObject(); + inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0])); } else { return null; } try { - for (Iterator iter = inputList.iterator(); iter.hasNext();) { - CMLChemFile file = (CMLChemFile) iter.next(); + for (CMLChemFile file : inputList) { String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); - List moleculeList = ChemFileManipulator.getAllAtomContainers(file); + List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); try { Draw2DStructure.draw(moleculeList, tab, ofor, fileName); comment.add("done"); @@ -92,7 +91,7 @@ } catch (Exception exception) { throw new TaskExecutionException(exception); } - Map outputs = new HashMap(); + Map<String, DataThing> outputs = new HashMap<String, DataThing>(); outputs.put(outputNames[0], new DataThing(comment)); return outputs; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <tho...@us...> - 2008-03-27 15:02:47
|
Revision: 10566 http://cdk.svn.sourceforge.net/cdk/?rev=10566&view=rev Author: thomaskuhn Date: 2008-03-27 08:02:42 -0700 (Thu, 27 Mar 2008) Log Message: ----------- Some clean up and upgrade to Java 5 standards Modified Paths: -------------- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java 2008-03-27 15:02:28 UTC (rev 10565) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateJPGWith2DStructures.java 2008-03-27 15:02:42 UTC (rev 10566) @@ -79,7 +79,7 @@ } try { for (CMLChemFile file : inputList) { - String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); + String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(FileNameGenerator.FILENAME), ""); List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); try { Draw2DStructure.draw(moleculeList, tab, ofor, fileName); Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java 2008-03-27 15:02:28 UTC (rev 10565) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePDFWith2DStructures.java 2008-03-27 15:02:42 UTC (rev 10566) @@ -85,7 +85,7 @@ try { for (CMLChemFile file : inputList) { if (first){ - fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); + fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(FileNameGenerator.FILENAME), ""); first = false; } List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java 2008-03-27 15:02:28 UTC (rev 10565) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreatePNGWith2DStructures.java 2008-03-27 15:02:42 UTC (rev 10566) @@ -79,7 +79,7 @@ } try { for (CMLChemFile file : inputList) { - String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); + String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(FileNameGenerator.FILENAME), ""); List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); try { Draw2DStructure.draw(moleculeList, tab, ofor, fileName); Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java 2008-03-27 15:02:28 UTC (rev 10565) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java 2008-03-27 15:02:42 UTC (rev 10566) @@ -79,7 +79,7 @@ } try { for (CMLChemFile file : inputList) { - String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(fileNameGenerator.FILENAME), ""); + String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(FileNameGenerator.FILENAME), ""); List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); try { Draw2DStructure.draw(moleculeList, tab, ofor, fileName); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <tho...@us...> - 2008-05-30 12:33:01
|
Revision: 11222 http://cdk.svn.sourceforge.net/cdk/?rev=11222&view=rev Author: thomaskuhn Date: 2008-05-30 05:32:57 -0700 (Fri, 30 May 2008) Log Message: ----------- Modified Paths: -------------- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/Draw2DStructure.java Removed Paths: ------------- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java Deleted: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java 2008-05-30 12:32:43 UTC (rev 11221) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/CreateSVGWith2DStructures.java 2008-05-30 12:32:57 UTC (rev 11222) @@ -1,100 +0,0 @@ -/* - * $Author$ - * $Date$ - * $Revision$ - * - * Copyright (C) 2006 by Mario Baseda <mar...@us...> - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * All we ask is that proper credit is given for our work, which includes - * - but is not limited to - adding the above copyright notice to the beginning - * of your source code files, and to any copyright notice that you may distribute - * with programs based on this work. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ - -package org.openscience.cdk.applications.taverna.renderers; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.embl.ebi.escience.baclava.DataThing; -import org.openscience.cdk.applications.taverna.CMLChemFile; -import org.openscience.cdk.applications.taverna.LocalWorkerCDK; -import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper; -import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator; -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.manipulator.ChemFileManipulator; - -import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException; - -public class CreateSVGWith2DStructures implements LocalWorkerCDK { - - private String[] inputNames = new String[] { "inputStructures" }; - private String[] outputNames = new String[] { "Comment" }; - - // Region: input and output definition - - public String[] inputNames() { - return inputNames; - } - public String[] inputTypes() { - return new String[] {LocalWorkerCDK.CMLChemFileList}; - } - - public String[] outputNames() { - return outputNames; - } - public String[] outputTypes() { - return new String[] {LocalWorkerCDK.STRING_ARRAY}; - } - - // End of region - - // Region: local worker execution - - public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException { - FileNameGenerator fileNameGenerator = new FileNameGenerator(); - boolean tab = false; - String ofor = "svg"; - List<CMLChemFile> inputList = null; - List<String> comment = new ArrayList<String>(); - if (inputs.get(inputNames[0]) != null) { - inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0])); - } else { - return null; - } - try { - for (CMLChemFile file : inputList) { - String fileName = fileNameGenerator.generateFileNameAndPathFromList((List<String>) file.getProperty(FileNameGenerator.FILENAME), ""); - List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file); - try { - Draw2DStructure.draw(moleculeList, tab, ofor, fileName); - comment.add("done"); - } catch (Exception e){ - comment.add("Error"); - } - } - } catch (Exception exception) { - throw new TaskExecutionException(exception); - } - Map<String, DataThing> outputs = new HashMap<String, DataThing>(); - outputs.put(outputNames[0], new DataThing(comment)); - return outputs; - } -} - // End of Region - Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/Draw2DStructure.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/Draw2DStructure.java 2008-05-30 12:32:43 UTC (rev 11221) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/renderers/Draw2DStructure.java 2008-05-30 12:32:57 UTC (rev 11222) @@ -44,7 +44,6 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; -import java.io.FileWriter; import java.io.IOException; import java.text.DecimalFormat; import java.util.Iterator; @@ -62,10 +61,9 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.io.SVGWriter; import org.openscience.cdk.layout.StructureDiagramGenerator; import org.openscience.cdk.math.RandomNumbersTool; -import org.openscience.cdk.renderer.Renderer2D; +import org.openscience.cdk.renderer.Java2DRenderer; import org.openscience.cdk.renderer.Renderer2DModel; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; @@ -318,7 +316,7 @@ cdke.printStackTrace(); } r2dm = new Renderer2DModel(); - renderer = new Renderer2D(r2dm); + renderer = new Java2DRenderer(r2dm); Dimension screenSize = new Dimension(this.width, this.height); setPreferredSize(screenSize); r2dm.setBackgroundDimension(screenSize); // make sure it is synched with the JPanel size @@ -396,7 +394,7 @@ public void paint(Graphics g) { super.paint(g); - renderer.paintMolecule(this.mol, (Graphics2D) g, false, true); + renderer.paintMolecule(this.mol, (Graphics2D) g); } public void close() throws Exception { @@ -434,12 +432,12 @@ IAtomContainer mol; Renderer2DModel r2dm; - Renderer2D renderer; + Java2DRenderer renderer; public displayStructure() { } - /**This method generate a jpg, png or svg files which contains the drawn molecules + /**This method generate a jpg or png files which contains the drawn molecules * @param withH boolean whether hydrogens explicit should be shown * <p> true means yes</p> * <p> false means no</p> @@ -469,11 +467,7 @@ } else if (oformat.equalsIgnoreCase("pdf")) { suffix = ".pdf"; oformat = "PDF"; - } else if (oformat.equalsIgnoreCase("svg")) { - suffix = ".svg"; - oformat = "SVG"; - } - + } this.frame = new JFrame(); } @@ -490,7 +484,7 @@ } r2dm = new Renderer2DModel(); - renderer = new Renderer2D(r2dm); + renderer = new Java2DRenderer(r2dm); Dimension screenSize = new Dimension(this.width, this.height); setPreferredSize(screenSize); r2dm.setBackgroundDimension(screenSize); // make sure it is synched with the JPanel size @@ -572,24 +566,12 @@ System.err.println(ioe.getMessage()); } document.close(); - } else if (oformat.equalsIgnoreCase("svg")) { - try { - SVGWriter cow = new SVGWriter(new FileWriter(name)); - if (cow != null) { - cow.writeAtomContainer(this.mol); - cow.close(); - } - } catch (IOException ioe) { - ioe.printStackTrace(); - } catch (CDKException cdke) { - cdke.printStackTrace(); - } } } public void paint(Graphics g) { super.paint(g); - renderer.paintMolecule(this.mol, (Graphics2D) g, false, true); + renderer.paintMolecule(this.mol, (Graphics2D) g); } public void close() throws Exception { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |