Created
July 3, 2012 16:44
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patch by Wayne Volkmuth for cpy/paste via MDLCT, issue #85
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| diff -C3 -r org.openscience.cdk.jchempaint30/src/main/org/openscience/jchempaint/action/CopyPasteAction.java org.openscience.cdk.jchempaint.patched/src/main/org/openscience/jchempaint/action/CopyPasteAction.java | |
| *** org.openscience.cdk.jchempaint30/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-12-08 03:48:25.000000000 -0800 | |
| --- org.openscience.cdk.jchempaint.patched/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2010-09-13 11:07:35.000000000 -0700 | |
| *************** | |
| *** 28,41 **** | |
| */ | |
| package org.openscience.jchempaint.action; | |
| - import java.awt.Toolkit; | |
| import java.awt.datatransfer.Clipboard; | |
| import java.awt.datatransfer.ClipboardOwner; | |
| import java.awt.datatransfer.DataFlavor; | |
| import java.awt.datatransfer.Transferable; | |
| import java.awt.datatransfer.UnsupportedFlavorException; | |
| import java.awt.event.ActionEvent; | |
| import java.io.ByteArrayInputStream; | |
| import java.io.StringBufferInputStream; | |
| import java.io.StringReader; | |
| import java.io.StringWriter; | |
| --- 28,43 ---- | |
| */ | |
| package org.openscience.jchempaint.action; | |
| import java.awt.datatransfer.Clipboard; | |
| import java.awt.datatransfer.ClipboardOwner; | |
| import java.awt.datatransfer.DataFlavor; | |
| + import java.awt.datatransfer.SystemFlavorMap; | |
| import java.awt.datatransfer.Transferable; | |
| import java.awt.datatransfer.UnsupportedFlavorException; | |
| import java.awt.event.ActionEvent; | |
| import java.io.ByteArrayInputStream; | |
| + import java.io.IOException; | |
| + import java.io.InputStream; | |
| import java.io.StringBufferInputStream; | |
| import java.io.StringReader; | |
| import java.io.StringWriter; | |
| *************** | |
| *** 64,69 **** | |
| --- 66,72 ---- | |
| import org.openscience.cdk.io.IChemObjectWriter; | |
| import org.openscience.cdk.io.INChIPlainTextReader; | |
| import org.openscience.cdk.io.ISimpleChemObjectReader; | |
| + import org.openscience.cdk.io.MDLCTV2000Reader; | |
| import org.openscience.cdk.io.MDLReader; | |
| import org.openscience.cdk.io.MDLWriter; | |
| import org.openscience.cdk.io.ReaderFactory; | |
| *************** | |
| *** 103,108 **** | |
| --- 106,113 ---- | |
| private DataFlavor molFlavor = new DataFlavor( | |
| "chemical/x-mdl-molfile", "mdl mol file format"); | |
| + private DataFlavor ctFlavor = new DataFlavor( | |
| + "chemical/x-mdlct-molfile", "mdl CT mol file format, used on clipboards by ISIS/Draw and ChemDraw"); | |
| private DataFlavor svgFlavor = new DataFlavor( | |
| "image/svg+xml", "scalable vector graphics"); | |
| private DataFlavor cmlFlavor = new DataFlavor( | |
| *************** | |
| *** 124,129 **** | |
| --- 129,141 ---- | |
| return transfer != null && transfer.isDataFlavorSupported(flavor); | |
| } | |
| + public CopyPasteAction() { | |
| + super(); | |
| + SystemFlavorMap sfm = (SystemFlavorMap) SystemFlavorMap.getDefaultFlavorMap(); | |
| + sfm.setFlavorsForNative("MDLCT", new DataFlavor[]{ctFlavor}); | |
| + sfm.setNativesForFlavor(ctFlavor, new String[]{"MDLCT"}); | |
| + } | |
| + | |
| public void actionPerformed(ActionEvent e) { | |
| logger.info(" type ", type); | |
| logger.debug(" source ", e.getSource()); | |
| *************** | |
| *** 242,257 **** | |
| if (supported(transfer, molFlavor) ) { | |
| try { | |
| ! StringBufferInputStream sbis = (StringBufferInputStream) transfer.getTransferData(molFlavor); | |
| int x; | |
| StringBuffer sb = new StringBuffer(); | |
| while((x=sbis.read())!=-1){ | |
| sb.append((char)x); | |
| } | |
| reader = new MDLReader(new StringReader(sb.toString())); | |
| } catch (Exception e1) { | |
| e1.printStackTrace(); | |
| } | |
| } else if (supported(transfer, DataFlavor.stringFlavor) ) { | |
| try { | |
| content = (String) transfer.getTransferData(DataFlavor.stringFlavor); | |
| --- 254,279 ---- | |
| if (supported(transfer, molFlavor) ) { | |
| try { | |
| ! InputStream sbis = (InputStream) transfer.getTransferData(molFlavor); | |
| int x; | |
| StringBuffer sb = new StringBuffer(); | |
| while((x=sbis.read())!=-1){ | |
| sb.append((char)x); | |
| } | |
| reader = new MDLReader(new StringReader(sb.toString())); | |
| + flip=true; | |
| } catch (Exception e1) { | |
| e1.printStackTrace(); | |
| } | |
| + } else if (supported(transfer, ctFlavor)) { | |
| + try { | |
| + InputStream sbis = (InputStream) transfer.getTransferData(ctFlavor); | |
| + StringBuffer sb = getMolFromCTStream(sbis); | |
| + reader = new MDLReader(new StringReader(sb.toString())); | |
| + flip=true; | |
| + } catch (Exception e1) { | |
| + e1.printStackTrace(); | |
| + } | |
| } else if (supported(transfer, DataFlavor.stringFlavor) ) { | |
| try { | |
| content = (String) transfer.getTransferData(DataFlavor.stringFlavor); | |
| *************** | |
| *** 265,270 **** | |
| --- 287,293 ---- | |
| // if looks like CML - InputStream required. Reader throws error. | |
| if(content!=null && content.indexOf("cml")>-1) { | |
| reader = new CMLReader(new ByteArrayInputStream(content.getBytes())); | |
| + flip=true; | |
| } | |
| IMolecule toPaste = null; | |
| *************** | |
| *** 482,487 **** | |
| --- 505,555 ---- | |
| /** | |
| + * Convert the data from a stream holding MDLCT format data into MDL | |
| + * Mol format. MDLCT format is Mol format where each line is converted | |
| + * into a string prepended with its length, and newline removed. | |
| + * @throws IOException | |
| + */ | |
| + private StringBuffer getMolFromCTStream(InputStream sbis) throws IOException { | |
| + StringBuffer sb = new StringBuffer(); | |
| + // In MDLCT format lines are prepended with their length. There are | |
| + // no newline characters (i.e. a line is just like a Pascal string) | |
| + // So, loop over lines and read them in. | |
| + int len; | |
| + while ((len = sbis.read()) != -1) { | |
| + if (len > 0) { | |
| + byte[] cbuf = new byte[len]; | |
| + // attempt to read all characters in the "line" | |
| + int rd = sbis.read(cbuf, 0, len); | |
| + // unless we read that number of characters, something is wrong | |
| + if (rd == -1) { | |
| + throw new IOException("MDLCT line specified length of " + len + " characters for line, found EOF"); | |
| + } else if (rd != len) { | |
| + throw new IOException("MDLCT input specified length of " + len + " characters for line, found " + rd); | |
| + } | |
| + sb.append(new String(cbuf)); | |
| + } | |
| + sb.append(System.getProperty("line.separator")); | |
| + } | |
| + return sb; | |
| + } | |
| + | |
| + /** | |
| + * Convert the data from a MDL Mol data into MDLCT format. MDLCT | |
| + * format is Mol format where each line is converted into a string | |
| + * prepended with its length, and newline removed. | |
| + */ | |
| + private String getCTStringFromMol(String mol) { | |
| + StringBuffer sb = new StringBuffer(); | |
| + for (String s : mol.toString().split(System.getProperty("line.separator"))) { | |
| + int len = s.length(); | |
| + sb.append((char) len); | |
| + sb.append(s); | |
| + } | |
| + return sb.toString(); | |
| + } | |
| + | |
| + /** | |
| * A workaround for reading structure from file, these tend to get | |
| * in upside down | |
| * TODO remove when obsolete. | |
| *************** | |
| *** 572,591 **** | |
| class JcpSelection implements Transferable, ClipboardOwner { | |
| private DataFlavor [] supportedFlavors = { | |
| ! molFlavor, DataFlavor.stringFlavor, svgFlavor, cmlFlavor, smilesFlavor | |
| }; | |
| String mol; | |
| String smiles; | |
| String svg; | |
| String cml; | |
| @SuppressWarnings("unchecked") | |
| public JcpSelection(IAtomContainer tocopy1) throws Exception { | |
| IMolecule tocopy= tocopy1.getBuilder().newMolecule(tocopy1); | |
| // MDL mol output | |
| StringWriter sw = new StringWriter(); | |
| new MDLWriter(sw).writeMolecule(tocopy); | |
| this.mol=sw.toString(); | |
| SmilesGenerator sg=new SmilesGenerator(); | |
| smiles = sg.createSMILES(tocopy); | |
| // SVG output | |
| --- 640,662 ---- | |
| class JcpSelection implements Transferable, ClipboardOwner { | |
| private DataFlavor [] supportedFlavors = { | |
| ! molFlavor, ctFlavor, DataFlavor.stringFlavor, svgFlavor, cmlFlavor, smilesFlavor | |
| }; | |
| String mol; | |
| String smiles; | |
| + String mdlct; | |
| String svg; | |
| String cml; | |
| @SuppressWarnings("unchecked") | |
| public JcpSelection(IAtomContainer tocopy1) throws Exception { | |
| IMolecule tocopy= tocopy1.getBuilder().newMolecule(tocopy1); | |
| + flipStructure(tocopy); | |
| // MDL mol output | |
| StringWriter sw = new StringWriter(); | |
| new MDLWriter(sw).writeMolecule(tocopy); | |
| this.mol=sw.toString(); | |
| + this.mdlct = getCTStringFromMol(sw.toString()); | |
| SmilesGenerator sg=new SmilesGenerator(); | |
| smiles = sg.createSMILES(tocopy); | |
| // SVG output | |
| *************** | |
| *** 629,634 **** | |
| --- 700,707 ---- | |
| return new StringBufferInputStream(smiles); | |
| } else if(parFlavor.equals(DataFlavor.stringFlavor)) { | |
| return mol; | |
| + } else if(parFlavor.equals(ctFlavor)) { | |
| + return new StringBufferInputStream(mdlct); | |
| } else if(parFlavor.equals(cmlFlavor)) { | |
| return new StringBufferInputStream(cml); | |
| } else if(parFlavor.equals(svgFlavor)) { |
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