X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f19a2c0e315e362b641228e524e90d1b2486e594;hb=ffa3ea1a2a3e3b0fd8da65fdb619ac2815fe5af7;hp=4a3fb20a4d99c69c842e4defb0f8361bdc37ed51;hpb=28bfc1385cb1addc479bc04eb5a5b992e0c8f1bd;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4a3fb20..f19a2c0 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview 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 @@ -23,8 +23,15 @@ import java.awt.*; import java.awt.event.*; import javax.swing.*; +import javax.xml.parsers.ParserConfigurationException; + +import org.xml.sax.SAXException; + +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; -import MCview.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; @@ -71,6 +78,7 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); @@ -84,8 +92,9 @@ public class PopupMenu extends JPopupMenu JMenu sequenceMenu = new JMenu(); JMenuItem sequenceName = new JMenuItem(); - + JMenuItem sequenceDetails = new JMenuItem(); + JMenuItem sequenceSelDetails = new JMenuItem(); SequenceI sequence; @@ -165,8 +174,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, - Vector groupLinks) + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, + Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -192,6 +201,7 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); + colours.add(RNAInteractionColour); // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) @@ -239,8 +249,10 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence - new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); + // TODO re JAL-860: optionally open dialog or provide a menu entry + // allowing user to open just one structure per sequence + new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] + { pdb })[0], null, ap); // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } @@ -260,28 +272,41 @@ public class PopupMenu extends JPopupMenu { if (ap.av.getAlignment().isNucleotide() == false) { - structureMenu.remove(viewStructureMenu); + structureMenu.remove(viewStructureMenu); } // structureMenu.remove(colStructureMenu); } if (ap.av.getAlignment().isNucleotide() == true) { - AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { if (aa[i].getRNAStruc() != null) { final String rnastruc = aa[i].getRNAStruc(); - final String structureLine=aa[i].label; + final String structureLine = aa[i].label; menuItem = new JMenuItem(); - menuItem.setText("2D RNA "+structureLine); + menuItem.setText("2D RNA " + structureLine); menuItem.addActionListener(new java.awt.event.ActionListener() + { public void actionPerformed(ActionEvent e) { - new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq - .getName(), ap); + //System.out.println("1:"+structureLine); + System.out.println("1:sname"+seq.getName()); + System.out.println("2:seq"+seq); + + //System.out.println("3:"+seq.getSequenceAsString()); + System.out.println("3:strucseq"+rnastruc); + //System.out.println("4:struc"+seq.getRNA()); + System.out.println("5:name"+seq.getName()); + System.out.println("6:ap"+ap); + new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq + .getName(), ap); + //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap); + System.out.println("end"); } }); viewStructureMenu.add(menuItem); @@ -298,17 +323,19 @@ public class PopupMenu extends JPopupMenu if (seqAnno[i].getRNAStruc() != null) { final String rnastruc = seqAnno[i].getRNAStruc(); - - // TODO: make rnastrucF a bit more nice + + // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText("2D RNA - "+seq.getName()); + menuItem.setText("2D RNA - " + seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq - .getName(), ap); + + new AppVarna(seq.getName() + " structure", seq, seq + .getSequenceAsString(), rnastruc, seq.getName(), + ap); } }); viewStructureMenu.add(menuItem); @@ -316,7 +343,6 @@ public class PopupMenu extends JPopupMenu } } - } menuItem = new JMenuItem("Hide Sequences"); @@ -367,7 +393,8 @@ public class PopupMenu extends JPopupMenu } } // for the case when no sequences are even visible - if (ap.av.hasHiddenRows()) { + if (ap.av.hasHiddenRows()) + { { menuItem = new JMenuItem("Reveal All"); menuItem.addActionListener(new ActionListener() @@ -389,9 +416,9 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null&& sg.getSize()>0) + if (sg != null && sg.getSize() > 0) { - groupName.setText("Name: "+sg.getName()); + groupName.setText("Name: " + sg.getName()); groupName.setText("Edit name and description of current group."); if (sg.cs instanceof ZappoColourScheme) @@ -442,6 +469,8 @@ public class PopupMenu extends JPopupMenu { purinePyrimidineColour.setSelected(true); } + + /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } @@ -465,36 +494,43 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe=new Hashtable(); - SequenceI sqass=null; - for (SequenceI sq: ap.av.getSequenceSelection()) + Hashtable pdbe = new Hashtable(); + SequenceI sqass = null; + for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); - if (pes!=null) { - for (PDBEntry pe: pes) + Vector pes = (Vector) sq.getDatasetSequence() + .getPDBId(); + if (pes != null) + { + for (PDBEntry pe : pes) { - pdbe.put(pe.getId(), pe); - if (sqass==null) + pdbe.put(pe.getId(), pe); + if (sqass == null) { sqass = sq; } } } } - if (pdbe.size()>0) + if (pdbe.size() > 0) { - final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); + final PDBEntry[] pe = pdbe.values().toArray( + new PDBEntry[pdbe.size()]); final JMenuItem gpdbview; - if (pdbe.size()==1) + if (pdbe.size() == 1) { - structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false))); - } else { - structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures.")); + structureMenu.add(gpdbview = new JMenuItem("View structure for " + + sqass.getDisplayId(false))); + } + else + { + structureMenu.add(gpdbview = new JMenuItem("View all " + + pdbe.size() + " structures.")); } gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); gpdbview.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { @@ -545,7 +581,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (seq!=null && urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs @@ -904,14 +940,17 @@ public class PopupMenu extends JPopupMenu public void actionPerformed(ActionEvent e) { sequenceDetails_actionPerformed(); - }}); + } + }); sequenceSelDetails.setText("Sequence Details ..."); - sequenceSelDetails.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sequenceSelectionDetails_actionPerformed(); - }}); + sequenceSelDetails + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); PIDColour.setFocusPainted(false); unGroupMenuItem.setText("Remove Group"); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -1021,9 +1060,40 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - pdbFromFile_actionPerformed(); + try { + pdbFromFile_actionPerformed(); + } catch (Exception e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } } }); +// RNAFold.setText("From RNA Fold with predict2D"); +// RNAFold.addActionListener(new ActionListener() +// { +// public void actionPerformed(ActionEvent e) +// { +// try { +// RNAFold_actionPerformed(); +// } catch (Exception e1) { +// // TODO Auto-generated catch block +// e1.printStackTrace(); +// } +// } +// }); +// ContraFold.setText("From Contra Fold with predict2D"); +// ContraFold.addActionListener(new ActionListener() +// { +// public void actionPerformed(ActionEvent e) +// { +// try { +// ContraFold_actionPerformed(); +// } catch (Exception e1) { +// // TODO Auto-generated catch block +// e1.printStackTrace(); +// } +// } +// }); enterPDB.setText("Enter PDB Id"); enterPDB.addActionListener(new ActionListener() { @@ -1069,7 +1139,7 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); - + /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void @@ -1100,6 +1170,8 @@ public class PopupMenu extends JPopupMenu colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); if (ap.getAlignment().isNucleotide()) { + // JBPNote - commented since the colourscheme isn't functional + // colourMenu.add(RNAInteractionColour); colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); @@ -1263,6 +1335,8 @@ public class PopupMenu extends JPopupMenu purinePyrimidineColour_actionPerformed(); } }); + + /* * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { @@ -1287,31 +1361,35 @@ public class PopupMenu extends JPopupMenu protected void sequenceDetails_actionPerformed() { - createSequenceDetailsReport(new SequenceI[]{sequence}); + createSequenceDetailsReport(new SequenceI[] + { sequence }); } + public void createSequenceDetailsReport(SequenceI[] sequences) { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); StringBuffer contents = new StringBuffer(); - for (SequenceI seq:sequences) - { - contents.append("

Annotation for "+seq.getDisplayId(true)+"

"); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport( - contents, - seq, - true, - true,false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax - : null); - contents.append("

"); + for (SequenceI seq : sequences) + { + contents.append("

Annotation for " + seq.getDisplayId(true) + + "

"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("

"); } cap.setText("" + contents.toString() + ""); - - Desktop.instance.addInternalFrame(cap, - "Sequence Details for " + (sequences.length==1 ? sequences[0].getDisplayId(true) : "Selection") -, 500, 400); - + + Desktop.instance.addInternalFrame(cap, "Sequence Details for " + + (sequences.length == 1 ? sequences[0].getDisplayId(true) + : "Selection"), 500, 400); + } protected void showNonconserved_actionPerformed() @@ -1340,8 +1418,7 @@ public class PopupMenu extends JPopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme( - sg,ap.av.getHiddenRepSequences()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -1447,6 +1524,7 @@ public class PopupMenu extends JPopupMenu refresh(); } + /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1468,8 +1546,8 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1522,8 +1600,8 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1540,8 +1618,8 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1575,8 +1653,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -1858,8 +1936,8 @@ public class PopupMenu extends JPopupMenu } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1885,7 +1963,8 @@ public class PopupMenu extends JPopupMenu ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation(); + AlignmentAnnotation[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) @@ -1899,13 +1978,15 @@ public class PopupMenu extends JPopupMenu oal = null; } - public void pdbFromFile_actionPerformed() + public void pdbFromFile_actionPerformed() throws Exception { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false)); - chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'"); + chooser.setDialogTitle("Select a PDB file for " + + sequence.getDisplayId(false)); + chooser.setToolTipText("Load a PDB file and associate it with sequence '" + + sequence.getDisplayId(false) + "'"); int value = chooser.showOpenDialog(null); @@ -1913,7 +1994,8 @@ public class PopupMenu extends JPopupMenu { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); } } @@ -1999,8 +2081,8 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure( - sequence, pdbid); + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots);