X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=c35496433f92978d338d81e03c7b7e80ec3bdf87;hb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;hp=ca6b199f6b83b44b159d930eb366f107ca56af9f;hpb=f60bd625292b277e70cda0125f04756ac7ca05de;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index ca6b199..c354964 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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 * * This file is part of Jalview. * @@ -23,6 +23,14 @@ 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.*; @@ -70,6 +78,12 @@ 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(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -79,8 +93,11 @@ public class PopupMenu extends JPopupMenu JMenu sequenceMenu = new JMenu(); JMenuItem sequenceName = new JMenuItem(); + + JMenuItem sequenceDetails = new JMenuItem(); + JMenuItem sequenceSelDetails = new JMenuItem(); - Sequence sequence; + SequenceI sequence; JMenuItem unGroupMenuItem = new JMenuItem(); @@ -157,7 +174,7 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// @@ -183,6 +200,9 @@ public class PopupMenu extends JPopupMenu colours.add(userDefinedColour); 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++) { @@ -248,10 +268,81 @@ public class PopupMenu extends JPopupMenu } else { + if (ap.av.getAlignment().isNucleotide() == false) + { structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } + if (ap.av.getAlignment().isNucleotide() == true) + { + 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; + menuItem = new JMenuItem(); + menuItem.setText("2D RNA "+structureLine); + menuItem.addActionListener(new java.awt.event.ActionListener() + + { + public void actionPerformed(ActionEvent e) + { + //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); + } + } + + // SequenceFeatures[] test = seq.getSequenceFeatures(); + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation seqAnno[] = seq.getAnnotation(); + for (int i = 0; i < seqAnno.length; i++) + { + if (seqAnno[i].getRNAStruc() != null) + { + final String rnastruc = seqAnno[i].getRNAStruc(); + + // TODO: make rnastrucF a bit more nice + menuItem = new JMenuItem(); + 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,rnastruc,seq.getRNA(), seq.getName(), ap); + new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq + .getName(), ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + } + + + } + menuItem = new JMenuItem("Hide Sequences"); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -276,9 +367,9 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows) + if (ap.av.hasHiddenRows()) { - final int index = ap.av.alignment.findIndex(seq); + final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) @@ -300,7 +391,7 @@ 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() @@ -371,6 +462,19 @@ public class PopupMenu extends JPopupMenu { clustalColour.setSelected(true); } + else if (sg.cs instanceof PurinePyrimidineColourScheme) + { + purinePyrimidineColour.setSelected(true); + } + + else if (sg.cs instanceof RNAInteractionColourScheme) + { + RNAInteractionColour.setSelected(true); + } + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -391,6 +495,7 @@ public class PopupMenu extends JPopupMenu } // Add a 'show all structures' for the current selection Hashtable pdbe=new Hashtable(); + SequenceI sqass=null; for (SequenceI sq: ap.av.getSequenceSelection()) { Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); @@ -398,6 +503,10 @@ public class PopupMenu extends JPopupMenu for (PDBEntry pe: pes) { pdbe.put(pe.getId(), pe); + if (sqass==null) + { + sqass = sq; + } } } } @@ -405,7 +514,12 @@ public class PopupMenu extends JPopupMenu { final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); final JMenuItem gpdbview; - structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures.")); + 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.")); + } 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() { @@ -424,7 +538,7 @@ public class PopupMenu extends JPopupMenu editMenu.setVisible(false); } - if (!ap.av.alignment.getGroups().contains(sg)) + if (!ap.av.getAlignment().getGroups().contains(sg)) { unGroupMenuItem.setVisible(false); } @@ -435,7 +549,7 @@ public class PopupMenu extends JPopupMenu structureMenu.setVisible(false); } - if (seq !=null && links != null && links.size() > 0) + if (links != null && links.size() > 0) { JMenu linkMenu = new JMenu("Link"); @@ -460,7 +574,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq!=null && urlLink.isDynamic()) { // collect matching db-refs @@ -813,6 +927,20 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); + sequenceDetails.setText("Sequence Details ..."); + sequenceDetails.addActionListener(new java.awt.event.ActionListener() + { + 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(); + }}); PIDColour.setFocusPainted(false); unGroupMenuItem.setText("Remove Group"); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -922,7 +1050,30 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - pdbFromFile_actionPerformed(); + try { + pdbFromFile_actionPerformed(); + } catch (ExceptionFileFormatOrSyntax e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (ParserConfigurationException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (SAXException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (ExceptionPermissionDenied e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (ExceptionLoadingFailed e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (InterruptedException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } catch (ExceptionUnmatchedClosingParentheses e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } } }); enterPDB.setText("Enter PDB Id"); @@ -970,15 +1121,15 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void * actionPerformed(ActionEvent actionEvent) { * annotationMenuItem_actionPerformed(actionEvent); } }); */ - + groupMenu.add(sequenceSelDetails); add(groupMenu); - add(sequenceMenu); this.add(structureMenu); groupMenu.add(editMenu); @@ -986,6 +1137,7 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceFeature); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); + sequenceMenu.add(sequenceDetails); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -999,6 +1151,11 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); + colourMenu.add(RNAInteractionColour); + if (ap.getAlignment().isNucleotide()) { + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1150,6 +1307,31 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); + purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + + RNAInteractionColour.setText("RNA Interaction type"); + RNAInteractionColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + RNAInteractionColour_actionPerformed(); + } + }); + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + conservationMenuItem.setText("Conservation"); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -1161,6 +1343,40 @@ public class PopupMenu extends JPopupMenu }); } + protected void sequenceSelectionDetails_actionPerformed() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void sequenceDetails_actionPerformed() + { + 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("

"); + } + cap.setText("" + contents.toString() + ""); + + Desktop.instance.addInternalFrame(cap, + "Sequence Details for " + (sequences.length==1 ? sequences[0].getDisplayId(true) : "Selection") +, 500, 400); + + } + protected void showNonconserved_actionPerformed() { getGroup().setShowNonconserved(displayNonconserved.isSelected()); @@ -1188,8 +1404,7 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.hiddenRepSequences), - ap.av.alignment.getWidth()); + sg,ap.av.getHiddenRepSequences()); refresh(); } @@ -1289,6 +1504,21 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + protected void RNAInteractionColour_actionPerformed() + { + getGroup().cs = new RNAInteractionColourScheme(); + refresh(); + } + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * @@ -1306,7 +1536,7 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() @@ -1360,7 +1590,7 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1378,7 +1608,7 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); @@ -1414,11 +1644,11 @@ public class PopupMenu extends JPopupMenu { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + c.verdict(false, ap.av.getConsPercGaps()); sg.cs.setConservation(c); @@ -1488,7 +1718,7 @@ public class PopupMenu extends JPopupMenu // this method won't add a new group if it already exists if (sg != null) { - ap.av.alignment.addGroup(sg); + ap.av.getAlignment().addGroup(sg); } return sg; @@ -1542,7 +1772,7 @@ public class PopupMenu extends JPopupMenu void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); refresh(); } @@ -1696,7 +1926,7 @@ public class PopupMenu extends JPopupMenu } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1723,7 +1953,7 @@ 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.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) @@ -1737,7 +1967,7 @@ public class PopupMenu extends JPopupMenu oal = null; } - public void pdbFromFile_actionPerformed() + public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); @@ -1772,9 +2002,9 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] { sequence } - : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { public void run() @@ -1843,10 +2073,10 @@ public class PopupMenu extends JPopupMenu AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots); - ap.av.alignment.addAnnotation(an); + ap.av.getAlignment().addAnnotation(an); an.createSequenceMapping(sequence, 0, true); // an.adjustForAlignment(); - ap.av.alignment.setAnnotationIndex(an, 0); + ap.av.getAlignment().setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); @@ -1873,8 +2103,8 @@ public class PopupMenu extends JPopupMenu EditCommand editCommand = new EditCommand("Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), - sg.getSequencesAsArray(ap.av.hiddenRepSequences), - sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand);