X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1a367c5e58d494e8354f494db9ba1e9ad797ea25;hb=be7129c40859bc2434e59ad0a54149c99ea569ef;hp=d44ecdfd911823469b1f99a2d7b26f648e83e856;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d44ecdf..1a367c5 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 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 @@ -21,9 +21,9 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; -import MCview.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; @@ -69,6 +69,11 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -79,7 +84,11 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + JMenuItem sequenceDetails = new JMenuItem(); + + JMenuItem sequenceSelDetails = new JMenuItem(); + + SequenceI sequence; JMenuItem unGroupMenuItem = new JMenuItem(); @@ -156,8 +165,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, Sequence 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 @@ -182,6 +191,8 @@ public class PopupMenu extends JPopupMenu colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -207,11 +218,11 @@ public class PopupMenu extends JPopupMenu e.printStackTrace(); } + JMenuItem menuItem; if (seq != null) { sequenceMenu.setText(sequence.getName()); - JMenuItem menuItem; if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) { @@ -228,33 +239,13 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - Vector seqs = new Vector(); - for (int i = 0; i < ap.av.alignment.getHeight(); i++) - { - Vector pdbs = ap.av.alignment.getSequenceAt(i) - .getDatasetSequence().getPDBId(); - if (pdbs == null) - continue; - - for (int p = 0; p < pdbs.size(); p++) - { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) - { - if (!seqs.contains(ap.av.alignment.getSequenceAt(i))) - seqs.addElement(ap.av.alignment.getSequenceAt(i)); - - continue; - } - } - } - - SequenceI[] seqs2 = new SequenceI[seqs.size()]; - seqs.toArray(seqs2); - - new AppJmol(pdb, seqs2, 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); } + }); viewStructureMenu.add(menuItem); @@ -269,10 +260,68 @@ public class PopupMenu extends JPopupMenu } else { - structureMenu.remove(viewStructureMenu); + 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) + { + new AppVarna(structureLine, seq, seq.getSequenceAsString(), + rnastruc, seq.getName(), ap); + } + }); + 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, seq + .getSequenceAsString(), rnastruc, seq.getName(), + ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + } + + } + menuItem = new JMenuItem("Hide Sequences"); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -297,9 +346,9 @@ 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) @@ -318,7 +367,12 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); } - + } + } + // for the case when no sequences are even visible + if (ap.av.hasHiddenRows()) + { + { menuItem = new JMenuItem("Reveal All"); menuItem.addActionListener(new ActionListener() { @@ -339,9 +393,9 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + 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) @@ -388,6 +442,14 @@ public class PopupMenu extends JPopupMenu { clustalColour.setSelected(true); } + else if (sg.cs instanceof PurinePyrimidineColourScheme) + { + purinePyrimidineColour.setSelected(true); + } + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -406,6 +468,51 @@ 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()) + { + Vector pes = (Vector) sq.getDatasetSequence() + .getPDBId(); + if (pes != null) + { + for (PDBEntry pe : pes) + { + pdbe.put(pe.getId(), pe); + if (sqass == null) + { + sqass = sq; + } + } + } + } + if (pdbe.size() > 0) + { + final PDBEntry[] pe = pdbe.values().toArray( + new PDBEntry[pdbe.size()]); + final JMenuItem gpdbview; + 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() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + } + }); + } } else { @@ -413,7 +520,7 @@ 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); } @@ -449,7 +556,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs @@ -802,6 +909,23 @@ 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() @@ -959,15 +1083,15 @@ 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); @@ -975,6 +1099,7 @@ 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); @@ -988,6 +1113,11 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); + if (ap.getAlignment().isNucleotide()) + { + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1139,6 +1269,21 @@ 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(); + } + }); + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + conservationMenuItem.setText("Conservation"); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -1150,6 +1295,44 @@ 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()); @@ -1176,9 +1359,7 @@ public class PopupMenu extends JPopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.hiddenRepSequences), - ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -1278,6 +1459,16 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * @@ -1295,8 +1486,8 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1349,8 +1540,8 @@ 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.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1367,8 +1558,8 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1402,12 +1593,12 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + ResidueProperties.propHash, 3, 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); @@ -1477,7 +1668,7 @@ 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; @@ -1531,7 +1722,7 @@ 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(); } @@ -1685,8 +1876,8 @@ public class PopupMenu extends JPopupMenu } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1712,7 +1903,8 @@ 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.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) @@ -1731,8 +1923,10 @@ public class PopupMenu extends JPopupMenu 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); @@ -1740,7 +1934,8 @@ 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); } } @@ -1761,9 +1956,9 @@ 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() @@ -1826,16 +2021,16 @@ 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); - 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(); @@ -1862,8 +2057,8 @@ 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);