X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=c1bbc8d58d0167bab19eb405f995533f9ee27a1b;hb=27d1490bba5753b3f9c8fac0647cfe8148c53310;hp=7a82a965084af1f6d165f1d26e95fc75532a103c;hpb=28c13a67af0d57c53de532d0d50add7ab83f7d42;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java old mode 100755 new mode 100644 index 7a82a96..c1bbc8d --- 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. * @@ -21,6 +21,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import MCview.*; @@ -37,7 +38,7 @@ import jalview.util.UrlLink; * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.118 $ */ public class PopupMenu extends JPopupMenu { @@ -69,6 +70,11 @@ 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 +85,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + SequenceI sequence; JMenuItem unGroupMenuItem = new JMenuItem(); @@ -156,7 +162,7 @@ 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) { // ///////////////////////////////////////////////////////// @@ -182,6 +188,8 @@ 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 +215,11 @@ 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 +236,11 @@ 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 +255,67 @@ 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) + { + 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 +340,9 @@ 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 +361,11 @@ 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 +386,10 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + if (sg != null&& sg.getSize()>0) { - groupName.setText(sg.getName()); + groupName.setText("Name: "+sg.getName()); + groupName.setText("Edit name and description of current group."); if (sg.cs instanceof ZappoColourScheme) { @@ -387,6 +435,14 @@ 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); @@ -405,6 +461,44 @@ 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 { @@ -412,7 +506,7 @@ 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); } @@ -448,7 +542,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq!=null && urlLink.isDynamic()) { // collect matching db-refs @@ -987,6 +1081,10 @@ 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) @@ -1138,6 +1236,21 @@ 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() @@ -1176,8 +1289,7 @@ 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(); } @@ -1277,6 +1389,16 @@ 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! * @@ -1294,7 +1416,7 @@ 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() @@ -1348,7 +1470,7 @@ 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(); } @@ -1366,7 +1488,7 @@ 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(); @@ -1402,11 +1524,11 @@ 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); @@ -1476,7 +1598,7 @@ 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; @@ -1530,7 +1652,7 @@ 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(); } @@ -1684,7 +1806,7 @@ 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); @@ -1711,7 +1833,7 @@ 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++) @@ -1760,9 +1882,9 @@ 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() @@ -1825,17 +1947,16 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = jalview.structure.StructureSelectionManager - .getStructureSelectionManager().colourSequenceFromStructure( + 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 +1983,8 @@ 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);