X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=c1bbc8d58d0167bab19eb405f995533f9ee27a1b;hb=27d1490bba5753b3f9c8fac0647cfe8148c53310;hp=a4808cff4bb48e766954f5e9f48dd7fff8545231;hpb=c45ff77fed27bdee9025cca9b16a3c03d8e21674;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index a4808cf..c1bbc8d 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. * @@ -69,10 +69,11 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - - //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); @@ -84,7 +85,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + SequenceI sequence; JMenuItem unGroupMenuItem = new JMenuItem(); @@ -161,8 +162,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links, - final 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 @@ -188,7 +189,7 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); - //colours.add(covariationColour); + // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -214,11 +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) { @@ -253,40 +254,67 @@ public class PopupMenu extends JPopupMenu } } else - { - if(ap.av.alignment.isNucleotide()==false){ - structureMenu.remove(viewStructureMenu); - } + { + if (ap.av.getAlignment().isNucleotide() == false) + { + structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } - - if(ap.av.alignment.isNucleotide()==true){ - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - String rnastruc=new String(); - for(int i=0; i 1) @@ -333,7 +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() { @@ -354,7 +386,7 @@ 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("Edit name and description of current group."); @@ -405,12 +437,12 @@ public class PopupMenu extends JPopupMenu } else if (sg.cs instanceof PurinePyrimidineColourScheme) { - purinePyrimidineColour.setSelected(true); + purinePyrimidineColour.setSelected(true); } - /* else if (sg.cs instanceof CovariationColourScheme) - { - covariationColour.setSelected(true); - }*/ + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -431,6 +463,7 @@ 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(); @@ -438,6 +471,10 @@ public class PopupMenu extends JPopupMenu for (PDBEntry pe: pes) { pdbe.put(pe.getId(), pe); + if (sqass==null) + { + sqass = sq; + } } } } @@ -445,7 +482,12 @@ 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() { @@ -464,7 +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); } @@ -500,7 +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 @@ -1039,8 +1081,10 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); - colourMenu.add(purinePyrimidineColour); - //colourMenu.add(covariationColour); + if (ap.getAlignment().isNucleotide()) { + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1193,22 +1237,20 @@ public class PopupMenu extends JPopupMenu } }); 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(); - } - });*/ - + 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() @@ -1247,8 +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(); } @@ -1347,19 +1388,17 @@ public class PopupMenu extends JPopupMenu getGroup().cs = new NucleotideColourScheme(); refresh(); } - + protected void purinePyrimidineColour_actionPerformed() { getGroup().cs = new PurinePyrimidineColourScheme(); refresh(); } + /* - protected void covariationColour_actionPerformed() - { - getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]); - refresh(); - } -*/ + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * @@ -1377,7 +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() @@ -1431,7 +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(); } @@ -1449,7 +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(); @@ -1485,11 +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); @@ -1559,7 +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; @@ -1613,7 +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(); } @@ -1767,7 +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); @@ -1794,7 +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++) @@ -1843,9 +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() @@ -1914,10 +1953,10 @@ 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(); @@ -1944,8 +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);