X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=037f0070997b302d4913198437b53744c3d9a477;hb=f3df97a8d39f8124610d661f8c141677f73d86b0;hp=f2f41a32e6ff6d48d6dba7418ee258446e85f03a;hpb=7b7397a32734f990b14ea0a3bf49d3a9e1d928c3;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index f2f41a3..037f007 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
@@ -24,7 +24,6 @@ import java.awt.event.*;
import javax.swing.*;
-import MCview.*;
import jalview.analysis.*;
import jalview.commands.*;
import jalview.datamodel.*;
@@ -71,6 +70,7 @@ 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();
@@ -85,8 +85,12 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
+ JMenuItem sequenceDetails = new JMenuItem();
+
+ JMenuItem sequenceSelDetails = new JMenuItem();
+ SequenceI sequence;
+ JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
@@ -118,7 +122,11 @@ public class PopupMenu extends JPopupMenu
JMenu pdbMenu = new JMenu();
JMenuItem pdbFromFile = new JMenuItem();
-
+ // JBPNote: Commented these out - Should add these services via the web services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
@@ -162,8 +170,8 @@ 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
@@ -189,6 +197,7 @@ 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++)
@@ -215,11 +224,11 @@ 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)
{
@@ -257,30 +266,43 @@ public class PopupMenu extends JPopupMenu
}
else
{
- if (ap.av.alignment.isNucleotide() == false)
+ if (ap.av.getAlignment().isNucleotide() == false)
{
structureMenu.remove(viewStructureMenu);
}
// structureMenu.remove(colStructureMenu);
}
- if (ap.av.alignment.isNucleotide() == true)
+ if (ap.av.getAlignment().isNucleotide() == true)
{
- AlignmentAnnotation[] aa = ap.av.alignment.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;
menuItem = new JMenuItem();
- menuItem.setText("RNA structure - consensus");
+ menuItem.setText("2D RNA " + structureLine);
menuItem.addActionListener(new java.awt.event.ActionListener()
+
{
public void actionPerformed(ActionEvent e)
{
- new AppVarna(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);
@@ -297,17 +319,19 @@ 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("RNA structure - "+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.getSequenceAsString(), rnastruc, seq
- .getName(), ap);
+
+ new AppVarna(seq.getName() + " structure", seq, seq
+ .getSequenceAsString(), rnastruc, seq.getName(),
+ ap);
}
});
viewStructureMenu.add(menuItem);
@@ -315,7 +339,6 @@ public class PopupMenu extends JPopupMenu
}
}
-
}
menuItem = new JMenuItem("Hide Sequences");
@@ -342,9 +365,9 @@ 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)
@@ -363,7 +386,12 @@ 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()
{
@@ -383,9 +411,10 @@ public class PopupMenu extends JPopupMenu
}
SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
- if (sg != null)
- {
+ if (sg != null && sg.getSize() > 0)
+ {
groupName.setText("Name: " + sg.getName());
groupName.setText("Edit name and description of current group.");
@@ -437,6 +466,8 @@ public class PopupMenu extends JPopupMenu
{
purinePyrimidineColour.setSelected(true);
}
+
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
@@ -461,6 +492,7 @@ public class PopupMenu extends JPopupMenu
}
// Add a 'show all structures' for the current selection
HashtableAnnotation 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()); @@ -1279,9 +1428,7 @@ 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(); } @@ -1387,6 +1534,7 @@ public class PopupMenu extends JPopupMenu refresh(); } + /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1407,9 +1555,9 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1461,9 +1609,9 @@ 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.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1479,9 +1627,9 @@ 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.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1515,12 +1663,12 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(ap.av.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1); + 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); @@ -1544,11 +1692,11 @@ public class PopupMenu extends JPopupMenu return; } - AnnotationColourGradient acg = new AnnotationColourGradient(sequence - .getAnnotation()[0], null, + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); - acg.predefinedColours = true; + acg.setPredefinedColours(true); sg.cs = acg; refresh(); @@ -1564,9 +1712,10 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); - EditNameDialog dialog = new EditNameDialog(sg.getName(), sg - .getDescription(), " Group Name ", "Group Description ", - "Edit Group Name/Description", ap.alignFrame); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), " Group Name ", + "Group Description ", "Edit Group Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1589,7 +1738,7 @@ 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; @@ -1603,8 +1752,8 @@ public class PopupMenu extends JPopupMenu */ void sequenceName_actionPerformed() { - EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence - .getDescription(), " Sequence Name ", + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), " Sequence Name ", "Sequence Description ", "Edit Sequence Name/Description", ap.alignFrame); @@ -1643,10 +1792,15 @@ 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(); } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + refresh(); + } /** * DOCUMENT ME! @@ -1796,9 +1950,9 @@ public class PopupMenu extends JPopupMenu caseChange = ChangeCaseCommand.TO_LOWER; } - ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg - .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1812,8 +1966,8 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); String[] omitHidden = null; @@ -1824,7 +1978,8 @@ 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++) @@ -1845,9 +2000,8 @@ public class PopupMenu extends JPopupMenu 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.setToolTipText("Load a PDB file and associate it with sequence '" + + sequence.getDisplayId(false) + "'"); int value = chooser.showOpenDialog(null); @@ -1860,7 +2014,18 @@ public class PopupMenu extends JPopupMenu } } - + // JBNote: commented out - these won't be instantiated here...! +// public void RNAFold_actionPerformed() throws Exception +// { +// Predict2D P2D = new Predict2D(); +// P2D.getStructure2DFromRNAFold("toto"); +// } +// +// public void ContraFold_actionPerformed() throws Exception +// { +// Predict2D P2D = new Predict2D(); +// P2D.getStructure2DFromContraFold("toto"); +// } public void enterPDB_actionPerformed() { String id = JOptionPane.showInternalInputDialog(Desktop.desktop, @@ -1877,9 +2042,9 @@ 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() @@ -1948,10 +2113,10 @@ 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(); @@ -1968,17 +2133,18 @@ public class PopupMenu extends JPopupMenu if (sequence == null) sequence = (Sequence) sg.getSequenceAt(0); - EditNameDialog dialog = new EditNameDialog(sequence - .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), - null, "Edit Sequence ", null, "Edit Sequence", ap.alignFrame); + EditNameDialog dialog = new EditNameDialog( + sequence.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), null, "Edit Sequence ", null, + "Edit Sequence", ap.alignFrame); if (dialog.accept) { 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); + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand);