/*
- * 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
import jalview.schemes.*;
import jalview.util.UrlLink;
import jalview.io.AppletFormatAdapter;
+import jalview.io.SequenceAnnotationReport;
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
MenuItem editSequence = new MenuItem("Edit Sequence");
+ MenuItem sequenceDetails = new MenuItem("Sequence Details ...");
+
+ MenuItem selSeqDetails = new MenuItem("Sequence Details ...");
+
Sequence seq;
MenuItem revealAll = new MenuItem();
MenuItem revealSeq = new MenuItem();
+
/**
* index of sequence to be revealed
*/
- int revealSeq_index=-1;
+ int revealSeq_index = -1;
+
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel("Name: "+sg.getName());
+ editGroupName.setLabel("Name: " + sg.getName());
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
displayNonconserved.setState(sg.getShowNonconserved());
- if (!ap.av.alignment.getGroups().contains(sg))
+ if (!ap.av.getAlignment().getGroups().contains(sg))
{
groupMenu.remove(unGroupMenuItem);
}
remove(groupMenu);
}
- if (seq!=null && links != null && links.size() > 0)
+ if (links != null && links.size() > 0)
{
Menu linkMenu = new Menu("Link");
String link;
final String target = urlLink.getTarget(); // link.substring(0,
// link.indexOf("|"));
final String label = urlLink.getLabel();
- if (seq!=null && urlLink.isDynamic())
+ if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
remove(seqMenu);
}
- if (!ap.av.hasHiddenRows)
+ if (!ap.av.hasHiddenRows())
{
remove(revealAll);
remove(revealSeq);
- } else {
- final int index = ap.av.alignment.findIndex(seq);
+ }
+ else
+ {
+ final int index = ap.av.getAlignment().findIndex(seq);
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- revealSeq_index=index;
- } else {
+ revealSeq_index = index;
+ }
+ else
+ {
remove(revealSeq);
}
}
{
editName();
}
+ else if (source == sequenceDetails)
+ {
+ showSequenceDetails();
+ }
+ else if (source == selSeqDetails)
+ {
+ showSequenceSelectionDetails();
+ }
else if (source == pdb)
{
addPDB();
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);
Vector regions = new Vector();
if (sg != null)
{
- int start = sg.getStartRes();
- int end = sg.getEndRes() + 1;
-
- do
- {
- if (ap.av.hasHiddenColumns)
- {
- if (start == 0)
- {
- start = ap.av.colSel.adjustForHiddenColumns(start);
- }
-
- end = ap.av.colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = sg.getEndRes() + 1;
- }
- if (end > sg.getEndRes())
- {
- end = sg.getEndRes() + 1;
- }
- }
-
- regions.addElement(new int[]
- { start, end });
-
- if (ap.av.hasHiddenColumns)
- {
- start = ap.av.colSel.adjustForHiddenColumns(end);
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < sg.getEndRes());
-
- int[][] startEnd = new int[regions.size()][2];
- for (int i = 0; i < regions.size(); i++)
- {
- startEnd[i] = (int[]) regions.elementAt(i);
- }
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
}
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
- sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
"Selection output - " + e.getActionCommand(), 600, 500);
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
+ // now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
e.getActionCommand(),
}
+ protected void showSequenceSelectionDetails()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void showSequenceDetails()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { seq });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
+ + "</h2></p><p>");
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ : null);
+ contents.append("</p>");
+ }
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+ : "Selection"), 600, 500);
+ cap.setText("<html>" + contents.toString() + "</html>");
+ }
+
void editName()
{
EditNameDialog dialog = new EditNameDialog(seq.getName(),
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Paste PDB file for sequence " + seq.getName(), 400, 300);
}
}
showBoxes.setState(true);
showBoxes.addItemListener(this);
sequenceName.addActionListener(this);
+ sequenceDetails.addActionListener(this);
+ selSeqDetails.addActionListener(this);
displayNonconserved.setLabel("Show Nonconserved");
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
this.add(hideSeqs);
this.add(revealSeq);
this.add(revealAll);
+ // groupMenu.add(selSeqDetails);
groupMenu.add(editGroupName);
groupMenu.add(editMenu);
groupMenu.add(outputmenu);
toLower.addActionListener(this);
editMenu.add(toggleCase);
seqMenu.add(sequenceName);
+ // seqMenu.add(sequenceDetails);
+
if (!ap.av.applet.useXtrnalSviewer)
{
seqMenu.add(pdb);
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();
}
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
}
sg.cs = new Blosum62ColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
}
if (conservationMenuItem.getState())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(ap.av.hiddenRepSequences), 0,
- ap.av.alignment.getWidth());
-
- c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
-
- sg.cs.setConservation(c);
-
+ sg.cs.setConservation(Conservation.calculateConservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment()
+ .getWidth(), false, ap.av.getConsPercGaps(), false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
// 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;
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
ap.paintAlignment(true);
}
git://source.jalview.org / jalview.git / blobdiff