/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
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());
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(revealAll);
remove(revealSeq);
- } else {
+ }
+ 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);
}
}
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
Vector regions = new Vector();
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
- sg.getEndRes() + 1);
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
}
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
- caseChange);
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
}
-
void outputText(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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
+ // 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(
ap.av.showJVSuffix));
}
+
protected void showSequenceSelectionDetails()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
protected void showSequenceDetails()
{
- createSequenceDetailsReport(new SequenceI[]{seq});
+ createSequenceDetailsReport(new SequenceI[]
+ { seq });
}
+
public void createSequenceDetailsReport(SequenceI[] sequences)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
-
+
StringBuffer contents = new StringBuffer();
- for (SequenceI seq:sequences)
+ 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>");
+ 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);
+ jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+ : "Selection"), 600, 500);
cap.setText("<html>" + contents.toString() + "</html>");
}
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file for sequence "+seq.getName(), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Paste PDB file for sequence " + seq.getName(), 400, 300);
}
}
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,ap.av.getHiddenRepSequences());
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
refresh();
}
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()), 0,
- ap.av.getAlignment().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.getHiddenRepSequences()), 0,
- ap.av.getAlignment().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.getHiddenRepSequences()), 0,
- ap.av.getAlignment().getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
}
{
sg.cs.setConservation(Conservation.calculateConservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(ap.av.getHiddenRepSequences()), 0,
- ap.av.getAlignment().getWidth(),
- false, ap.av.getConsPercGaps(),false));
+ 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();
}
git://source.jalview.org / jalview.git / blobdiff