JMenu sequenceMenu = new JMenu();
JMenuItem sequenceName = new JMenuItem();
+
+ JMenuItem sequenceDetails = new JMenuItem();
+ JMenuItem sequenceSelDetails = new JMenuItem();
SequenceI sequence;
}
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
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
.getName(), ap);
}
});
// 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
+ new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
.getName(), ap);
}
});
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)
}
}
// for the case when no sequences are even visible
- if (ap.av.hasHiddenRows) {
+ if (ap.av.hasHiddenRows()) {
{
menuItem = new JMenuItem("Reveal All");
menuItem.addActionListener(new ActionListener()
editMenu.setVisible(false);
}
- if (!ap.av.alignment.getGroups().contains(sg))
+ if (!ap.av.getAlignment().getGroups().contains(sg))
{
unGroupMenuItem.setVisible(false);
}
sequenceName_actionPerformed();
}
});
+ sequenceDetails.setText("Sequence Details ...");
+ sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceDetails_actionPerformed();
+ }});
+ sequenceSelDetails.setText("Sequence Details ...");
+ sequenceSelDetails.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }});
PIDColour.setFocusPainted(false);
unGroupMenuItem.setText("Remove Group");
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
editSequence_actionPerformed(actionEvent);
}
});
+
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
* actionPerformed(ActionEvent actionEvent) {
* annotationMenuItem_actionPerformed(actionEvent); } });
*/
-
+ groupMenu.add(sequenceSelDetails);
add(groupMenu);
-
add(sequenceMenu);
this.add(structureMenu);
groupMenu.add(editMenu);
groupMenu.add(sequenceFeature);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
colourMenu.add(textColour);
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
});
}
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void sequenceDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(new SequenceI[]{sequence});
+ }
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ 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>");
+ }
+ cap.setText("<html>" + contents.toString() + "</html>");
+
+ 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());
{
SequenceGroup sg = getGroup();
sg.cs = new ClustalxColourScheme(
- sg.getSequences(ap.av.hiddenRepSequences),
- ap.av.alignment.getWidth());
+ sg,ap.av.getHiddenRepSequences());
refresh();
}
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()
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();
}
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();
{
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);
// 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);
refresh();
}
}
ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
- sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
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++)
public void discoverPDB_actionPerformed()
{
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[]
+ 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()
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();
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);