import java.awt.event.*;
import javax.swing.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
import MCview.*;
import jalview.analysis.*;
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
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++)
}
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(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
+ System.out.println("end");
}
});
viewStructureMenu.add(menuItem);
// 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,rnastruc,seq.getRNA(),
+ seq.getName(), ap);
}
});
viewStructureMenu.add(menuItem);
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()
{
purinePyrimidineColour.setSelected(true);
}
+
+ else if (sg.cs instanceof RNAInteractionColourScheme)
+ {
+ RNAInteractionColour.setSelected(true);
+ }
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
editMenu.setVisible(false);
}
- if (!ap.av.alignment.getGroups().contains(sg))
+ if (!ap.av.getAlignment().getGroups().contains(sg))
{
unGroupMenuItem.setVisible(false);
}
{
public void actionPerformed(ActionEvent e)
{
- pdbFromFile_actionPerformed();
+ try {
+ pdbFromFile_actionPerformed();
+ } catch (ExceptionFileFormatOrSyntax e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (ParserConfigurationException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (SAXException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (ExceptionPermissionDenied e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (ExceptionLoadingFailed e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (InterruptedException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
});
enterPDB.setText("Enter PDB Id");
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(RNAInteractionColour);
if (ap.getAlignment().isNucleotide()) {
colourMenu.add(purinePyrimidineColour);
}
purinePyrimidineColour_actionPerformed();
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed();
+ }
+ });
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
{
SequenceGroup sg = getGroup();
sg.cs = new ClustalxColourScheme(
- sg.getSequences(ap.av.hiddenRepSequences),
- ap.av.alignment.getWidth());
+ sg,ap.av.getHiddenRepSequences());
refresh();
}
refresh();
}
+ protected void RNAInteractionColour_actionPerformed()
+ {
+ getGroup().cs = new RNAInteractionColourScheme();
+ refresh();
+ }
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); 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++)
oal = null;
}
- public void pdbFromFile_actionPerformed()
+ public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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);
git://source.jalview.org / jalview.git / blobdiff