import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
|| evt.isShiftDown() || evt.isAltDown());
}
break;
-
+
+ case KeyEvent.VK_A:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertNucAtCursor(false,"A");
+ //System.out.println("A");
+ }
+ break;
+ /*
+ case KeyEvent.VK_CLOSE_BRACKET:
+ if (viewport.cursorMode)
+ {
+ System.out.println("closing bracket");
+ }
+ break;
+ */
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
}
}
progressBars.put(lId, progressPanel);
}
// update GUI
- setMenusForViewport();
+ // setMenusForViewport();
validate();
}
changeColour(new NucleotideColourScheme());
}
+ public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ /*
+ public void covariationColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0]));
+ }
+ */
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
+
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
/**
* DOCUMENT ME!
sortByTreeMenu.add(item);
}
}
+
public boolean sortBy(AlignmentOrder alorder, String undoname)
{
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
- if (undoname!=null)
+ if (undoname != null)
{
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.alignment));
}
alignPanel.paintAlignment(true);
return true;
}
+
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
featuresFile = new FeaturesFile(file, type)
.parse(viewport.alignment.getDataset(),
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- false,jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ false, jalview.bin.Cache.getDefault(
+ "RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
ex.printStackTrace();
if (pdbfn.length() > 0)
{
// attempt to find a match in the alignment
- SequenceI mtch = idm.findIdMatch(pdbfn);
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
int l = 0, c = pdbfn.indexOf(".");
while (mtch == null && c != -1)
{
- while ((c = pdbfn.indexOf(".", l)) > l)
+ do
{
l = c;
- }
+ } while ((c = pdbfn.indexOf(".", l)) > l);
if (l > -1)
{
pdbfn = pdbfn.substring(0, l);
}
- mtch = idm.findIdMatch(pdbfn);
+ mtch = idm.findAllIdMatches(pdbfn);
}
if (mtch != null)
{
// try and associate
// TODO: may want to set a standard ID naming formalism for
// associating PDB files which have no IDs.
+ for (SequenceI toassoc: (SequenceI[])fm[2]) {
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0], (String) fm[1],
- (SequenceI) fm[2], false);
+ toassoc, false);
if (pe != null)
{
System.err
.println("Associated file : " + ((String) fm[0])
+ " with "
- + ((SequenceI) fm[2]).getDisplayId(true));
+ + toassoc.getDisplayId(true));
assocfiles++;
}
+ }
alignPanel.paintAlignment(true);
}
}
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
alignPanel.paintAlignment(true);
+ System.out.println("Hallo");
}
} catch (Exception ex)
{
alignPanel.paintAlignment(true);
}
}
+
+ /**
+ * make the given alignmentPanel the currently selected tab
+ *
+ * @param alignmentPanel
+ */
+ public void setDisplayedView(AlignmentPanel alignmentPanel)
+ {
+ if (!viewport.getSequenceSetId().equals(
+ alignmentPanel.av.getSequenceSetId()))
+ {
+ throw new Error(
+ "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+ }
+ if (tabbedPane != null
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
+ {
+ tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+ }
+ }
}
class PrintThread extends Thread