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;
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!
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);
}
}