import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.JalviewColourScheme;
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
- Vector<String> links)
+ List<String> links)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
*
* @param cs
*/
- protected void setSelectedColour(CollectionColourSchemeI cs)
+ protected void setSelectedColour(ResidueShaderI cs)
{
if (cs == null || cs.getColourScheme() == null)
{
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg,
+ sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
refresh();
}
protected void taylorColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
refresh();
}
protected void helixColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
refresh();
}
protected void strandColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
refresh();
}
protected void turnColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
refresh();
}
protected void buriedColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(
+ getGroup().cs = new ResidueShader(
new PurinePyrimidineColourScheme());
refresh();
}
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new PIDColourScheme());
+ sg.cs = new ResidueShader(new PIDColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
+ sg.cs = new ResidueShader(new Blosum62ColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));