import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
}
if (viewport.getAlignment().isNucleotide())
{
+ conservationMenuItem.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
viewport.updateStrucConsensus(alignPanel);
if (viewport.getAlignment().hasRNAStructure())
{
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
+ "Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
+ "Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
+ "Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
+ "Average distance tree using BLOSUM62");
}
void NewTreePanel(String type, String pwType, String title)