protected void outputText_actionPerformed(ActionEvent e)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
JInternalFrame frame = new JInternalFrame();
- cap.formatForOutput();
frame.setContentPane(cap);
Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- HTMLOutput htmlOutput = new HTMLOutput(viewport);
- htmlOutput = null;
+ new HTMLOutput(viewport);
}
protected void createPNG_actionPerformed(ActionEvent e)
public void clustalColour_actionPerformed(ActionEvent e)
{
- abovePIDThreshold.setSelected(false);
changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
}
ccs.setConsensus( viewport.vconsensus );
viewport.setGlobalColourScheme(ccs);
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+ ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
}
else
{
SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
- if (cs instanceof ClustalxColourScheme)
- {
+ if(cs==null)
+ sg.cs = null;
+ else if (cs instanceof ClustalxColourScheme)
sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
- }
- else if(cs!=null)
- {
+ else if (cs instanceof UserColourScheme)
+ sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
+ else
try{
sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }catch(Exception ex){ex.printStackTrace();}
- }
+ }catch(Exception ex){}
if(viewport.getAbovePIDThreshold())
{
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+ new UserDefinedColours( alignPanel, null);
}
public void PIDColour_actionPerformed(ActionEvent e)
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
void NewTreePanel(String type, String pwType, String title)