import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
-import javax.swing.JOptionPane;
-
/**
* DOCUMENT ME!
*
System.err.println("Couldn't locate Jalview XML file : " + ex
+ "\n");
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new String[] { file }), MessageManager
.getString("label.url_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.error_loading_file_params", new String[]
{ file }), MessageManager
.getString("label.error_loading_jalview_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
}
else
{
- cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(groups[i].getPidThreshold(), true);
+ cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
}
-
}
+ int pidThreshold = groups[i].getPidThreshold();
Vector seqs = new Vector();
int[] ids = groups[i].getSeq();
seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
+ sg.getGroupColourScheme().setThreshold(pidThreshold, true);
sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.getRanges().setStartRes(view.getStartRes());
+ af.viewport.getRanges().setStartSeq(view.getStartSeq());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setColourText(view.getShowColourText());
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
- }
+ // if (cs != null)
+ // {
+ // cs.setThreshold(view.getPidThreshold(), true);
+ // cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ // }
}
- af.viewport.setGlobalColourScheme(cs);
+ af.viewport.getResidueShading().setThreshold(
+ view.getPidThreshold(), true);
+ af.viewport.getResidueShading().setConsensus(
+ af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
- cs.setConservationInc(view.getConsThreshold());
+ af.viewport.getResidueShading().setConservationInc(
+ view.getConsThreshold());
}
af.viewport.setColourAppliesToAllGroups(true);