/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
/**
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.161 $
*/
public class AlignmentPanel extends GAlignmentPanel implements
AdjustmentListener, Printable, AlignmentViewPanel
}
validateAnnotationDimensions(true);
addNotify();
- repaint();
+ paintAlignment(true);
}
/**
* calculate the annotation dimensions and refresh slider values accordingly.
if (updateOverview)
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sequenceColoursChanged(this);
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
{
pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
alabels.drawComponent((Graphics2D) pg, idWidth);
pg.translate(idWidth + 3, 0);
- annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+ annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
*/
public void closePanel()
{
- jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager
- .getStructureSelectionManager();
- ssm.removeStructureViewerListener(seqPanel, null);
- ssm.removeSelectionListener(seqPanel);
PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(idPanel.idCanvas);
PaintRefresher.RemoveComponent(this);
if (av != null)
{
+ jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+ ssm.removeStructureViewerListener(seqPanel, null);
+ ssm.removeSelectionListener(seqPanel);
av.alignment = null;
av = null;
}
boolean cons = av.isShowGroupConsensus();
boolean showprf = av.isShowSequenceLogo();
boolean showConsHist = av.isShowConsensusHistogram();
+ boolean normLogo = av.isNormaliseSequenceLogo();
boolean sortg = true;
// set defaults for this group's conservation/consensus
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
+ sg.setNormaliseSequenceLogo(normLogo);
}
if (conv)
{
alignFrame.setDisplayedView(this);
}
}
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return av.getStructureSelectionManager();
+ }
}