* @author $author$
* @version $Revision$
*/
-public class AlignFrame
- extends GAlignFrame implements DropTargetListener, FeatureListener
+public class AlignFrame extends GAlignFrame implements DropTargetListener
{
/** DOCUMENT ME!! */
public static final int DEFAULT_WIDTH = 700;
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- if (viewport.vconsensus == null)
+ if (viewport.conservation == null)
{
- //Out of memory calculating consensus.
BLOSUM62Colour.setEnabled(false);
- PIDColour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
- abovePIDThreshold.setEnabled(false);
- modifyPID.setEnabled(false);
+ // PIDColour.setEnabled(false);
+ // abovePIDThreshold.setEnabled(false);
+ // modifyPID.setEnabled(false);
}
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
}
+ ap.av.updateConsensus(ap);
+ ap.av.updateConservation(ap);
+
ap.av.addPropertyChangeListener(new PropertyChangeListener()
{
}
}
- public void comeBackLater(FeatureEvent evt)
- {}
-
- public void newFeatures(FeatureEvent evt)
- {
- if (evt.getFeatures().length > 0)
- {
- alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
- alignPanel.repaint();
- }
- }
Hashtable progressBars;
public void setProgressBar(String message, long id)
}
+
+
/*
Added so Castor Mapping file can obtain Jalview Version
*/
*/
void updateEditMenuBar()
{
- if (historyList.size() > 0)
+ /* if (historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
{
redoMenuItem.setEnabled(false);
redoMenuItem.setText("Redo");
- }
+ }*/
}
/**
for (int i = 0; i < sg.getSize(false); i++)
{
SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
-
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
// If the cut affects all sequences, remove highlighted columns
viewport.getAlignment().deleteSequence(seq);
PaintRefresher.Refresh(alignPanel,alignPanel.av.getSequenceSetId(),seq,null);
}
- else
- {
- viewport.getAlignment().getSequences().setElementAt(seq, index);
- }
}
viewport.setSelectionGroup(null);
if (av.padGaps)
av.getAlignment().padGaps();
- if (av.vconsensus != null && av.autoCalculateConsensus)
+ if (av.hconsensus != null && av.autoCalculateConsensus)
{
- av.updateConsensus();
- av.updateConservation();
+ av.updateConsensus(ap);
+ av.updateConservation(ap);
+ ap.annotationPanel.repaint();
}
resetAllColourSchemes();
viewport.alignment.getWidth());
}
- cs.setConsensus(viewport.vconsensus);
+ cs.setConsensus(viewport.hconsensus);
if (cs.conservationApplied())
{
Alignment al = (Alignment) viewport.alignment;
cs.setConservation(null);
}
- cs.setConsensus(viewport.vconsensus);
+ cs.setConsensus(viewport.hconsensus);
}
viewport.setGlobalColourScheme(cs);
{
return ShowNewickTree(nf,title,600,500,4,5);
}
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+ {
+ return ShowNewickTree(nf,title, input, 600,500,4,5);
+ }
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+ return ShowNewickTree(nf, title, null, w, h, x, y);
+ }
/**
- * DOCUMENT ME!
+ * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
*
- * @param nf DOCUMENT ME!
- * @param title DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @param nf the tree
+ * @param title tree viewer title
+ * @param input Associated alignment input data (or null)
+ * @param w width
+ * @param h height
+ * @param x position
+ * @param y position
+ * @return TreePanel handle
*/
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
- {
+ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
TreePanel tp = null;
try
tp = new TreePanel(alignPanel,
"FromFile",
title,
- nf);
+ nf, input);
tp.setSize(w,h);
if (msa.getSequences().length == 1)
{
// Single Sequence prediction
- new jalview.ws.JPredClient(sh, title, false, msa, af);
+ new jalview.ws.JPredClient(sh, title, false, msa, af, true);
}
else
{
{
// Sequence profile based prediction
new jalview.ws.JPredClient(sh,
- title, true, msa, af);
+ title, true, msa, af, true);
}
}
}