/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import java.awt.*;
import java.awt.event.*;
-import java.util.Hashtable;
import jalview.analysis.*;
import jalview.datamodel.*;
NJTree tree;
+ AlignmentPanel ap;
+
AlignViewport av;
public NJTree getTree()
return tree;
}
+ public void finalize() throws Throwable
+ {
+ ap = null;
+ av = null;
+ super.finalize();
+ }
+
/**
* Creates a new TreePanel object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqVector
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwtype
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public TreePanel(AlignViewport av, String type, String pwtype)
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)
{
try
{
ex.printStackTrace();
}
- initTreePanel(av, type, pwtype, null);
+ initTreePanel(ap, type, pwtype, null);
}
/**
* Creates a new TreePanel object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqVector
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param pwtype
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public TreePanel(AlignViewport av, String type, String pwtype,
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
NewickFile newtree)
{
try
e.printStackTrace();
}
- initTreePanel(av, type, pwtype, newtree);
+ initTreePanel(ap, type, pwtype, newtree);
}
- void initTreePanel(AlignViewport av, String type, String pwtype,
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
NewickFile newTree)
{
- this.av = av;
+ this.ap = ap;
+ this.av = ap.av;
this.type = type;
this.pwtype = pwtype;
- treeCanvas = new TreeCanvas(av, scrollPane);
+ treeCanvas = new TreeCanvas(ap, scrollPane);
TreeLoader tl = new TreeLoader(newTree);
tl.start();
embedMenuIfNeeded(treeCanvas);
{
if (odata == null)
{
- tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
}
else
{
- tree = new NJTree(av.alignment.getSequencesArray(), odata,
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
newtree);
}
{
int start, end;
SequenceI[] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av
- .getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
+ boolean selview = (av.getSelectionGroup() != null)
+ && (av.getSelectionGroup().getSize() > 1);
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
{
start = 0;
- end = av.alignment.getWidth();
- seqs = av.alignment.getSequencesArray();
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
}
else
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ seqs = av.getSelectionGroup().getSequencesInOrder(
+ av.getAlignment());
}
tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
treeCanvas.setTree(tree);
if (newtree != null)
{
- distanceMenu.setState(newtree.HasDistances());
- bootstrapMenu.setState(newtree.HasBootstrap());
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());
- treeCanvas.setShowDistances(newtree.HasDistances());
+ // Set default view, paying lip service to any overriding tree view
+ // parameter settings
+ boolean showDist = newtree.HasDistances()
+ && av.applet.getDefaultParameter("showTreeDistances",
+ newtree.HasDistances());
+ boolean showBoots = newtree.HasBootstrap()
+ && av.applet.getDefaultParameter("showTreeBootstraps",
+ newtree.HasBootstrap());
+ distanceMenu.setState(showDist);
+ bootstrapMenu.setState(showBoots);
+ treeCanvas.setShowBootstrap(showBoots);
+ treeCanvas.setShowDistances(showDist);
+ treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
+ "showUnlinkedTreeNodes", false));
}
treeCanvas.repaint();
public void newickOutput_actionPerformed()
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
- .getTopNode());
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
String output = fout.print(false, true);
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
cap.setText(output);
git://source.jalview.org / jalview.git / blobdiff