/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* 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 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.
- *
+ *
* 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
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class TreePanel
- extends GTreePanel
+public class TreePanel extends GTreePanel
{
String type;
+
String pwtype;
+
TreeCanvas treeCanvas;
+
NJTree tree;
+
AlignViewport av;
/**
* Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- * @param s DOCUMENT ME!
- * @param e DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
*/
public TreePanel(AlignmentPanel ap, String type, String pwtype)
{
super();
initTreePanel(ap, type, pwtype, null, null);
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+ // We know this tree has distances. JBPNote TODO: prolly should add this as
+ // a userdefined default
// showDistances(true);
}
/**
* Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param newtree DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param newtree
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
*/
- public TreePanel(AlignmentPanel ap,
- String type,
- String pwtype,
- NewickFile newtree)
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newtree)
{
super();
initTreePanel(ap, type, pwtype, newtree, null);
}
- public TreePanel(AlignmentPanel av,
- String type,
- String pwtype,
- NewickFile newtree, AlignmentView inputData)
+ public TreePanel(AlignmentPanel av, String type, String pwtype,
+ NewickFile newtree, AlignmentView inputData)
{
super();
initTreePanel(av, type, pwtype, newtree, inputData);
}
void initTreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newTree, AlignmentView inputData)
+ NewickFile newTree, AlignmentView inputData)
{
av = ap.av;
}
if (evt.getNewValue() == null)
{
- System.out.println("new alignment sequences vector value is null");
+ System.out
+ .println("new alignment sequences vector value is null");
}
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
- treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
+ tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ // rectangles and leafnodes
repaint();
}
}
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
- getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
if (aps.length == 1 && treeCanvas.ap == aps[0])
{
associateLeavesMenu.setVisible(false);
associateLeavesMenu.setVisible(true);
- if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
}
- class TreeLoader
- extends Thread
+ class TreeLoader extends Thread
{
NewickFile newtree;
+
jalview.datamodel.AlignmentView odata = null;
+
public TreeLoader(NewickFile newtree)
{
this.newtree = newtree;
{
if (odata == null)
{
- tree = new NJTree(av.alignment.getSequencesArray(),
- newtree);
+ tree = new NJTree(av.alignment.getSequencesArray(), newtree);
}
else
{
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+ tree = new NJTree(av.alignment.getSequencesArray(), odata,
+ newtree);
}
if (!tree.hasOriginalSequenceData())
{
{
int start, end;
SequenceI[] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+ AlignmentView seqStrings = av.getAlignmentView(av
+ .getSelectionGroup() != null);
if (av.getSelectionGroup() == null)
{
start = 0;
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public NJTree getTree()
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void textbox_actionPerformed(ActionEvent e)
{
Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
+ .getTopNode());
cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
- tree.isHasRootDistance()));
+ tree.isHasRootDistance()));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void saveAsNewick_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save tree as newick file");
chooser.setToolTipText("Save");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
try
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
- String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
- tree.isHasRootDistance());
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
- FileWriter(
- choice));
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
+ .getTopNode());
+ String output = fout.print(tree.isHasBootstrap(), tree
+ .isHasDistances(), tree.isHasRootDistance());
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(choice));
out.println(output);
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void printMenu_actionPerformed(ActionEvent e)
{
- //Putting in a thread avoids Swing painting problems
+ // Putting in a thread avoids Swing painting problems
treeCanvas.startPrinting();
}
{
if (!tree.hasOriginalSequenceData())
{
- jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log
+ .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // decide if av alignment is sufficiently different to original data to
+ // warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions
+ // yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
char gc = '-';
- try {
+ try
+ {
// we try to get the associated view's gap character
// but this may fail if the view was closed...
- gc = av.
- getGapCharacter();
-
- } catch (Exception ex) {};
+ gc = av.getGapCharacter();
+
+ } catch (Exception ex)
+ {
+ }
+ ;
Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
- Alignment dataset = (av!=null && av.getAlignment()!=null) ? av.getAlignment().getDataset() : null;
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment dataset = (av != null && av.getAlignment() != null) ? av
+ .getAlignment().getDataset() : null;
if (dataset != null)
{
al.setDataset(dataset);
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT
- );
+ AlignFrame af = new AlignFrame(al,
+ (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- //>>>This is a fix for the moment, until a better solution is found!!<<<
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void fitToWindow_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void distanceMenu_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
+ "Prompt each time");
// If we need to prompt, and if the GUI is visible then
// Prompt for EPS rendering style
if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !
- (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
EPSOptions eps = new EPSOptions();
renderStyle = eps.getValue();
try
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[]
- {"eps"},
- new String[]
- {"Encapsulated Postscript"},
- "Encapsulated Postscript");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "eps" }, new String[]
+ { "Encapsulated Postscript" }, "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Create EPS file from tree");
chooser.setToolTipText("Save");
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
- height);
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
pg.setAccurateTextMode(accurateText);
pg.flush();
pg.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void pngTree_actionPerformed(ActionEvent e)
{
try
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[]
- {"png"},
- new String[]
- {"Portable network graphics"},
- "Portable network graphics");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "png" }, new String[]
+ { "Portable network graphics" }, "Portable network graphics");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Create PNG image from tree");
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
BufferedImage bi = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_RGB);
+ BufferedImage.TYPE_INT_RGB);
Graphics png = bi.getGraphics();
treeCanvas.draw(png, width, height);
ImageIO.write(bi, "png", out);
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
git://source.jalview.org / jalview.git / blobdiff