-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
-\r
-public class TreePanel\r
- extends GTreePanel\r
-{\r
- SequenceI[] seq;\r
- String type;\r
- String pwtype;\r
- AlignViewport av;\r
- int start;\r
- int end;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
-\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- public TreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e)\r
- {\r
- super();\r
-\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- start = s;\r
- end = e;\r
-\r
- String longestName = "";\r
- seq = new Sequence[seqVector.size()];\r
- for (int i = 0; i < seqVector.size(); i++)\r
- {\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- if (seq[i].getName().length() > longestName.length())\r
- {\r
- longestName = seq[i].getName();\r
- }\r
- }\r
-\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
-\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- scrollPane.add(treeCanvas);\r
-\r
- }\r
-\r
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
- {\r
- super();\r
- // These are probably only arbitrary strings reflecting source of tree\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- start = 0;\r
- end = seqVector.size();\r
-\r
- String longestName = "";\r
- seq = new Sequence[seqVector.size()];\r
- for (int i = 0; i < seqVector.size(); i++)\r
- {\r
- seq[i] = (Sequence) seqVector.elementAt(i);\r
- }\r
- // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
- tree = new NJTree(seq, newtree);\r
- // Now have to calculate longest name based on the leaves\r
- Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
-\r
- for (int i = 0; i < leaves.size(); i++)\r
- {\r
- if (longestName.length() <\r
- ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().\r
- length())\r
- {\r
- longestName = TreeCanvas.PLACEHOLDER +\r
- ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).\r
- getName();\r
- }\r
- }\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
-\r
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- distanceMenu.setState(newtree.HasDistances());\r
- bootstrapMenu.setState(newtree.HasBootstrap());\r
- if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
- {\r
- placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
- }\r
- scrollPane.add(treeCanvas);\r
-\r
- }\r
-\r
- public String getText(String format)\r
- {\r
- return null;\r
- }\r
-\r
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.getState();\r
- repaint();\r
- }\r
-\r
- public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
- {\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(false, true);\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- cap.setText(output);\r
- java.awt.Frame frame = new java.awt.Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);\r
- }\r
-\r
- protected void fontSize_actionPerformed(ActionEvent e)\r
- {\r
- /* if( treeCanvas==null )\r
- return;\r
-\r
- String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
-\r
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,"Font Size - "+size);\r
- if(selection!=null)\r
- {\r
- fontSize.setText("Font Size - " + selection);\r
-\r
- int i = Integer.parseInt(selection.toString());\r
- treeCanvas.setFontSize(i);\r
- }\r
- scrollPane.setViewportView(treeCanvas);\r
- */\r
- }\r
-\r
- protected void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.getState());\r
- }\r
-\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
- }\r
-\r
- protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.ScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+public class TreePanel extends EmbmenuFrame implements ActionListener,
+ ItemListener
+{
+ SequenceI[] seq;
+
+ String type;
+
+ String pwtype;
+
+ int start;
+
+ int end;
+
+ TreeCanvas treeCanvas;
+
+ 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!
+ * @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)
+ {
+ try
+ {
+ jbInit();
+ this.setMenuBar(jMenuBar1);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ initTreePanel(ap, type, pwtype, null);
+ }
+
+ /**
+ * 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!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newtree)
+ {
+ try
+ {
+ jbInit();
+ this.setMenuBar(jMenuBar1);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ initTreePanel(ap, type, pwtype, newtree);
+ }
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree)
+ {
+
+ this.ap = ap;
+ this.av = ap.av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(ap, scrollPane);
+ TreeLoader tl = new TreeLoader(newTree);
+ tl.start();
+ embedMenuIfNeeded(treeCanvas);
+ scrollPane.add(treeCanvas, BorderLayout.CENTER);
+ }
+
+ void showOriginalData()
+ {
+ // 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[])
+ if (tree.seqData != null)
+ {
+ char gc = '-';
+ 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)
+ {
+ }
+ ;
+ Object[] alAndColsel = tree.seqData
+ .getAlignmentAndColumnSelection(gc);
+
+ if (alAndColsel != null && alAndColsel[0] != null)
+ {
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignFrame af = new AlignFrame(al, av.applet,
+ "Original Data for Tree", false);
+
+ af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+ }
+ }
+ else
+ {
+ System.out.println("Original Tree Data not available");
+ }
+ }
+
+ class TreeLoader extends Thread
+ {
+ NewickFile newtree;
+
+ jalview.datamodel.AlignmentView odata = null;
+
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ }
+
+ public void run()
+ {
+ if (newtree != null)
+ {
+ if (odata == null)
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ }
+ else
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
+ newtree);
+ }
+
+ }
+ else
+ {
+ int start, end;
+ SequenceI[] seqs;
+ boolean selview = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 1;
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
+ {
+ start = 0;
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes() + 1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(
+ av.getAlignment());
+ }
+ ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ if (sm instanceof ViewBasedAnalysisI)
+ {
+ try
+ {
+ sm = sm.getClass().newInstance();
+ ((ViewBasedAnalysisI) sm)
+ .configureFromAlignmentView(treeCanvas.ap);
+ } catch (Exception q)
+ {
+ System.err.println("Couldn't create a scoremodel instance for "
+ + sm.getName());
+ q.printStackTrace();
+ }
+ tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ }
+ else
+ {
+ tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+ end);
+ }
+ }
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ if (newtree != null)
+ {
+ // 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();
+
+ av.setCurrentTree(tree);
+
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == newickOutput)
+ {
+ newickOutput_actionPerformed();
+ }
+ else if (evt.getSource() == fontSize)
+ {
+ fontSize_actionPerformed();
+ }
+ else if (evt.getSource() == inputData)
+ {
+ showOriginalData();
+ }
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == fitToWindow)
+ {
+ treeCanvas.fitToWindow = fitToWindow.getState();
+ }
+
+ else if (evt.getSource() == distanceMenu)
+ {
+ treeCanvas.setShowDistances(distanceMenu.getState());
+ }
+
+ else if (evt.getSource() == bootstrapMenu)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+ }
+
+ else if (evt.getSource() == placeholdersMenu)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+ }
+
+ treeCanvas.repaint();
+ }
+
+ public void newickOutput_actionPerformed()
+ {
+ 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);
+ java.awt.Frame frame = new java.awt.Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
+ }
+
+ public java.awt.Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
+
+ public void setTreeFont(java.awt.Font font)
+ {
+ treeCanvas.font = font;
+ treeCanvas.repaint();
+ }
+
+ protected void fontSize_actionPerformed()
+ {
+ if (treeCanvas == null)
+ {
+ return;
+ }
+
+ new FontChooser(this);
+ }
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ protected ScrollPane scrollPane = new ScrollPane();
+
+ MenuBar jMenuBar1 = new MenuBar();
+
+ Menu jMenu2 = new Menu();
+
+ protected MenuItem fontSize = new MenuItem();
+
+ protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+
+ Menu fileMenu = new Menu();
+
+ MenuItem newickOutput = new MenuItem();
+
+ MenuItem inputData = new MenuItem();
+
+ private void jbInit() throws Exception
+ {
+ setLayout(borderLayout1);
+ this.setBackground(Color.white);
+ this.setFont(new java.awt.Font("Verdana", 0, 12));
+ jMenu2.setLabel(MessageManager.getString("action.view"));
+ fontSize.setLabel(MessageManager.getString("action.font"));
+ fontSize.addActionListener(this);
+ bootstrapMenu.setLabel(MessageManager
+ .getString("label.show_bootstrap_values"));
+ bootstrapMenu.addItemListener(this);
+ distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
+ distanceMenu.addItemListener(this);
+ placeholdersMenu.setLabel(MessageManager
+ .getString("label.mark_unassociated_leaves"));
+ placeholdersMenu.addItemListener(this);
+ fitToWindow.setState(true);
+ fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
+ fitToWindow.addItemListener(this);
+ fileMenu.setLabel(MessageManager.getString("action.file"));
+ newickOutput.setLabel(MessageManager.getString("label.newick_format"));
+ newickOutput.addActionListener(this);
+ inputData.setLabel(MessageManager.getString("label.input_data"));
+
+ add(scrollPane, BorderLayout.CENTER);
+ jMenuBar1.add(fileMenu);
+ jMenuBar1.add(jMenu2);
+ jMenu2.add(fitToWindow);
+ jMenu2.add(fontSize);
+ jMenu2.add(distanceMenu);
+ jMenu2.add(bootstrapMenu);
+ jMenu2.add(placeholdersMenu);
+ fileMenu.add(newickOutput);
+ fileMenu.add(inputData);
+ inputData.addActionListener(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff