-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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
-package MCview;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.appletgui.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-\r
-public class AppletPDBViewer\r
- extends Frame implements ActionListener, ItemListener\r
-{\r
- AppletPDBCanvas pdbcanvas;\r
-\r
- public AppletPDBViewer(PDBEntry pdbentry,\r
- SequenceI[] seq,\r
- String [] chains,\r
- AlignmentPanel ap,\r
- String protocol)\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);\r
-\r
-\r
- add(pdbcanvas, BorderLayout.CENTER);\r
-\r
- StringBuffer title = new StringBuffer(seq[0].getName()\r
- + ":"\r
- + pdbcanvas.pdbentry.getFile());\r
-\r
- jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);\r
-\r
- }\r
-\r
-\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if (evt.getSource() == mapping)\r
- {\r
- jalview.appletgui.CutAndPasteTransfer cap\r
- = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,\r
- 600);\r
- cap.setText(pdbcanvas.mappingDetails.toString());\r
-\r
- }\r
- else if (evt.getSource() == charge)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setChargeColours();\r
- }\r
-\r
- else if (evt.getSource() == chain)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setChainColours();\r
- }\r
- else if (evt.getSource() == seqButton)\r
- {\r
- pdbcanvas.bysequence = true;\r
- pdbcanvas.colourBySequence();\r
-\r
- }\r
- else if (evt.getSource() == zappo)\r
- {\r
- pdbcanvas.setColours(new ZappoColourScheme());\r
- }\r
- else if (evt.getSource() == taylor)\r
- {\r
- pdbcanvas.setColours(new TaylorColourScheme());\r
- }\r
- else if (evt.getSource() == hydro)\r
- {\r
- pdbcanvas.setColours(new HydrophobicColourScheme());\r
- }\r
- else if (evt.getSource() == helix)\r
- {\r
- pdbcanvas.setColours(new HelixColourScheme());\r
- }\r
- else if (evt.getSource() == strand)\r
- {\r
- pdbcanvas.setColours(new StrandColourScheme());\r
- }\r
- else if (evt.getSource() == turn)\r
- {\r
- pdbcanvas.setColours(new TurnColourScheme());\r
- }\r
- else if (evt.getSource() == buried)\r
- {\r
- pdbcanvas.setColours(new BuriedColourScheme());\r
- }\r
- else if (evt.getSource() == user)\r
- {\r
- pdbcanvas.bysequence = false;\r
- new jalview.appletgui.UserDefinedColours(pdbcanvas);\r
- }\r
-\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
-\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt.getSource() == allchains)\r
- {\r
- pdbcanvas.setAllchainsVisible(allchains.getState());\r
- }\r
- else if (evt.getSource() == wire)\r
- {\r
- pdbcanvas.wire = !pdbcanvas.wire;\r
- }\r
- else if (evt.getSource() == depth)\r
- {\r
- pdbcanvas.depthcue = !pdbcanvas.depthcue;\r
- }\r
- else if (evt.getSource() == zbuffer)\r
- {\r
- pdbcanvas.zbuffer = !pdbcanvas.zbuffer;\r
- }\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- setMenuBar(jMenuBar1);\r
- fileMenu.setLabel("File");\r
- coloursMenu.setLabel("Colours");\r
- mapping.setLabel("View Mapping");\r
- mapping.addActionListener(this);\r
- wire.setLabel("Wireframe");\r
- wire.addItemListener(this);\r
- depth.setState(true);\r
- depth.setLabel("Depthcue");\r
- depth.addItemListener(this);\r
- zbuffer.setState(true);\r
- zbuffer.setLabel("Z Buffering");\r
- zbuffer.addItemListener(this);\r
- charge.setLabel("Charge & Cysteine");\r
- charge.addActionListener(this);\r
- hydro.setLabel("Hydrophobicity");\r
- hydro.addActionListener(this);\r
- chain.setLabel("By Chain");\r
- chain.addActionListener(this);\r
- seqButton.setLabel("By Sequence");\r
- seqButton.addActionListener(this);\r
- allchains.setLabel("All Chains Visible");\r
- allchains.addItemListener(this);\r
- viewMenu.setLabel("View");\r
- zappo.setLabel("Zappo");\r
- zappo.addActionListener(this);\r
- taylor.setLabel("Taylor");\r
- taylor.addActionListener(this);\r
- helix.setLabel("Helix Propensity");\r
- helix.addActionListener(this);\r
- strand.setLabel("Strand Propensity");\r
- strand.addActionListener(this);\r
- turn.setLabel("Turn Propensity");\r
- turn.addActionListener(this);\r
- buried.setLabel("Buried Index");\r
- buried.addActionListener(this);\r
- user.setLabel("User Defined...");\r
- user.addActionListener(this);\r
- jMenuBar1.add(fileMenu);\r
- jMenuBar1.add(coloursMenu);\r
- jMenuBar1.add(viewMenu);\r
- fileMenu.add(mapping); ;\r
-\r
- coloursMenu.add(seqButton);\r
- coloursMenu.add(chain);\r
- coloursMenu.add(charge);\r
- coloursMenu.add(zappo);\r
- coloursMenu.add(taylor);\r
- coloursMenu.add(hydro);\r
- coloursMenu.add(helix);\r
- coloursMenu.add(strand);\r
- coloursMenu.add(turn);\r
- coloursMenu.add(buried);\r
- coloursMenu.add(user);\r
- viewMenu.add(wire);\r
- viewMenu.add(depth);\r
- viewMenu.add(zbuffer);\r
- viewMenu.add(allchains);\r
- allchains.setState(true);\r
- }\r
-\r
- MenuBar jMenuBar1 = new MenuBar();\r
- Menu fileMenu = new Menu();\r
- Menu coloursMenu = new Menu();\r
- MenuItem mapping = new MenuItem();\r
- CheckboxGroup bg = new CheckboxGroup();\r
- CheckboxMenuItem wire = new CheckboxMenuItem();\r
- CheckboxMenuItem depth = new CheckboxMenuItem();\r
- CheckboxMenuItem zbuffer = new CheckboxMenuItem();\r
-\r
- MenuItem charge = new MenuItem();\r
- MenuItem hydro = new MenuItem();\r
- MenuItem chain = new MenuItem();\r
- MenuItem seqButton = new MenuItem();\r
-\r
- CheckboxMenuItem allchains = new CheckboxMenuItem();\r
- Menu viewMenu = new Menu();\r
- MenuItem turn = new MenuItem();\r
- MenuItem strand = new MenuItem();\r
- MenuItem helix = new MenuItem();\r
- MenuItem taylor = new MenuItem();\r
- MenuItem zappo = new MenuItem();\r
- MenuItem buried = new MenuItem();\r
- MenuItem user = new MenuItem();\r
-\r
-\r
-//End StructureListener\r
-////////////////////////////\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ */
+package MCview;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.appletgui.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+
+public class AppletPDBViewer
+ extends EmbmenuFrame implements ActionListener, ItemListener
+{
+ AppletPDBCanvas pdbcanvas;
+
+ public AppletPDBViewer(PDBEntry pdbentry,
+ SequenceI[] seq,
+ String [] chains,
+ AlignmentPanel ap,
+ String protocol)
+ {
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
+
+ embedMenuIfNeeded(pdbcanvas);
+ add(pdbcanvas, BorderLayout.CENTER);
+
+ StringBuffer title = new StringBuffer(seq[0].getName()
+ + ":"
+ + pdbcanvas.pdbentry.getFile());
+
+ jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
+
+ }
+
+
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == mapping)
+ {
+ jalview.appletgui.CutAndPasteTransfer cap
+ = new jalview.appletgui.CutAndPasteTransfer(false, null);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,
+ 600);
+ cap.setText(pdbcanvas.mappingDetails.toString());
+
+ }
+ else if (evt.getSource() == charge)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChargeColours();
+ }
+
+ else if (evt.getSource() == chain)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChainColours();
+ }
+ else if (evt.getSource() == seqButton)
+ {
+ pdbcanvas.bysequence = true;
+ pdbcanvas.colourBySequence();
+
+ }
+ else if (evt.getSource() == zappo)
+ {
+ pdbcanvas.setColours(new ZappoColourScheme());
+ }
+ else if (evt.getSource() == taylor)
+ {
+ pdbcanvas.setColours(new TaylorColourScheme());
+ }
+ else if (evt.getSource() == hydro)
+ {
+ pdbcanvas.setColours(new HydrophobicColourScheme());
+ }
+ else if (evt.getSource() == helix)
+ {
+ pdbcanvas.setColours(new HelixColourScheme());
+ }
+ else if (evt.getSource() == strand)
+ {
+ pdbcanvas.setColours(new StrandColourScheme());
+ }
+ else if (evt.getSource() == turn)
+ {
+ pdbcanvas.setColours(new TurnColourScheme());
+ }
+ else if (evt.getSource() == buried)
+ {
+ pdbcanvas.setColours(new BuriedColourScheme());
+ }
+ else if (evt.getSource() == user)
+ {
+ pdbcanvas.bysequence = false;
+ new jalview.appletgui.UserDefinedColours(pdbcanvas);
+ }
+
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == allchains)
+ {
+ pdbcanvas.setAllchainsVisible(allchains.getState());
+ }
+ else if (evt.getSource() == wire)
+ {
+ pdbcanvas.wire = !pdbcanvas.wire;
+ }
+ else if (evt.getSource() == depth)
+ {
+ pdbcanvas.depthcue = !pdbcanvas.depthcue;
+ }
+ else if (evt.getSource() == zbuffer)
+ {
+ pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+ }
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ setMenuBar(jMenuBar1);
+ fileMenu.setLabel("File");
+ coloursMenu.setLabel("Colours");
+ mapping.setLabel("View Mapping");
+ mapping.addActionListener(this);
+ wire.setLabel("Wireframe");
+ wire.addItemListener(this);
+ depth.setState(true);
+ depth.setLabel("Depthcue");
+ depth.addItemListener(this);
+ zbuffer.setState(true);
+ zbuffer.setLabel("Z Buffering");
+ zbuffer.addItemListener(this);
+ charge.setLabel("Charge & Cysteine");
+ charge.addActionListener(this);
+ hydro.setLabel("Hydrophobicity");
+ hydro.addActionListener(this);
+ chain.setLabel("By Chain");
+ chain.addActionListener(this);
+ seqButton.setLabel("By Sequence");
+ seqButton.addActionListener(this);
+ allchains.setLabel("All Chains Visible");
+ allchains.addItemListener(this);
+ viewMenu.setLabel("View");
+ zappo.setLabel("Zappo");
+ zappo.addActionListener(this);
+ taylor.setLabel("Taylor");
+ taylor.addActionListener(this);
+ helix.setLabel("Helix Propensity");
+ helix.addActionListener(this);
+ strand.setLabel("Strand Propensity");
+ strand.addActionListener(this);
+ turn.setLabel("Turn Propensity");
+ turn.addActionListener(this);
+ buried.setLabel("Buried Index");
+ buried.addActionListener(this);
+ user.setLabel("User Defined...");
+ user.addActionListener(this);
+ jMenuBar1.add(fileMenu);
+ jMenuBar1.add(coloursMenu);
+ jMenuBar1.add(viewMenu);
+ fileMenu.add(mapping); ;
+
+ coloursMenu.add(seqButton);
+ coloursMenu.add(chain);
+ coloursMenu.add(charge);
+ coloursMenu.add(zappo);
+ coloursMenu.add(taylor);
+ coloursMenu.add(hydro);
+ coloursMenu.add(helix);
+ coloursMenu.add(strand);
+ coloursMenu.add(turn);
+ coloursMenu.add(buried);
+ coloursMenu.add(user);
+ viewMenu.add(wire);
+ viewMenu.add(depth);
+ viewMenu.add(zbuffer);
+ viewMenu.add(allchains);
+ allchains.setState(true);
+ }
+
+ MenuBar jMenuBar1 = new MenuBar();
+ Menu fileMenu = new Menu();
+ Menu coloursMenu = new Menu();
+ MenuItem mapping = new MenuItem();
+ CheckboxGroup bg = new CheckboxGroup();
+ CheckboxMenuItem wire = new CheckboxMenuItem();
+ CheckboxMenuItem depth = new CheckboxMenuItem();
+ CheckboxMenuItem zbuffer = new CheckboxMenuItem();
+
+ MenuItem charge = new MenuItem();
+ MenuItem hydro = new MenuItem();
+ MenuItem chain = new MenuItem();
+ MenuItem seqButton = new MenuItem();
+
+ CheckboxMenuItem allchains = new CheckboxMenuItem();
+ Menu viewMenu = new Menu();
+ MenuItem turn = new MenuItem();
+ MenuItem strand = new MenuItem();
+ MenuItem helix = new MenuItem();
+ MenuItem taylor = new MenuItem();
+ MenuItem zappo = new MenuItem();
+ MenuItem buried = new MenuItem();
+ MenuItem user = new MenuItem();
+
+
+//End StructureListener
+////////////////////////////
+
+
+}
import jalview.schemes.*;
-public class AppletJmol extends Frame
+public class AppletJmol extends EmbmenuFrame
implements StructureListener, JmolStatusListener,
KeyListener, ActionListener, ItemListener
//PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
//FOR NOW, LETS JUST OPEN A NEW WINDOW
}
-
- renderPanel = new RenderPanel();
-
- this.add(renderPanel, BorderLayout.CENTER);
- viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
-
- viewer.setAppletContext("jalview",
- ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(),
- null);
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
-
- this.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- closeViewer();
- }
- });
-
MenuBar menuBar = new MenuBar();
menuBar.add(fileMenu);
fileMenu.add(mappingMenuItem);
helpMenu.add(jmolHelp);
- this.setMenuBar(menuBar);
+ setMenuBar(menuBar);
+
+ renderPanel = new RenderPanel();
+ embedMenuIfNeeded(renderPanel);
+ this.add(renderPanel, BorderLayout.CENTER);
+ viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter());
+
+ viewer.setAppletContext("jalview",
+ ap.av.applet.getDocumentBase(),
+ ap.av.applet.getCodeBase(),
+ null);
+
+ viewer.setJmolStatusListener(this);
+
+ jmolpopup = JmolPopup.newJmolPopup(viewer);
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ closeViewer();
+ }
+ });
+
if(pdbentry.getFile()!=null)
{
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-\r
-public class PCAPanel\r
- extends Frame implements Runnable, ActionListener, ItemListener\r
-{\r
- PCA pca;\r
- int top;\r
- RotatableCanvas rc;\r
- AlignViewport av;\r
- SequenceI[] seqs;\r
- AlignmentView seqstrings;\r
-\r
- public PCAPanel(AlignViewport av)\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- for (int i = 1; i < 8; i++)\r
- {\r
- xCombobox.addItem("dim " + i);\r
- yCombobox.addItem("dim " + i);\r
- zCombobox.addItem("dim " + i);\r
- }\r
-\r
- this.av = av;\r
- seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);\r
- if (av.getSelectionGroup() == null)\r
- {\r
- seqs = av.alignment.getSequencesArray();\r
- }\r
- else\r
- {\r
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
- }\r
- SeqCigar sq[] = seqstrings.getSequences();\r
- int length = sq[0].getWidth();\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (sq[i].getWidth() != length)\r
- {\r
- System.out.println("Sequences must be equal length for PCA analysis");\r
- return;\r
- }\r
- }\r
-\r
- rc = new RotatableCanvas(av);\r
- add(rc, BorderLayout.CENTER);\r
-\r
- jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",\r
- 400, 400);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- pca = new PCA(seqstrings.getSequenceStrings(' '));\r
- pca.run();\r
-\r
- // Now find the component coordinates\r
- int ii = 0;\r
-\r
- while ( (ii < seqs.length) && (seqs[ii] != null))\r
- {\r
- ii++;\r
- }\r
-\r
- double[][] comps = new double[ii][ii];\r
-\r
- for (int i = 0; i < ii; i++)\r
- {\r
- if (pca.getEigenvalue(i) > 1e-4)\r
- {\r
- comps[i] = pca.component(i);\r
- }\r
- }\r
-\r
- //////////////////\r
- xCombobox.select(0);\r
- yCombobox.select(1);\r
- zCombobox.select(2);\r
-\r
- top = pca.getM().rows - 1;\r
-\r
- Vector points = new Vector();\r
- float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);\r
-\r
- for (int i = 0; i < pca.getM().rows; i++)\r
- {\r
- SequencePoint sp = new SequencePoint(seqs[i], scores[i]);\r
- points.addElement(sp);\r
- }\r
-\r
- rc.setPoints(points, pca.getM().rows);\r
- rc.repaint();\r
- seqs = null;\r
- this.repaint();\r
- }\r
-\r
- void doDimensionChange()\r
- {\r
- if (top == 0)\r
- {\r
- return;\r
- }\r
-\r
- int dim1 = top - xCombobox.getSelectedIndex();\r
- int dim2 = top - yCombobox.getSelectedIndex();\r
- int dim3 = top - zCombobox.getSelectedIndex();\r
-\r
- float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);\r
- for (int i = 0; i < pca.getM().rows; i++)\r
- {\r
- ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];\r
- }\r
-\r
- rc.img = null;\r
- rc.rotmat.setIdentity();\r
- rc.initAxes();\r
- rc.paint(rc.getGraphics());\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if (evt.getSource() == inputData)\r
- {\r
- showOriginalData();\r
- }\r
- else\r
- {\r
- values_actionPerformed();\r
- }\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt.getSource() == xCombobox)\r
- {\r
- xCombobox_actionPerformed();\r
- }\r
- else if (evt.getSource() == yCombobox)\r
- {\r
- yCombobox_actionPerformed();\r
- }\r
- else if (evt.getSource() == zCombobox)\r
- {\r
- zCombobox_actionPerformed();\r
- }\r
- }\r
-\r
- protected void xCombobox_actionPerformed()\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- protected void yCombobox_actionPerformed()\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- protected void zCombobox_actionPerformed()\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- public void values_actionPerformed()\r
- {\r
-\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);\r
-\r
- cap.setText(pca.getDetails());\r
- }\r
-\r
- void showOriginalData()\r
- {\r
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
- // or create a selection box around columns in alignment view\r
- // test Alignment(SeqCigar[])\r
- Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.\r
- getGapCharacter());\r
-\r
- if (alAndColsel != null && alAndColsel[0] != null)\r
- {\r
- Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
- AlignFrame af = new AlignFrame(al,\r
- av.applet,\r
- "Original Data for PCA",\r
- false);\r
-\r
- af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);\r
- }\r
- }\r
-\r
- public void labels_itemStateChanged(ItemEvent itemEvent)\r
- {\r
- rc.showLabels(labels.getState());\r
- }\r
-\r
- Panel jPanel2 = new Panel();\r
- Label jLabel1 = new Label();\r
- Label jLabel2 = new Label();\r
- Label jLabel3 = new Label();\r
- protected Choice xCombobox = new Choice();\r
- protected Choice yCombobox = new Choice();\r
- protected Choice zCombobox = new Choice();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- MenuBar menuBar1 = new MenuBar();\r
- Menu menu1 = new Menu();\r
- Menu menu2 = new Menu();\r
- protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
- MenuItem values = new MenuItem();\r
- MenuItem inputData = new MenuItem();\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(borderLayout1);\r
- jPanel2.setLayout(flowLayout1);\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel1.setText("x=");\r
- jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel2.setText("y=");\r
- jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel3.setText("z=");\r
- jPanel2.setBackground(Color.white);\r
- zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- zCombobox.addItemListener(this);\r
- yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- yCombobox.addItemListener(this);\r
- xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- xCombobox.addItemListener(this);\r
- this.setMenuBar(menuBar1);\r
- menu1.setLabel("File");\r
- menu2.setLabel("View");\r
- labels.setLabel("Labels");\r
- labels.addItemListener(this);\r
- values.setLabel("Output Values...");\r
- values.addActionListener(this);\r
- inputData.setLabel("Input Data...");\r
- this.add(jPanel2, BorderLayout.SOUTH);\r
- jPanel2.add(jLabel1, null);\r
- jPanel2.add(xCombobox, null);\r
- jPanel2.add(jLabel2, null);\r
- jPanel2.add(yCombobox, null);\r
- jPanel2.add(jLabel3, null);\r
- jPanel2.add(zCombobox, null);\r
- menuBar1.add(menu1);\r
- menuBar1.add(menu2);\r
- menu2.add(labels);\r
- menu1.add(values);\r
- menu1.add(inputData);\r
- inputData.addActionListener(this);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+public class PCAPanel
+ extends EmbmenuFrame implements Runnable, ActionListener, ItemListener
+{
+ PCA pca;
+ int top;
+ RotatableCanvas rc;
+ AlignViewport av;
+ SequenceI[] seqs;
+ AlignmentView seqstrings;
+
+ public PCAPanel(AlignViewport av)
+ {
+ try
+ {
+ jbInit();
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ for (int i = 1; i < 8; i++)
+ {
+ xCombobox.addItem("dim " + i);
+ yCombobox.addItem("dim " + i);
+ zCombobox.addItem("dim " + i);
+ }
+
+ this.av = av;
+ seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
+ if (av.getSelectionGroup() == null)
+ {
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
+ {
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
+ SeqCigar sq[] = seqstrings.getSequences();
+ int length = sq[0].getWidth();
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (sq[i].getWidth() != length)
+ {
+ System.out.println("Sequences must be equal length for PCA analysis");
+ return;
+ }
+ }
+
+ rc = new RotatableCanvas(av);
+ embedMenuIfNeeded(rc);
+ add(rc, BorderLayout.CENTER);
+
+ jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
+ 400, 400);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run()
+ {
+ pca = new PCA(seqstrings.getSequenceStrings(' '));
+ pca.run();
+
+ // Now find the component coordinates
+ int ii = 0;
+
+ while ( (ii < seqs.length) && (seqs[ii] != null))
+ {
+ ii++;
+ }
+
+ double[][] comps = new double[ii][ii];
+
+ for (int i = 0; i < ii; i++)
+ {
+ if (pca.getEigenvalue(i) > 1e-4)
+ {
+ comps[i] = pca.component(i);
+ }
+ }
+
+ //////////////////
+ xCombobox.select(0);
+ yCombobox.select(1);
+ zCombobox.select(2);
+
+ top = pca.getM().rows - 1;
+
+ Vector points = new Vector();
+ float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+ for (int i = 0; i < pca.getM().rows; i++)
+ {
+ SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+ points.addElement(sp);
+ }
+
+ rc.setPoints(points, pca.getM().rows);
+ rc.repaint();
+ seqs = null;
+ this.repaint();
+ }
+
+ void doDimensionChange()
+ {
+ if (top == 0)
+ {
+ return;
+ }
+
+ int dim1 = top - xCombobox.getSelectedIndex();
+ int dim2 = top - yCombobox.getSelectedIndex();
+ int dim3 = top - zCombobox.getSelectedIndex();
+
+ float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+ for (int i = 0; i < pca.getM().rows; i++)
+ {
+ ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
+ }
+
+ rc.img = null;
+ rc.rotmat.setIdentity();
+ rc.initAxes();
+ rc.paint(rc.getGraphics());
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == inputData)
+ {
+ showOriginalData();
+ }
+ else
+ {
+ values_actionPerformed();
+ }
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == xCombobox)
+ {
+ xCombobox_actionPerformed();
+ }
+ else if (evt.getSource() == yCombobox)
+ {
+ yCombobox_actionPerformed();
+ }
+ else if (evt.getSource() == zCombobox)
+ {
+ zCombobox_actionPerformed();
+ }
+ }
+
+ protected void xCombobox_actionPerformed()
+ {
+ doDimensionChange();
+ }
+
+ protected void yCombobox_actionPerformed()
+ {
+ doDimensionChange();
+ }
+
+ protected void zCombobox_actionPerformed()
+ {
+ doDimensionChange();
+ }
+
+ public void values_actionPerformed()
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
+
+ cap.setText(pca.getDetails());
+ }
+
+ 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[])
+ Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
+ getGapCharacter());
+
+ if (alAndColsel != null && alAndColsel[0] != null)
+ {
+ Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+ AlignFrame af = new AlignFrame(al,
+ av.applet,
+ "Original Data for PCA",
+ false);
+
+ af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+ }
+ }
+
+ public void labels_itemStateChanged(ItemEvent itemEvent)
+ {
+ rc.showLabels(labels.getState());
+ }
+
+ Panel jPanel2 = new Panel();
+ Label jLabel1 = new Label();
+ Label jLabel2 = new Label();
+ Label jLabel3 = new Label();
+ protected Choice xCombobox = new Choice();
+ protected Choice yCombobox = new Choice();
+ protected Choice zCombobox = new Choice();
+ FlowLayout flowLayout1 = new FlowLayout();
+ BorderLayout borderLayout1 = new BorderLayout();
+ MenuBar menuBar1 = new MenuBar();
+ Menu menu1 = new Menu();
+ Menu menu2 = new Menu();
+ protected CheckboxMenuItem labels = new CheckboxMenuItem();
+ MenuItem values = new MenuItem();
+ MenuItem inputData = new MenuItem();
+
+ private void jbInit()
+ throws Exception
+ {
+ this.setLayout(borderLayout1);
+ jPanel2.setLayout(flowLayout1);
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+ jLabel1.setText("x=");
+ jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+ jLabel2.setText("y=");
+ jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+ jLabel3.setText("z=");
+ jPanel2.setBackground(Color.white);
+ zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+ zCombobox.addItemListener(this);
+ yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+ yCombobox.addItemListener(this);
+ xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+ xCombobox.addItemListener(this);
+ this.setMenuBar(menuBar1);
+ menu1.setLabel("File");
+ menu2.setLabel("View");
+ labels.setLabel("Labels");
+ labels.addItemListener(this);
+ values.setLabel("Output Values...");
+ values.addActionListener(this);
+ inputData.setLabel("Input Data...");
+ this.add(jPanel2, BorderLayout.SOUTH);
+ jPanel2.add(jLabel1, null);
+ jPanel2.add(xCombobox, null);
+ jPanel2.add(jLabel2, null);
+ jPanel2.add(yCombobox, null);
+ jPanel2.add(jLabel3, null);
+ jPanel2.add(zCombobox, null);
+ menuBar1.add(menu1);
+ menuBar1.add(menu2);
+ menu2.add(labels);
+ menu1.add(values);
+ menu1.add(inputData);
+ inputData.addActionListener(this);
+ }
+
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-\r
-public class TreePanel\r
- extends Frame implements ActionListener, ItemListener\r
-{\r
- SequenceI[] seq;\r
- String type;\r
- String pwtype;\r
- int start;\r
- int end;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
- AlignViewport av;\r
-\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- * @param e DOCUMENT ME!\r
- */\r
- public TreePanel(AlignViewport av, String type, String pwtype)\r
- {\r
- try\r
- {\r
- jbInit();\r
- this.setMenuBar(jMenuBar1);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- initTreePanel(av, type, pwtype, null);\r
- }\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param newtree DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- */\r
- public TreePanel(AlignViewport av,\r
- String type,\r
- String pwtype,\r
- NewickFile newtree)\r
- {\r
- try\r
- {\r
- jbInit();\r
- this.setMenuBar(jMenuBar1);\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- initTreePanel(av, type, pwtype, newtree);\r
- }\r
-\r
- void initTreePanel(AlignViewport av,\r
- String type,\r
- String pwtype,\r
- NewickFile newTree)\r
- {\r
-\r
- this.av = av;\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- treeCanvas = new TreeCanvas(av, scrollPane);\r
- scrollPane.add(treeCanvas);\r
-\r
- TreeLoader tl = new TreeLoader(newTree);\r
- tl.start();\r
-\r
- }\r
-\r
- void showOriginalData()\r
- {\r
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
- // or create a selection box around columns in alignment view\r
- // test Alignment(SeqCigar[])\r
- if (tree.seqData != null)\r
- {\r
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
- getGapCharacter());\r
-\r
- if (alAndColsel != null && alAndColsel[0] != null)\r
- {\r
- Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
- AlignFrame af = new AlignFrame(al,\r
- av.applet,\r
- "Original Data for Tree",\r
- false);\r
-\r
- af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);\r
- }\r
- }\r
- else\r
- {\r
- System.out.println("Original Tree Data not available");\r
- }\r
- }\r
-\r
- class TreeLoader\r
- extends Thread\r
- {\r
- NewickFile newtree;\r
- jalview.datamodel.AlignmentView odata = null;\r
-\r
- public TreeLoader(NewickFile newtree)\r
- {\r
- this.newtree = newtree;\r
- }\r
-\r
- public void run()\r
- {\r
- if (newtree != null)\r
- {\r
- if (odata == null)\r
- {\r
- tree = new NJTree(av.alignment.getSequencesArray(),\r
- newtree);\r
- }\r
- else\r
- {\r
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
- }\r
-\r
- }\r
- else\r
- {\r
- int start, end;\r
- SequenceI[] seqs;\r
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);\r
- if (av.getSelectionGroup() == null)\r
- {\r
- start = 0;\r
- end = av.alignment.getWidth();\r
- seqs = av.alignment.getSequencesArray();\r
- }\r
- else\r
- {\r
- start = av.getSelectionGroup().getStartRes();\r
- end = av.getSelectionGroup().getEndRes() + 1;\r
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
- }\r
-\r
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
- }\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- treeCanvas.setTree(tree);\r
- if (newtree != null)\r
- {\r
- distanceMenu.setState(newtree.HasDistances());\r
- bootstrapMenu.setState(newtree.HasBootstrap());\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- }\r
-\r
- treeCanvas.repaint();\r
-\r
- av.setCurrentTree(tree);\r
-\r
- }\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if (evt.getSource() == newickOutput)\r
- {\r
- newickOutput_actionPerformed();\r
- }\r
- else if (evt.getSource() == fontSize)\r
- {\r
- fontSize_actionPerformed();\r
- }\r
- else if (evt.getSource() == inputData)\r
- {\r
- showOriginalData();\r
- }\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt.getSource() == fitToWindow)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.getState();\r
- }\r
-\r
- else if (evt.getSource() == distanceMenu)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.getState());\r
- }\r
-\r
- else if (evt.getSource() == bootstrapMenu)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
- }\r
-\r
- else if (evt.getSource() == placeholdersMenu)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
- }\r
-\r
- treeCanvas.repaint();\r
- }\r
-\r
- public void newickOutput_actionPerformed()\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, null);\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
- public java.awt.Font getTreeFont()\r
- {\r
- return treeCanvas.font;\r
- }\r
-\r
- public void setTreeFont(java.awt.Font font)\r
- {\r
- treeCanvas.font = font;\r
- treeCanvas.repaint();\r
- }\r
-\r
- protected void fontSize_actionPerformed()\r
- {\r
- if (treeCanvas == null)\r
- {\r
- return;\r
- }\r
-\r
- new FontChooser(this);\r
- }\r
-\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected ScrollPane scrollPane = new ScrollPane();\r
- MenuBar jMenuBar1 = new MenuBar();\r
- Menu jMenu2 = new Menu();\r
- protected MenuItem fontSize = new MenuItem();\r
- protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
- Menu fileMenu = new Menu();\r
- MenuItem newickOutput = new MenuItem();\r
- MenuItem inputData = new MenuItem();\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- setLayout(borderLayout1);\r
- this.setBackground(Color.white);\r
- this.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jMenu2.setLabel("View");\r
- fontSize.setLabel("Font...");\r
- fontSize.addActionListener(this);\r
- bootstrapMenu.setLabel("Show Bootstrap Values");\r
- bootstrapMenu.addItemListener(this);\r
- distanceMenu.setLabel("Show Distances");\r
- distanceMenu.addItemListener(this);\r
- placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
- placeholdersMenu.addItemListener(this);\r
- fitToWindow.setState(true);\r
- fitToWindow.setLabel("Fit To Window");\r
- fitToWindow.addItemListener(this);\r
- fileMenu.setLabel("File");\r
- newickOutput.setLabel("Newick Format");\r
- newickOutput.addActionListener(this);\r
- inputData.setLabel("Input Data...");\r
-\r
- add(scrollPane, BorderLayout.CENTER);\r
- jMenuBar1.add(fileMenu);\r
- jMenuBar1.add(jMenu2);\r
- jMenu2.add(fitToWindow);\r
- jMenu2.add(fontSize);\r
- jMenu2.add(distanceMenu);\r
- jMenu2.add(bootstrapMenu);\r
- jMenu2.add(placeholdersMenu);\r
- fileMenu.add(newickOutput);\r
- fileMenu.add(inputData);\r
- inputData.addActionListener(this);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ */
+
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Hashtable;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class TreePanel
+ extends EmbmenuFrame implements ActionListener, ItemListener
+{
+ SequenceI[] seq;
+ String type;
+ String pwtype;
+ int start;
+ int end;
+ TreeCanvas treeCanvas;
+ NJTree tree;
+ AlignViewport av;
+
+ public NJTree getTree()
+ {
+ return tree;
+ }
+
+ /**
+ * 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(AlignViewport av, String type, String pwtype)
+ {
+ try
+ {
+ jbInit();
+ this.setMenuBar(jMenuBar1);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ initTreePanel(av, 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(AlignViewport av,
+ String type,
+ String pwtype,
+ NewickFile newtree)
+ {
+ try
+ {
+ jbInit();
+ this.setMenuBar(jMenuBar1);
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ initTreePanel(av, type, pwtype, newtree);
+ }
+ void initTreePanel(AlignViewport av,
+ String type,
+ String pwtype,
+ NewickFile newTree)
+ {
+
+ this.av = av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+
+ TreeLoader tl = new TreeLoader(newTree);
+ tl.start();
+ treeCanvas = new TreeCanvas(av, scrollPane);
+ 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)
+ {
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+ getGapCharacter());
+
+ 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.alignment.getSequencesArray(),
+ newtree);
+ }
+ else
+ {
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+ }
+
+ }
+ else
+ {
+ int start, end;
+ SequenceI[] seqs;
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+ if (av.getSelectionGroup() == null)
+ {
+ start = 0;
+ end = av.alignment.getWidth();
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes() + 1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
+
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ }
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ if (newtree != null)
+ {
+ distanceMenu.setState(newtree.HasDistances());
+ bootstrapMenu.setState(newtree.HasBootstrap());
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+ treeCanvas.setShowDistances(newtree.HasDistances());
+ }
+
+ 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("View");
+ fontSize.setLabel("Font...");
+ fontSize.addActionListener(this);
+ bootstrapMenu.setLabel("Show Bootstrap Values");
+ bootstrapMenu.addItemListener(this);
+ distanceMenu.setLabel("Show Distances");
+ distanceMenu.addItemListener(this);
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");
+ placeholdersMenu.addItemListener(this);
+ fitToWindow.setState(true);
+ fitToWindow.setLabel("Fit To Window");
+ fitToWindow.addItemListener(this);
+ fileMenu.setLabel("File");
+ newickOutput.setLabel("Newick Format");
+ newickOutput.addActionListener(this);
+ inputData.setLabel("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 / commitdiff