-/*\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.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
-\r
-public class PCAPanel\r
- extends GPCAPanel implements Runnable\r
-{\r
- PCA pca;\r
- int top;\r
- RotatableCanvas rc;\r
- AlignViewport av;\r
- SequenceI [] seqs;\r
-\r
-\r
- public PCAPanel(AlignViewport av, SequenceI[] s)\r
- {\r
-\r
- this.av = av;\r
- if (av.getSelectionGroup().getSize() > 3)\r
- {\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
- for (int i = 0; i < s.length; i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- }\r
- }\r
-\r
- if (seqs == null)\r
- {\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
- }\r
- rc = new RotatableCanvas(av);\r
- add(rc, BorderLayout.CENTER);\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(seqs);\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
- }\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
- protected void xCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- protected void yCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
-\r
- protected void zCombobox_actionPerformed(ActionEvent e)\r
- {\r
- doDimensionChange();\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.viewmodel.PCAModel;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.CheckboxMenuItem;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+public class PCAPanel extends EmbmenuFrame implements Runnable,
+ ActionListener, ItemListener
+{
+ RotatableCanvas rc;
+
+ AlignViewport av;
+
+ PCAModel pcaModel;
+
+ int top = 0;
+
+ 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;
+ boolean selected = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 0;
+ AlignmentView seqstrings = av.getAlignmentView(selected);
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ SequenceI[] seqs;
+ if (!selected)
+ {
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ }
+ 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;
+ }
+ }
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+
+ rc = new RotatableCanvas(av);
+ embedMenuIfNeeded(rc);
+ add(rc, BorderLayout.CENTER);
+
+ jalview.bin.JalviewLite.addFrame(this,
+ MessageManager.getString("label.principal_component_analysis"),
+ 475, 400);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run()
+ {
+ // TODO progress indicator
+ calcSettings.setEnabled(false);
+ rc.setEnabled(false);
+ try
+ {
+ nuclSetting.setState(pcaModel.isNucleotide());
+ protSetting.setState(!pcaModel.isNucleotide());
+ pcaModel.run();
+ // ////////////////
+ xCombobox.select(0);
+ yCombobox.select(1);
+ zCombobox.select(2);
+
+ pcaModel.updateRc(rc);
+ // rc.invalidate();
+ top = pcaModel.getTop();
+ } catch (OutOfMemoryError x)
+ {
+ System.err.println("Out of memory when calculating PCA.");
+ return;
+ }
+ calcSettings.setEnabled(true);
+
+ // TODO revert progress indicator
+ rc.setEnabled(true);
+ rc.repaint();
+ this.repaint();
+ }
+
+ void doDimensionChange()
+ {
+ if (top == 0)
+ {
+ return;
+ }
+
+ int dim1 = top - xCombobox.getSelectedIndex();
+ int dim2 = top - yCombobox.getSelectedIndex();
+ int dim3 = top - zCombobox.getSelectedIndex();
+ pcaModel.updateRcView(dim1, dim2, dim3);
+ rc.img = null;
+ rc.rotmat.setIdentity();
+ rc.initAxes();
+ rc.paint(rc.getGraphics());
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == inputData)
+ {
+ showOriginalData();
+ }
+ if (evt.getSource() == resetButton)
+ {
+ xCombobox.select(0);
+ yCombobox.select(1);
+ zCombobox.select(2);
+ doDimensionChange();
+ }
+ if (evt.getSource() == values)
+ {
+ 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();
+ }
+ else if (evt.getSource() == labels)
+ {
+ labels_itemStateChanged(evt);
+ }
+ else if (evt.getSource() == nuclSetting)
+ {
+ if (!pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(true);
+ new Thread(this).start();
+ }
+ }
+ else if (evt.getSource() == protSetting)
+ {
+ if (pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(false);
+ new Thread(this).start();
+ }
+ }
+ }
+
+ 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,
+ MessageManager.getString("label.pca_details"), 500, 500);
+
+ cap.setText(pcaModel.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[])
+ 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 = pcaModel.getSeqtrings()
+ .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 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();
+
+ protected Button resetButton = new Button();
+
+ FlowLayout flowLayout1 = new FlowLayout();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ MenuBar menuBar1 = new MenuBar();
+
+ Menu menu1 = new Menu();
+
+ Menu menu2 = new Menu();
+
+ Menu calcSettings = new Menu();
+
+ protected CheckboxMenuItem labels = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem nuclSetting = 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);
+ resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
+ resetButton.setLabel(MessageManager.getString("action.reset"));
+ resetButton.addActionListener(this);
+ this.setMenuBar(menuBar1);
+ menu1.setLabel(MessageManager.getString("action.file"));
+ menu2.setLabel(MessageManager.getString("action.view"));
+ calcSettings.setLabel(MessageManager.getString("action.change_params"));
+ labels.setLabel(MessageManager.getString("label.labels"));
+ labels.addItemListener(this);
+ values.setLabel(MessageManager.getString("label.output_values"));
+ values.addActionListener(this);
+ inputData.setLabel(MessageManager.getString("label.input_data"));
+ nuclSetting.setLabel(MessageManager
+ .getString("label.nucleotide_matrix"));
+ nuclSetting.addItemListener(this);
+ protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
+ protSetting.addItemListener(this);
+ 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);
+ jPanel2.add(resetButton, null);
+ menuBar1.add(menu1);
+ menuBar1.add(menu2);
+ menuBar1.add(calcSettings);
+ menu2.add(labels);
+ menu1.add(values);
+ menu1.add(inputData);
+ calcSettings.add(nuclSetting);
+ calcSettings.add(protSetting);
+ inputData.addActionListener(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff