+/*\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 jalview.datamodel.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbappletgui.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
\r
-public class PCAPanel extends GPCAPanel implements Runnable\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 void run()\r
+ public PCAPanel(AlignViewport av)\r
{\r
- // do stuff\r
- }\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
\r
- public PCAPanel(AlignViewport av, SequenceI[] s) {\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
- if(av.getSelectionGroup().getSize()>3)\r
+ seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);\r
+ if (av.getSelectionGroup() == null)\r
{\r
- s = new Sequence[av.getSelectionGroup().getSize()];\r
- for(int i=0; i<s.length; i++)\r
- s[i] = av.getSelectionGroup().getSequenceAt(i);\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
-\r
- if(s==null)\r
+ for (int i = 0; i < seqs.length; i++)\r
{\r
- s = new Sequence[av.getAlignment().getHeight()];\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- s[i] = av.getAlignment().getSequenceAt(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
-//////////////////////This part was done in PCATHread originally. Is it too slow???\r
- pca = new PCA(s);\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
- while (ii < s.length && s[ii] != null)\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
+ for (int i = 0; i < ii; i++)\r
{\r
if (pca.getEigenvalue(i) > 1e-4)\r
{\r
- comps[i] = pca.component(i);\r
+ comps[i] = pca.component(i);\r
}\r
}\r
\r
//////////////////\r
-\r
xCombobox.select(0);\r
yCombobox.select(1);\r
zCombobox.select(2);\r
\r
- top = pca.getM().rows-1;\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
+ float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);\r
\r
- for (int i =0; i < pca.getM().rows; i++ )\r
+ for (int i = 0; i < pca.getM().rows; i++)\r
{\r
- SequencePoint sp = new SequencePoint(s[i],scores[i]);\r
+ SequencePoint sp = new SequencePoint(seqs[i], scores[i]);\r
points.addElement(sp);\r
}\r
\r
- rc = new RotatableCanvas(av,points,pca.getM().rows);\r
-\r
- //rc.printPoints();\r
-\r
- add(rc, BorderLayout.CENTER);\r
+ rc.setPoints(points, pca.getM().rows);\r
+ rc.repaint();\r
+ seqs = null;\r
+ this.repaint();\r
}\r
\r
-\r
void doDimensionChange()\r
{\r
- if(top==0)\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
- ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];\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.paint(rc.getGraphics());\r
}\r
\r
- protected void xCombobox_actionPerformed(ActionEvent e)\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(ActionEvent e)\r
+ protected void yCombobox_actionPerformed()\r
{\r
doDimensionChange();\r
}\r
\r
- protected void zCombobox_actionPerformed(ActionEvent e)\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
git://source.jalview.org / jalview.git / blobdiff