*/\r
package jalview.gui;\r
\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
\r
-public class PCAPanel\r
- extends GPCAPanel implements Runnable\r
-{\r
- PCA pca;\r
- int top;\r
- RotatableCanvas rc;\r
- AlignViewport av;\r
+import jalview.jbgui.*;\r
\r
- public PCAPanel(AlignViewport av, SequenceI[] s)\r
- {\r
- this.av = av;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
\r
- if ( (av.getSelectionGroup() != null) &&\r
- (av.getSelectionGroup().getSize() > 3))\r
- {\r
- s = new Sequence[av.getSelectionGroup().getSize()];\r
+import java.util.*;\r
\r
- for (int i = 0; i < s.length; i++)\r
- {\r
- s[i] = av.getSelectionGroup().getSequenceAt(i);\r
- }\r
- }\r
\r
- if (s == null)\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class PCAPanel extends GPCAPanel implements Runnable\r
+{\r
+ PCA pca;\r
+ int top;\r
+ RotatableCanvas rc;\r
+ AlignViewport av;\r
+ SequenceI [] seqs;\r
+\r
+ /**\r
+ * Creates a new PCAPanel object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ */\r
+ public PCAPanel(AlignViewport av, SequenceI[] s)\r
{\r
- s = new Sequence[av.getAlignment().getHeight()];\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- s[i] = av.getAlignment().getSequenceAt(i);\r
- }\r
+ this.av = av;\r
+\r
+ if ((av.getSelectionGroup() != null) &&\r
+ (av.getSelectionGroup().getSize() > 3))\r
+ {\r
+ seqs = new Sequence[av.getSelectionGroup().getSize()];\r
+\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
+ seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ }\r
+ }\r
+\r
+ if (s == null)\r
+ {\r
+ seqs = new Sequence[av.getAlignment().getHeight()];\r
+\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ seqs[i] = av.getAlignment().getSequenceAt(i);\r
+ }\r
+ }\r
+\r
+\r
+ rc = new RotatableCanvas(av);\r
+ add(rc, BorderLayout.CENTER);\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
}\r
\r
- //////////////////////This part was done in PCATHread originally. Is it too slow???\r
- pca = new PCA(s);\r
- pca.run();\r
\r
- // Now find the component coordinates\r
- int ii = 0;\r
\r
- while ( (ii < s.length) && (s[ii] != null))\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
{\r
- ii++;\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.setSelectedIndex(0);\r
+ yCombobox.setSelectedIndex(1);\r
+ zCombobox.setSelectedIndex(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
- double[][] comps = new double[ii][ii];\r
-\r
- for (int i = 0; i < ii; i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void doDimensionChange()\r
{\r
- if (pca.getEigenvalue(i) > 1e-4)\r
- {\r
- comps[i] = pca.component(i);\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
+\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
- //////////////////\r
- xCombobox.setSelectedIndex(0);\r
- yCombobox.setSelectedIndex(1);\r
- zCombobox.setSelectedIndex(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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void xCombobox_actionPerformed(ActionEvent e)\r
{\r
- SequencePoint sp = new SequencePoint(s[i], scores[i]);\r
- points.addElement(sp);\r
+ doDimensionChange();\r
}\r
\r
- rc = new RotatableCanvas(av, points, pca.getM().rows);\r
-\r
- //rc.printPoints();\r
- add(rc, BorderLayout.CENTER);\r
- }\r
-\r
- public void run()\r
- {\r
- // do stuff\r
- }\r
-\r
- void doDimensionChange()\r
- {\r
- if (top == 0)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void yCombobox_actionPerformed(ActionEvent e)\r
{\r
- return;\r
+ doDimensionChange();\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
-\r
- for (int i = 0; i < pca.getM().rows; i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void zCombobox_actionPerformed(ActionEvent e)\r
{\r
- ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];\r
+ doDimensionChange();\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
git://source.jalview.org / jalview.git / blobdiff