/*\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
+ * 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
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbgui.*;\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
+import jalview.jbgui.*;\r
\r
-public class PCAPanel extends GPCAPanel implements Runnable\r
+public class PCAPanel\r
+ extends GPCAPanel implements Runnable\r
{\r
PCA pca;\r
int top;\r
RotatableCanvas rc;\r
AlignViewport av;\r
\r
- public void run()\r
+ public PCAPanel(AlignViewport av, SequenceI[] s)\r
{\r
- // do stuff\r
- }\r
-\r
- public PCAPanel(AlignViewport av, SequenceI[] s) {\r
-\r
this.av = av;\r
- if(av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>3)\r
+\r
+ if ( (av.getSelectionGroup() != null) &&\r
+ (av.getSelectionGroup().getSize() > 3))\r
{\r
s = new Sequence[av.getSelectionGroup().getSize()];\r
- for(int i=0; i<s.length; i++)\r
+\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
s[i] = av.getSelectionGroup().getSequenceAt(i);\r
+ }\r
}\r
\r
-\r
- if(s==null)\r
+ if (s == null)\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
+ }\r
+ }\r
\r
-//////////////////////This part was done in PCATHread originally. Is it too slow???\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
- while (ii < s.length && s[ii] != null)\r
+ int ii = 0;\r
+\r
+ while ( (ii < s.length) && (s[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.setSelectedIndex(0);\r
yCombobox.setSelectedIndex(1);\r
zCombobox.setSelectedIndex(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(s[i], scores[i]);\r
points.addElement(sp);\r
}\r
\r
- rc = new RotatableCanvas(av,points,pca.getM().rows);\r
+ rc = new RotatableCanvas(av, points, pca.getM().rows);\r
\r
//rc.printPoints();\r
-\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
+ 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
+\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
{\r
doDimensionChange();\r
}\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff