Display nucleotides

[jalview.git] / src / jalview / gui / PCAPanel.java

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 474a158..26f1160 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -28,6 +28,8 @@ import java.awt.*;
 import java.awt.event.*;\r
 \r
 import java.util.*;\r
+import javax.swing.JOptionPane;\r
+import javax.swing.JInternalFrame;\r
 \r
 \r
 /**\r
@@ -50,31 +52,61 @@ public class PCAPanel extends GPCAPanel implements Runnable
      * @param av DOCUMENT ME!\r
      * @param s DOCUMENT ME!\r
      */\r
-    public PCAPanel(AlignViewport av, SequenceI[] s)\r
+    public PCAPanel(AlignViewport av)\r
     {\r
         this.av = av;\r
 \r
+        boolean sameLength = true;\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
+            int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
+            for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
             {\r
                 seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
+                if(seqs[i].getLength()!=length)\r
+                {\r
+                  sameLength = false;\r
+                  break;\r
+                }\r
             }\r
         }\r
-\r
-        if (s == null)\r
+        else\r
         {\r
             seqs = new Sequence[av.getAlignment().getHeight()];\r
+            int length = av.alignment.getSequenceAt(0).getLength();\r
 \r
             for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
             {\r
                 seqs[i] = av.getAlignment().getSequenceAt(i);\r
+                if(seqs[i].getLength()!=length)\r
+               {\r
+                 sameLength = false;\r
+                 break;\r
+               }\r
+\r
             }\r
         }\r
 \r
+        if (!sameLength)\r
+        {\r
+          JOptionPane.showMessageDialog(Desktop.desktop,\r
+                                        "The sequences must be aligned before calculating PCA.\n" +\r
+                                        "Try using the Pad function in the edit menu,\n" +\r
+                                        "or one of the multiple sequence alignment web services.",\r
+                                        "Sequences not aligned",\r
+                                        JOptionPane.WARNING_MESSAGE);\r
+\r
+          return;\r
+        }\r
+\r
+        JInternalFrame frame = new JInternalFrame();\r
+        frame.setContentPane(this);\r
+        Desktop.addInternalFrame(frame, "Principal component analysis",\r
+                               400, 400);\r
+\r
 \r
         rc = new RotatableCanvas(av);\r
         add(rc, BorderLayout.CENTER);\r
@@ -89,46 +121,60 @@ public class PCAPanel extends GPCAPanel implements Runnable
      */\r
     public void run()\r
     {\r
-                pca = new PCA(seqs);\r
-                pca.run();\r
+      try{\r
+        pca = new PCA(seqs);\r
+        pca.run();\r
 \r
-                // Now find the component coordinates\r
-                int ii = 0;\r
+        // Now find the component coordinates\r
+        int ii = 0;\r
 \r
-                while ((ii < seqs.length) && (seqs[ii] != null))\r
-                {\r
-                    ii++;\r
-                }\r
+        while ( (ii < seqs.length) && (seqs[ii] != null))\r
+        {\r
+          ii++;\r
+        }\r
 \r
-                double[][] comps = new double[ii][ii];\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
+        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
+        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
+        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
+        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
+     catch(OutOfMemoryError er)\r
+      { JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                              "Out of memory calculating PCA!!"\r
+                                              +\r
+                                              "\nSee help files for increasing Java Virtual Machine memory."\r
+                                              , "Out of memory",\r
+                                              JOptionPane.WARNING_MESSAGE);\r
+        System.out.println("PCAPanel: "+er);\r
+        System.gc();\r
+\r
+      }\r
 \r
-                rc.setPoints(points, pca.getM().rows);\r
-                rc.repaint();\r
-                seqs = null;\r
     }\r
 \r
     /**\r