Jalview 2.6 source licence

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 9c852c5..084311f 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -36,6 +36,7 @@ import jalview.jbgui.*;
  */
 public class PCAPanel extends GPCAPanel implements Runnable
 {
+
   PCA pca;
 
   int top;
@@ -243,9 +244,14 @@ public class PCAPanel extends GPCAPanel implements Runnable
   public void outputValues_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap, "PCA details", 500, 500);
-
-    cap.setText(pca.getDetails());
+    try {
+      cap.setText(pca.getDetails());
+      Desktop.addInternalFrame(cap, "PCA details", 500, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("opening PCA details",oom);
+      cap.dispose();
+    }
   }
 
   public void showLabels_actionPerformed(ActionEvent e)
@@ -486,5 +492,80 @@ public class PCAPanel extends GPCAPanel implements Runnable
     associateViewsMenu.add(itemf);
 
   }
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void outputPoints_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    try {
+      cap.setText(getPointsasCsv(false));
+      Desktop.addInternalFrame(cap, "Points for "+getTitle(), 500, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("exporting PCA points",oom);
+      cap.dispose();
+    }
+  }
+
+  private String getPointsasCsv(boolean transformed)
+  {
+    StringBuffer csv = new StringBuffer();
+    csv.append("\"Sequence\"");
+    if (transformed) {
+      csv.append(",");
+      csv.append(xCombobox.getSelectedIndex());
+      csv.append(",");
+      csv.append(yCombobox.getSelectedIndex());
+      csv.append(",");
+      csv.append(zCombobox.getSelectedIndex());
+    } else {
+      for (int d=1,dmax=pca.component(1).length;d<=dmax;d++)
+      {
+        csv.append(","+d);
+      }
+    }
+    csv.append("\n");
+    for (int s=0;s<seqs.length;s++)
+    {
+      csv.append("\""+seqs[s].getName()+"\"");
+      double fl[];
+      if (!transformed) {
+        // output pca in correct order
+        fl = pca.component(s);
+        for (int d=fl.length-1; d>=0;d--)
+        {
+          csv.append(",");
+          csv.append(fl[d]);
+        }
+    } else {
+      // output current x,y,z coords for points
+        fl = rc.getPointPosition(s);
+        for (int d=0; d<fl.length;d++)
+        {
+          csv.append(",");
+          csv.append(fl[d]);
+        }
+      }
+      csv.append("\n");
+    }
+    return csv.toString();
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void outputProjPoints_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    try {
+      cap.setText(getPointsasCsv(true));
+      Desktop.addInternalFrame(cap, "Transformed points for "+getTitle(), 500, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("exporting transformed PCA points",oom);
+      cap.dispose();
+    }
+  }
 
 }