(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 9c852c5..fe0c4f9 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
@@ -68,11 +69,11 @@ public class PCAPanel extends GPCAPanel implements Runnable
     seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
     if (av.getSelectionGroup() == null)
     {
-      seqs = av.alignment.getSequencesArray();
+      seqs = av.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
     SeqCigar sq[] = seqstrings.getSequences();
     int length = sq[0].getWidth();
@@ -99,9 +100,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
       return;
     }
 
-    Desktop
-            .addInternalFrame(this, "Principal component analysis", 400,
-                    400);
+    Desktop.addInternalFrame(this, "Principal component analysis", 400, 400);
 
     PaintRefresher.Register(this, av.getSequenceSetId());
 
@@ -243,9 +242,15 @@ 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)
@@ -408,8 +413,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
     else
     {
       im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
-              "Make EPS file from PCA", width, height, null, this
-                      .getTitle());
+              "Make EPS file from PCA", width, height, null,
+              this.getTitle());
     }
 
     if (im.getGraphics() != null)
@@ -487,4 +492,97 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
   }
 
+  /*
+   * (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();
+    }
+  }
+
 }