X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=084311fa6b8942e46247dd52abeb2d55249ad660;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=b397cf598a6bd0372c9534c6ddbd6ce6412ec6e2;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index b397cf5..084311f 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -37,6 +36,7 @@ import jalview.jbgui.*;
  */
 public class PCAPanel extends GPCAPanel implements Runnable
 {
+
   PCA pca;
 
   int top;
@@ -55,9 +55,9 @@ public class PCAPanel extends GPCAPanel implements Runnable
    * Creates a new PCAPanel object.
    * 
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public PCAPanel(AlignmentPanel ap)
   {
@@ -212,7 +212,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void xCombobox_actionPerformed(ActionEvent e)
   {
@@ -223,7 +223,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void yCombobox_actionPerformed(ActionEvent e)
   {
@@ -234,7 +234,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void zCombobox_actionPerformed(ActionEvent e)
   {
@@ -244,9 +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)
@@ -322,8 +327,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
      * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
      * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
      * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
-     * "\n");
-     *  }
+     * "\n"); }
      * 
      * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
      */
@@ -377,7 +381,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -388,7 +392,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
@@ -488,5 +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();
+    }
+  }
 
 }