X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=ea4f44e2f7bc3ab40aee3dd63439053f70fbba44;hb=0b23947e2cdcd704d3f313b23ba271e43d097344;hp=371528aa9fcf5d46fa583c3594f803330dfc116f;hpb=ddf4180014d2316824c4ecd4bcbbe20be4033d43;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 371528a..ea4f44e 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, 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
@@ -44,7 +44,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     int top;
     RotatableCanvas rc;
     AlignViewport av;
-    String  [] seqstrings;
+    AlignmentView seqstrings;
     SequenceI  [] seqs;
 
     /**
@@ -59,9 +59,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         boolean sameLength = true;
 
-        seqstrings = av.getSelectionAsString();
-
-        if (av.getSelectionGroup() == null)
+        seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+        if(av.getSelectionGroup()==null)
         {
           seqs = av.alignment.getSequencesArray();
         }
@@ -69,12 +68,12 @@ public class PCAPanel extends GPCAPanel implements Runnable
         {
           seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
         }
-
-        int length = seqs[0].getLength();
+        SeqCigar sq[]=seqstrings.getSequences();
+        int length = sq[0].getWidth();
 
         for (int i = 0; i < seqs.length; i++)
         {
-          if (seqs[i].getLength() != length)
+          if (sq[i].getWidth() != length)
           {
             sameLength = false;
             break;
@@ -123,7 +122,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     public void run()
     {
       try{
-        pca = new PCA(seqstrings);
+        pca = new PCA(seqstrings.getSequenceStrings(' '));
         pca.run();
 
         // Now find the component coordinates
@@ -257,18 +256,62 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
     public void originalSeqData_actionPerformed(ActionEvent e)
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();
-      for (int i = 0; i < seqs.length; i++)
+      // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows
+      if (seqstrings==null)
       {
-        cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(
-            seqs[i].getName()));
-        cap.appendText(" " + seqstrings[i] + "\n");
-
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+        return;
       }
+      // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+      // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+      // or create a selection box around columns in alignment view
+      // test Alignment(SeqCigar[])
+      Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
+          getGapCharacter());
+
+
+      if (alAndColsel != null && alAndColsel[0]!=null)
+      {
+          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+          Alignment dataset = av.getAlignment().getDataset();
+          if (dataset != null)
+          {
+            al.setDataset(dataset);
+          }
+
+          if (true)
+          {
+              // make a new frame!
+              AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT
+);
+
+              //>>>This is a fix for the moment, until a better solution is found!!<<<
+              // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+              //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+              //                                     msaorder);
+
+              Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                       AlignFrame.DEFAULT_WIDTH,
+                                       AlignFrame.DEFAULT_HEIGHT);
+            }
+          }
+          /*      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");
 
-      Desktop.addInternalFrame(cap, "Original Data",
-          400, 400);
+                 }
 
+                 Desktop.addInternalFrame(cap, "Original Data",
+                     400, 400);
+           */
     }