X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=115f641e4288461f51497a41f9f8ac04f012095d;hb=927fababac20a4859004bbc53de9694390b50ca8;hp=64253b41ec5850047d9ba8a70e0a8c636e660708;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 64253b4..115f641 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -44,7 +44,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
     int top;
     RotatableCanvas rc;
     AlignViewport av;
-    SequenceI [] seqs;
+    AlignmentView seqstrings;
+    SequenceI  [] seqs;
 
     /**
      * Creates a new PCAPanel object.
@@ -58,36 +59,25 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         boolean sameLength = true;
 
-        if ((av.getSelectionGroup() != null) &&
-                (av.getSelectionGroup().getSize(false) > 3))
+        seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+        if(av.getSelectionGroup()==null)
         {
-            seqs = new Sequence[av.getSelectionGroup().getSize(false)];
-            int length = av.getSelectionGroup().getSequenceAt(0).getLength();
-            for (int i = 0; i < av.getSelectionGroup().getSize(false); i++)
-            {
-                seqs[i] = av.getSelectionGroup().getSequenceAt(i);
-                if(seqs[i].getLength()!=length)
-                {
-                  sameLength = false;
-                  break;
-                }
-            }
+          seqs = av.alignment.getSequencesArray();
         }
         else
         {
-            seqs = new Sequence[av.getAlignment().getHeight()];
-            int length = av.alignment.getSequenceAt(0).getLength();
-
-            for (int i = 0; i < av.getAlignment().getHeight(); i++)
-            {
-                seqs[i] = av.getAlignment().getSequenceAt(i);
-                if(seqs[i].getLength()!=length)
-               {
-                 sameLength = false;
-                 break;
-               }
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
+        SeqCigar sq[]=seqstrings.getSequences();
+        int length = sq[0].getWidth();
 
-            }
+        for (int i = 0; i < seqs.length; i++)
+        {
+          if (sq[i].getWidth() != length)
+          {
+            sameLength = false;
+            break;
+          }
         }
 
         if (!sameLength)
@@ -132,7 +122,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     public void run()
     {
       try{
-        pca = new PCA(seqs);
+        pca = new PCA(seqstrings.getSequenceStrings(' '));
         pca.run();
 
         // Now find the component coordinates
@@ -171,7 +161,6 @@ public class PCAPanel extends GPCAPanel implements Runnable
 
         rc.setPoints(points, pca.getM().rows);
         rc.repaint();
-        seqs = null;
       }
      catch(OutOfMemoryError er)
       { JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -265,6 +254,64 @@ public class PCAPanel extends GPCAPanel implements Runnable
       printer.start();
     }
 
+    public void originalSeqData_actionPerformed(ActionEvent e)
+    {
+      // 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)
+      {
+        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]);
+
+              //>>>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.NEW_WINDOW_WIDTH,
+                                       AlignFrame.NEW_WINDOW_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);
+           */
+    }
+
+
 
     class PCAPrinter extends Thread implements Printable
     {