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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index ffc5a76..ea4f44e 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -44,7 +44,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     int top;\r
     RotatableCanvas rc;\r
     AlignViewport av;\r
-    String  [] seqstrings;\r
+    AlignmentView seqstrings;\r
     SequenceI  [] seqs;\r
 \r
     /**\r
@@ -59,9 +59,8 @@ public class PCAPanel extends GPCAPanel implements Runnable
 \r
         boolean sameLength = true;\r
 \r
-        seqstrings = av.getViewAsString(true);\r
-\r
-        if (av.getSelectionGroup() == null)\r
+        seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+        if(av.getSelectionGroup()==null)\r
         {\r
           seqs = av.alignment.getSequencesArray();\r
         }\r
@@ -69,12 +68,12 @@ public class PCAPanel extends GPCAPanel implements Runnable
         {\r
           seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
         }\r
-\r
-        int length = seqs[0].getLength();\r
+        SeqCigar sq[]=seqstrings.getSequences();\r
+        int length = sq[0].getWidth();\r
 \r
         for (int i = 0; i < seqs.length; i++)\r
         {\r
-          if (seqs[i].getLength() != length)\r
+          if (sq[i].getWidth() != length)\r
           {\r
             sameLength = false;\r
             break;\r
@@ -123,7 +122,7 @@ public class PCAPanel extends GPCAPanel implements Runnable
     public void run()\r
     {\r
       try{\r
-        pca = new PCA(seqstrings);\r
+        pca = new PCA(seqstrings.getSequenceStrings(' '));\r
         pca.run();\r
 \r
         // Now find the component coordinates\r
@@ -257,18 +256,62 @@ public class PCAPanel extends GPCAPanel implements Runnable
 \r
     public void originalSeqData_actionPerformed(ActionEvent e)\r
     {\r
-      CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-      for (int i = 0; i < seqs.length; i++)\r
+      // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows\r
+      if (seqstrings==null)\r
       {\r
-        cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(\r
-            seqs[i].getName()));\r
-        cap.appendText(" " + seqstrings[i] + "\n");\r
-\r
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
+        return;\r
       }\r
+      // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+      // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+      // or create a selection box around columns in alignment view\r
+      // test Alignment(SeqCigar[])\r
+      Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.\r
+          getGapCharacter());\r
+\r
+\r
+      if (alAndColsel != null && alAndColsel[0]!=null)\r
+      {\r
+          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
+\r
+          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);\r
+          Alignment dataset = av.getAlignment().getDataset();\r
+          if (dataset != null)\r
+          {\r
+            al.setDataset(dataset);\r
+          }\r
+\r
+          if (true)\r
+          {\r
+              // make a new frame!\r
+              AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
+                                           AlignFrame.DEFAULT_WIDTH,\r
+                                           AlignFrame.DEFAULT_HEIGHT\r
+);\r
+\r
+              //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+              // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
+              //           af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+              //                                     msaorder);\r
+\r
+              Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
+                                       AlignFrame.DEFAULT_WIDTH,\r
+                                       AlignFrame.DEFAULT_HEIGHT);\r
+            }\r
+          }\r
+          /*      CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+                 for (int i = 0; i < seqs.length; i++)\r
+                 {\r
+                   cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(\r
+            seqs[i].getName()));\r
+                   cap.appendText(" " + seqstrings[i] + "\n");\r
 \r
-      Desktop.addInternalFrame(cap, "Original Data",\r
-          400, 400);\r
+                 }\r
 \r
+                 Desktop.addInternalFrame(cap, "Original Data",\r
+                     400, 400);\r
+           */\r
     }\r
 \r
 \r