Applet has hidden regions

[jalview.git] / src / jalview / appletgui / PairwiseAlignPanel.java

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index e58dd76..b8a15d5 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -42,21 +42,35 @@ public class PairwiseAlignPanel
     catch (Exception e)\r
     {\r
       e.printStackTrace();\r
-  }\r
+    }\r
     this.ap = ap;\r
-    float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
-        getHeight()];\r
+    sequences = new Vector();\r
+\r
+    SequenceI[] seqs;\r
+    String[] seqStrings = ap.av.getViewAsString(true);\r
+\r
+    if (ap.av.getSelectionGroup() == null)\r
+    {\r
+      seqs = ap.av.alignment.getSequencesArray();\r
+    }\r
+    else\r
+    {\r
+      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);\r
+    }\r
+\r
+    float scores[][] = new float[seqs.length][seqs.length];\r
     double totscore = 0;\r
     int count = ap.av.getSelectionGroup().getSize(false);\r
 \r
     Sequence seq;\r
+\r
     for (int i = 1; i < count; i++)\r
     {\r
       for (int j = 0; j < i; j++)\r
       {\r
-        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
-                                   ap.av.getSelectionGroup().getSequenceAt(j),\r
-                                   "pep");\r
+\r
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
+                                   seqs[j], seqStrings[j], "pep");\r
 \r
         if (as.s1str.length() == 0 || as.s2str.length() == 0)\r
         {\r
@@ -65,29 +79,41 @@ public class PairwiseAlignPanel
 \r
         as.calcScoreMatrix();\r
         as.traceAlignment();\r
+\r
         as.printAlignment(System.out);\r
         scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
         totscore = totscore + scores[i][j];\r
 \r
         textarea.append(as.getOutput());\r
-\r
         seq = new Sequence(as.getS1().getName(),\r
                            as.getAStr1(),\r
-                           as.getS1().getStart(), as.getS1().getEnd()\r
+                           as.getS1().getStart(),\r
+                           as.getS1().getEnd()\r
             );\r
         sequences.addElement(seq);\r
 \r
         seq = new Sequence(as.getS2().getName(),\r
                            as.getAStr2(),\r
-                           as.getS2().getStart(), as.getS2().getEnd()\r
-            );\r
-\r
+                           as.getS2().getStart(),\r
+                           as.getS2().getEnd());\r
         sequences.addElement(seq);\r
       }\r
     }\r
 \r
     if (count > 2)\r
     {\r
+      System.out.println(\r
+          "Pairwise alignment scaled similarity score matrix\n");\r
+\r
+      for (int i = 0; i < count; i++)\r
+      {\r
+        jalview.util.Format.print(System.out, "%s \n",\r
+                                  ("" + i) + " " +\r
+                                  seqs[i].getName());\r
+      }\r
+\r
+      System.out.println("\n");\r
+\r
       for (int i = 0; i < count; i++)\r
       {\r
         for (int j = 0; j < i; j++)\r
@@ -96,9 +122,10 @@ public class PairwiseAlignPanel
                                     scores[i][j] / totscore);\r
         }\r
       }\r
+\r
+      System.out.println("\n");\r
     }\r
   }\r
-\r
   public void actionPerformed(ActionEvent evt)\r
   {\r
     if(evt.getSource()==viewInEditorButton)\r
@@ -116,7 +143,7 @@ public class PairwiseAlignPanel
     }\r
 \r
     new AlignFrame(new Alignment(seq),\r
-                                   ap.alignFrame.applet,\r
+                                   ap.av.applet,\r
                                    "Pairwise Aligned Sequences",\r
                                    false);\r
 \r