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 d5243e3..b8a15d5 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -25,48 +25,95 @@ import java.awt.event.*;
 \r
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
+import java.awt.*;\r
 \r
 public class PairwiseAlignPanel\r
-    extends GPairwiseAlignPanel\r
+    extends Panel implements ActionListener\r
 {\r
   Vector sequences = new Vector();\r
   AlignmentPanel ap;\r
 \r
   public PairwiseAlignPanel(AlignmentPanel ap)\r
   {\r
-    super();\r
+    try\r
+    {\r
+      jbInit();\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\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();\r
+    int count = ap.av.getSelectionGroup().getSize(false);\r
+\r
+    Sequence seq;\r
 \r
-    int acount = 0;\r
     for (int i = 1; i < count; i++)\r
     {\r
       for (int j = 0; j < i; j++)\r
       {\r
-        acount++;\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
+          continue;\r
+        }\r
 \r
         as.calcScoreMatrix();\r
         as.traceAlignment();\r
-        as.printAlignment();\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
-        sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));\r
-        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));\r
-\r
+        seq = new Sequence(as.getS1().getName(),\r
+                           as.getAStr1(),\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(),\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
@@ -75,10 +122,17 @@ public class PairwiseAlignPanel
                                     scores[i][j] / totscore);\r
         }\r
       }\r
+\r
+      System.out.println("\n");\r
     }\r
   }\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    if(evt.getSource()==viewInEditorButton)\r
+      viewInEditorButton_actionPerformed();\r
+  }\r
 \r
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
+  protected void viewInEditorButton_actionPerformed()\r
   {\r
 \r
     Sequence[] seq = new Sequence[sequences.size()];\r
@@ -89,9 +143,28 @@ public class PairwiseAlignPanel
     }\r
 \r
     new AlignFrame(new Alignment(seq),\r
-                                   ap.alignFrame.applet,\r
-                                   "Pairwise Aligned Sequences");\r
+                                   ap.av.applet,\r
+                                   "Pairwise Aligned Sequences",\r
+                                   false);\r
 \r
   }\r
+  protected ScrollPane scrollPane = new ScrollPane();\r
+  protected TextArea textarea = new TextArea();\r
+  protected Button viewInEditorButton = new Button();\r
+  Panel jPanel1 = new Panel();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+  private void jbInit() throws Exception {\r
+      this.setLayout(borderLayout1);\r
+      textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
+      textarea.setText("");\r
+      viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
+      viewInEditorButton.setLabel("View in alignment editor");\r
+      viewInEditorButton.addActionListener(this);\r
+      this.add(scrollPane, BorderLayout.CENTER);\r
+      scrollPane.add(textarea);\r
+      this.add(jPanel1, BorderLayout.SOUTH);\r
+      jPanel1.add(viewInEditorButton, null);\r
+  }\r
 \r
 }\r