Reduced jar size by 20%

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

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 55cf2cc..26836cd 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -25,22 +25,29 @@ 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
-  AlignViewport av;\r
+  AlignmentPanel ap;\r
 \r
-  public PairwiseAlignPanel(AlignViewport av)\r
+  public PairwiseAlignPanel(AlignmentPanel ap)\r
   {\r
-    super();\r
-    this.av = av;\r
-    float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().\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
     double totscore = 0;\r
-    int count = av.getSelectionGroup().getSize();\r
+    int count = ap.av.getSelectionGroup().getSize();\r
 \r
     int acount = 0;\r
     for (int i = 1; i < count; i++)\r
@@ -48,13 +55,13 @@ public class PairwiseAlignPanel
       for (int j = 0; j < i; j++)\r
       {\r
         acount++;\r
-        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
-                                   av.getSelectionGroup().getSequenceAt(j),\r
+        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
+                                   ap.av.getSelectionGroup().getSequenceAt(j),\r
                                    "pep");\r
 \r
         as.calcScoreMatrix();\r
         as.traceAlignment();\r
-        as.printAlignment();\r
+        as.printAlignment(System.out);\r
         scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
         totscore = totscore + scores[i][j];\r
 \r
@@ -78,7 +85,13 @@ public class PairwiseAlignPanel
     }\r
   }\r
 \r
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    if(evt.getSource()==viewInEditorButton)\r
+      viewInEditorButton_actionPerformed();\r
+  }\r
+\r
+  protected void viewInEditorButton_actionPerformed()\r
   {\r
 \r
     Sequence[] seq = new Sequence[sequences.size()];\r
@@ -88,11 +101,28 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);\r
     }\r
 \r
-    AlignFrame af = new AlignFrame(new Alignment(seq));\r
-    jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",\r
-                                     AlignFrame.NEW_WINDOW_WIDTH,\r
-                                     AlignFrame.NEW_WINDOW_HEIGHT);\r
+    new AlignFrame(new Alignment(seq),\r
+                                   ap.alignFrame.applet,\r
+                                   "Pairwise Aligned Sequences");\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