From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 26 Nov 2014 16:58:04 +0000 (+0000)
Subject: Merge branch 'bug/JAL-207_pairwise-alignment-context-loss' into develop
X-Git-Tag: Jalview_2_9~141
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e2e6110281b107d8cc5d79ca567f830f7b06e17e;hp=249af5c14861435f049c2191cac8c84592ec9dc6;p=jalview.git

Merge branch 'bug/JAL-207_pairwise-alignment-context-loss' into develop
---

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 9afc70b..5a3b56c 100644
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -20,15 +20,21 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
+
 public class PairwiseAlignPanel extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
@@ -89,13 +95,8 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.addElement(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.addElement(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq1());
       }
     }
 
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index dcddf88..69b6ba6 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -20,14 +20,16 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
 
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+
 /**
  * DOCUMENT ME!
  * 
@@ -97,13 +99,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.add(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.add(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq1());
       }
     }