From 2732a03c243a8d57c559e8e33c0e36bcd5d57624 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Nov 2005 14:20:37 +0000
Subject: [PATCH] AlignSeq takes printstream as arg

---
 src/jalview/analysis/AlignSeq.java            |    6 ++++--
 src/jalview/analysis/NJTree.java              |    4 ++--
 src/jalview/appletgui/PairwiseAlignPanel.java |    2 +-
 src/jalview/gui/AlignFrame.java               |    5 -----
 src/jalview/gui/PairwiseAlignPanel.java       |    2 +-
 src/jalview/gui/SeqCanvas.java                |    6 ++++++
 6 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 9d8f008..092928f 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -406,7 +406,7 @@ public class AlignSeq
     /**
      * DOCUMENT ME!
      */
-    public void printAlignment()
+    public void printAlignment(java.io.PrintStream os)
     {
         // Find the biggest id length for formatting purposes
         int maxid = s1.getName().length();
@@ -499,7 +499,9 @@ public class AlignSeq
         pid = pid / (float) (aseq1.length - count) * 100;
         output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
 
-        System.out.println(output.toString());
+        try{
+          os.println(output.toString());
+        }catch(Exception ex){}
     }
 
     /**
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 46a2ced..0683265 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -375,7 +375,7 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
         float dist)
     {
-     
+
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
 
@@ -658,7 +658,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
                     as.calcScoreMatrix();
                     as.traceAlignment();
-                    as.printAlignment();
+                    as.printAlignment(System.out);
                     distance[i][j] = (float) as.maxscore;
 
                     if (max < distance[i][j])
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index d5243e3..e187663 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -54,7 +54,7 @@ public class PairwiseAlignPanel
 
         as.calcScoreMatrix();
         as.traceAlignment();
-        as.printAlignment();
+        as.printAlignment(System.out);
         scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0cef877..dcb3f44 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -162,11 +162,6 @@ public class AlignFrame
 
   }
 
-  public AlignViewport getViewport()
-  {
-    return viewport;
-  }
-
 
   /*
    Added so Castor Mapping file can obtain Jalview Version
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 6509063..31efd84 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -77,7 +77,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                         (SequenceI) selsubset.elementAt(j), "pep");
                 as.calcScoreMatrix();
                 as.traceAlignment();
-                as.printAlignment();
+                as.printAlignment(System.out);
                 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
                 totscore = totscore + scores[i][j];
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c3972ee..f86441a 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -81,6 +81,12 @@ public class SeqCanvas extends JComponent
       pdbViewer = pc;
     }
 
+    public AlignViewport getViewport()
+    {
+      return av;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
-- 
1.7.10.2