From: jprocter <Jim Procter>
Date: Wed, 11 Jan 2006 13:27:21 +0000 (+0000)
Subject: refactored Alignframe padGaps code to Alignment and Added AlignmentI method.
X-Git-Tag: Root_VamJalview_2_07b+~219
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=20403dbf83a2caa650a4ccd37f5a6dae7d0bd0f3;p=jalview.git

refactored Alignframe padGaps code to Alignment and Added AlignmentI method.
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f0aeed9..e9af7f4 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -734,4 +734,21 @@ public class Alignment implements AlignmentI
       return dataset;
     }
 
+    public boolean padGaps() {
+      boolean modified=false;
+      int Width = getWidth();
+      SequenceI current;
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, gapCharacter);
+          modified=true;
+        }
+      }
+      return modified;
+    }
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2a39847..59610b3 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -300,6 +300,11 @@ public interface AlignmentI
     public Alignment getDataset();
 
     public void setDataset(Alignment dataset);
+    /**
+     * pads sequences with gaps (to ensure the set looks like an alignment)
+     * @return boolean true if alignment was modified
+     */
+    public boolean padGaps();
 
 
 }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d2b5fc8..bfdc40b 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1259,22 +1259,8 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-
-    SequenceI current;
-    int Width = viewport.getAlignment().getWidth();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size();
-         i++)
-    {
-      current = viewport.getAlignment().getSequenceAt(i);
-
-      if (current.getLength() < Width)
-      {
-        current.insertCharAt(Width - 1, viewport.getGapCharacter());
-      }
-    }
-
-    alignmentChanged();
+    if (viewport.getAlignment().padGaps())
+      alignmentChanged();
   }
 
   /**