refactored Alignframe padGaps code to Alignment and Added AlignmentI method.

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f0aeed9..e9af7f4 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -734,4 +734,21 @@ public class Alignment implements AlignmentI
       return dataset;\r
     }\r
 \r
+    public boolean padGaps() {\r
+      boolean modified=false;\r
+      int Width = getWidth();\r
+      SequenceI current;\r
+      for (int i = 0; i < sequences.size();\r
+           i++)\r
+      {\r
+        current = getSequenceAt(i);\r
+\r
+        if (current.getLength() < Width)\r
+        {\r
+          current.insertCharAt(Width - 1, gapCharacter);\r
+          modified=true;\r
+        }\r
+      }\r
+      return modified;\r
+    }\r
 }\r