Works on strings, not seqs

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index d3dfc9b..464abb0 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -98,7 +98,6 @@ public class AlignSeq
     String type;\r
     Runtime rt;\r
 \r
-\r
     /**\r
      * Creates a new AlignSeq object.\r
      *\r
@@ -109,7 +108,24 @@ public class AlignSeq
     public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
     {\r
         rt = Runtime.getRuntime();\r
-        SeqInit(s1, s2, type);\r
+        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);\r
+    }\r
+\r
+    /**\r
+     * Creates a new AlignSeq object.\r
+     *\r
+     * @param s1 DOCUMENT ME!\r
+     * @param s2 DOCUMENT ME!\r
+     * @param type DOCUMENT ME!\r
+     */\r
+    public AlignSeq(SequenceI s1,\r
+                    String string1,\r
+                    SequenceI s2,\r
+                    String string2,\r
+                    String type)\r
+    {\r
+        rt = Runtime.getRuntime();\r
+        SeqInit(s1, string1, s2,  string2,  type);\r
     }\r
 \r
     /**\r
@@ -239,10 +255,14 @@ public class AlignSeq
      * @param s2 DOCUMENT ME!\r
      * @param type DOCUMENT ME!\r
      */\r
-    public void SeqInit(SequenceI s1, SequenceI s2, String type)\r
+    public void SeqInit(SequenceI s1,\r
+                        String string1,\r
+                        SequenceI s2,\r
+                        String string2,\r
+                        String type)\r
     {\r
-        s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());\r
-        s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());\r
+        s1str = extractGaps(jalview.util.Comparison.GapChars, string1);\r
+        s2str = extractGaps(jalview.util.Comparison.GapChars, string2);\r
 \r
         this.s1 = s1;\r
         this.s2 = s2;\r