parseResult takes the title as string. usually null

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2a39847..ebd95d9 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -248,6 +248,14 @@ public interface AlignmentI
     public void addAnnotation(AlignmentAnnotation aa);\r
 \r
     /**\r
+     * Adds a new AlignmentAnnotation to this alignment,\r
+     *  associated to Sequence starting at sequence index\r
+     */\r
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
+\r
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
+\r
+    /**\r
      * Deletes a specific AlignmentAnnotation from the alignment.\r
      *\r
      * @param aa DOCUMENT ME!\r
@@ -300,6 +308,13 @@ public interface AlignmentI
     public Alignment getDataset();\r
 \r
     public void setDataset(Alignment dataset);\r
+    /**\r
+     * pads sequences with gaps (to ensure the set looks like an alignment)\r
+     * @return boolean true if alignment was modified\r
+     */\r
+    public boolean padGaps();\r
+\r
+     public void adjustSequenceAnnotations();\r
 \r
 \r
 }\r