2.08, not 2.07

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 4399b39..7fe4627 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -125,14 +125,6 @@ public interface AlignmentI
      */\r
     public SequenceI findName(String name);\r
 \r
-    /**\r
-     * Finds sequence in alignment using full displayId as query.\r
-     *\r
-     * @param name displayId, ie <em>NAME/25-100</em>\r
-     *\r
-     * @return Sequence matching query, if found. If not found returns null.\r
-     */\r
-    public SequenceI findbyDisplayId(String name);\r
 \r
     /**\r
      * Finds index of a given sequence in the alignment.\r
@@ -227,33 +219,19 @@ public interface AlignmentI
      */\r
     public void deleteAllGroups();\r
 \r
-    /**\r
-     * Adds a super group. A SuperGroup is a group of groups.\r
-     *\r
-     * @param sg Adds a new SuperGroup to alignment\r
-     */\r
-    public void addSuperGroup(SuperGroup sg);\r
 \r
     /**\r
-     * Removes SuperGroup from alignment.\r
-     *\r
-     * @param sg This SuperGroup will be deleted from alignment.\r
+     * Adds a new AlignmentAnnotation to this alignment\r
      */\r
-    public void removeSuperGroup(SuperGroup sg);\r
+    public void addAnnotation(AlignmentAnnotation aa);\r
 \r
     /**\r
-     * Finds any SuperGroup that a given SequenceGroup may be part of.\r
-     *\r
-     * @param sg SequenceGroup to search for.\r
-     *\r
-     * @return SuperGroup that contains the given SequenceGroup.\r
+     * Adds a new AlignmentAnnotation to this alignment,\r
+     *  associated to Sequence starting at sequence index\r
      */\r
-    public SuperGroup getSuperGroup(SequenceGroup sg);\r
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
 \r
-    /**\r
-     * Adds a new AlignmentAnnotation to this alignment\r
-     */\r
-    public void addAnnotation(AlignmentAnnotation aa);\r
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
 \r
     /**\r
      * Deletes a specific AlignmentAnnotation from the alignment.\r
@@ -304,4 +282,18 @@ public interface AlignmentI
      */\r
     public void setNucleotide(boolean b);\r
 \r
+\r
+    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
+    public HiddenSequences getHiddenSequences();\r
+\r
 }\r