X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=7fe4627294d84d8674dadf08c25a4f4cb7b5bc86;hb=9175e97621ea51c3e98145545b3957842126c09e;hp=4399b39f04f0bc84127f701921da117637d19acf;hpb=bb99b11825ccc8f9d7dd7b4b0dfcc2f64ebe0b75;p=jalview.git

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