X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=06e93d7a4322aea1f8b8feb2267d0a071e4f2c22;hb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;hp=416be69750e1e2b52652b27b4b9ff198cdb87dec;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 416be69..06e93d7 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -61,6 +61,13 @@ public interface AlignmentI
     public Vector getSequences();
 
     /**
+     * Gets sequences as a SequenceI[]
+     *
+     * @return All sequences in alignment.
+     */
+    public SequenceI [] getSequencesArray();
+
+    /**
      * Find a specific sequence in this alignment.
      *
      * @param i Index of required sequence.
@@ -104,17 +111,8 @@ public interface AlignmentI
      * @param start Start index of columns to delete.
      * @param end End index to columns to delete.
      */
-    public void deleteColumns(int start, int end);
+    public void deleteColumns(SequenceI seqs [], int start, int end);
 
-    /**
-     * Deletes all residues in every sequence of alignment within given columns.
-     *
-     * @param seq1 Index of first sequence to delete columns from.
-     * @param seq2 Index of last sequence to delete columns from.
-     * @param start Start index of columns to delete.
-     * @param end End index of columns to delete.
-     */
-    public void deleteColumns(int seq1, int seq2, int start, int end);
 
     /**
      * Finds sequence in alignment using sequence name as query.
@@ -125,14 +123,6 @@ 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.
@@ -162,25 +152,7 @@ public interface AlignmentI
      */
     public void removeGaps();
 
-    /**
-     * Removes redundant sequences from alignment.
-     *
-     * @param threshold Remove all sequences above the given threshold.
-     * @param sel Set of sequences which will have redundant sequences removed from.
-     *
-     * @return All sequences below redundancy threshold.
-     */
-    public Vector removeRedundancy(float threshold, Vector sel);
 
-    /**
-     * Finds group that sequence at index i in alignment is part of.
-     *
-     * @param i Index in alignment.
-     *
-     * @return First group found for sequence at position i. WARNING :
-     * Sequences may be members of several groups. This method is incomplete.
-     */
-    public SequenceGroup findGroup(int i);
 
     /**
      * Finds group that given sequence is part of.
@@ -227,34 +199,15 @@ 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.
-     */
-    public void removeSuperGroup(SuperGroup sg);
-
-    /**
-     * Finds any SuperGroup that a given SequenceGroup may be part of.
-     *
-     * @param sg SequenceGroup to search for.
-     *
-     * @return SuperGroup that contains the given SequenceGroup.
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg);
 
     /**
      * 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.
      *
@@ -289,4 +242,37 @@ public interface AlignmentI
      * @return DOCUMENT ME!
      */
     public Vector getAAFrequency();
+
+    /**
+     * Returns true if alignment is nucleotide sequence
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isNucleotide();
+
+    /**
+     * Set true if the alignment is a nucleotide sequence
+     *
+     * @return
+     */
+    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();
+    /**
+     * Compact representation of alignment
+     * @return CigarArray
+     */
+    public CigarArray getCompactAlignment();
 }