sequences are private in SequenceGroup

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 416be69..dbf3c35 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -61,6 +61,13 @@ public interface AlignmentI
     public Vector getSequences();\r
 \r
     /**\r
+     * Gets sequences as a SequenceI[]\r
+     *\r
+     * @return All sequences in alignment.\r
+     */\r
+    public SequenceI [] getSequencesArray();\r
+\r
+    /**\r
      * Find a specific sequence in this alignment.\r
      *\r
      * @param i Index of required sequence.\r
@@ -125,14 +132,6 @@ 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
@@ -162,25 +161,7 @@ public interface AlignmentI
      */\r
     public void removeGaps();\r
 \r
-    /**\r
-     * Removes redundant sequences from alignment.\r
-     *\r
-     * @param threshold Remove all sequences above the given threshold.\r
-     * @param sel Set of sequences which will have redundant sequences removed from.\r
-     *\r
-     * @return All sequences below redundancy threshold.\r
-     */\r
-    public Vector removeRedundancy(float threshold, Vector sel);\r
 \r
-    /**\r
-     * Finds group that sequence at index i in alignment is part of.\r
-     *\r
-     * @param i Index in alignment.\r
-     *\r
-     * @return First group found for sequence at position i. WARNING :\r
-     * Sequences may be members of several groups. This method is incomplete.\r
-     */\r
-    public SequenceGroup findGroup(int i);\r
 \r
     /**\r
      * Finds group that given sequence is part of.\r
@@ -227,34 +208,15 @@ 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
-     */\r
-    public void removeSuperGroup(SuperGroup sg);\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
-     */\r
-    public SuperGroup getSuperGroup(SequenceGroup sg);\r
 \r
     /**\r
      * Adds a new AlignmentAnnotation to this alignment\r
      */\r
     public void addAnnotation(AlignmentAnnotation aa);\r
 \r
+\r
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
+\r
     /**\r
      * Deletes a specific AlignmentAnnotation from the alignment.\r
      *\r
@@ -289,4 +251,33 @@ public interface AlignmentI
      * @return DOCUMENT ME!\r
      */\r
     public Vector getAAFrequency();\r
+\r
+    /**\r
+     * Returns true if alignment is nucleotide sequence\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public boolean isNucleotide();\r
+\r
+    /**\r
+     * Set true if the alignment is a nucleotide sequence\r
+     *\r
+     * @return\r
+     */\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