X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=8ddba6c56b9a6e4de36b7cecf56711fd9fd77b34;hb=6fc163433164d93374330fa0a603eea1e1fd42b3;hp=f1238ffda2a975f196f890d8a62594051ef76a40;hpb=36dceb54710feb97a81f4bd69ad051f316141dc3;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index f1238ff..8ddba6c 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -41,7 +41,8 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
-   * @return Greatest sequence length within alignment.
+   * @return Greatest sequence length within alignment, or -1 if no sequences
+   *         present
    */
   @Override
   int getWidth();
@@ -107,11 +108,14 @@ public interface AlignmentI extends AnnotatedCollectionI
    * Used to set a particular index of the alignment with the given sequence.
    * 
    * @param i
-   *          Index of sequence to be updated.
+   *          Index of sequence to be updated. if i>length, sequence will be
+   *          added to end, with no intervening positions.
    * @param seq
-   *          New sequence to be inserted.
+   *          New sequence to be inserted. The existing sequence at position i
+   *          will be replaced.
+   * @return existing sequence (or null if i>current length)
    */
-  void setSequenceAt(int i, SequenceI seq);
+  SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
    * Deletes a sequence from the alignment
@@ -363,14 +367,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   void addCodonFrame(AlignedCodonFrame codons);
 
   /**
-   * add a set of aligned codons mappings for this alignment, apart from any
-   * duplicates which are ignored
-   * 
-   * @param codons
-   */
-  void addCodonFrames(Iterable<AlignedCodonFrame> codons);
-
-  /**
    * remove a particular codon frame reference from this alignment
    * 
    * @param codons
@@ -430,7 +426,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @param results
    * @return -1 or index of sequence in alignment
    */
-  int findIndex(SearchResults results);
+  int findIndex(SearchResultsI results);
 
   /**
    * append sequences and annotation from another alignment object to this one.
@@ -560,4 +556,16 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
+  /**
+   * resolve a contact list instance (if any) associated with the annotation row
+   * and column position
+   * 
+   * @param _aa
+   * @param column
+   * @return
+   */
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
+
+  AlignmentAnnotation addContactList(ContactMatrixI cm);
 }