X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=c15bb99b84c393da6f4b0afacc731f3aa5c1f95c;hb=90ad4273c7105b7763247192e1c6739eed30ba4c;hp=8194bf0fa4a0c77534d63d1daec30fd392cfd15a;hpb=72738726bce0733f652a5dbcc9db7c5a13bc2d80;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 8194bf0..c15bb99 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -305,7 +305,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return Alignment containing dataset sequences or null of this is a
    *         dataset.
    */
-  Alignment getDataset();
+  AlignmentI getDataset();
 
   /**
    * Set the associated dataset for the alignment, or create one.
@@ -313,7 +313,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @param dataset
    *          The dataset alignment or null to construct one.
    */
-  void setDataset(Alignment dataset);
+  void setDataset(AlignmentI dataset);
 
   /**
    * pads sequences with gaps (to ensure the set looks like an alignment)
@@ -375,12 +375,12 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return
    */
-  Set<AlignedCodonFrame> getCodonFrames();
+  List<AlignedCodonFrame> getCodonFrames();
 
   /**
-   * Set the codon frame mappings (replacing any existing set).
+   * Set the codon frame mappings (replacing any existing list).
    */
-  void setCodonFrames(Set<AlignedCodonFrame> acfs);
+  void setCodonFrames(List<AlignedCodonFrame> acfs);
 
   /**
    * get codon frames involving sequenceI
@@ -473,9 +473,8 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return existing annotation matching the given attributes
    */
-  AlignmentAnnotation findOrCreateAnnotation(String name,
-          String calcId, boolean autoCalc, SequenceI seqRef,
-          SequenceGroup groupRef);
+  AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+          boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
 
   /**
    * move the given group up or down in the alignment by the given number of
@@ -525,4 +524,32 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public boolean hasValidSequence();
+
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  int realiseMappings(List<SequenceI> seqs);
+
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+
+  /**
+   * Calculate the visible start and end index of an alignment. The result is
+   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+   * 
+   * @param hiddenCols
+   * @return
+   */
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
 }