JAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(AlignmentAnnotation ala) - calls...

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5fb16d6..cea1c5b 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -48,15 +48,29 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 
-   * Calculates the maximum width of the alignment, including gaps.
+   * Answers the width of the alignment, including gaps, that is, the length of
+   * the longest sequence, or -1 if there are no sequences. Avoid calling this
+   * method repeatedly where possible, as it has to perform a calculation. Note
+   * that this width includes any hidden columns.
    * 
-   * @return Greatest sequence length within alignment, or -1 if no sequences
-   *         present
+   * @return
+   * @see AlignmentI#getVisibleWidth()
    */
   @Override
   int getWidth();
 
   /**
+   * 
+   * Answers the visible width of the alignment, including gaps, that is, the
+   * length of the longest sequence, excluding any hidden columns. Answers -1 if
+   * there are no sequences. Avoid calling this method repeatedly where
+   * possible, as it has to perform a calculation.
+   * 
+   * @return
+   */
+  int getVisibleWidth();
+
+  /**
    * Calculates if this set of sequences (visible and invisible) are all the
    * same length
    * 
@@ -504,8 +518,6 @@ public interface AlignmentI extends AnnotatedCollectionI
    *          - null or specific sequence reference
    * @param groupRef
    *          - null or specific group reference
-   * @param method
-   *          - CalcId for the annotation (must match)
    * 
    * @return existing annotation matching the given attributes
    */
@@ -513,6 +525,17 @@ public interface AlignmentI extends AnnotatedCollectionI
           boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
 
   /**
+   * like findOrCreateAnnotation - looks for an existing alignment annotation
+   * row with matching name, calcId, sequenceRef, groupRef and autoCalculated
+   * flag and updates it from the annotation. If none is found the annotation is
+   * added directly.
+   * 
+   * @param ala
+   * @return ala or the annotation row that was updated.
+   */
+  AlignmentAnnotation updateFromOrCopyAnnotation(AlignmentAnnotation ala);
+
+  /**
    * move the given group up or down in the alignment by the given number of
    * rows. Implementor assumes given group is already present on alignment - no
    * recalculations are triggered.
@@ -581,11 +604,23 @@ public interface AlignmentI extends AnnotatedCollectionI
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
   /**
-   * Set the hidden columns collection on the alignment
+   * Set the hidden columns collection on the alignment. Answers true if the
+   * hidden column selection changed, else false.
    * 
    * @param cols
+   * @return
    */
-  public void setHiddenColumns(HiddenColumns cols);
+  public boolean setHiddenColumns(HiddenColumns cols);
+
+  /**
+   * Insert a sequence at a position in an alignment
+   * 
+   * @param i
+   *          The index of the position.
+   * @param snew
+   *          The new sequence.
+   */
+  void insertSequenceAt(int i, SequenceI snew);
 
   /**
    * Set the first sequence as representative and hide its insertions. Typically
@@ -607,5 +642,4 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   public HiddenColumns propagateInsertions(SequenceI profileseq,
           AlignmentView input);
-
 }