X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=7386d4b6677648265bb1cebb9421a84ab9b546b3;hb=3714de3baf8f4ee3fc11e93a0fdc8bee96c1594f;hp=b076ea78c41264265241eb0c79d258f2fe27b977;hpb=621b23ed6783d2c4c7caaf6d58151217b2fa4f1d;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index b076ea7..7386d4b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -24,7 +24,6 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.function.Consumer;
 
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
@@ -49,15 +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
    * 
@@ -505,8 +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
    */
@@ -581,8 +592,43 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
-  public void setHiddenColumns(HiddenColumns cols);
+  /**
+   * Set the hidden columns collection on the alignment. Answers true if the
+   * hidden column selection changed, else false.
+   * 
+   * @param cols
+   * @return
+   */
+  public boolean setHiddenColumns(HiddenColumns cols);
 
-  public void forEachSequence(Consumer<SequenceI> c, int start, int end);
+  /**
+   * 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
+   * used when loading JPred files.
+   */
+  public void setupJPredAlignment();
 
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @param input
+   *          alignment view where sequence corresponding to profileseq is first
+   *          entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input);
 }