pdb files are global to all alignments with new mapping mechanism.

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index a81a965..ab198c1 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -157,6 +157,7 @@ public interface AlignmentI
    */
   public Vector getGroups();
 
+
   /**
    * Deletes all groups from this alignment.
    */
@@ -166,53 +167,64 @@ public interface AlignmentI
    * Adds a new AlignmentAnnotation to this alignment
    */
   public void addAnnotation(AlignmentAnnotation aa);
-
+  /**
+   * moves annotation to a specified index in alignment annotation display stack
+   * @param aa the annotation object to be moved
+   * @param index the destination position
+   */
   public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
   /**
    * Deletes a specific AlignmentAnnotation from the alignment.
    *
-   * @param aa DOCUMENT ME!
+   * @param aa the annotation to delete
    */
   public void deleteAnnotation(AlignmentAnnotation aa);
 
   /**
-   * DOCUMENT ME!
+   * Get the annotation associated with this alignment
    *
-   * @return DOCUMENT ME!
+   * @return array of AlignmentAnnotation objects
    */
   public AlignmentAnnotation[] getAlignmentAnnotation();
 
   /**
-   * DOCUMENT ME!
+   * Change the gap character used in this alignment to 'gc'
    *
-   * @param gc DOCUMENT ME!
+   * @param gc the new gap character.
    */
   public void setGapCharacter(char gc);
 
   /**
-   * DOCUMENT ME!
+   * Get the gap character used in this alignment
    *
-   * @return DOCUMENT ME!
+   * @return gap character
    */
   public char getGapCharacter();
 
   /**
-   * Returns true if alignment is nucleotide sequence
+   * Test for all nucleotide alignment
    *
-   * @return DOCUMENT ME!
+   * @return true if alignment is nucleotide sequence
    */
   public boolean isNucleotide();
 
   /**
-   * Set true if the alignment is a nucleotide sequence
+   * Set alignment to be a nucleotide sequence
    *
-   * @return
    */
   public void setNucleotide(boolean b);
 
+  /**
+   * Get the associated dataset for the alignment.
+   * @return Alignment containing dataset sequences or null of this is a dataset.
+   */
   public Alignment getDataset();
 
+  /**
+   * Set the associated dataset for the alignment, or create one.
+   * @param dataset The dataset alignment or null to construct one. 
+   */
   public void setDataset(Alignment dataset);
 
   /**