javadoc

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index b4075a0..d9791f1 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -122,7 +122,7 @@ public interface AlignmentI
    * @param s
    *                Sequence to look for.
    * 
-   * @return Index of sequence within the alignment.
+   * @return Index of sequence within the alignment or -1 if not found
    */
   public int findIndex(SequenceI s);
 
@@ -359,4 +359,26 @@ public interface AlignmentI
    */
   public SequenceI findName(SequenceI startAfter, String token, boolean b);
 
+  /**
+   * find first sequence in alignment which is involved in the given search result object
+   * @param results
+   * @return -1 or index of sequence in alignment
+   */
+  public int findIndex(SearchResults results);
+
+  /**
+   * append sequences and annotation from another alignment object to this one.
+   * Note: this is a straight transfer of object references, and may result in 
+   * toappend's dependent data being transformed to fit the alignment (changing gap characters, etc...).
+   * If you are uncertain, use the copy Alignment copy constructor to create a new version
+   * which can be appended without side effect.
+   * @param toappend - the alignment to be appended. 
+   */
+  public void append(AlignmentI toappend);
+  /**
+   * Justify the sequences to the left or right by deleting and inserting gaps before the initial residue or after the terminal residue
+   * @param right true if alignment padded to right, false to justify to left
+   * @return true if alignment was changed
+   */
+  public boolean justify(boolean right);
 }