X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=64dcabb51b6ed1580be9563426aef487f24e672e;hb=3d4951e92e9a212eb9f6857bbcc4056bf69b36a3;hp=7810f2bfdbe2549bed64697966d640d7f8b3bc5c;hpb=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7810f2b..64dcabb 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -22,7 +22,7 @@ import java.util.*;
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
-public interface AlignmentI
+public interface AlignmentI extends AnnotatedCollectionI
 {
   /**
    * Calculates the number of sequences in an alignment
@@ -36,6 +36,7 @@ public interface AlignmentI
    * 
    * @return Greatest sequence length within alignment.
    */
+  @Override
   public int getWidth();
 
   /**
@@ -56,11 +57,12 @@ public interface AlignmentI
   public boolean isAligned(boolean includeHidden);
 
   /**
-   * Gets sequences as a Vector
+   * Gets sequences as a Synchronized collection
    * 
    * @return All sequences in alignment.
    */
-  public Vector getSequences();
+  @Override
+  public List<SequenceI> getSequences();
 
   /**
    * Gets sequences as a SequenceI[]
@@ -175,9 +177,9 @@ public interface AlignmentI
   /**
    * Get all the groups associated with this alignment.
    * 
-   * @return All groups as a Vector.
+   * @return All groups as a list.
    */
-  public Vector getGroups();
+  public List<SequenceGroup> getGroups();
 
   /**
    * Deletes all groups from this alignment.
@@ -236,6 +238,7 @@ public interface AlignmentI
    * 
    * @return array of AlignmentAnnotation objects
    */
+  @Override
   public AlignmentAnnotation[] getAlignmentAnnotation();
 
   /**
@@ -431,4 +434,45 @@ public interface AlignmentI
    * @param i
    */
   public void addAnnotation(AlignmentAnnotation consensus, int i);
+
+  /**
+   * search for or create a specific annotation row on the alignment
+   * 
+   * @param name
+   *          name for annotation (must match)
+   * @param calcId
+   *          calcId for the annotation (null or must match)
+   * @param autoCalc
+   *          - value of autocalc flag for the annotation
+   * @param seqRef
+   *          - 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
+   */
+  public 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
+   * rows. Implementor assumes given group is already present on alignment - no
+   * recalculations are triggered.
+   * 
+   * @param sg
+   * @param map
+   * @param up
+   * @param i
+   */
+  public void moveSelectedSequencesByOne(SequenceGroup sg,
+          Map<SequenceI, SequenceCollectionI> map, boolean up);
+
+  /**
+   * validate annotation after an edit and update any alignment state flags accordingly
+   * @param alignmentAnnotation
+   */
+  public void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
 }