X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=68903bb11ccf073a71893e6b2476322466963c04;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=ec35124c914e8f0357ed6d32ba1bdb3dd3ed5922;hpb=ef23315db576f5451de0fcb850f645c5db222b20;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index ec35124..68903bb 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
@@ -36,6 +37,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return Greatest sequence length within alignment.
    */
+  @Override
   public int getWidth();
 
   /**
@@ -56,11 +58,12 @@ public interface AlignmentI extends AnnotatedCollectionI
   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 +178,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   /**
    * 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 +239,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return array of AlignmentAnnotation objects
    */
+  @Override
   public AlignmentAnnotation[] getAlignmentAnnotation();
 
   /**
@@ -434,13 +438,42 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * search for or create a specific annotation row on the alignment
-   *  
-   * @param method - CalcId for the annotation (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 
-   * @return existing annotation matching the given attributes 
-   */
-  public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
-          SequenceI seqRef, SequenceGroup groupRef);
+   * 
+   * @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);
 }