Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index 95afb3d..e2bb5a6 100644 (file)
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
 
@@ -22,25 +25,62 @@ import java.util.Map;
 
 public interface SequenceCollectionI
 {
+  /**
+   * 
+   * @return (visible) sequences in this collection. This may be a direct
+   *         reference to the collection so not thread safe
+   */
   List<SequenceI> getSequences();
 
+  /**
+   * FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
+   * contract!
+   * 
+   * @param hiddenReps
+   * @return the full set of sequences in this collection, including any
+   *         sequences represented by sequences in the collection.
+   */
   List<SequenceI> getSequences(
           Map<SequenceI, SequenceCollectionI> hiddenReps);
+
   int getWidth();
+
   /**
    * 
    * @return true if getSeqrep doesn't return null
    */
   boolean hasSeqrep();
+
   /**
    * get the reference or representative sequence within this collection
+   * 
    * @return null or the current reference sequence
    */
   SequenceI getSeqrep();
+
   /**
-   * set the reference or representative sequence for this collection. 
-   * Reference is assumed to be present within the collection.
+   * set the reference or representative sequence for this collection. Reference
+   * is assumed to be present within the collection.
+   * 
    * @return
    */
   void setSeqrep(SequenceI refseq);
+
+  /**
+   * @return the first column included in this collection. Runs from 0<=i<N_cols
+   */
+  int getStartRes();
+
+  /**
+   * 
+   * @return the last column in this collection. Runs from 0<=i<N_cols
+   */
+  int getEndRes();
+
+  /**
+   * Answers true if sequence data is nucleotide (according to some heuristic)
+   * 
+   * @return
+   */
+  boolean isNucleotide();
 }