Merge branch 'releases/Release_2_10_0_Branch'

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

diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index db79b4d..afd4094 100644 (file)
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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;
 
 import java.util.List;
@@ -6,7 +26,42 @@ import java.util.Map;
 public interface SequenceCollectionI
 {
   List<SequenceI> getSequences();
-  List<SequenceI> getSequences(Map<SequenceI,SequenceCollectionI> hiddenReps);
+
+  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.
+   * 
+   * @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();
+
 }