X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=8376047444fb4cff5840e33e4ec2d7c036f44554;hb=d3a2fdc864b586b5c604335dd715ec215b679197;hp=285b7a89c667ae12250ec6cc507a0428acf85e07;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 285b7a8..8376047 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,25 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
+import java.util.List;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
@@ -132,10 +137,12 @@ public interface SequenceI
* create a new sequence object from start to end of this sequence
*
* @param start
- * int
+ * int index for start position
* @param end
- * int
+ * int index for end position
+ *
* @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
*/
public SequenceI getSubSequence(int start, int end);
@@ -184,7 +191,7 @@ public interface SequenceI
* Returns the sequence position for an alignment position
*
* @param i
- * column index in alignment (from 1)
+ * column index in alignment (from 0.. getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
- * references on the sequence onto the dataset.
+ * references on the sequence onto the dataset. It will also make a duplicate
+ * of existing annotation rows for the dataset sequence, rather than relocate
+ * them in order to preserve external references (since 2.8.2).
*
* @return dataset sequence for this sequence
*/
@@ -348,7 +368,9 @@ public interface SequenceI
/**
* Transfer any database references or annotation from entry under a sequence
- * mapping.
+ * mapping.
+ * Note: DOES NOT transfer sequence associated alignment
+ * annotation
*
* @param entry
* @param mp
@@ -367,4 +389,16 @@ public interface SequenceI
*/
public int getIndex();
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna
+ * The RNA.
+ */
+ public void setRNA(RNA rna);
+
}