X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=64a57bae376b10bbfbdf36ed1d56233348679118;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=5afdc5a8d297123c866f93f88f6c084d2dfdb6ac;hpb=8d2724b83aca38ef75d68787cc5939d950467e63;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 5afdc5a..64a57ba 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,24 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* 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;
@@ -135,10 +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);
@@ -187,7 +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
*/
@@ -351,7 +370,9 @@ 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
@@ -369,17 +390,17 @@ public interface SequenceI
* @return The index of the sequence in the alignment
*/
public int getIndex();
-
+
/**
* @return The RNA of the sequence in the alignment
*/
-
+
public RNA getRNA();
-
+
/**
- * @param rna The RNA.
+ * @param rna
+ * The RNA.
*/
public void setRNA(RNA rna);
-
}