X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=e9259ddab23903e495451276e718476a4c2617eb;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=57d25690511e4f037ac598fc33ec9ac96798eb68;hpb=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 57d2569..e9259dd 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,23 +1,25 @@
/*
- * 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 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.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
@@ -100,21 +102,21 @@ public interface SequenceI
public String getSequenceAsString();
/**
- * get a range on the seuqence as a string
+ * get a range on the sequence as a string
*
* @param start
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
* @param end
- * DOCUMENT ME!
+ * position relative to start of sequence including gaps (from 0)
*
- * @return DOCUMENT ME!
+ * @return String containing all gap and symbols in specified range
*/
public String getSequenceAsString(int start, int end);
/**
- * DOCUMENT ME!
+ * Get the sequence as a character array
*
- * @return DOCUMENT ME!
+ * @return seqeunce and any gaps
*/
public char[] getSequence();
@@ -368,17 +370,17 @@ 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);
-
}