JAL-1065 - Visualize T-Coffee quality scores for an alignment

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 10bee55..87c964f 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,24 +1,23 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -44,7 +43,7 @@ public interface SequenceI
    * Set start position of first non-gapped symbol in sequence
    * 
    * @param start
-   *                new start position
+   *          new start position
    */
   public void setStart(int start);
 
@@ -88,7 +87,7 @@ public interface SequenceI
    * Replace the sequence with the given string
    * 
    * @param sequence
-   *                new sequence string
+   *          new sequence string
    */
   public void setSequence(String sequence);
 
@@ -101,9 +100,9 @@ public interface SequenceI
    * get a range on the seuqence as a string
    * 
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -120,9 +119,9 @@ public interface SequenceI
    * get stretch of sequence characters in an array
    * 
    * @param start
-   *                absolute index into getSequence()
+   *          absolute index into getSequence()
    * @param end
-   *                exclusive index of last position in segment to be returned.
+   *          exclusive index of last position in segment to be returned.
    * 
    * @return char[max(0,end-start)];
    */
@@ -132,9 +131,9 @@ public interface SequenceI
    * create a new sequence object from start to end of this sequence
    * 
    * @param start
-   *                int
+   *          int
    * @param end
-   *                int
+   *          int
    * @return SequenceI
    */
   public SequenceI getSubSequence(int start, int end);
@@ -143,7 +142,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -153,7 +152,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc);
 
@@ -168,7 +167,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param pos
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -178,7 +177,7 @@ public interface SequenceI
    * Returns the sequence position for an alignment position
    * 
    * @param i
-   *                column index in alignment (from 1)
+   *          column index in alignment (from 1)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */
@@ -207,9 +206,9 @@ public interface SequenceI
    * if necessary and adjusting start and end positions accordingly.
    * 
    * @param i
-   *                first column in range to delete
+   *          first column in range to delete
    * @param j
-   *                last column in range to delete
+   *          last column in range to delete
    */
   public void deleteChars(int i, int j);
 
@@ -217,9 +216,9 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void insertCharAt(int i, char c);
 
@@ -227,9 +226,9 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void insertCharAt(int i, int length, char c);
 
@@ -244,7 +243,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param v
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
@@ -252,7 +251,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param id
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setPDBId(Vector ids);
 
@@ -326,7 +325,7 @@ public interface SequenceI
    * Get one or more alignment annotations with a particular label.
    * 
    * @param label
-   *                string which each returned annotation must have as a label.
+   *          string which each returned annotation must have as a label.
    * @return null or array of annotations.
    */
   public AlignmentAnnotation[] getAnnotation(String label);
@@ -346,8 +345,18 @@ public interface SequenceI
    * 
    * @param entry
    * @param mp
-   *                null or mapping from entry's numbering to local start/end
+   *          null or mapping from entry's numbering to local start/end
    */
   public void transferAnnotation(SequenceI entry, Mapping mp);
+  
+  /**
+   * @param index The sequence index in the MSA 
+   */
+  public void setIndex(int index);
+  
+  /**
+   * @return The index of the sequence in the alignment
+   */
+  public int getIndex();
 
 }