X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=8376047444fb4cff5840e33e4ec2d7c036f44554;hb=d3a2fdc864b586b5c604335dd715ec215b679197;hp=3e9c4c7ab56af5bcec2c19a54e27245ac1af40c1;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 3e9c4c7..8376047 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,24 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.*;
+import java.util.List;
+import java.util.Vector;
+
+import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * DOCUMENT ME!
@@ -44,7 +49,7 @@ 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 +93,7 @@ public interface SequenceI
    * Replace the sequence with the given string
    * 
    * @param sequence
-   *                new sequence string
+   *          new sequence string
    */
   public void setSequence(String sequence);
 
@@ -98,21 +103,21 @@ 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();
 
@@ -120,9 +125,9 @@ 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)];
    */
@@ -132,10 +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);
 
@@ -143,7 +150,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -153,7 +160,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc);
 
@@ -165,12 +172,18 @@ public interface SequenceI
   public String getDescription();
 
   /**
-   * DOCUMENT ME!
+   * Return the alignment column for a sequence position * Return the alignment
+   * position for a sequence position
    * 
    * @param pos
-   *                DOCUMENT ME!
+   *          lying from start to end
+   * 
+   * @return aligned column for residue (0 if residue is upstream from
+   *         alignment, -1 if residue is downstream from alignment) note.
+   *         Sequence object returns sequence.getEnd() for positions upstream
+   *         currently. TODO: change sequence for
+   *         assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
    * 
-   * @return DOCUMENT ME!
    */
   public int findIndex(int pos);
 
@@ -178,7 +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..<length)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */
@@ -207,9 +220,9 @@ 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 +230,9 @@ 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 +240,9 @@ 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 +257,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param v
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
@@ -252,7 +265,7 @@ public interface SequenceI
    * DOCUMENT ME!
    * 
    * @param id
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setPDBId(Vector ids);
 
@@ -326,15 +339,28 @@ 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);
 
   /**
+   * Return a list of any annotations which match the given calcId (source) and
+   * label (type). Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   * @return
+   */
+  public List<AlignmentAnnotation> 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
    */
@@ -342,12 +368,37 @@ public interface SequenceI
 
   /**
    * Transfer any database references or annotation from entry under a sequence
-   * mapping.
+   * mapping. <br/>
+   * <strong>Note: DOES NOT transfer sequence associated alignment
+   * annotation </strong><br/>
    * 
    * @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();
+
+  /**
+   * @return The RNA of the sequence in the alignment
+   */
+
+  public RNA getRNA();
+
+  /**
+   * @param rna
+   *          The RNA.
+   */
+  public void setRNA(RNA rna);
+
 }