X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=64a57bae376b10bbfbdf36ed1d56233348679118;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=a1a7bc223cc2f01b3e0e48de99f1a822b8cb5c84;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index a1a7bc2..64a57ba 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,23 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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!
@@ -97,21 +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();
 
@@ -131,10 +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);
 
@@ -164,12 +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);
 
@@ -177,7 +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
    */
@@ -303,6 +317,8 @@ public interface SequenceI
 
   public AlignmentAnnotation[] getAnnotation();
 
+  public boolean hasAnnotation(AlignmentAnnotation ann);
+
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
@@ -331,9 +347,22 @@ public interface SequenceI
   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
    */
@@ -341,7 +370,9 @@ 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
@@ -349,4 +380,27 @@ public interface SequenceI
    */
   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);
+
 }