X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=338aa627c01c85833414953a851dcdf883199a84;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=cd817ab3063d3abe61187fd70f3dffa32f315dc2;hpb=ad315220a610542fe2ba24b33bf506636c330d99;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cd817ab..338aa62 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,28 +1,34 @@
 /*
- * 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 <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 jalview.analysis.AlignSeq;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -50,18 +56,22 @@ public class Sequence implements SequenceI
 
   DBRefEntry[] dbrefs;
 
+  RNA rna;
+
   /**
    * This annotation is displayed below the alignment but the positions are tied
    * to the residues of this sequence
+   *
+   * TODO: change to List<>
    */
-  Vector annotation;
+  Vector<AlignmentAnnotation> annotation;
 
   /**
    * The index of the sequence in a MSA
    */
   int index = -1;
 
-  /** array of seuqence features - may not be null for a valid sequence object */
+  /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
   /**
@@ -483,7 +493,9 @@ public class Sequence implements SequenceI
   public char[] getSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
+    }
     // JBPNote - left to user to pad the result here (TODO:Decide on this
     // policy)
     if (start >= sequence.length)
@@ -502,16 +514,7 @@ public class Sequence implements SequenceI
     return reply;
   }
 
-  /**
-   * make a new Sequence object from start to end (including gaps) over this
-   * seqeunce
-   * 
-   * @param start
-   *          int
-   * @param end
-   *          int
-   * @return SequenceI
-   */
+  @Override
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
@@ -611,14 +614,7 @@ public class Sequence implements SequenceI
     }
   }
 
-  /**
-   * Returns the sequence position for an alignment position
-   * 
-   * @param i
-   *          column index in alignment (from 1)
-   * 
-   * @return residue number for residue (left of and) nearest ith column
-   */
+  @Override
   public int findPosition(int i)
   {
     int j = 0;
@@ -708,7 +704,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
-      j=sequence.length;
+      j = sequence.length;
     }
     else
     {
@@ -883,22 +879,30 @@ public class Sequence implements SequenceI
     return datasetSequence;
   }
 
+  /**
+   * Returns a new array containing this sequence's annotations, or null.
+   */
   public AlignmentAnnotation[] getAnnotation()
   {
-    if (annotation == null)
-    {
-      return null;
-    }
-
-    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
-    for (int r = 0; r < ret.length; r++)
-    {
-      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
-    }
+    return annotation == null ? null : annotation
+            .toArray(new AlignmentAnnotation[annotation.size()]);
+  }
 
-    return ret;
+  /**
+   * Returns true if this sequence has the given annotation (by object
+   * identity).
+   */
+  @Override
+  public boolean hasAnnotation(AlignmentAnnotation ann)
+  {
+    return annotation == null ? false : annotation.contains(ann);
   }
 
+  /**
+   * Add the given annotation, if not already added, and set its sequence ref to
+   * be this sequence. Does nothing if this sequence's annotations already
+   * include this annotation (by identical object reference).
+   */
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
@@ -918,7 +922,9 @@ public class Sequence implements SequenceI
     {
       this.annotation.removeElement(annotation);
       if (this.annotation.size() == 0)
+      {
         this.annotation = null;
+      }
     }
   }
 
@@ -999,14 +1005,13 @@ public class Sequence implements SequenceI
       datasetSequence.updatePDBIds();
       if (annotation != null)
       {
-        Vector<AlignmentAnnotation> _annot = annotation;
-        annotation = null;
-        for (AlignmentAnnotation aa : _annot)
+        for (AlignmentAnnotation aa : annotation)
         {
-          aa.sequenceRef = datasetSequence;
-          aa.adjustForAlignment(); // uses annotation's own record of
+          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+          _aa.sequenceRef = datasetSequence;
+          _aa.adjustForAlignment(); // uses annotation's own record of
                                    // sequence-column mapping
-          datasetSequence.addAlignmentAnnotation(aa);
+          datasetSequence.addAlignmentAnnotation(_aa);
         }
       }
     }
@@ -1031,7 +1036,9 @@ public class Sequence implements SequenceI
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] != null)
+        {
           addAlignmentAnnotation(annotations[i]);
+        }
       }
     }
   }
@@ -1217,4 +1224,39 @@ public class Sequence implements SequenceI
   {
     index = value;
   }
+
+  public void setRNA(RNA r)
+  {
+    rna = r;
+  }
+
+  public RNA getRNA()
+  {
+    return rna;
+  }
+
+  /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source) and label (type). Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   */
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label)
+  {
+    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    if (this.annotation != null) {
+      for (AlignmentAnnotation ann : annotation) {
+        if (ann.calcId != null && ann.calcId.equals(calcId)
+                && ann.label != null && ann.label.equals(label))
+        {
+          result.add(ann);
+        }
+      }
+    }
+    return result;
+  }
+
 }