X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=f4795f1cb993f1d1f64a5856716822e27bdca324;hb=7d76e402efd4e04e179bc9bb264551bc2d3df936;hp=fa063ff40efec2716d95361aaf912661a901272a;hpb=507800557a9b27cc6e1a3f831cbb7d18c9d173d0;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index fa063ff..f4795f1 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,27 +1,34 @@
 /*
- * 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 <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.
@@ -49,18 +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;
 
   /**
@@ -315,13 +326,26 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Returns the sequence features (if any), looking first on the sequence, then
+   * on its dataset sequence, and so on until a non-null value is found (or
+   * none). This supports retrieval of sequence features stored on the sequence
+   * (as in the applet) or on the dataset sequence (as in the Desktop version).
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   public SequenceFeature[] getSequenceFeatures()
   {
-    return sequenceFeatures;
+    SequenceFeature[] features = sequenceFeatures;
+
+    SequenceI seq = this;
+    int count = 0; // failsafe against loop in sequence.datasetsequence...
+    while (features == null && seq.getDatasetSequence() != null
+            && count++ < 10)
+    {
+      seq = seq.getDatasetSequence();
+      features = ((Sequence) seq).sequenceFeatures;
+    }
+    return features;
   }
 
   public void addPDBId(PDBEntry entry)
@@ -482,7 +506,9 @@ 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)
@@ -501,16 +527,7 @@ 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)
@@ -610,14 +627,7 @@ 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;
@@ -664,11 +674,7 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#findPositionMap()
-   */
+  @Override
   public int[] findPositionMap()
   {
     int map[] = new int[sequence.length];
@@ -688,11 +694,43 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
-   */
+  @Override
+  public List<int[]> getInsertions()
+  {
+    ArrayList<int[]> map = new ArrayList<int[]>();
+    int lastj = -1, j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < seqlen))
+    {
+      if (jalview.util.Comparison.isGap(sequence[j]))
+      {
+        if (lastj == -1)
+        {
+          lastj = j;
+        }
+      }
+      else
+      {
+        if (lastj != -1)
+        {
+          map.add(new int[]
+          { lastj, j - 1 });
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
+    {
+      map.add(new int[]
+      { lastj, j - 1 });
+      lastj = -1;
+    }
+    return map;
+  }
+
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
@@ -707,7 +745,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
-      j=sequence.length;
+      j = sequence.length;
     }
     else
     {
@@ -771,16 +809,7 @@ public class Sequence implements SequenceI
     sequence = tmp;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * @param c
-   *          DOCUMENT ME!
-   * @param chop
-   *          DOCUMENT ME!
-   */
+  @Override
   public void insertCharAt(int i, int length, char c)
   {
     char[] tmp = new char[sequence.length + length];
@@ -810,26 +839,31 @@ public class Sequence implements SequenceI
     sequence = tmp;
   }
 
+  @Override
   public void insertCharAt(int i, char c)
   {
     insertCharAt(i, 1, c);
   }
 
+  @Override
   public String getVamsasId()
   {
     return vamsasId;
   }
 
+  @Override
   public void setVamsasId(String id)
   {
     vamsasId = id;
   }
 
+  @Override
   public void setDBRef(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
 
+  @Override
   public DBRefEntry[] getDBRef()
   {
     if (dbrefs == null && datasetSequence != null
@@ -840,6 +874,7 @@ public class Sequence implements SequenceI
     return dbrefs;
   }
 
+  @Override
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
@@ -872,32 +907,33 @@ public class Sequence implements SequenceI
     dbrefs = temp;
   }
 
+  @Override
   public void setDatasetSequence(SequenceI seq)
   {
     datasetSequence = seq;
   }
 
+  @Override
   public SequenceI getDatasetSequence()
   {
     return datasetSequence;
   }
 
+  @Override
   public AlignmentAnnotation[] getAnnotation()
   {
-    if (annotation == null)
-    {
-      return null;
-    }
+    return annotation == null ? null : annotation
+            .toArray(new AlignmentAnnotation[annotation.size()]);
+  }
 
-    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
-    for (int r = 0; r < ret.length; r++)
-    {
-      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
-    }
 
-    return ret;
+  @Override
+  public boolean hasAnnotation(AlignmentAnnotation ann)
+  {
+    return annotation == null ? false : annotation.contains(ann);
   }
 
+  @Override
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
@@ -917,7 +953,9 @@ public class Sequence implements SequenceI
     {
       this.annotation.removeElement(annotation);
       if (this.annotation.size() == 0)
+      {
         this.annotation = null;
+      }
     }
   }
 
@@ -941,11 +979,7 @@ public class Sequence implements SequenceI
     return true;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#deriveSequence()
-   */
+  @Override
   public SequenceI deriveSequence()
   {
     SequenceI seq = new Sequence(this);
@@ -996,6 +1030,17 @@ public class Sequence implements SequenceI
       datasetSequence.setPDBId(getPDBId());
       setPDBId(null);
       datasetSequence.updatePDBIds();
+      if (annotation != null)
+      {
+        for (AlignmentAnnotation aa : annotation)
+        {
+          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+          _aa.sequenceRef = datasetSequence;
+          _aa.adjustForAlignment(); // uses annotation's own record of
+                                   // sequence-column mapping
+          datasetSequence.addAlignmentAnnotation(_aa);
+        }
+      }
     }
     return datasetSequence;
   }
@@ -1018,16 +1063,14 @@ public class Sequence implements SequenceI
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] != null)
+        {
           addAlignmentAnnotation(annotations[i]);
+        }
       }
     }
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
-   */
+  @Override
   public AlignmentAnnotation[] getAnnotation(String label)
   {
     if (annotation == null || annotation.size() == 0)
@@ -1060,6 +1103,7 @@ public class Sequence implements SequenceI
     return anns;
   }
 
+  @Override
   public boolean updatePDBIds()
   {
     if (datasetSequence != null)
@@ -1113,13 +1157,7 @@ public class Sequence implements SequenceI
     return false;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
-   * jalview.datamodel.Mapping)
-   */
+  @Override
   public void transferAnnotation(SequenceI entry, Mapping mp)
   {
     if (datasetSequence != null)
@@ -1204,4 +1242,32 @@ public class Sequence implements SequenceI
   {
     index = value;
   }
+
+  public void setRNA(RNA r)
+  {
+    rna = r;
+  }
+
+  public RNA getRNA()
+  {
+    return rna;
+  }
+
+  @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;
+  }
+
 }