X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=b60813950ae4c84a22587a8e3c769765fa0a966d;hb=960206d9ae05d85b42552025c3dec4b5f7b14c15;hp=0207575aea6f9c2dda68a4e6de94f6ba03428c9d;hpb=7d3c15518c8a237ff2ef0c135b6553891485462d;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0207575..b608139 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,19 +20,18 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Enumeration;
 import java.util.HashMap;
-import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 /**
  * DOCUMENT ME!
  * 
@@ -41,6 +40,15 @@ import java.util.Map.Entry;
  */
 public class AlignmentAnnotation
 {
+  /*
+   * Identifers for different types of profile data
+   */
+  public static final int SEQUENCE_PROFILE = 0;
+
+  public static final int STRUCTURE_PROFILE = 1;
+
+  public static final int CDNA_PROFILE = 2;
+
   /**
    * If true, this annotations is calculated every edit, eg consensus, quality
    * or conservation graphs
@@ -75,9 +83,10 @@ public class AlignmentAnnotation
   public SequenceFeature[] _rnasecstr = null;
 
   /**
-   * position of annotation resulting in invalid WUSS parsing or -1
+   * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+   * there was no RNA structure in this annotation
    */
-  private long invalidrnastruc = -1;
+  private long invalidrnastruc = -2;
 
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
@@ -118,6 +127,7 @@ public class AlignmentAnnotation
 
   private void _markRnaHelices()
   {
+    int mxval = 0;
     // Figure out number of helices
     // Length of rnasecstr is the number of pairs of positions that base pair
     // with each other in the secondary structure
@@ -133,6 +143,10 @@ public class AlignmentAnnotation
       try
       {
         val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+        if (mxval < val)
+        {
+          mxval = val;
+        }
       } catch (NumberFormatException q)
       {
       }
@@ -141,14 +155,15 @@ public class AlignmentAnnotation
       annotations[_rnasecstr[x].getBegin()].value = val;
       annotations[_rnasecstr[x].getEnd()].value = val;
 
-      annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
-      annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
     }
+    setScore(mxval);
   }
   /**
    * map of positions in the associated annotation
    */
-  public java.util.Hashtable<Integer, Annotation> sequenceMapping;
+  private Map<Integer, Annotation> sequenceMapping;
 
   /** DOCUMENT ME!! */
   public float graphMin;
@@ -486,13 +501,13 @@ public class AlignmentAnnotation
     @Override
     public char charAt(int index)
     {
-      String dc;
       return ((index + offset < 0) || (index + offset) >= max
-              || annotations[index + offset] == null || (dc = annotations[index
-              + offset].displayCharacter.trim()).length() < 1) ? '.' : dc
-              .charAt(0);
+              || annotations[index + offset] == null || (annotations[index
+ + offset].secondaryStructure < ' ') ? ' '
+              : annotations[index + offset].secondaryStructure);
     }
 
+    @Override
     public String toString()
     {
       char[] string = new char[max - offset];
@@ -500,9 +515,8 @@ public class AlignmentAnnotation
 
       for (int i = offset; i < mx; i++)
       {
-        String dc;
-        string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
-                .trim()).length() < 1) ? '.' : dc.charAt(0);
+        string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' '
+                : annotations[i].secondaryStructure;
       }
       return new String(string);
     }
@@ -705,12 +719,13 @@ public class AlignmentAnnotation
       if (annotation.sequenceMapping != null)
       {
         Integer p = null;
-        sequenceMapping = new Hashtable();
-        Enumeration pos = annotation.sequenceMapping.keys();
-        while (pos.hasMoreElements())
+        sequenceMapping = new HashMap<Integer, Annotation>();
+        Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+                .iterator();
+        while (pos.hasNext())
         {
           // could optimise this!
-          p = (Integer) pos.nextElement();
+          p = pos.next();
           Annotation a = annotation.sequenceMapping.get(p);
           if (a == null)
           {
@@ -784,11 +799,11 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Hashtable newmapping = new Hashtable();
-        Enumeration e = sequenceMapping.keys();
-        while (e.hasMoreElements())
+        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Iterator<Integer> e = sequenceMapping.keySet().iterator();
+        while (e.hasNext())
         {
-          Integer pos = (Integer) e.nextElement();
+          Integer pos = e.next();
           if (pos.intValue() >= spos && pos.intValue() <= epos)
           {
             newmapping.put(pos, sequenceMapping.get(pos));
@@ -831,9 +846,10 @@ public class AlignmentAnnotation
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String toString()
   {
-    StringBuffer buffer = new StringBuffer();
+    StringBuilder buffer = new StringBuilder(256);
 
     for (int i = 0; i < annotations.length; i++)
     {
@@ -906,7 +922,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new java.util.Hashtable();
+    sequenceMapping = new HashMap<Integer, Annotation>();
 
     int seqPos;
 
@@ -1218,7 +1234,7 @@ public class AlignmentAnnotation
             .getTo() == sq.getDatasetSequence()) : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Hashtable<Integer, Annotation> mapForsq = new Hashtable();
+    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1270,7 +1286,8 @@ public class AlignmentAnnotation
   {
     if (mapping != null)
     {
-      Hashtable<Integer, Annotation> old = sequenceMapping, remap = new Hashtable<Integer, Annotation>();
+      Map<Integer, Annotation> old = sequenceMapping;
+      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
       int index = -1;
       for (int mp[] : mapping)
       {
@@ -1342,8 +1359,21 @@ public class AlignmentAnnotation
   {
     if (properties == null)
     {
-      return Collections.EMPTY_LIST;
+      return Collections.emptyList();
     }
     return properties.keySet();
   }
+
+  /**
+   * Returns the Annotation for the given sequence position (base 1) if any,
+   * else null
+   * 
+   * @param position
+   * @return
+   */
+  public Annotation getAnnotationForPosition(int position)
+  {
+    return sequenceMapping == null ? null : sequenceMapping.get(position);
+
+  }
 }