X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=3cf9244267844f0f5e4885092310ae1a59442813;hb=bb3f28791ddb1a4f55e78a3bcd2ff4a591ebe95d;hp=236e8ee0cb95d0d05742333eacd04f108d5f71dc;hpb=63cbb86a2d771d2d99d2f38a7b6cf639bf5c19c8;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 236e8ee..3cf9244 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 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,6 +17,9 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
+
 import java.util.Enumeration;
 import java.util.Hashtable;
 
@@ -35,7 +38,7 @@ public class AlignmentAnnotation
   public boolean autoCalculated = false;
 
   public String annotationId;
-
+  
   public SequenceI sequenceRef;
 
   /** DOCUMENT ME!! */
@@ -47,6 +50,46 @@ public class AlignmentAnnotation
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
 
+  /**
+   * RNA secondary structure contact positions
+   */
+  public SequenceFeature[] _rnasecstr = null;
+  /**
+   * position of annotation resulting in invalid WUSS parsing or -1
+   */
+  private long invalidrnastruc=-1;
+  /**
+   * Updates the _rnasecstr field Determines the positions that base pair and
+   * the positions of helices based on secondary structure from a Stockholm file
+   * 
+   * @param RNAannot
+   */
+  private void _updateRnaSecStr(CharSequence RNAannot)
+  {
+    try {
+    _rnasecstr = Rna.GetBasePairs(RNAannot);
+    invalidrnastruc=-1;
+    }
+    catch (WUSSParseException px)
+    {
+      invalidrnastruc=px.getProblemPos();
+    }
+    if (invalidrnastruc>-1)
+    {
+      return;
+    }
+    Rna.HelixMap(_rnasecstr);
+    // setRNAStruc(RNAannot);
+    
+    if (_rnasecstr != null && _rnasecstr.length > 0)
+    {
+      // show all the RNA secondary structure annotation symbols.
+      isrna=true;
+      showAllColLabels = true;
+      scaleColLabel = true;
+    }
+    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+  }
   public java.util.Hashtable sequenceMapping;
 
   /** DOCUMENT ME!! */
@@ -117,6 +160,8 @@ public class AlignmentAnnotation
    */
   public boolean centreColLabels = false;
 
+  private boolean isrna;
+
   /*
    * (non-Javadoc)
    * 
@@ -167,9 +212,16 @@ public class AlignmentAnnotation
     validateRangeAndDisplay();
   }
 
+  /**
+   * Checks if annotation labels represent secondary structures
+   * 
+   */
   void areLabelsSecondaryStructure()
   {
     boolean nonSSLabel = false;
+    isrna = false;
+    StringBuffer rnastring = new StringBuffer();
+
     char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
@@ -182,9 +234,22 @@ public class AlignmentAnnotation
       {
         hasIcons |= true;
       }
+      else
+      // Check for RNA secondary structure
+      {
+        if (annotations[i].secondaryStructure == 'S')
+        {
+          hasIcons |= true;
+          isrna |= true;
+        }
+      }
+
+      // System.out.println("displaychar " + annotations[i].displayCharacter);
 
-      if (annotations[i].displayCharacter == null)
+      if (annotations[i].displayCharacter == null
+              || annotations[i].displayCharacter.length() == 0)
       {
+        rnastring.append('.');
         continue;
       }
       if (annotations[i].displayCharacter.length() == 1)
@@ -205,6 +270,7 @@ public class AlignmentAnnotation
                 firstChar != ' '
                 && firstChar != 'H'
                 && firstChar != 'E'
+                && firstChar != 'S'
                 && firstChar != '-'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
@@ -219,6 +285,10 @@ public class AlignmentAnnotation
           }
         }
       }
+      else
+      {
+        rnastring.append(annotations[i].displayCharacter.charAt(1));
+      }
 
       if (annotations[i].displayCharacter.length() > 0)
       {
@@ -241,11 +311,83 @@ public class AlignmentAnnotation
 
       }
     }
+    else
+    {
+      if (isrna)
+      {
+        _updateRnaSecStr(new AnnotCharSequence());
+      }
+    }
 
     annotationId = this.hashCode() + "";
   }
-
   /**
+   * flyweight access to positions in the alignment annotation row for RNA processing
+   * @author jimp
+   *
+   */
+  private class AnnotCharSequence  implements CharSequence 
+  {
+    int offset=0;
+    int max=0;
+    
+    public AnnotCharSequence() {
+      this(0,annotations.length);
+    }
+    public AnnotCharSequence(int start, int end) {
+      offset=start;
+      max=end;
+    }
+    @Override
+    public CharSequence subSequence(int start, int end)
+    {
+      return new AnnotCharSequence(offset+start, offset+end);
+    }
+    
+    @Override
+    public int length()
+    {
+      return max-offset;
+    }
+    
+    @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);
+    }
+    public String toString()
+    {
+      char[] string=new char[max-offset];
+      int mx=annotations.length;
+        
+      for (int i=offset;i<mx;i++)
+      {
+        String dc;
+        string[i]=(annotations[i]==null || (dc=annotations[i].displayCharacter.trim()).length()<1 )? '.' : dc.charAt(0);
+      }
+      return new String(string);
+    }
+  };
+  
+  private long _lastrnaannot=-1;
+  public String getRNAStruc(){
+    if (isrna)
+    {
+      String rnastruc = new AnnotCharSequence().toString();
+      if (_lastrnaannot!=rnastruc.hashCode())
+      {
+        // ensure rna structure contacts are up to date
+        _lastrnaannot=rnastruc.hashCode();
+        _updateRnaSecStr(rnastruc);
+      }
+      return rnastruc;
+    }
+    return null;
+  }
+
+/**
    * Creates a new AlignmentAnnotation object.
    * 
    * @param label
@@ -280,7 +422,7 @@ public class AlignmentAnnotation
    * checks graphMin and graphMax, secondary structure symbols, sets graphType
    * appropriately, sets null labels to the empty string if appropriate.
    */
-  private void validateRangeAndDisplay()
+  public void validateRangeAndDisplay()
   {
 
     if (annotations == null)
@@ -813,8 +955,24 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
+      int i=description.toLowerCase().indexOf("<html>");
+      if (i>-1)
+      {
+        // move the html tag to before the sequence reference.
+        return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+      }
       return sequenceRef.getName() + " : " + description;
     }
     return description;
   }
+
+  public boolean isValidStruc()
+  {
+    return invalidrnastruc==-1;
+  }
+  public long getInvalidStrucPos()
+  {
+    return invalidrnastruc;
+  }
+  
 }