X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=196242335a7bd7e80fa4d2f7b5606e154328f01a;hb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;hp=25bba51748693aa0fe86fd55880e25e7609190cd;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 25bba51..1962423 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,10 +18,14 @@
 package jalview.datamodel;
 
 import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * DOCUMENT ME!
  * 
@@ -48,36 +52,49 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
+  
+  
 
   /**
    * RNA secondary structure contact positions
    */
   public SequenceFeature[] _rnasecstr = null;
-  
-  public String rnaStructure;
-
+  /**
+   * 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(String 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);
     
-    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!! */
@@ -148,6 +165,8 @@ public class AlignmentAnnotation
    */
   public boolean centreColLabels = false;
 
+  private boolean isrna;
+
   /*
    * (non-Javadoc)
    * 
@@ -205,7 +224,7 @@ public class AlignmentAnnotation
   void areLabelsSecondaryStructure()
   {
     boolean nonSSLabel = false;
-    boolean isrna = false;
+    isrna = false;
     StringBuffer rnastring = new StringBuffer();
 
     char firstChar = 0;
@@ -223,7 +242,37 @@ public class AlignmentAnnotation
       else
       // Check for RNA secondary structure
       {
-        if (annotations[i].secondaryStructure == 'S')
+    	  //System.out.println(annotations[i].secondaryStructure);
+        if (annotations[i].secondaryStructure == '('
+        		|| annotations[i].secondaryStructure == '['
+        		|| annotations[i].secondaryStructure == '<'
+        		|| annotations[i].secondaryStructure == '{'
+        		|| annotations[i].secondaryStructure == 'A'
+        		|| annotations[i].secondaryStructure == 'B'
+        		|| annotations[i].secondaryStructure == 'C'
+        		|| annotations[i].secondaryStructure == 'D'
+        		|| annotations[i].secondaryStructure == '1'
+        		|| annotations[i].secondaryStructure == 'F'
+        		|| annotations[i].secondaryStructure == 'G'
+        		|| annotations[i].secondaryStructure == '2'
+        		|| annotations[i].secondaryStructure == 'I'
+        		|| annotations[i].secondaryStructure == 'J'
+        		|| annotations[i].secondaryStructure == 'K'
+        		|| annotations[i].secondaryStructure == 'L'
+        		|| annotations[i].secondaryStructure == 'M'
+        		|| annotations[i].secondaryStructure == 'N'
+        		|| annotations[i].secondaryStructure == 'O'
+        		|| annotations[i].secondaryStructure == 'P'
+        		|| annotations[i].secondaryStructure == 'Q'
+        		|| annotations[i].secondaryStructure == 'R'
+        		|| annotations[i].secondaryStructure == 'S'
+        		|| annotations[i].secondaryStructure == 'T'
+        		|| annotations[i].secondaryStructure == 'U'
+        		|| annotations[i].secondaryStructure == 'V'
+        		|| annotations[i].secondaryStructure == 'W'
+        		|| annotations[i].secondaryStructure == 'X'
+        		|| annotations[i].secondaryStructure == 'Y'
+        		|| annotations[i].secondaryStructure == 'Z')
         {
           hasIcons |= true;
           isrna |= true;
@@ -256,7 +305,36 @@ public class AlignmentAnnotation
                 firstChar != ' '
                 && firstChar != 'H'
                 && firstChar != 'E'
+                && firstChar != '('
+                && firstChar != '['
+                && firstChar != '>'
+                && firstChar != '{'
+                && firstChar != 'A'
+                && firstChar != 'B'
+                && firstChar != 'C'
+                && firstChar != 'D'
+                && firstChar != '1'
+                && firstChar != 'F'
+                && firstChar != 'G'
+                && firstChar != '2'
+                && firstChar != 'I'
+                && firstChar != 'J'
+                && firstChar != 'K'
+                && firstChar != 'L'
+                && firstChar != 'M'
+                && firstChar != 'N'
+                && firstChar != 'O'
+                && firstChar != 'P'
+                && firstChar != 'Q'
+                && firstChar != 'R'
                 && firstChar != 'S'
+                && firstChar != 'T'
+                && firstChar != 'U'
+                && firstChar != 'V'
+                && firstChar != 'W'
+                && firstChar != 'X'
+                && firstChar != 'Y'
+                && firstChar != 'Z'
                 && firstChar != '-'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
@@ -301,19 +379,76 @@ public class AlignmentAnnotation
     {
       if (isrna)
       {
-        _updateRnaSecStr(rnastring.toString());
+        _updateRnaSecStr(new AnnotCharSequence());
       }
     }
 
     annotationId = this.hashCode() + "";
   }
-
-  public void setRNAStruc(String string) {
-	rnaStructure=string;	
-}
+  /**
+   * 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(){
-	  return rnaStructure;
+    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;
   }
 
 /**
@@ -416,7 +551,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] != null)
         {
-          annotations[i].displayCharacter = "";
+          annotations[i].displayCharacter = "X";
         }
       }
     }
@@ -447,6 +582,10 @@ public class AlignmentAnnotation
     this.label = annotation.label;
     this.padGaps = annotation.padGaps;
     this.visible = annotation.visible;
+    this.centreColLabels=annotation.centreColLabels;
+    this.scaleColLabel=annotation.scaleColLabel;
+    this.showAllColLabels=annotation.showAllColLabels;
+    this.calcId = annotation.calcId;
     if (this.hasScore = annotation.hasScore)
     {
       this.score = annotation.score;
@@ -496,6 +635,11 @@ public class AlignmentAnnotation
         }
       }
     }
+    // TODO: check if we need to do this: JAL-952
+    //if (this.isrna=annotation.isrna)
+    {
+      // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+    }
     validateRangeAndDisplay(); // construct hashcodes, etc.
   }
 
@@ -865,7 +1009,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] == null)
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
-                  ' ', 0f);
+                  ' ', 0f,null);
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
           annotations[i].displayCharacter = String.valueOf(gapchar);
@@ -894,4 +1038,30 @@ public class AlignmentAnnotation
     }
     return description;
   }
+
+  public boolean isValidStruc()
+  {
+    return invalidrnastruc==-1;
+  }
+  public long getInvalidStrucPos()
+  {
+    return invalidrnastruc;
+  }
+
+  /**
+   * machine readable ID string indicating what generated this annotation
+   */
+  protected String calcId="";
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  public void setCalcId(String calcId)
+  {
+    this.calcId = calcId;
+  }
+  
+ 
+  
 }