X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=f5d34a64835791d768e7809a3b709c7fe79877c0;hb=3d731dad51b259b16c50834ec24550280fb7dd64;hp=22d637b985ce1398e90b2a3b42fb2a0e21f21751;hpb=b7a8120335d2b6be10ce363b3d9353ddca751a77;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 22d637b..f5d34a6 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,23 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, 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 program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.WUSSParseException;
+
 import java.util.Enumeration;
 import java.util.Hashtable;
 
@@ -36,7 +38,7 @@ public class AlignmentAnnotation
   public boolean autoCalculated = false;
 
   public String annotationId;
-
+  
   public SequenceI sequenceRef;
 
   /** DOCUMENT ME!! */
@@ -48,6 +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!! */
@@ -76,7 +118,7 @@ public class AlignmentAnnotation
   /** Indicates if annotation has a graphical symbol track */
   public boolean hasIcons; //
 
-  /** Indicates if annotation has a text character label  */
+  /** Indicates if annotation has a text character label */
   public boolean hasText;
 
   /** is the row visible */
@@ -101,13 +143,13 @@ public class AlignmentAnnotation
 
   public boolean belowAlignment = true;
 
-  public SequenceGroup groupRef =null ;
+  public SequenceGroup groupRef = null;
 
   /**
    * display every column label, even if there is a row of identical labels
    */
-  public boolean showAllColLabels=false;
-  
+  public boolean showAllColLabels = false;
+
   /**
    * scale the column label to fit within the alignment column.
    */
@@ -118,12 +160,16 @@ public class AlignmentAnnotation
    */
   public boolean centreColLabels = false;
 
-  
-  /* (non-Javadoc)
+  private boolean isrna;
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see java.lang.Object#finalize()
    */
   protected void finalize() throws Throwable
   {
+    sequenceRef = null;
     groupRef = null;
     super.finalize();
   }
@@ -148,11 +194,11 @@ public class AlignmentAnnotation
    * Creates a new AlignmentAnnotation object.
    * 
    * @param label
-   *                short label shown under sequence labels
+   *          short label shown under sequence labels
    * @param description
-   *                text displayed on mouseover
+   *          text displayed on mouseover
    * @param annotations
-   *                set of positional annotation elements
+   *          set of positional annotation elements
    */
   public AlignmentAnnotation(String label, String description,
           Annotation[] annotations)
@@ -166,9 +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++)
     {
@@ -181,9 +234,22 @@ public class AlignmentAnnotation
       {
         hasIcons |= true;
       }
+      else
+      // Check for RNA secondary structure
+      {
+        if (annotations[i].secondaryStructure == 'S')
+        {
+          hasIcons |= true;
+          isrna |= true;
+        }
+      }
 
-      if (annotations[i].displayCharacter == null)
+      // System.out.println("displaychar " + annotations[i].displayCharacter);
+
+      if (annotations[i].displayCharacter == null
+              || annotations[i].displayCharacter.length() == 0)
       {
+        rnastring.append('.');
         continue;
       }
       if (annotations[i].displayCharacter.length() == 1)
@@ -191,25 +257,38 @@ public class AlignmentAnnotation
         firstChar = annotations[i].displayCharacter.charAt(0);
         // check to see if it looks like a sequence or is secondary structure
         // labelling.
-        if (annotations[i].secondaryStructure!=' ' && !hasIcons &&
-        // Uncomment to only catch case where displayCharacter==secondary
-        // Structure
-        // to correctly redisplay SS annotation imported from Stockholm,
-        // exported to JalviewXML and read back in again.
-        // &&
-        // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
-        firstChar != ' '
+        if (annotations[i].secondaryStructure != ' '
+                && !hasIcons
+                &&
+                // Uncomment to only catch case where
+                // displayCharacter==secondary
+                // Structure
+                // to correctly redisplay SS annotation imported from Stockholm,
+                // exported to JalviewXML and read back in again.
+                // &&
+                // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+                firstChar != ' '
                 && firstChar != 'H'
                 && firstChar != 'E'
+                && firstChar != 'S'
                 && firstChar != '-'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO: parameterise to gap symbol number
+          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+                                                                         // parameterise
+                                                                         // to
+                                                                         // gap
+                                                                         // symbol
+                                                                         // number
           {
             nonSSLabel = true;
           }
         }
       }
+      else
+      {
+        rnastring.append(annotations[i].displayCharacter.charAt(1));
+      }
 
       if (annotations[i].displayCharacter.length() > 0)
       {
@@ -232,25 +311,97 @@ 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
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param description
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param annotations
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param min
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param max
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param winLength
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public AlignmentAnnotation(String label, String description,
           Annotation[] annotations, float min, float max, int graphType)
@@ -271,7 +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)
@@ -312,14 +463,17 @@ public class AlignmentAnnotation
         }
       }
       // ensure zero is origin for min/max ranges on only one side of zero
-      if (min>0) {
+      if (min > 0)
+      {
         min = 0;
-      } else {
-        if (max<0)
+      }
+      else
+      {
+        if (max < 0)
         {
           max = 0;
         }
-        }
+      }
     }
 
     graphMin = min;
@@ -364,11 +518,15 @@ 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;
     }
-    if (threshold != null)
+    if (annotation.threshold != null)
     {
       threshold = new GraphLine(annotation.threshold);
     }
@@ -413,6 +571,11 @@ 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.
   }
 
@@ -472,7 +635,7 @@ public class AlignmentAnnotation
    * set the annotation row to be at least length Annotations
    * 
    * @param length
-   *                minimum number of columns required in the annotation row
+   *          minimum number of columns required in the annotation row
    * @return false if the annotation row is greater than length
    */
   public boolean padAnnotation(int length)
@@ -480,7 +643,7 @@ public class AlignmentAnnotation
     if (annotations == null)
     {
       return true; // annotation row is correct - null == not visible and
-                    // undefined length
+      // undefined length
     }
     if (annotations.length < length)
     {
@@ -523,7 +686,7 @@ public class AlignmentAnnotation
       buffer.append(", ");
     }
     // TODO: remove disgusting hack for 'special' treatment of consensus line.
-    if (label.indexOf("Consensus")==0)
+    if (label.indexOf("Consensus") == 0)
     {
       buffer.append("\n");
 
@@ -725,7 +888,7 @@ public class AlignmentAnnotation
 
   /**
    * @param score
-   *                the score to set
+   *          the score to set
    */
   public void setScore(double score)
   {
@@ -801,8 +964,38 @@ 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;
+  }
+
+  /**
+   * 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;
+  }
+  
 }