X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=9659cd75503d94a28a994011cfa0230bd129287a;hb=d197025c26793dc26ef790633ee6ab394c8eff85;hp=196242335a7bd7e80fa4d2f7b5606e154328f01a;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 1962423..9659cd7 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,23 +1,28 @@
 /*
- * 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
+ * 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.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
@@ -41,7 +46,7 @@ public class AlignmentAnnotation
   public boolean autoCalculated = false;
 
   public String annotationId;
-  
+
   public SequenceI sequenceRef;
 
   /** DOCUMENT ME!! */
@@ -52,17 +57,19 @@ public class AlignmentAnnotation
 
   /** DOCUMENT ME!! */
   public Annotation[] annotations;
-  
-  
+
+  public ArrayList<SimpleBP> bps = null;
 
   /**
    * RNA secondary structure contact positions
    */
   public SequenceFeature[] _rnasecstr = null;
+
   /**
    * position of annotation resulting in invalid WUSS parsing or -1
    */
-  private long invalidrnastruc=-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
@@ -71,30 +78,33 @@ public class AlignmentAnnotation
    */
   private void _updateRnaSecStr(CharSequence RNAannot)
   {
-    try {
-    _rnasecstr = Rna.GetBasePairs(RNAannot);
-    invalidrnastruc=-1;
-    }
-    catch (WUSSParseException px)
+    try
+    {
+      _rnasecstr = Rna.GetBasePairs(RNAannot);
+      bps = Rna.GetModeleBP(RNAannot);
+      invalidrnastruc = -1;
+    } catch (WUSSParseException px)
     {
-      invalidrnastruc=px.getProblemPos();
+      // DEBUG System.out.println(px);
+      invalidrnastruc = px.getProblemPos();
     }
-    if (invalidrnastruc>-1)
+    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;
+      isrna = true;
       showAllColLabels = true;
       scaleColLabel = true;
     }
     // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
   }
+
   public java.util.Hashtable sequenceMapping;
 
   /** DOCUMENT ME!! */
@@ -195,6 +205,12 @@ public class AlignmentAnnotation
     }
   }
 
+  // JBPNote: what does this do ?
+  public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+  {
+    bps = Rna.GetModeleBP(RNAannot);
+  }
+
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -242,37 +258,38 @@ public class AlignmentAnnotation
       else
       // Check for RNA secondary structure
       {
-    	  //System.out.println(annotations[i].secondaryStructure);
+        // System.out.println(annotations[i].secondaryStructure);
+        // TODO: 2.8.2 should this ss symbol validation check be a function in RNA/ResidueProperties ?
         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')
+                || 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 == 'E'
+                || annotations[i].secondaryStructure == 'F'
+                || annotations[i].secondaryStructure == 'G'
+                || annotations[i].secondaryStructure == 'H'
+                || 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;
@@ -303,8 +320,8 @@ public class AlignmentAnnotation
                 // &&
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
-                && firstChar != 'H'
-                && firstChar != 'E'
+                && firstChar != '$'
+                && firstChar != 0xCE
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -313,10 +330,10 @@ public class AlignmentAnnotation
                 && firstChar != 'B'
                 && firstChar != 'C'
                 && firstChar != 'D'
-                && firstChar != '1'
+                && firstChar != 'E'
                 && firstChar != 'F'
                 && firstChar != 'G'
-                && firstChar != '2'
+                && firstChar != 'H'
                 && firstChar != 'I'
                 && firstChar != 'J'
                 && firstChar != 'K'
@@ -385,65 +402,79 @@ public class AlignmentAnnotation
 
     annotationId = this.hashCode() + "";
   }
+
   /**
-   * flyweight access to positions in the alignment annotation row for RNA processing
+   * flyweight access to positions in the alignment annotation row for RNA
+   * processing
+   * 
    * @author jimp
-   *
+   * 
    */
-  private class AnnotCharSequence  implements CharSequence 
+  private class AnnotCharSequence implements CharSequence
   {
-    int offset=0;
-    int max=0;
-    
-    public AnnotCharSequence() {
-      this(0,annotations.length);
+    int offset = 0;
+
+    int max = 0;
+
+    public AnnotCharSequence()
+    {
+      this(0, annotations.length);
     }
-    public AnnotCharSequence(int start, int end) {
-      offset=start;
-      max=end;
+
+    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);
+      return new AnnotCharSequence(offset + start, offset + end);
     }
-    
+
     @Override
     public int length()
     {
-      return max-offset;
+      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);
+      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++)
+      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);
+        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(){
+
+  private long _lastrnaannot = -1;
+
+  public String getRNAStruc()
+  {
     if (isrna)
     {
       String rnastruc = new AnnotCharSequence().toString();
-      if (_lastrnaannot!=rnastruc.hashCode())
+      if (_lastrnaannot != rnastruc.hashCode())
       {
         // ensure rna structure contacts are up to date
-        _lastrnaannot=rnastruc.hashCode();
+        _lastrnaannot = rnastruc.hashCode();
         _updateRnaSecStr(rnastruc);
       }
       return rnastruc;
@@ -451,7 +482,7 @@ public class AlignmentAnnotation
     return null;
   }
 
-/**
+  /**
    * Creates a new AlignmentAnnotation object.
    * 
    * @param label
@@ -499,7 +530,7 @@ public class AlignmentAnnotation
     float min = graphMin;
     float max = graphMax;
     boolean drawValues = true;
-
+    _linecolour = null;
     if (min == max)
     {
       min = 999999999;
@@ -525,6 +556,10 @@ public class AlignmentAnnotation
         {
           min = annotations[i].value;
         }
+        if (_linecolour == null && annotations[i].colour != null)
+        {
+          _linecolour = annotations[i].colour;
+        }
       }
       // ensure zero is origin for min/max ranges on only one side of zero
       if (min > 0)
@@ -582,9 +617,9 @@ 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.centreColLabels = annotation.centreColLabels;
+    this.scaleColLabel = annotation.scaleColLabel;
+    this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
     if (this.hasScore = annotation.hasScore)
     {
@@ -600,7 +635,14 @@ public class AlignmentAnnotation
       this.annotations = new Annotation[ann.length];
       for (int i = 0; i < ann.length; i++)
       {
-        annotations[i] = new Annotation(ann[i]);
+        if (ann[i] != null)
+        {
+          annotations[i] = new Annotation(ann[i]);
+          if (_linecolour != null)
+          {
+            _linecolour = annotations[i].colour;
+          }
+        }
       }
       ;
       if (annotation.sequenceRef != null)
@@ -636,7 +678,7 @@ public class AlignmentAnnotation
       }
     }
     // TODO: check if we need to do this: JAL-952
-    //if (this.isrna=annotation.isrna)
+    // if (this.isrna=annotation.isrna)
     {
       // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
     }
@@ -1009,7 +1051,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] == null)
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
-                  ' ', 0f,null);
+                  ' ', 0f, null);
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
           annotations[i].displayCharacter = String.valueOf(gapchar);
@@ -1028,11 +1070,12 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
-      int i=description.toLowerCase().indexOf("<html>");
-      if (i>-1)
+      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 "<html>" + sequenceRef.getName() + " : "
+                + description.substring(i + 6);
       }
       return sequenceRef.getName() + " : " + description;
     }
@@ -1041,8 +1084,9 @@ public class AlignmentAnnotation
 
   public boolean isValidStruc()
   {
-    return invalidrnastruc==-1;
+    return invalidrnastruc == -1;
   }
+
   public long getInvalidStrucPos()
   {
     return invalidrnastruc;
@@ -1051,7 +1095,14 @@ public class AlignmentAnnotation
   /**
    * machine readable ID string indicating what generated this annotation
    */
-  protected String calcId="";
+  protected String calcId = "";
+
+  /**
+   * base colour for line graphs. If null, will be set automatically by
+   * searching the alignment annotation
+   */
+  public java.awt.Color _linecolour;
+
   public String getCalcId()
   {
     return calcId;
@@ -1061,7 +1112,4 @@ public class AlignmentAnnotation
   {
     this.calcId = calcId;
   }
-  
- 
-  
 }