X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=13d1d55951c9218d2328a8954bd9a430572035e1;hb=97f870ff4890ebfadcbb73e6793c83f856948658;hp=47aebd1eb832a44cb1d3ffd6a4144d3656536ca7;hpb=516ce4f35f75fe4775f3299742b2f453ae7d21fe;p=jalview.git

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 47aebd1..13d1d55 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,89 +1,179 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
-import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.io.TCoffeeScoreFile;
 
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.IdentityHashMap;
-import java.util.TreeMap;
+import java.util.List;
+import java.util.Map;
 
 /**
- * Defines the color score for T-Coffee MSA 
+ * Defines the color score for T-Coffee MSA
  * <p>
  * See http://tcoffee.org
  * 
  * 
  * @author Paolo Di Tommaso
- *
+ * 
  */
-public class TCoffeeColourScheme extends ResidueColourScheme {
+public class TCoffeeColourScheme extends ResidueColourScheme
+{
+  IdentityHashMap<SequenceI, Color[]> seqMap;
+
+  /**
+   * Default constructor (required for Class.newInstance())
+   */
+  public TCoffeeColourScheme()
+  {
+
+  }
+
+  /**
+   * the color scheme needs to look at the alignment to get and cache T-COFFEE
+   * scores
+   * 
+   * @param alignment
+   *          - annotated sequences to be searched
+   */
+  public TCoffeeColourScheme(AnnotatedCollectionI alignment)
+  {
+    alignmentChanged(alignment, null);
+  }
+
+  /**
+   * Finds the TCoffeeScore annotation (if any) for each sequence and notes the
+   * annotation colour for each column position. The colours are fixed for
+   * scores 0-9 and are set when annotation is parsed.
+   * 
+   * @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
+   */
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    // TODO: if sequences have been represented and they have scores, could
+    // compute an average sequence score for the representative
+
+    // assume only one set of TCOFFEE scores - but could have more than one
+    // potentially.
+    List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+    // Search alignment to get all tcoffee annotation and pick one set of
+    // annotation to use to colour seqs.
+    seqMap = new IdentityHashMap<SequenceI, Color[]>();
+    AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+            : alignment.getContext();
+    if (alcontext == null)
+    {
+      return;
+    }
+    int w = 0;
+    for (AlignmentAnnotation al : alcontext
+            .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
+    {
+      if (al.sequenceRef != null && !al.belowAlignment)
+      {
+        annots.add(al);
+        if (w < al.annotations.length)
+        {
+          w = al.annotations.length;
+        }
+        Color[] scores = new Color[al.annotations.length];
+        int i = 0;
+        for (Annotation an : al.annotations)
+        {
+          scores[i++] = (an != null) ? an.colour : Color.white;
+        }
+        seqMap.put(al.sequenceRef, scores);
+      }
+    }
+    // TODO: compute average colour for each symbol type in each column - gives
+    // a second order colourscheme for colouring a sequence logo derived from
+    // the alignment (colour reflects quality of alignment for each residue
+    // class)
+  }
+
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    if (seqMap == null)
+    {
+      return Color.WHITE;
+    }
+    Color[] cols = seqMap.get(seq);
+    if (cols == null)
+    {
+      // see above TODO about computing a colour for each residue in each
+      // column: cc = _rcols[i][indexFor[c]];
+      return Color.white;
+    }
+
+    if (j < 0 || j >= cols.length)
+    {
+      return Color.white;
+    }
+    return cols[j];
+  }
 
-	static final Color[] colors = {
-		new Color( 102, 102, 255 ),	// #6666FF
-		new Color( 0, 255, 0),		// #00FF00
-		new Color( 102, 255, 0),	// #66FF00
-		new Color( 204, 255, 0),	// #CCFF00
-		new Color( 255, 255, 0),	// #FFFF00
-		new Color( 255, 204, 0),	// #FFCC00
-		new Color( 255, 153, 0),	// #FF9900
-		new Color( 255, 102, 0),	// #FF6600
-		new Color( 255, 51, 0), 	// #FF3300
-		new Color( 255, 34, 0)		// #FF2000
-	};
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    return new TCoffeeColourScheme(sg);
+  }
 
+  /**
+   * Answers true if the data has TCoffee score annotation
+   */
+  @Override
+  public boolean isApplicableTo(AnnotatedCollectionI ac)
+  {
+    AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac : ac
+            .getContext();
+    if (alcontext == null)
+    {
+      return false;
+    }
+    Iterable<AlignmentAnnotation> anns = alcontext
+            .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
+    return anns.iterator().hasNext();
+  }
 
-	IdentityHashMap<SequenceI, Color[]> seqMap;
-	/**
-	 * the color scheme needs to look at the alignment to get and cache T-COFFEE scores 
-	 * 
-	 * @param alignment - annotated sequences to be searched
-	 */
-	public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
-	  alignmentChanged(alignment);
-	}
-	@Override public void alignmentChanged(AnnotatedCollectionI alignment)
-	{
-          // assume only one set of TCOFFEE scores - but could have more than one potentially.
-          ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
-          // Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
-          seqMap = new IdentityHashMap<SequenceI, Color[]>();
-          int w=0;
-          for (AlignmentAnnotation al:alignment.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
-          {
-            if (al.sequenceRef!=null && !al.belowAlignment)
-            {
-              annots.add(al);
-              if (w<al.annotations.length)
-              {
-                w=al.annotations.length;
-              }
-              Color[] scores=new Color[al.annotations.length];
-              int i=0;
-              for (Annotation an:al.annotations)
-              {
-                scores[i++]=(an!=null) ? an.colour : Color.white;
-              }
-              seqMap.put(al.sequenceRef, scores);
-            }
-          }
-	}
-	@Override
-	public Color findColour(char c, int j, SequenceI seq) {
-          Color[] cols;
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.TCoffee.toString();
+  }
 
-	  if( seqMap==null || (cols=seqMap.get(seq))==null) {
-	    return Color.white;
-	  }
-	  
-	  if( j < 0 || j>= cols.length ) {
-	    return Color.white;
-	  }
-	  return cols[j];
-	}
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
 }