JAL-3675 release notes for JAL-3750 JAL-3751

[jalview.git] / src / jalview / schemes / PIDColourScheme.java

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 18fc6e4..3a5c066 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,93 +1,105 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import java.awt.Color;
 
 public class PIDColourScheme extends ResidueColourScheme
 {
-  public Color[] pidColours;
+  private static final Color[] pidColours = { new Color(100, 100, 255),
+      new Color(153, 153, 255), new Color(204, 204, 255), };
 
-  public float[] thresholds;
+  private static final float[] thresholds = { 80, 60, 40, };
 
   SequenceGroup group;
 
   public PIDColourScheme()
   {
-    this.pidColours = ResidueProperties.pidColours;
-    this.thresholds = ResidueProperties.pidThresholds;
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq,
+          String consensusResidue, float pid)
   {
+    /*
+     * compare as upper case; note consensusResidue is 
+     * always computed as uppercase
+     */
     if ('a' <= c && c <= 'z')
     {
       c -= ('a' - 'A');
     }
 
-    if (consensus == null || j >= consensus.length || consensus[j] == null)
-    {
-      return Color.white;
-    }
-
-    if ((threshold != 0) && !aboveThreshold(c, j))
+    if (consensusResidue == null || Comparison.isGap(c))
     {
       return Color.white;
     }
 
-    Color currentColour = Color.white;
+    Color colour = Color.white;
 
-    double sc = 0;
-
-    if (consensus.length <= j)
-    {
-      return Color.white;
-    }
-
-    if ((Integer
-            .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
-            && consensus[j].contains(String.valueOf(c)))
+    /*
+     * test whether this is the consensus (or joint consensus) residue
+     */
+    boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
+    if (matchesConsensus)
     {
-      sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
-
-      if (!jalview.util.Comparison.isGap(c))
+      for (int i = 0; i < thresholds.length; i++)
       {
-        for (int i = 0; i < thresholds.length; i++)
+        if (pid > thresholds[i])
         {
-          if (sc > thresholds[i])
-          {
-            currentColour = pidColours[i];
-
-            break;
-          }
+          colour = pidColours[i];
+          break;
         }
       }
     }
 
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
+    return colour;
+  }
 
-    return currentColour;
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.PID.toString();
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
+  {
+    return new PIDColourScheme();
+  }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
   }
 }