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 34c47ed..3a5c066 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,105 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-\r
-package jalview.schemes;\r
-\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class PIDColourScheme extends ResidueColourScheme {\r
-    public Color[] pidColours;\r
-    public float[] thresholds;\r
-\r
-    SequenceGroup group;\r
-\r
-    public PIDColourScheme() {\r
-       this.pidColours = ResidueProperties.pidColours;\r
-       this.thresholds = ResidueProperties.pidThresholds;\r
-    }\r
-\r
-\r
-\r
-  public Color findColour(String s, int j) {\r
-\r
-    if( threshold!=0 && !aboveThreshold(s,j))\r
-      return Color.white;\r
-\r
-    Color     c    = Color.white;\r
-      Hashtable hash =  (Hashtable)consensus.elementAt(j);\r
-\r
-      double sc = 0;\r
-      if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
-      {\r
-        sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
-        // MC Should be isGap\r
-        if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
-        {\r
-          for (int i = 0; i < thresholds.length; i++)\r
-          {\r
-            if (sc > thresholds[i])\r
-            {\r
-              c = pidColours[i];\r
-              break;\r
-            }\r
-          }\r
-        }\r
-\r
-      }\r
-      return c;\r
-  }\r
-}\r
+/*
+ * 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.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+  private static final Color[] pidColours = { new Color(100, 100, 255),
+      new Color(153, 153, 255), new Color(204, 204, 255), };
+
+  private static final float[] thresholds = { 80, 60, 40, };
+
+  SequenceGroup group;
+
+  public PIDColourScheme()
+  {
+  }
+
+  @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 (consensusResidue == null || Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+
+    Color colour = Color.white;
+
+    /*
+     * test whether this is the consensus (or joint consensus) residue
+     */
+    boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
+    if (matchesConsensus)
+    {
+      for (int i = 0; i < thresholds.length; i++)
+      {
+        if (pid > thresholds[i])
+        {
+          colour = pidColours[i];
+          break;
+        }
+      }
+    }
+
+    return colour;
+  }
+
+  @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;
+  }
+}