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 8061e67..3a5c066 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,90 +1,105 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.analysis.AAFrequency;\r
-\r
-public class PIDColourScheme\r
-    extends ResidueColourScheme\r
-{\r
-  public Color[] pidColours;\r
-  public float[] thresholds;\r
-  SequenceGroup group;\r
-\r
-  public PIDColourScheme()\r
-  {\r
-    this.pidColours = ResidueProperties.pidColours;\r
-    this.thresholds = ResidueProperties.pidThresholds;\r
-  }\r
-\r
-  public Color findColour(String s, int j)\r
-  {\r
-    char res = s.charAt(0);\r
-    if ('a' <= res && res <= 'z')\r
-    {\r
-      s = String.valueOf(res -= ('a' - 'A'));\r
-    }\r
-\r
-    if (consensus == null\r
-        || j >= consensus.length\r
-        || consensus[j]==null)\r
-    {\r
-      return Color.white;\r
-    }\r
-\r
-    if ( (threshold != 0) && !aboveThreshold(s, j))\r
-    {\r
-      return Color.white;\r
-    }\r
-\r
-    currentColour = Color.white;\r
-\r
-    double sc = 0;\r
-\r
-    if(consensus.length<=j)\r
-      return Color.white;\r
-\r
-      if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1) &&\r
-          consensus[j].contains(s))\r
-      {\r
-        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
-\r
-        if (!jalview.util.Comparison.isGap(res))\r
-        {\r
-          for (int i = 0; i < thresholds.length; i++)\r
-          {\r
-            if (sc > thresholds[i])\r
-            {\r
-              currentColour = pidColours[i];\r
-\r
-              break;\r
-            }\r
-          }\r
-        }\r
-      }\r
-\r
-    if(conservationColouring)\r
-         applyConservation(j);\r
-\r
-    return currentColour;\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;
+  }
+}