JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 69cd269..9dd763d 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,59 +1,97 @@
-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
-  public Color getColour(SequenceI seq, int j,Vector aa) {\r
-    Color c = Color.white;\r
-\r
-    String       s = seq.getSequence(j,j+1);\r
-\r
-    if (aa != null && j < aa.size()) {\r
-       c = findColour(seq,s,j,aa);\r
-    }\r
-\r
-    return c;\r
-  }\r
-\r
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
-      Color     c    = Color.white;\r
-      Hashtable hash = null;\r
-\r
-      if (aa != null) {\r
-         hash = (Hashtable)aa.elementAt(j);\r
-      }\r
-      else\r
-        return c;\r
-\r
-      String    max  = (String)hash.get("maxResidue");\r
-\r
-      double sc = 0;\r
-      if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {\r
-         sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));\r
-\r
-         // MC Should be isGap\r
-         if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {\r
-             for (int i=0; i < thresholds.length; i++) {\r
-                 if (sc > thresholds[i]) {\r
-                     c = pidColours[i];\r
-                     break;\r
-                 }\r
-             }\r
-         } else {\r
-             c = Color.white;\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.analysis.AAFrequency;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+  public Color[] pidColours;
+
+  public float[] thresholds;
+
+  SequenceGroup group;
+
+  public PIDColourScheme()
+  {
+    this.pidColours = ResidueProperties.pidColours;
+    this.thresholds = ResidueProperties.pidThresholds;
+  }
+
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    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))
+    {
+      return Color.white;
+    }
+
+    Color currentColour = 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)))
+    {
+      sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
+
+      if (!jalview.util.Comparison.isGap(c))
+      {
+        for (int i = 0; i < thresholds.length; i++)
+        {
+          if (sc > thresholds[i])
+          {
+            currentColour = pidColours[i];
+
+            break;
+          }
+        }
+      }
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+}