X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=a64bf20f1a749af03df2482ae9a884468b770585;hb=863467bf6c59c0bc5368c8f3a03d9d5a4f10700d;hp=7f4bebeae89016568d89bbe635c565f09fc6a1fe;hpb=0bdaa0deb6ee514912d2ed730e19f618bc44cb69;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 7f4bebe..a64bf20 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,89 +1,95 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.analysis.AAFrequency;
-
-public class PIDColourScheme
-    extends ResidueColourScheme
-{
-  public Color[] pidColours;
-  public float[] thresholds;
-  SequenceGroup group;
-
-  public PIDColourScheme()
-  {
-    this.pidColours = ResidueProperties.pidColours;
-    this.thresholds = ResidueProperties.pidThresholds;
-  }
-
-  public Color findColour(String s, int j)
-  {
-    char res = s.charAt(0);
-    if ('a' <= res && res <= 'z')
-    {
-      s = String.valueOf(res -= ('a' - 'A'));
-    }
-
-    if (consensus == null ||
-        j >= consensus.length)
-    {
-      return Color.white;
-    }
-
-    if ( (threshold != 0) && !aboveThreshold(s, j))
-    {
-      return Color.white;
-    }
-
-    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(s))
-      {
-        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
-
-        if (!jalview.util.Comparison.isGap(res))
-        {
-          for (int i = 0; i < thresholds.length; i++)
-          {
-            if (sc > thresholds[i])
-            {
-              currentColour = pidColours[i];
-
-              break;
-            }
-          }
-        }
-      }
-
-    if(conservationColouring)
-         applyConservation(j);
-
-    return currentColour;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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;
+  }
+}