updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

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

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 8cea507..d9fd7bd 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,70 +1,83 @@
-/*\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
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\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
-    if ( (threshold != 0) && !aboveThreshold(s, j))\r
-    {\r
-      return Color.white;\r
-    }\r
-\r
-    Color c = Color.white;\r
-\r
-    double sc = 0;\r
-\r
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
-        consensus[j].contains(s))\r
-    {\r
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
-\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
-\r
-            break;\r
-          }\r
-        }\r
-      }\r
-    }\r
-\r
-    return c;\r
-  }\r
-}\r
+/*
+ * 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.*;
+
+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 ( (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("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;
+  }
+}