X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=9dd763defefdca617f86b56d20e10a8d9e9f69c3;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=253515434b247888b857816e7cb27e0f76579065;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 2535154..9dd763d 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,97 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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 jalview.datamodel.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-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) {
-        if ((threshold != 0) && !aboveThreshold(s, j)) {
-            return Color.white;
-        }
-
-        Color c = Color.white;
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
-
-        double sc = 0;
-
-        if ((Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
-                hash.contains(s)) {
-            sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
-                    "size")).intValue();
-
-            // MC Should be isGap
-            if (!jalview.util.Comparison.isGap((s.charAt(0)))) {
-                for (int i = 0; i < thresholds.length; i++) {
-                    if (sc > thresholds[i]) {
-                        c = pidColours[i];
-
-                        break;
-                    }
-                }
-            }
-        }
-
-        return c;
-    }
-}
+/*
+ * 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;
+  }
+}