X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=fc922b936dc50605078944ddfe1cba2f407e0396;hb=004a35d07335854184fdd335920b7210eebd66d9;hp=253515434b247888b857816e7cb27e0f76579065;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 2535154..fc922b9 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,67 +1,106 @@
-/*
-* 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.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+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(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
+  {
+    return new PIDColourScheme();
+  }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
+}