Set size for mac users

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 3bd9bca..71f12c1 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,62 +1,154 @@
+/*\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.util.*;\r
 import java.awt.*;\r
 \r
-public class ResidueColourScheme implements ColourSchemeI{\r
-    Color    [] colors;\r
-    int       threshold = 0;\r
-    public Vector   consensus;\r
+import java.util.*;\r
+\r
 \r
-    public ResidueColourScheme(Color[] colors, int threshold) {\r
-        this.colors    = colors;\r
-       this.threshold = threshold;\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ResidueColourScheme implements ColourSchemeI\r
+{\r
+    Color[] colors;\r
+    int threshold = 0;\r
+\r
+    /* Set when threshold colouring to either pid_gaps or pid_nogaps*/\r
+    protected String ignoreGaps = "pid_gaps";\r
+\r
+    /** DOCUMENT ME!! */\r
+    public Hashtable [] consensus;\r
+\r
+    /**\r
+     * Creates a new ResidueColourScheme object.\r
+     *\r
+     * @param colors DOCUMENT ME!\r
+     * @param threshold DOCUMENT ME!\r
+     */\r
+    public ResidueColourScheme(Color[] colors, int threshold)\r
+    {\r
+        this.colors = colors;\r
+        this.threshold = threshold;\r
     }\r
 \r
+    /**\r
+     * Creates a new ResidueColourScheme object.\r
+     */\r
     public ResidueColourScheme()\r
-    {   }\r
+    {\r
+    }\r
 \r
-    public void setConsensus(Vector consensus)\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param consensus DOCUMENT ME!\r
+     */\r
+    public void setConsensus(Vector vconsensus)\r
     {\r
-      this.consensus = consensus;\r
+       int i, iSize=vconsensus.size();\r
+       consensus = new Hashtable[iSize];\r
+       for(i=0; i<iSize; i++)\r
+        consensus[i] = (Hashtable)vconsensus.elementAt(i);\r
     }\r
 \r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param aa DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
     public Color findColour(String aa)\r
     {\r
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
+        return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
     }\r
 \r
-    public Color findColour(String s, int j) {\r
-\r
-       if( threshold==0 || aboveThreshold(s,j))\r
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
-       else\r
-          return Color.white;\r
-\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param s DOCUMENT ME!\r
+     * @param j DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public Color findColour(String s, int j)\r
+    {\r
+        if ((threshold == 0) || aboveThreshold(s, j))\r
+        {\r
+            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
+        }\r
+        else\r
+        {\r
+            return Color.white;\r
+        }\r
     }\r
 \r
-    public int getThreshold() {\r
-       return threshold;\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public int getThreshold()\r
+    {\r
+        return threshold;\r
     }\r
 \r
-    public void setThreshold(int ct) {\r
-       threshold = ct;\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param ct DOCUMENT ME!\r
+     */\r
+    public void setThreshold(int ct, boolean ignoreGaps)\r
+    {\r
+        threshold = ct;\r
+        if(ignoreGaps)\r
+          this.ignoreGaps = "pid_nogaps";\r
+        else\r
+          this.ignoreGaps = "pid_gaps";\r
     }\r
 \r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param s DOCUMENT ME!\r
+     * @param j DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
     public boolean aboveThreshold(String s, int j)\r
     {\r
-       Hashtable hash = (Hashtable)consensus.elementAt(j);\r
-\r
-        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))\r
+        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
+                consensus[j].contains(s))\r
         {\r
-               ////  resCount////////////////////                  ///////////////seq count////////////\r
-          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();\r
-\r
-          if (sc >= threshold)\r
-            return true;\r
+            float ratio =  ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
 \r
+            if (ratio >= threshold)\r
+            {\r
+                return true;\r
+            }\r
         }\r
 \r
-       return false;\r
+        return false;\r
     }\r
 }\r