From 96786b7b949dc261a9556e13a17870166915d0e9 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 15 Aug 2005 12:13:33 +0000
Subject: [PATCH] Percentage precalculated in aafrequency

---
 src/jalview/schemes/PIDColourScheme.java     |   12 +++-------
 src/jalview/schemes/ResidueColourScheme.java |   32 ++++++++++++++++----------
 src/jalview/schemes/ResidueProperties.java   |   20 ++++++++++++++++
 3 files changed, 43 insertions(+), 21 deletions(-)

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index cfc9f94..8cea507 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -18,8 +18,6 @@
  */
 package jalview.schemes;
 
-import java.util.*;
-
 import java.awt.*;
 
 import jalview.datamodel.*;
@@ -45,18 +43,14 @@ public class PIDColourScheme
     }
 
     Color c = Color.white;
-    Hashtable hash = (Hashtable) consensus.elementAt(j);
 
     double sc = 0;
 
-    if ( (Integer.parseInt(hash.get("maxCount").toString()) != -1) &&
-        hash.contains(s))
+    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+        consensus[j].contains(s))
     {
-      sc = ( ( (Integer) hash.get(s)).intValue() * 100.0) /
-          ( (Integer) hash.get(
-              "size")).intValue();
+      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
 
-      // MC Should be isGap
       if (!jalview.util.Comparison.isGap( (s.charAt(0))))
       {
         for (int i = 0; i < thresholds.length; i++)
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 9c10e7d..3181cf4 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -34,8 +34,11 @@ public class ResidueColourScheme implements ColourSchemeI
     Color[] colors;
     int threshold = 0;
 
+    /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
+    protected String ignoreGaps = "pid_gaps";
+
     /** DOCUMENT ME!! */
-    public Vector consensus;
+    public Hashtable [] consensus;
 
     /**
      * Creates a new ResidueColourScheme object.
@@ -61,9 +64,12 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @param consensus DOCUMENT ME!
      */
-    public void setConsensus(Vector consensus)
+    public void setConsensus(Vector vconsensus)
     {
-        this.consensus = consensus;
+       int i, iSize=vconsensus.size();
+       consensus = new Hashtable[iSize];
+       for(i=0; i<iSize; i++)
+        consensus[i] = (Hashtable)vconsensus.elementAt(i);
     }
 
     /**
@@ -113,9 +119,13 @@ public class ResidueColourScheme implements ColourSchemeI
      *
      * @param ct DOCUMENT ME!
      */
-    public void setThreshold(int ct)
+    public void setThreshold(int ct, boolean ignoreGaps)
     {
         threshold = ct;
+        if(ignoreGaps)
+          this.ignoreGaps = "pid_nogaps";
+        else
+          this.ignoreGaps = "pid_gaps";
     }
 
     /**
@@ -128,16 +138,14 @@ public class ResidueColourScheme implements ColourSchemeI
      */
     public boolean aboveThreshold(String s, int j)
     {
-        Hashtable hash = (Hashtable) consensus.elementAt(j);
-
-        if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
-                hash.contains(s))
+      if(consensus==null)
+        System.out.println("its null");
+        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
+                consensus[j].contains(s))
         {
-            ////  resCount////////////////////                  ///////////////seq count////////////
-            double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
-                    "size")).intValue();
+            float ratio =  ((Float)consensus[j].get(ignoreGaps)).floatValue();
 
-            if (sc >= threshold)
+            if (ratio >= threshold)
             {
                 return true;
             }
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 14479a7..0b71381 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -138,25 +138,45 @@ public class ResidueProperties
   static
   {
     aa2Triplet.put("A", "ALA");
+    aa2Triplet.put("a", "ALA");
     aa2Triplet.put("R", "ARG");
+    aa2Triplet.put("r", "ARG");
     aa2Triplet.put("N", "ASN");
+    aa2Triplet.put("n", "ASN");
     aa2Triplet.put("D", "ASP");
+    aa2Triplet.put("d", "ASP");
     aa2Triplet.put("C", "CYS");
+    aa2Triplet.put("c", "CYS");
     aa2Triplet.put("Q", "GLN");
+    aa2Triplet.put("q", "GLN");
     aa2Triplet.put("E", "GLU");
+    aa2Triplet.put("e", "GLU");
     aa2Triplet.put("G", "GLY");
+    aa2Triplet.put("g", "GLY");
     aa2Triplet.put("H", "HIS");
+    aa2Triplet.put("h", "HIS");
     aa2Triplet.put("I", "ILE");
+    aa2Triplet.put("i", "ILE");
     aa2Triplet.put("L", "LEU");
+    aa2Triplet.put("l", "LEU");
     aa2Triplet.put("K", "LYS");
+    aa2Triplet.put("k", "LYS");
     aa2Triplet.put("M", "MET");
+    aa2Triplet.put("m", "MET");
     aa2Triplet.put("F", "PHE");
+    aa2Triplet.put("f", "PHE");
     aa2Triplet.put("P", "PRO");
+    aa2Triplet.put("p", "PRO");
     aa2Triplet.put("S", "SER");
+    aa2Triplet.put("s", "SER");
     aa2Triplet.put("T", "THR");
+    aa2Triplet.put("t", "THR");
     aa2Triplet.put("W", "TRP");
+    aa2Triplet.put("w", "TRP");
     aa2Triplet.put("Y", "TYR");
+    aa2Triplet.put("y", "TYR");
     aa2Triplet.put("V", "VAL");
+    aa2Triplet.put("v", "VAL");
   }
 
   public static String[] aa =
-- 
1.7.10.2