isGap method implemented in utils, and optimized

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e587fee..cc050d5 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -16,7 +16,7 @@ public class PIDColourScheme extends ResidueColourScheme {
     }\r
 \r
 \r
-  public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
+  public Color findColour(String s, int j,Vector aa) {\r
       Color     c    = Color.white;\r
       Hashtable hash = null;\r
 \r
@@ -31,10 +31,9 @@ public class PIDColourScheme extends ResidueColourScheme {
       double sc = 0;\r
       if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
       {\r
-\r
         sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
         // MC Should be isGap\r
-        if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
+        if (!jalview.util.Comparison.isGap((s.charAt(0))))\r
         {\r
           for (int i = 0; i < thresholds.length; i++)\r
           {\r
@@ -45,8 +44,7 @@ public class PIDColourScheme extends ResidueColourScheme {
             }\r
           }\r
         }\r
-        else\r
-          c = Color.white;\r
+\r
       }\r
       return c;\r
   }\r

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f16bcca..b0a5caa 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -6,7 +6,7 @@ import java.awt.*;
 \r
 public class ResidueColourScheme implements ColourSchemeI{\r
     Color    [] colors;\r
-    int         threshold = 90;\r
+    int       threshold = 0;\r
 \r
     public ResidueColourScheme(Color[] colors, int threshold) {\r
        this.colors    = colors;\r
@@ -21,31 +21,14 @@ public class ResidueColourScheme implements ColourSchemeI{
       return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
     }\r
 \r
-    public Color findColour(SequenceI seq,String s, int j, Vector aa) {\r
-  try {\r
-           return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
-       } catch (Exception e) {\r
-           return Color.white;\r
-       }\r
-    }\r
-\r
-    // aa should maybe be a class\r
-  /*  public Color getColour(SequenceI seq, int j,Vector aa) {\r
-\r
-       Color  c       = Color.white;\r
-       String s       = seq.getSequence(j,j+1);\r
-\r
-       if (threshold > 0 && aa != null)\r
-        {\r
-           if (aboveThreshold(aa,seq,j,threshold))\r
-               c = findColour(seq,s,j,aa);\r
-       }\r
-        else\r
-           c = findColour(seq,s,j,aa);\r
+    public Color findColour(String s, int j, Vector aa) {\r
 \r
+       if( threshold==0 || aboveThreshold(aa,s,j))\r
+          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
+       else\r
+          return Color.white;\r
 \r
-      return c;\r
-    }*/\r
+    }\r
 \r
     public int getThreshold() {\r
        return threshold;\r
@@ -55,29 +38,21 @@ public class ResidueColourScheme implements ColourSchemeI{
        threshold = ct;\r
     }\r
 \r
-    public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {\r
-       String    s    = seq.getSequence(j,j+1);\r
-       Hashtable hash = (Hashtable)aa.elementAt(j);\r
+    public boolean aboveThreshold(Vector aa,String s, int j)\r
+    {\r
 \r
-       if (j < aa.size()) {\r
-           String maxRes = (String)hash.get("maxResidue");\r
+       Hashtable hash = (Hashtable)aa.elementAt(j);\r
 \r
-           double sc = 0;\r
+        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.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 (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {\r
-               int maxCount = ((Integer)hash.get("maxCount")).intValue();\r
-               int resCount = ((Integer)hash.get(s)).intValue();\r
+          if (sc >= threshold)\r
+            return true;\r
 \r
-               sc = resCount * 100.0 / resCount;\r
+        }\r
 \r
-               // This should be isGap somewhere\r
-               if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {\r
-                   if (sc >= (double)threshold) {\r
-                       return true;\r
-                   }\r
-               }\r
-           }\r
-       }\r
        return false;\r
     }\r
 \r