Draw helices correctly

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 7c36208..df90500 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -52,12 +52,6 @@ public class ResidueColourScheme implements ColourSchemeI
    /** DOCUMENT ME!! */\r
    int inc = 30;\r
 \r
-   /**\r
-    * The colour to be calculated, manipulated and returned\r
-    */\r
-   Color currentColour = null;\r
-\r
-\r
 \r
     /**\r
      * Creates a new ResidueColourScheme object.\r
@@ -81,21 +75,20 @@ public class ResidueColourScheme implements ColourSchemeI
     /**\r
     * Find a colour without an index in a sequence\r
     */\r
-   public Color findColour(String aa)\r
+   public Color findColour(char c)\r
    {\r
-       return colors[ResidueProperties.aaIndex[aa.charAt(0)]];\r
+       return colors[ResidueProperties.aaIndex[c]];\r
    }\r
 \r
 \r
 \r
-   public Color findColour(String s, int j)\r
+   public Color findColour(char c, int j)\r
    {\r
+       Color currentColour;\r
 \r
-       int index = ResidueProperties.aaIndex[s.charAt(0)];\r
-\r
-       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
+       if ((threshold == 0) || aboveThreshold(c, j))\r
        {\r
-           currentColour = colors[index];\r
+           currentColour = colors[ResidueProperties.aaIndex[c]];\r
        }\r
        else\r
        {\r
@@ -103,7 +96,7 @@ public class ResidueColourScheme implements ColourSchemeI
        }\r
 \r
        if(conservationColouring)\r
-         applyConservation(j);\r
+         currentColour = applyConservation(currentColour, j);\r
 \r
 \r
        return currentColour;\r
@@ -142,25 +135,25 @@ public class ResidueColourScheme implements ColourSchemeI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public boolean aboveThreshold(String s, int j)\r
+    public boolean aboveThreshold(char c, int j)\r
     {\r
-      char c = s.charAt(0);\r
       if ('a' <= c && c <= 'z')\r
         {\r
           // TO UPPERCASE !!!\r
           //Faster than toUpperCase\r
           c -= ('a' - 'A');\r
-          s = String.valueOf(c);\r
         }\r
 \r
+        if (consensus == null || consensus[j] == null)\r
+          return false;\r
 \r
-      if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&\r
-                consensus[j].contains(s))\r
+        if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&\r
+            consensus[j].contains(String.valueOf(c)))\r
         {\r
-            if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
-            {\r
-                return true;\r
-            }\r
+          if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
+          {\r
+            return true;\r
+          }\r
         }\r
 \r
         return false;\r
@@ -225,7 +218,7 @@ public class ResidueColourScheme implements ColourSchemeI
     * @return DOCUMENT ME!\r
     */\r
 \r
-   void applyConservation(int i)\r
+   Color applyConservation(Color currentColour, int i)\r
    {\r
 \r
      if ((conservation[i] != '*') && (conservation[i] != '+'))\r
@@ -239,8 +232,7 @@ public class ResidueColourScheme implements ColourSchemeI
          float t = 11 - (conservation[i] - '0');\r
          if(t==0)\r
          {\r
-           currentColour = Color.white;\r
-           return;\r
+           return Color.white;\r
          }\r
 \r
          int red = currentColour.getRed();\r
@@ -265,6 +257,7 @@ public class ResidueColourScheme implements ColourSchemeI
            currentColour = new Color(red, green, blue);\r
        }\r
        }\r
+       return currentColour;\r
    }\r
 \r
 \r