Formatting

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

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 00f8f6f..81947b3 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
@@ -18,18 +18,19 @@
  */\r
 package jalview.schemes;\r
 \r
+import java.util.*;\r
+\r
 import java.awt.*;\r
-import java.util.StringTokenizer;\r
 \r
 public class UserColourScheme\r
     extends ResidueColourScheme\r
 {\r
-  Color [] lowerCaseColours;\r
+  Color[] lowerCaseColours;\r
 \r
   protected String schemeName;\r
 \r
   public UserColourScheme()\r
-  {  }\r
+  {}\r
 \r
   public UserColourScheme(Color[] newColors)\r
   {\r
@@ -40,15 +41,17 @@ public class UserColourScheme
   {\r
     Color col = getColourFromString(colour);\r
 \r
-    if(col==null)\r
+    if (col == null)\r
     {\r
-      System.out.println("Unknown colour!! "+colour);\r
+      System.out.println("Unknown colour!! " + colour);\r
       col = createColourFromName(colour);\r
     }\r
 \r
     colors = new Color[24];\r
-    for(int i=0; i<24; i++)\r
+    for (int i = 0; i < 24; i++)\r
+    {\r
       colors[i] = col;\r
+    }\r
   }\r
 \r
   public Color[] getColours()\r
@@ -85,7 +88,9 @@ public class UserColourScheme
     {}\r
 \r
     if (col == null)\r
+    {\r
       col = ColourSchemeProperty.getAWTColorFromName(colour);\r
+    }\r
 \r
     if (col == null)\r
     {\r
@@ -119,7 +124,9 @@ public class UserColourScheme
     start = end;\r
     end += lsize / 3;\r
     if (end > lsize)\r
+    {\r
       end = lsize;\r
+    }\r
 \r
     g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;\r
 \r
@@ -134,8 +141,9 @@ public class UserColourScheme
   {\r
     StringTokenizer st = new StringTokenizer(paramValue, ";");\r
     StringTokenizer st2;\r
-    String token=null, colour, residues;\r
-    try{\r
+    String token = null, colour, residues;\r
+    try\r
+    {\r
       while (st.hasMoreElements())\r
       {\r
         token = st.nextToken().trim();\r
@@ -147,72 +155,85 @@ public class UserColourScheme
         {\r
           token = st2.nextToken();\r
 \r
-          if (ResidueProperties.aaIndex[token.charAt(0)]==-1)\r
+          if (ResidueProperties.aaIndex[token.charAt(0)] == -1)\r
+          {\r
             continue;\r
+          }\r
 \r
           int colIndex = ResidueProperties.aaIndex[token.charAt(0)];\r
 \r
-          if(token.equalsIgnoreCase("lowerCase"))\r
+          if (token.equalsIgnoreCase("lowerCase"))\r
           {\r
             if (lowerCaseColours == null)\r
+            {\r
               lowerCaseColours = new Color[23];\r
+            }\r
             for (int i = 0; i < 23; i++)\r
+            {\r
               if (lowerCaseColours[i] == null)\r
+              {\r
                 lowerCaseColours[i] = getColourFromString(colour);\r
+              }\r
+            }\r
 \r
-              continue;\r
+            continue;\r
           }\r
 \r
-          if(token.equals(token.toLowerCase()))\r
+          if (token.equals(token.toLowerCase()))\r
           {\r
-            if(lowerCaseColours==null)\r
+            if (lowerCaseColours == null)\r
             {\r
               lowerCaseColours = new Color[23];\r
             }\r
             lowerCaseColours[colIndex] = getColourFromString(colour);\r
           }\r
           else\r
+          {\r
             colors[colIndex] = getColourFromString(colour);\r
+          }\r
         }\r
       }\r
     }\r
-    catch(Exception ex)\r
-  {\r
-    System.out.println("Error parsing userDefinedColours:\n"\r
-                       +token+"\n"+ex);\r
-  }\r
+    catch (Exception ex)\r
+    {\r
+      System.out.println("Error parsing userDefinedColours:\n"\r
+                         + token + "\n" + ex);\r
+    }\r
 \r
   }\r
 \r
-\r
-\r
   public Color findColour(char c, int j)\r
   {\r
-      Color currentColour;\r
-      int index = ResidueProperties.aaIndex[c];\r
+    Color currentColour;\r
+    int index = ResidueProperties.aaIndex[c];\r
 \r
-      if ((threshold == 0) || aboveThreshold(c, j))\r
+    if ( (threshold == 0) || aboveThreshold(c, j))\r
+    {\r
+      if (lowerCaseColours != null && 'a' <= c && c <= 'z')\r
       {\r
-        if(lowerCaseColours!=null && 'a' <= c && c <= 'z')\r
-          currentColour = lowerCaseColours[index];\r
-        else\r
-          currentColour = colors[index];\r
+        currentColour = lowerCaseColours[index];\r
       }\r
       else\r
       {\r
-          currentColour = Color.white;\r
+        currentColour = colors[index];\r
       }\r
+    }\r
+    else\r
+    {\r
+      currentColour = Color.white;\r
+    }\r
 \r
-      if(conservationColouring)\r
-       currentColour =  applyConservation(currentColour, j);\r
-\r
+    if (conservationColouring)\r
+    {\r
+      currentColour = applyConservation(currentColour, j);\r
+    }\r
 \r
-      return currentColour;\r
-   }\r
+    return currentColour;\r
+  }\r
 \r
-   public void setLowerCaseColours(Color [] lcolours)\r
-   {\r
-     lowerCaseColours = lcolours;\r
-   }\r
+  public void setLowerCaseColours(Color[] lcolours)\r
+  {\r
+    lowerCaseColours = lcolours;\r
+  }\r
 \r
 }\r