formatting

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

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 895ee86..9341509 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -90,42 +90,49 @@ public class ScoreMatrix
   {\r
     return outputMatrix(false);\r
   }\r
+\r
   public String outputMatrix(boolean html)\r
   {\r
-    StringBuffer sb=new StringBuffer();\r
-    int[] symbols=(type==0) ? ResidueProperties.aaIndex : ResidueProperties.nucleotideIndex;\r
-    int symMax = (type==0) ? ResidueProperties.maxProteinIndex :ResidueProperties.maxNucleotideIndex;\r
-    boolean header=true;\r
+    StringBuffer sb = new StringBuffer();\r
+    int[] symbols = (type == 0) ? ResidueProperties.aaIndex\r
+            : ResidueProperties.nucleotideIndex;\r
+    int symMax = (type == 0) ? ResidueProperties.maxProteinIndex\r
+            : ResidueProperties.maxNucleotideIndex;\r
+    boolean header = true;\r
     if (html)\r
     {\r
       sb.append("<table>");\r
     }\r
-    for (char sym='A';sym<='Z';sym++)\r
+    for (char sym = 'A'; sym <= 'Z'; sym++)\r
     {\r
-      if (symbols[sym]>=0 && symbols[sym]<symMax)\r
+      if (symbols[sym] >= 0 && symbols[sym] < symMax)\r
       {\r
-        if (header) {\r
-          sb.append(html ? "<tr><td></td>" : "");\r
-        for (char sym2='A';sym2<='Z';sym2++)\r
+        if (header)\r
         {\r
-          if (symbols[sym2]>=0 && symbols[sym2]<symMax)\r
+          sb.append(html ? "<tr><td></td>" : "");\r
+          for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)\r
           {\r
-            sb.append((html ? "<td>&nbsp;" : "\t")+sym2 +(html ? "&nbsp;</td>": ""));\r
+            if (symbols[sym2] >= 0 && symbols[sym2] < symMax)\r
+            {\r
+              sb.append((html ? "<td>&nbsp;" : "\t") + sym2\r
+                      + (html ? "&nbsp;</td>" : ""));\r
+            }\r
           }\r
+          header = false;\r
+          sb.append(html ? "</tr>\n" : "\n");\r
         }\r
-        header=false;\r
-        sb.append(html ? "</tr>\n" : "\n");\r
-        } \r
         if (html)\r
         {\r
           sb.append("<tr>");\r
         }\r
-        sb.append((html ? "<td>" : "")+sym+(html ? "</td>" : ""));\r
-        for (char sym2='A';sym2<='Z';sym2++)\r
+        sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));\r
+        for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)\r
         {\r
-          if (symbols[sym2]>=0 && symbols[sym2]<symMax)\r
+          if (symbols[sym2] >= 0 && symbols[sym2] < symMax)\r
           {\r
-            sb.append((html ? "<td>" : "\t")+matrix[symbols[sym]][symbols[sym2]]+(html ? "</td>" : ""));\r
+            sb.append((html ? "<td>" : "\t")\r
+                    + matrix[symbols[sym]][symbols[sym2]]\r
+                    + (html ? "</td>" : ""));\r
           }\r
         }\r
         sb.append(html ? "</tr>\n" : "\n");\r