JAL-2418 source formatting

[jalview.git] / src / jalview / io / ScoreMatrixFile.java

diff --git a/src/jalview/io/ScoreMatrixFile.java b/src/jalview/io/ScoreMatrixFile.java
index 6b2f891..ad1527c 100644 (file)
--- a/src/jalview/io/ScoreMatrixFile.java
+++ b/src/jalview/io/ScoreMatrixFile.java
@@ -30,8 +30,8 @@ import java.util.StringTokenizer;
  * and the substitution scores
  * </pre>
  */
-public class ScoreMatrixFile extends AlignFile implements
-        AlignmentFileReaderI
+public class ScoreMatrixFile extends AlignFile
+        implements AlignmentFileReaderI
 {
   // first non-comment line identifier - also checked in IdentifyFile
   public static final String SCOREMATRIX = "SCOREMATRIX";
@@ -186,9 +186,9 @@ public class ScoreMatrixFile extends AlignFile implements
      */
     if (row < size)
     {
-      err = String
-              .format("Expected %d rows of score data in score matrix but only found %d",
-                      size, row);
+      err = String.format(
+              "Expected %d rows of score data in score matrix but only found %d",
+              size, row);
       throw new FileFormatException(err);
     }
 
@@ -312,9 +312,9 @@ public class ScoreMatrixFile extends AlignFile implements
       String symbol = scoreLine.nextToken();
       if (symbol.length() > 1 || symbol.charAt(0) != alphabet[row])
       {
-        err = String
-                .format("Error parsing score matrix at line %d, expected '%s' but found '%s'",
-                        lineNo, alphabet[row], symbol);
+        err = String.format(
+                "Error parsing score matrix at line %d, expected '%s' but found '%s'",
+                lineNo, alphabet[row], symbol);
         throw new FileFormatException(err);
       }
       tokenCount = scoreLine.countTokens(); // excluding guide symbol
@@ -328,7 +328,7 @@ public class ScoreMatrixFile extends AlignFile implements
       err = String.format(
               "Expected %d scores at line %d: '%s' but found %d", row + 1,
               lineNo, data, tokenCount);
-        throw new FileFormatException(err);
+      throw new FileFormatException(err);
     }
 
     if (!isLowerDiagonalOnly && tokenCount != size)
@@ -359,9 +359,8 @@ public class ScoreMatrixFile extends AlignFile implements
         col++;
       } catch (NumberFormatException e)
       {
-        err = String.format(
-                "Invalid score value '%s' at line %d column %d", value,
-                lineNo, col);
+        err = String.format("Invalid score value '%s' at line %d column %d",
+                value, lineNo, col);
         throw new FileFormatException(err);
       }
     }
@@ -387,7 +386,7 @@ public class ScoreMatrixFile extends AlignFile implements
   {
     String err = "Unexpected aaIndex score matrix data at line " + lineNo
             + ": " + data;
-    
+
     try
     {
       String[] toks = data.split(",");