Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/io/ScoreMatrixFile.java b/src/jalview/io/ScoreMatrixFile.java
index 6b2f891..0b70dce 100644 (file)
--- a/src/jalview/io/ScoreMatrixFile.java
+++ b/src/jalview/io/ScoreMatrixFile.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.analysis.scoremodels.ScoreMatrix;
@@ -30,8 +50,8 @@ 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 +206,9 @@ 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 +332,9 @@ 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 +348,7 @@ 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 +379,8 @@ 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 +406,7 @@ public class ScoreMatrixFile extends AlignFile implements
   {
     String err = "Unexpected aaIndex score matrix data at line " + lineNo
             + ": " + data;
-    
+
     try
     {
       String[] toks = data.split(",");