* 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";
*/
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);
}
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
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)
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);
}
}
{
String err = "Unexpected aaIndex score matrix data at line " + lineNo
+ ": " + data;
-
+
try
{
String[] toks = data.split(",");