X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=ac02ee5a3c395db30319bede783c8b0e553a9a1d;hb=8ba93f7655ea7165579539158b6a5eb076135bba;hp=ab603e15fbf958e72d38b7db957a23aea31220a3;hpb=27b77d2219147d3741d4af7377e13918a8ae972a;p=jalview.git
diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index ab603e1..ac02ee5 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
@@ -21,10 +23,11 @@ package jalview.schemes;
import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
import jalview.api.analysis.ScoreModelI;
-public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
+public class ScoreMatrix extends PairwiseSeqScoreModel implements
+ ScoreModelI
{
String name;
-
+
@Override
public String getName()
{
@@ -40,11 +43,15 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
* 0 for Protein Score matrix. 1 for dna score matrix
*/
int type;
+
/**
*
- * @param name Unique, human readable name for the matrix
- * @param matrix Pairwise scores indexed according to appropriate symbol alphabet
- * @param type 0 for Protein, 1 for NA
+ * @param name
+ * Unique, human readable name for the matrix
+ * @param matrix
+ * Pairwise scores indexed according to appropriate symbol alphabet
+ * @param type
+ * 0 for Protein, 1 for NA
*/
ScoreMatrix(String name, int[][] matrix, int type)
{
@@ -58,6 +65,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
{
return type == 1;
}
+
@Override
public boolean isProtein()
{
@@ -119,7 +127,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements ScoreModelI
boolean header = true;
if (html)
{
- sb.append("
");
+ sb.append("");
}
for (char sym = 'A'; sym <= 'Z'; sym++)
{