X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=97de459be5f199ea3e3dceeafa71bc93d5b5f9ac;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=274f532448b47508da1715f97c4184fef9f9425a;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 274f532..97de459 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.io;
@@ -89,7 +91,6 @@ import java.util.regex.Pattern;
*/
public class TCoffeeScoreFile extends AlignFile
{
-
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
@@ -396,8 +397,9 @@ public class TCoffeeScoreFile extends AlignFile
}
}
- static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern.compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
-
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
/**
* Read a scores block ihe provided stream.
*
@@ -458,10 +460,11 @@ public class TCoffeeScoreFile extends AlignFile
String val = line.substring(p + 1).trim();
Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
- if( m.matches() ) {
- val = m.group(1);
+ if (m.matches())
+ {
+ val = m.group(1);
}
-
+
result.items.put(id, val);
} while ((line = reader.nextLine()) != null);
@@ -522,8 +525,7 @@ public class TCoffeeScoreFile extends AlignFile
/**
* TCOFFEE score colourscheme
*/
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
new Color(0, 255, 0), // #00FF00
new Color(102, 255, 0), // #66FF00
new Color(204, 255, 0), // #CCFF00
@@ -550,8 +552,11 @@ public class TCoffeeScoreFile extends AlignFile
{
if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
{
- String info = String.format("align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(), al.getHeight(), getWidth(), getHeight() );
- warningMessage = "Alignment shape does not match T-Coffee score file shape -- " + info;
+ String info = String.format(
+ "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
+ al.getHeight(), getWidth(), getHeight());
+ warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
+ + info;
return false;
}
boolean added = false;