/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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;
*/
public class TCoffeeScoreFile extends AlignFile
{
-
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
}
- 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.
*
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);
/**
* 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
{
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;