X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=c3ec9514f77a99b68700071947b5d6be16d236ca;hb=46f8b484bb166375423eab4387dca05b48a9a8ff;hp=158ba6b2ae61565db40697f99c9491b38635a5c5;hpb=2bd43f464e725844b02a106c2d2f187c2c3655a6;p=jalview.git
diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 158ba6b..c3ec951 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -1,19 +1,22 @@
/*
- * 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 .
+ * 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;
@@ -86,11 +89,12 @@ import java.util.regex.Pattern;
* @author Paolo Di Tommaso
*
*/
-public class TCoffeeScoreFile extends AlignFile {
-
- public TCoffeeScoreFile(String inFile, String type) throws IOException
+public class TCoffeeScoreFile extends AlignFile
+{
+ public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, fileSourceType);
}
@@ -210,6 +214,7 @@ public class TCoffeeScoreFile extends AlignFile {
return result;
}
+ @Override
public void parse() throws IOException
{
/*
@@ -394,8 +399,9 @@ 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.
*
@@ -456,10 +462,11 @@ 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);
@@ -520,8 +527,7 @@ 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
@@ -548,8 +554,11 @@ 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;
@@ -636,7 +645,7 @@ public class TCoffeeScoreFile extends AlignFile {
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
// TODO Auto-generated method stub
return "Not valid.";