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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
io
/
TCoffeeScoreFile.java
diff --git
a/src/jalview/io/TCoffeeScoreFile.java
b/src/jalview/io/TCoffeeScoreFile.java
index
7e5f0c3
..
07d7be4
100644
(file)
--- a/
src/jalview/io/TCoffeeScoreFile.java
+++ b/
src/jalview/io/TCoffeeScoreFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-89,7
+89,8
@@
import java.util.regex.Pattern;
* @author Paolo Di Tommaso
*
*/
* @author Paolo Di Tommaso
*
*/
-public class TCoffeeScoreFile extends AlignFile {
+public class TCoffeeScoreFile extends AlignFile
+{
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
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.
*
/**
* 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);
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);
result.items.put(id, val);
} while ((line = reader.nextLine()) != null);
@@
-522,8
+525,7
@@
public class TCoffeeScoreFile extends AlignFile {
/**
* TCOFFEE score colourscheme
*/
/**
* 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
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())
{
{
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;
return false;
}
boolean added = false;