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JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,
[jalview.git]
/
src
/
jalview
/
io
/
TCoffeeScoreFile.java
diff --git
a/src/jalview/io/TCoffeeScoreFile.java
b/src/jalview/io/TCoffeeScoreFile.java
index
ca8a22a
..
c3ec951
100644
(file)
--- a/
src/jalview/io/TCoffeeScoreFile.java
+++ b/
src/jalview/io/TCoffeeScoreFile.java
@@
-91,9
+91,10
@@
import java.util.regex.Pattern;
*/
public class TCoffeeScoreFile extends AlignFile
{
*/
public class TCoffeeScoreFile extends AlignFile
{
- public TCoffeeScoreFile(String inFile, String type) throws IOException
+ public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ throws IOException
{
{
- super(inFile, type);
+ super(inFile, fileSourceType);
}
}
@@
-213,6
+214,7
@@
public class TCoffeeScoreFile extends AlignFile
return result;
}
return result;
}
+ @Override
public void parse() throws IOException
{
/*
public void parse() throws IOException
{
/*
@@
-525,8
+527,7
@@
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
@@
-644,7
+645,7
@@
public class TCoffeeScoreFile extends AlignFile
}
@Override
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
// TODO Auto-generated method stub
return "Not valid.";
{
// TODO Auto-generated method stub
return "Not valid.";