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JAL-4290 new CommandsTest.headlessOrGuiImageOutputTest - uses CommandLineOperations...
[jalview.git]
/
src
/
jalview
/
io
/
ClustalFile.java
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
a37afd9
..
b6f36e8
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-77,7
+77,9
@@
public class ClustalFile extends AlignFile
{
top = true;
}
{
top = true;
}
- if (line.indexOf(" ") != 0)
+ boolean isConservation = line.startsWith(SPACE)
+ || line.startsWith(TAB);
+ if (!isConservation)
{
str = new StringTokenizer(line);
{
str = new StringTokenizer(line);
@@
-138,7
+140,7
@@
public class ClustalFile extends AlignFile
}
} catch (IOException e)
{
}
} catch (IOException e)
{
- System.err.println("Exception parsing clustal file " + e);
+ jalview.bin.Console.errPrintln("Exception parsing clustal file " + e);
e.printStackTrace();
}
e.printStackTrace();
}
@@
-166,8
+168,9
@@
public class ClustalFile extends AlignFile
}
else
{
}
else
{
- System.err.println("Clustal File Reader: Can't find sequence for "
- + headers.elementAt(i));
+ jalview.bin.Console.errPrintln(
+ "Clustal File Reader: Can't find sequence for "
+ + headers.elementAt(i));
}
}
AlignmentAnnotation lastssa = null;
}
}
AlignmentAnnotation lastssa = null;