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JAL-629 Much better way of dealing with list of filenames/URLs without an --open...
[jalview.git]
/
src
/
jalview
/
io
/
MSFfile.java
diff --git
a/src/jalview/io/MSFfile.java
b/src/jalview/io/MSFfile.java
index
df2bed2
..
0a0520a
100755
(executable)
--- a/
src/jalview/io/MSFfile.java
+++ b/
src/jalview/io/MSFfile.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
@@
-134,7
+136,7
@@
public class MSFfile extends AlignFile
}
} catch (IOException e)
{
}
} catch (IOException e)
{
- System.err.println("Exception parsing MSFFile " + e);
+ jalview.bin.Console.errPrintln("Exception parsing MSFFile " + e);
e.printStackTrace();
}
e.printStackTrace();
}
@@
-167,7
+169,7
@@
public class MSFfile extends AlignFile
}
else
{
}
else
{
- System.err.println("MSFFile Parser: Can't find sequence for "
+ jalview.bin.Console.errPrintln("MSFFile Parser: Can't find sequence for "
+ headers.get(i));
}
}
+ headers.get(i));
}
}
@@
-184,7
+186,7
@@
public class MSFfile extends AlignFile
public int checkSum(String seq)
{
int check = 0;
public int checkSum(String seq)
{
int check = 0;
- String sequence = seq.toUpperCase();
+ String sequence = seq.toUpperCase(Locale.ROOT);
for (int i = 0; i < sequence.length(); i++)
{
for (int i = 0; i < sequence.length(); i++)
{
@@
-198,7
+200,7
@@
public class MSFfile extends AlignFile
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- System.err.println("Exception during MSF Checksum calculation");
+ jalview.bin.Console.errPrintln("Exception during MSF Checksum calculation");
e.printStackTrace();
}
}
e.printStackTrace();
}
}
@@
-370,8
+372,7
@@
public class MSFfile extends AlignFile
int end = start + 10;
int length = s[j].getLength();
int end = start + 10;
int length = s[j].getLength();
- if ((end < length)
- && (start < length))
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequence(start, end));
{
out.append(s[j].getSequence(start, end));