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tidied up system.out messages and moved many to stderr.
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
08f7d17
..
b2226db
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-62,7
+62,7
@@
public class JPredFile
public void parse()
throws IOException
{
public void parse()
throws IOException
{
-System.out.println("all read in ");
+ // JBPNote log.System.out.println("all read in ");
String line;
QuerySeqPosition = -1;
noSeqs = 0;
String line;
QuerySeqPosition = -1;
noSeqs = 0;
@@
-136,7
+136,7
@@
System.out.println("all read in ");
}
else if (id.equals("jnetconf"))
{
}
else if (id.equals("jnetconf"))
{
- System.out.println("here");
+ // log.debug System.out.println("here");
id = "Prediction Confidence";
this.conf = new Vector(numSymbols);
for (int i = 0; i < numSymbols; i++)
id = "Prediction Confidence";
this.conf = new Vector(numSymbols);
for (int i = 0; i < numSymbols; i++)
@@
-241,7
+241,7
@@
System.out.println("all read in ");
}
catch (java.io.IOException e)
{
}
catch (java.io.IOException e)
{
- System.out.println("Exception " + e);
+ System.err.println("Exception " + e);
e.printStackTrace();
}
}
e.printStackTrace();
}
}