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redirect error messages and exceptions to STDERR, not STDOUT #10

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redirect error messages and exceptions to STDERR, not STDOUT #10

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6b9122f
redirect error messages and exceptions to STDERR, not STDOUT
sjaenick Aug 5, 2015
263eea0
Merge branch 'rdpstaff:master' into master
sjaenick Dec 21, 2022
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4 changes: 2 additions & 2 deletions src/edu/msu/cme/rdp/classifier/ClassifierCmd.java
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ public void doClassify(String inputFile, String outFile, String propfile, Classi
wt.write(ClassificationResultFormatter.getOutput(result, format));

} catch (ShortSequenceException e) {
System.out.println(e.getMessage());
System.err.println(e.getMessage());
} catch (Exception e) {
e.printStackTrace();
}
Expand Down Expand Up @@ -181,7 +181,7 @@ public static void main(String[] args) throws Exception {
queryFile = args[0];

} catch (Exception e) {
System.out.println("Command Error: " + e.getMessage());
System.err.println("Command Error: " + e.getMessage());
new HelpFormatter().printHelp(120, "ClassifierCmd [options] <samplefile>\nNote this is the legacy command for one sample classification ", "", options, "");

return;
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8 changes: 4 additions & 4 deletions src/edu/msu/cme/rdp/classifier/comparison/ComparisonCmd.java
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Expand Up @@ -97,7 +97,7 @@ public void doClassify(String s1, String s2, String detailFile, String sigFile,
wt.write(ClassificationResultFormatter.getOutput(result, format));

} catch (ShortSequenceException e) {
System.out.println(e.getMessage());
System.err.println(e.getMessage());
} catch (Exception e) {
e.printStackTrace();
}
Expand All @@ -111,7 +111,7 @@ public void doClassify(String s1, String s2, String detailFile, String sigFile,
wt.write(ClassificationResultFormatter.getOutput(result, format));

} catch (ShortSequenceException e) {
System.out.println(e.getMessage());
System.err.println(e.getMessage());
} catch (Exception e) {
e.printStackTrace();
}
Expand Down Expand Up @@ -301,7 +301,7 @@ public static void main(String[] args) throws Exception {
}
}
} catch (Exception e) {
System.out.println("Command Error: " + e.getMessage());
System.err.println("Command Error: " + e.getMessage());
new HelpFormatter().printHelp(120, "ComparisonCmd", "", options, "", true);
return;
}
Expand All @@ -318,4 +318,4 @@ public static void main(String[] args) throws Exception {
cmd.doClassify(queryFile1, queryFile2, class_outputFile, compare_outputFile, format);

}
}
}
2 changes: 1 addition & 1 deletion src/edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker.java
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Expand Up @@ -162,7 +162,7 @@ public static void main(String[] args) throws FileNotFoundException,
}

} catch (Exception e) {
System.out.println("Command Error: " + e.getMessage());
System.err.println("Command Error: " + e.getMessage());
new HelpFormatter().printHelp(120, "train", "", options, "", true);
return;
}
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2 changes: 1 addition & 1 deletion src/edu/msu/cme/rdp/classifier/train/LineageSequenceParser.java
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Expand Up @@ -128,7 +128,7 @@ private String modifySequence(String s) {
out.close();
return out.toString();
} catch (IOException e) {
System.out.println("In StringReader or StringWriter exception : " + e.getMessage());
System.err.println("In StringReader or StringWriter exception : " + e.getMessage());
}
return null;
}
Expand Down
2 changes: 1 addition & 1 deletion src/edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTesterMain.java
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Expand Up @@ -177,7 +177,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
GoodWordIterator.setWordSize(kmer);
}*/
} catch (Exception e) {
System.out.println("Command Error: " + e.getMessage());
System.err.println("Command Error: " + e.getMessage());
new HelpFormatter().printHelp(120, "LeaveOneOutTesterMain", "", options, "", true);
return;
}
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2 changes: 1 addition & 1 deletion src/edu/msu/cme/rdp/classifier/utils/HierarchyVersion.java
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Expand Up @@ -26,7 +26,7 @@ public class HierarchyVersion {
try{
versionPattern = Pattern.compile(regex);
} catch(PatternSyntaxException pse){
System.out.println("There is a problem with the regular expression! " + regex);
System.err.println("There is a problem with the regular expression! " + regex);
}
}

Expand Down
2 changes: 1 addition & 1 deletion src/edu/msu/cme/rdp/multicompare/Main.java
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Expand Up @@ -239,7 +239,7 @@ public static void main(String[] args) throws Exception {
throw new IllegalArgumentException("Require at least one sample files");
}
}catch (Exception e) {
System.out.println("Command Error: " + e.getMessage());
System.err.println("Command Error: " + e.getMessage());
new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
return;
}
Expand Down
2 changes: 1 addition & 1 deletion src/edu/msu/cme/rdp/multicompare/Reprocess.java
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Expand Up @@ -169,7 +169,7 @@ public static void main(String [] args) throws Exception {

}
} catch (Exception e) {
System.out.println("Command Error: " + e.getMessage());
System.err.println("Command Error: " + e.getMessage());
new HelpFormatter().printHelp(120, "Reprocess [options] <Classification_allrank_result>[,idmappingfile] ...", "", options, "");
return;
}
Expand Down