clean up logging

etc/log4j.properties

@@ -31,7 +31,7 @@ log4j.logger.uk.ac.sanger.artemis.components.genebuilder.cv.GoBox=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.chado.ArtemisUtils=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.components.database.DatabaseJPanel=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.components.alignment.LookSeqPanel=DEBUG, R
-log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, stdout, R
+log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.io.ReadAndWriteEntry=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.util.FTPSeekableStream=DEBUG, R
 
@@ -53,8 +53,8 @@ log4j.logger.com.sshtools.j2ssh=WARN, R
 
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
-#log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) - %m%n
-log4j.appender.stdout.layout.ConversionPattern=%m%n
+log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) - %m%n
+#log4j.appender.stdout.layout.ConversionPattern=%m%n
 log4j.appender.Default=uk.ac.sanger.artemis.components.LogViewer
 log4j.appender.R=uk.ac.sanger.artemis.components.LogViewer
 log4j.appender.R.MaxLogLines=2000

uk/ac/sanger/artemis/components/variant/VCFRecord.java

@@ -399,8 +399,8 @@ public class VCFRecord
   
   protected static short checkSyn(CDSFeature gfeat, int basePosition, char variant)
   {
-    logger.info("CDSFEATURE\t"+gfeat);
-    logger.info("BASEANDVARIANT\t"+basePosition + "\t" + variant);
+    //logger.info("CDSFEATURE\t"+gfeat);
+    //logger.info("BASEANDVARIANT\t"+basePosition + "\t" + variant);
     if(gfeat.firstBase < basePosition && gfeat.lastBase > basePosition)
     {
       RangeVector ranges = gfeat.ranges;
@@ -443,11 +443,11 @@ public class VCFRecord
 
             char aaRef = AminoAcidSequence.getCodonTranslation(codon[0],
                   codon[1], codon[2]);
-            logger.info(String.format("%d %d %s%s%s", mod, codonStart, codon[0],codon[1],codon[2]));
+            //logger.info(String.format("%d %d %s%s%s", mod, codonStart, codon[0],codon[1],codon[2]));
             if(!gfeat.isFwd)
               variant = Bases.complement(variant);
             codon[mod] = variant;
-            logger.info(String.format("%d %d %s%s%s", mod, codonStart, codon[0],codon[1],codon[2]));
+            //logger.info(String.format("%d %d %s%s%s", mod, codonStart, codon[0],codon[1],codon[2]));
             char aaNew = AminoAcidSequence.getCodonTranslation(codon[0],
                 codon[1], codon[2]);
 

uk/ac/sanger/artemis/components/variant/VCFview.java

@@ -123,7 +123,7 @@ import uk.ac.sanger.artemis.util.OutOfRangeException;
 public class VCFview extends JPanel
              implements DisplayAdjustmentListener, SelectionChangeListener
 {
-  private static Logger logger = Logger.getLogger(VCFview.class);
+  
   private static final long serialVersionUID = 1L;
   private JScrollBar scrollBar;
   private JPanel vcfPanel;
@@ -1089,7 +1089,7 @@ public class VCFview extends JPanel
     try
     {
       VCFRecord record;
-      logger.info(
+      /*logger4j.info(
               String.format(
               "FILTER\t%s-%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
               sbeg, 
@@ -1100,7 +1100,7 @@ public class VCFview extends JPanel
               this.showInsertions, 
               this.showMultiAlleles, 
               this.showNonOverlappings,
-              this.showNonVariants));
+              this.showNonVariants));*/
       
       while((record = vcfReaders[i].getNextRecord(chr, sbeg, send)) != null)
         drawVariantCall(g, record, start, i, pixPerBase, features, vcfReaders[i].isVcf_v4());
@@ -1114,7 +1114,6 @@ public class VCFview extends JPanel
   
   protected FeatureVector getCDSFeaturesInRange(int start, int end)
   {
-    logger.info("getting cds features in range " + start + "-" + end);
     if(entryGroup == null)
       return null;
     try
@@ -1204,8 +1203,7 @@ public class VCFview extends JPanel
       return false;
     
     short isSyn = -1;
-    isSyn = record.getSynFlag(features, basePosition);
-    logger.info("ISSYNONYMOUS\t"+record.getPos() +"\t" + isSyn);
+    
     markAsNewStop = false;
     if(markNewStops.isSelected() &&
        !record.getAlt().isDeletion(vcf_v4) && 
@@ -1262,7 +1260,7 @@ public class VCFview extends JPanel
   {
     int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
     boolean show = showVariant(record, features, basePosition, vcf_v4);
-    logger.info(String.format("%s\t%s", (show) ? "SHOW" : "HIDE", record));
+    // logger4j.info(String.format("%s\t%s", (show) ? "SHOW" : "HIDE", record));
     if( !show )
       return;