From f45891439bad72cdb360296a0b1a38c855c4aba1 Mon Sep 17 00:00:00 2001
From: Giles Velarde <gv1@sanger.ac.uk>
Date: Fri, 29 Jul 2011 10:54:59 +0100
Subject: [PATCH] back to logging
---
etc/log4j.properties | 2 +-
uk/ac/sanger/artemis/components/variant/VCFRecord.java | 4 ++--
uk/ac/sanger/artemis/components/variant/VCFview.java | 6 +++---
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/etc/log4j.properties b/etc/log4j.properties
index b70338f31..c36f3d9b0 100644
--- a/etc/log4j.properties
+++ b/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.BCFReader=DEBUG, R
+log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, stdout, R
log4j.logger.uk.ac.sanger.artemis.io.ReadAndWriteEntry=DEBUG, R
log4j.logger.uk.ac.sanger.artemis.util.FTPSeekableStream=DEBUG, R
diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 543ba1fbe..d13008e75 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -398,8 +398,8 @@ public class VCFRecord
protected static short checkSyn(CDSFeature gfeat, int basePosition, char variant)
{
- System.out.println("CDSFEATURE\t"+gfeat);
- System.out.println("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;
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index e9e1f8ae6..d0af0a9b4 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -1089,7 +1089,7 @@ public class VCFview extends JPanel
try
{
VCFRecord record;
- System.out.println(
+ logger.info(
String.format(
"FILTER\t%s-%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
sbeg,
@@ -1204,7 +1204,7 @@ public class VCFview extends JPanel
short isSyn = -1;
isSyn = record.getSynFlag(features, basePosition);
- System.out.println("ISSYNONYMOUS\t"+record.getPos() +"\t" + isSyn);
+ logger.info("ISSYNONYMOUS\t"+record.getPos() +"\t" + isSyn);
markAsNewStop = false;
if(markNewStops.isSelected() &&
!record.getAlt().isDeletion(vcf_v4) &&
@@ -1261,7 +1261,7 @@ public class VCFview extends JPanel
{
int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
boolean show = showVariant(record, features, basePosition, vcf_v4);
- System.out.println(String.format("%s\t%s", (show) ? "SHOW" : "HIDE", record));
+ logger.info(String.format("%s\t%s", (show) ? "SHOW" : "HIDE", record));
if( !show )
return;
--
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