diff --git a/xtandempipeline/conf/log4j.properties b/xtandempipeline/conf/log4j.properties
index 2ddcc63a162b55a2579106c0f2c6547a764955eb..32c231b3c276b415367a0999e1c3cbb1d0050f21 100644
--- a/xtandempipeline/conf/log4j.properties
+++ b/xtandempipeline/conf/log4j.properties
@@ -1,10 +1,9 @@
-log4j.rootLogger=warn, stdout
+#log4j.rootLogger=warn, stdout
log4j.logger.org=error, stdout
log4j.logger.com=error, stdout
#log4j.logger.fr=info, stdout, rollingFile
-log4j.logger.fr.inra.pappso=rollingFile
-log4j.logger.fr.inra.pappso=trace,stdout
+log4j.logger.fr.inra.pappso=debug,stdout,rollingFile
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
@@ -13,7 +12,7 @@ log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
log4j.appender.stdout.layout.ConversionPattern=%-5p: [%d{yyyy-MM-dd HH:mm:ss,SSS}]-(%F:%-3L>%M): %m%n
log4j.appender.rollingFile=org.apache.log4j.RollingFileAppender
-log4j.appender.rollingFile.File=${user.home}/.local/log/XtandemPipeline.log
+log4j.appender.rollingFile.File=${user.home}/.config/xtandempipeline/XtandemPipeline.log
log4j.appender.rollingFile.MaxFileSize=1000KB
# Keep one backup file
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
index 38deabc572906e08904bb29426f64d2ebd69a98a..27cbef7b57f34ae60decabfe8deba62db071199c 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
@@ -106,7 +106,7 @@ public class Identification {
public void filtered_match(filter_base filter) {
int valid = filter.execute(this.protein_liste);
- logger.trace("Number of Valid Match " + valid);
+ logger.info("Number of Valid Match " + valid);
}
public void print_result(print_base print) throws Exception {
@@ -124,7 +124,7 @@ public class Identification {
public void setProteinListValideToGroupeSet() {
// Seul les match dans le groupSet sont valides
- logger.trace("Unvalide match not present in Group");
+ logger.info("Unvalide match not present in Group");
for (Match m : protein_liste.getMatchListes()) {
m.setIsvalidate(false);
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
index d7a2572810415653eb5b4544195940580d4c361d..5ddc50b99844f8ff0c49eda49a035d409ef4cebc 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
@@ -280,10 +280,10 @@ public class config {
File xml = new File(this.getRacinePath()
+ System.getProperty("file.separator") + "xtandempipeline.conf");
if (!xml.exists()){
- logger.trace("New configuration file");
+ logger.info("New configuration file");
return (false);
}
- logger.trace("Load properties configuration from : "+xml.getPath());
+ logger.info("Load properties configuration from : "+xml.getPath());
properties.loadFromXML(new FileInputStream(xml));
return (true);
}
@@ -291,7 +291,7 @@ public class config {
public void savePropertiestoXml() throws Exception {
File xml = new File(this.getRacinePath()
+ System.getProperty("file.separator") + "xtandempipeline.conf");
- logger.trace("Save properties condfiguration to : "+xml.getPath());
+ logger.info("Save properties condfiguration to : "+xml.getPath());
properties.storeToXML(new FileOutputStream(xml),
"Xtandem pipeline configuration file");
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr.java
index 425d9499de9bfa53d54642e8fbaf427824f86503..ed152a9afe1e2c99adc77f3f1dca181ab8beaae8 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr.java
@@ -21,7 +21,7 @@ public class calculation_peptide_fdr extends calculation_base_protein {
this.reverse = 0;
this.normal = 0;
this.peptide_view = new Hashtable<Integer,String>();
- logger.trace("Calculation of peptide FDR");
+ logger.info("Calculation of peptide FDR");
}
protected void processing_match(Match m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr_distribution.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr_distribution.java
index aec442190e4c4c60107a751c102f287117c39020..e0902424419191c94129c11acafb636bc3c9359a 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr_distribution.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_fdr_distribution.java
@@ -24,7 +24,7 @@ public class calculation_peptide_fdr_distribution extends
databases = new HashMap<String, String>();
fdrs = new HashMap<String, fdr_count>();
this.peptide_view = new HashMap<Integer,String>();
- logger.trace("Print peptide FDR distribution");
+ logger.info("Print peptide FDR distribution");
}
protected void processing_match(Match m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_mh_deviation.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_mh_deviation.java
index d120a90992d39eee2526cff43ad169f0cbb001af..f2b7e211f3f32eadfcf9772e49d1c805fa08893b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_mh_deviation.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_peptide_mh_deviation.java
@@ -18,7 +18,7 @@ public class calculation_peptide_mh_deviation extends calculation_base_peptide {
this.is_ppm = is_ppm;
list_value_diff = new ArrayList<Float>();
sum = 0;
- logger.trace("Calculation of peptide mass deviation");
+ logger.info("Calculation of peptide mass deviation");
}
protected void processing_peptide(Peptide pep) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr.java
index b6ed8f4cbf77224cd3ca58938dcf9d02cccb8244..8c20fa53078560cecfe6df25838d332e5e17564c 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr.java
@@ -21,7 +21,7 @@ public class calculation_protein_fdr extends calculation_base_protein{
this.reverse = 0;
this.normal = 0;
this.peptide_view = new HashMap<Integer,String>();
- logger.trace("Calculation of protein fdr");
+ logger.info("Calculation of protein fdr");
}
protected void processing_match(Match m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr_distribution.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr_distribution.java
index e6bb1cbef112a1961ea03ec50a1ec63e25e99321..8eb27be37c676001100244db6c26fb30e0f146d9 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr_distribution.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/calculation_protein_fdr_distribution.java
@@ -23,7 +23,7 @@ public class calculation_protein_fdr_distribution extends
databases = new HashMap<String, String>();
fdrs = new HashMap<String, fdr_count>();
this.peptide_view = new HashMap<Integer, String>();
- logger.trace("Print of protein fdr distribution");
+ logger.info("Print of protein fdr distribution");
}
protected void processing_match(Match m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_index_and_order_match_scan.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_index_and_order_match_scan.java
index 5f3f95e95fc329c8dd4f49e5d0589d9be99d36c7..856ded525773fce88a64f703b3091fefb6d95425 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_index_and_order_match_scan.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_index_and_order_match_scan.java
@@ -7,7 +7,7 @@ public class filter_index_and_order_match_scan extends filter_base {
public filter_index_and_order_match_scan() {
super();
- logger.trace("Index and order peptide liste in match");
+ logger.info("Index and order peptide liste in match");
}
public int execute(MatchList ms) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_isotopic_modifs.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_isotopic_modifs.java
index ac88d9ba39e124a5f3a33b2d79423a6d483aba2e..3a54464298abed7712ca7e566aac6b38434a46c3 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_isotopic_modifs.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_isotopic_modifs.java
@@ -14,7 +14,7 @@ public class filter_isotopic_modifs extends filter_base {
public filter_isotopic_modifs(ModifsList l) {
super();
this.list = l;
- logger.trace("Set isotopic modifs");
+ logger.info("Set isotopic modifs");
}
public int execute(MatchList m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_peptide_evalue.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_peptide_evalue.java
index 99621a0e75be23ed964029fc1e6e48277280ab98..e596a1ac77d5ac9c04b6babf5e90301a39132aaf 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_peptide_evalue.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_peptide_evalue.java
@@ -13,7 +13,7 @@ public class filter_peptide_evalue extends filter_base {
public filter_peptide_evalue(float evalue){
super();
this.peptide_evalue = evalue;
- logger.trace("Filter peptide on Evalue : "+evalue);
+ logger.info("Filter peptide on Evalue : "+evalue);
}
public int execute(MatchList m){
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_phospho_peptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_phospho_peptide.java
index 0b5728947259c17dc6b65f8b80fa687ee45d4194..d83efe4928a3f74ed6a3490e81a22f99058bc83c 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_phospho_peptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_phospho_peptide.java
@@ -10,7 +10,7 @@ public class filter_phospho_peptide extends filter_base {
public filter_phospho_peptide() {
super();
- logger.trace("Unvalidate match without phosphopeptide and non phosphopeptide");
+ logger.info("Unvalidate match without phosphopeptide and non phosphopeptide");
}
public int execute(MatchList m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue.java
index 19848fc9739b57ec8ef6aaccd43a0c2f1b479064..800814049db4be87f750fc76f661b825767d593f 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue.java
@@ -10,7 +10,7 @@ public class filter_protein_evalue extends filter_base {
public filter_protein_evalue(float evalue) {
super();
this.protein_evalue = evalue;
- logger.trace("Filter by Evalue protein < " + evalue);
+ logger.info("Filter by Evalue protein < " + evalue);
}
public int execute(MatchList m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue_to.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue_to.java
index fad7fa919de9197a21cba6461443a8032a818420..887de601b2258fb5d25aedfa054f2625c9ec6a2a 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue_to.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_protein_evalue_to.java
@@ -12,7 +12,7 @@ public class filter_protein_evalue_to extends filter_base {
public filter_protein_evalue_to(float evalue){
super();
this.protein_evalue = evalue;
- logger.trace("Filter by Evalue protein on sample < "+evalue);
+ logger.info("Filter by Evalue protein on sample < "+evalue);
}
public int execute(MatchList m){
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_recalcul_protein_evalue.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_recalcul_protein_evalue.java
index 6854247ca44bd0b8d77a28c7d7ee834389ac69b3..4893e770cdb59a1bbc607ff01e6696a5a8e88a9f 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_recalcul_protein_evalue.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_recalcul_protein_evalue.java
@@ -13,7 +13,7 @@ public class filter_recalcul_protein_evalue extends filter_base {
public filter_recalcul_protein_evalue() {
super();
- logger.trace("Recalcul protein evalue by product of unique valid peptide");
+ logger.info("Recalcul protein evalue by product of unique valid peptide");
}
public int execute(MatchList m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java
index d50faa7c0143eb3a5b7eaf66629ce02a081fa15c..75522280651e6e703c9bcef5aeea89891db5d7e9 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java
@@ -12,7 +12,7 @@ public class filter_unique_peptide_number_to extends filter_base {
public filter_unique_peptide_number_to(int pep_number) {
super();
this.peptide_number = pep_number;
- logger.trace("Unvalidate match with less than "+pep_number+" peptide number in at leat one sample");
+ logger.info("Unvalidate match with less than "+pep_number+" peptide number in at leat one sample");
}
public int execute(MatchList m) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar.java
index 8b721bd6b05df063c5796ca18d3c29f73fd1c5d5..3f67fae3f131e3fa0646123df63f7f1ef3f54bdf 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar.java
@@ -15,7 +15,7 @@ public class print_compar extends print_base {
public print_compar(msms_output out, MsRunSet samp) {
super(out, samp);
- logger.trace("Print Compar file");
+ logger.info("Print Compar file");
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar_phospho.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar_phospho.java
index 71929f1236d2d27830c4aad4d73ed668cac9405c..f2c24954e011feeab275f9edcbff915d2c984f6b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar_phospho.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar_phospho.java
@@ -15,7 +15,7 @@ public class print_compar_phospho extends print_base {
public print_compar_phospho(msms_output out, MsRunSet samp) {
super(out, samp);
- logger.trace("Print Compar file in phospho mode");
+ logger.info("Print Compar file in phospho mode");
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java
index 959f52b0e9f7935eaa1bf5a010dbe3c313f56495..5bf29d71fe6fb1583b8e9aa819eb37cd5a8a6ada 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java
@@ -13,7 +13,7 @@ public class print_fasta extends print_base {
public print_fasta() {
super();
- logger.trace("Print protein to fasta : "+this.toString());
+ logger.info("Print protein to fasta : "+this.toString());
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java
index 65f3cf768b31dbe14446105023779a6944d8134a..2eca2d188ec06c9b6c4779e1e0f0444a6baec2bb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java
@@ -14,7 +14,7 @@ public class print_pepnovo extends print_base {
public print_pepnovo(msms_output out, MsRunSet sample) {
super(out, sample);
- logger.trace("Print PepNovo file");
+ logger.info("Print PepNovo file");
}
public void print_header(String samp) throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list.java
index 019c4559fbdfff950d3db5eb6fae725f4e7d7c94..cc14c658869f8785f41f151d78fcb0a43203f074 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list.java
@@ -14,7 +14,7 @@ public class print_peptide_list extends print_base {
public print_peptide_list(msms_output out) {
super(out);
- logger.trace("Print Peptide liste file in normal mode");
+ logger.info("Print Peptide liste file in normal mode");
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
index b93db8b734cfcd0b5b7c3898a08fef63bd014039..a55a58a5dbc5971bfe900bd0c062c98ec494b2d1 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
@@ -17,7 +17,7 @@ public class print_peptide_list_to_phosphopeptide extends print_base {
public print_peptide_list_to_phosphopeptide(msms_output out) {
super(out);
- logger.trace("Print Peptide liste file in phospho mode");
+ logger.info("Print Peptide liste file in phospho mode");
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_combined.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_combined.java
index 89e53acd92e2c0587743af38ea6d5517cbdbcc52..5bf65feb26dae960f65b514874e0e87fc0967cfd 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_combined.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_combined.java
@@ -10,7 +10,7 @@ public class print_protein_to_combined extends print_base {
public print_protein_to_combined(msms_output out) {
super(out);
- logger.trace("Print Protein liste file in Combined mode");
+ logger.info("Print Protein liste file in Combined mode");
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_indiv.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_indiv.java
index e5fe1e1fa74e6851982fa714572bfeb9f57758a1..f3339ea5fb950ee474c25ae3f5dc8a05356d589f 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_indiv.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_indiv.java
@@ -12,7 +12,7 @@ public class print_protein_to_indiv extends print_base {
public print_protein_to_indiv(msms_output out, MsRunSet sample) {
super(out, sample);
- logger.trace("Print Protein liste file in Individual mode");
+ logger.info("Print Protein liste file in Individual mode");
}
public void print_header(MsRun samp) throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
index 50ff38f6e6e3e1512451e164c1a9c6caf6d207fe..e23e1e330ce136d40a4af4495adce61863edff9e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
@@ -11,7 +11,7 @@ public class print_protein_to_phosphopeptide extends print_base {
public print_protein_to_phosphopeptide(msms_output out) {
super(out);
- logger.trace("Print Protein liste file in Phospho mode");
+ logger.info("Print Protein liste file in Phospho mode");
}
public void print_header() throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
index f59ab5641fa75ec38df3e7e6c0d133f3397158f0..31825d4cd1b21656a7620b4776c9aa6e57ee2122 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
@@ -68,7 +68,7 @@ public class swt_table_peptide extends swt_table_base {
filter_value = "";
filtercolumn = "";
// filter = "";
- logger.trace("View SWT Peptide Table on type :" + type.getType());
+ logger.info("View SWT Peptide Table on type :" + type.getType());
}
protected boolean set_table_item(Group group) throws Exception {
@@ -82,7 +82,7 @@ public class swt_table_peptide extends swt_table_base {
if (!filter)
return false;
- logger.trace("View SWT peptide Table on protein:"
+ logger.info("View SWT peptide Table on protein:"
+ protein.getMatch().get_protein_match().get_cle_accession());
// filtrage de la table des peptides
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java
index 7f2199fe09499cd9676e646bf72a4dd8a23f90b9..ea1c8c5b1ccb458e3c679b04d32e81f4263edfa9 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java
@@ -59,7 +59,7 @@ public class swt_table_protein extends swt_table_base {
color = true;
filter = "";
subgroup_count = 0;
- logger.trace("View SWT Protein Table on type :" + type.getType());
+ logger.info("View SWT Protein Table on type :" + type.getType());
}
protected boolean set_table_item(Group group) throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
index aec1c667ba4d5c6856c9f2636923e5f3e9168dd0..1712c63efe25596384fafeed95224082dee67670 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
@@ -91,7 +91,7 @@ public class GroupSet {
public void removeGroupFromDatabase(File database) {
// TODO Remove Group from this database
- logger.trace("Remove Group from Database: " + database.getName());
+ logger.info("Remove Group from Database: " + database.getName());
for (Group group : this.getGroupList()) {
boolean isconta = false;
for (SubGroup sg : group.getSubGroupSet()) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQML.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQML.java
index 34c6f66351eca744f5b67eeae638ba0e4d787738..f0a176401e744e6565754cf37a49b6b650892bbb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQML.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQML.java
@@ -60,7 +60,7 @@ public class MassChroQML {
private Hashtable<String, String> sample_to_id;
public MassChroQML(File F) throws Exception {
- logger.trace("Save result in MassChroQ file");
+ logger.info("Save result in MassChroQ file");
this.qmscpp_file = F;
this.prot_to_id = new Hashtable<String, String>();
this.seq_to_element = new Hashtable<String, Element>();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
index bf456f557e0fb086bbe022242cf297294f1c8667..4466b77007ce8e268356e05d8a0fc7ccf8b57e42 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
@@ -98,7 +98,7 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
correction_scan = new Hashtable<String, String>();
correction_time = new Hashtable<String, String>();
peptide_list = new Vector<Peptide>();
- logger.trace("Parse Xtandem file in phospho Mode : "+sample_.getName());
+ logger.info("Parse Xtandem file in phospho Mode : "+sample_.getName());
}
public void endDocument() throws SAXException {
@@ -119,7 +119,7 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
// }
}
- logger.trace("Parse Xtandem file finish");
+ logger.info("Parse Xtandem file finish");
}
public void startElement(String namespaceURI, String simpleName,
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java
index 021ec2a1c26255317f3b9947985288909d379e3d..9e3bb0f86c99ed6bef3108306b4d40f6ea560a4b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java
@@ -61,11 +61,11 @@ public class load_project extends org.xml.sax.helpers.DefaultHandler {
Last_element_ = "";
Start_element_ = "";
C_data = "";
- logger.trace("Load project ...");
+ logger.info("Load project ...");
}
public void endDocument() throws SAXException {
- logger.trace("Load project finish");
+ logger.info("Load project finish");
}
public void startElement(String namespaceURI, String simpleName,
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java
index 30d4e97bf853003d3b24ef8e829c32f3b4aeb501..5b3ea70a49b74872eaf4053a3002bb48c4f138f8 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java
@@ -33,7 +33,7 @@ public class new_xtandem_param extends org.xml.sax.helpers.DefaultHandler {
Last_element_ = "";
Start_element_ = "";
C_data = "";
- logger.trace("Create new xtamde param");
+ logger.info("Create new xtamde param");
}
public void endDocument() throws SAXException {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
index 6b6502c818ed0ea72ee7ded499d13640bb4cb635..b370d7e20ac5f049040e33a1025fa45546f8c2c6 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
@@ -28,7 +28,7 @@ public class parse_file {
// on recupere le handler et le fichier à parser
this.handler = h;
this.file_to_parse = f;
- logger.trace("Parsing xml file : "+f.getName());
+ logger.info("Parsing xml file : "+f.getName());
if (!this.file_to_parse.exists())
throw new MSMSException("The file "
+ file_to_parse.getAbsolutePath()
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/proticdbml.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/proticdbml.java
index 11e19a6d96961179ddf9349fcad6a8a42bfa6a2f..872ba9efb7da0885c515ec201af31edb75241a38 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/proticdbml.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/proticdbml.java
@@ -47,7 +47,7 @@ public class proticdbml {
private Hashtable<String, String> msrun_to_id;
public proticdbml(File F) throws Exception {
- logger.trace("Save result in ProticDBml");
+ logger.info("Save result in ProticDBml");
this.proticfile = F;
this.prot_to_id = new Hashtable<String, String>();
this.pep_to_id = new Hashtable<String, String>();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java
index 958b9a0f9219683a5a50be0d299545defadfb476..15576acf1b1777b468c2108180dc0e29151d4a57 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java
@@ -40,7 +40,7 @@ public class save_project {
}
public void write_data_to(File save) throws Exception {
- logger.trace("Save project ...");
+ logger.info("Save project ...");
XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
//FileWriter output = new FileWriter(save);
@@ -77,7 +77,7 @@ public class save_project {
writer.close();
output.close();
- logger.trace("Save project finish");
+ logger.info("Save project finish");
}
private void write_result_to(Identification ident) throws Exception {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
index 6e24ec2bb8859c932aa22398741e61897d4300b5..2f459f5acf9f394a97518895db26292b1daf694b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
@@ -97,7 +97,7 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
correction_scan = new Hashtable<String, String>();
correction_time = new Hashtable<String, String>();
peptide_list = new Vector<Peptide>();
- logger.trace("Parse Xtandem file in normal Mode : " + sample_.getName());
+ logger.info("Parse Xtandem file in normal Mode : " + sample_.getName());
}
public void endDocument() throws SAXException {
@@ -117,7 +117,7 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
pep.set_RT(correction_time.get("" + pep.get_scan()));
// }
}
- logger.trace("Parse Xtandem file finish");
+ logger.info("Parse Xtandem file finish");
}
public void startElement(String namespaceURI, String simpleName,
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_ms2_spectra.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_ms2_spectra.java
index 42db4a56896b66681665a3ae5da0a009593e13f5..7deeb6b77a16ad193f068f7cf128a5d331f747ef 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_ms2_spectra.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_ms2_spectra.java
@@ -32,7 +32,7 @@ public class xtandem_ms2_spectra extends org.xml.sax.helpers.DefaultHandler {
public xtandem_ms2_spectra(Peptide p) {
super();
pep_ = p;
- logger.trace("Load MSMS spectra of : "+pep_.getHashSampleScan().toString());
+ logger.info("Load MSMS spectra of : "+pep_.getHashSampleScan().toString());
}
public void error(SAXParseException e) throws SAXParseException {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java
index 3ed8b4a27ec984c2ebb6f2060bb72f86f16cad1e..f710feb736edc5c61ec3c40427555caaeb8b0c83 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java
@@ -26,7 +26,7 @@ public class xtandem_params {
}
public void load_xml(File xml) throws Exception {
- logger.trace("Load xtandem param from : "+xml.getName());
+ logger.info("Load xtandem param from : "+xml.getName());
new parse_file(new xml_xtandem_param(this),xml);
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/base_shell.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/base_shell.java
index 9040a37d77ca771939da5a069797da81ea993312..c4a2e0bf7b3b7b1b72845d83944e09c3a5df1ebd 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/base_shell.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/base_shell.java
@@ -14,7 +14,7 @@ public class base_shell {
private StringBuilder stdout;
- private String error;
+ private Exception error;
private Process process_run;
@@ -23,7 +23,7 @@ public class base_shell {
public base_shell() {
application = "";
stdout = new StringBuilder();
- error = "";
+ error = null;
}
public void set_commande(String[] commande) {
@@ -55,14 +55,14 @@ public class base_shell {
System.out.println(mess);
}
- public String get_error() {
+ public Exception get_error() {
// gérer les erreurs
return (error);
}
- protected void set_error(String err) {
+ protected void set_error(Exception ioe) {
// gérer les erreurs
- this.error += err + "\n";
+ this.error = ioe;
}
public boolean status() {
@@ -97,7 +97,7 @@ public class base_shell {
test_result();
}
} catch (IOException ioe) {
- set_error(""+ioe);
+ set_error(ioe);
}
}
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java
index 512268891130d14c4baf7aaf233c8834aae7e4ec..a3cdb925506a2e52874b8801ee7658ead5fc8ff3 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java
@@ -30,7 +30,7 @@ public class combined extends process {
}
protected void processing() throws Exception {
- logger.trace("Process result in Combine mode");
+ logger.info("Process result in Combine mode");
// Ecrire le process et penser à relever des StopException
xtandem handler = new xtandem();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/filtered_and_create_grouping.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/filtered_and_create_grouping.java
index 3baed418b993888f0bef439d56e91c59335721bd..0561d56bd1f0cb8eed162a6e7549bd826f17a18c 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/filtered_and_create_grouping.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/filtered_and_create_grouping.java
@@ -24,7 +24,7 @@ public class filtered_and_create_grouping extends process {
}
protected void processing() throws Exception {
- logger.trace("Filtered result and create grouped");
+ logger.info("Filtered result and create grouped");
//restreindre la liste des protéines aux protéines identifiées
this.set_view("Removing redondant proteins");
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
index b35f598c756f92e3eebd62454085f079f7f6bad3..dc7d3305146097ed3d789fad68482b401fb07a0c 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
@@ -28,7 +28,7 @@ public class individual extends process {
}
protected void processing() throws Exception {
- logger.trace("Process result in Individual mode");
+ logger.info("Process result in Individual mode");
// Ecrire le process et penser à relever des StopException
for (int i = 0; i < xtandem.size(); i++) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java
index 1d06895c72d0f74fc92e6be914ea127592d50134..b7eb9c331a7757ad180d24fd3d0d612bb85b90e0 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java
@@ -30,7 +30,7 @@ public class phosphosite extends process {
}
protected void processing() throws Exception {
- logger.trace("Process result in Phopho mode");
+ logger.info("Process result in Phopho mode");
// Ecrire le process et penser à relever des StopException
XtandemPhospho handler = new XtandemPhospho();
for (int i = 0; i < xtandem.size(); i++) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
index 49403166309f045c9db12e78ac2bdb295e517f39..567e491776f4b57c4e89380841956d6fe41e9c88 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
@@ -37,25 +37,9 @@ public class printing_base extends process {
this.set_max_progress(8);
}
- public void run() {
- try {
- this.processing();
- } catch (StopException e) {
- } catch (Exception e) {
- e.printStackTrace();
- StackTraceElement[] f = e.getStackTrace();
- this.setError(e.getMessage() + "\nat : " + f[0].toString());
- // print error on screen!!!
- // stopping(""+e);
- this.set_view("Error:\n" + this.getError());
- this.setStop(true);
- e.printStackTrace();
- }
- }
-
protected void processing() throws Exception {
// Ecrire le process et penser à relever des StopException
- logger.trace("Printing to other format");
+ logger.info("Printing to other format");
msms_output output = new msms_output();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
index daddee12ab5d1f67ea7bb39fc537cf4ca7c75cf5..9bdd5f6deabffd8814505f7e01ef52d1be1f3d5e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
@@ -15,7 +15,7 @@ public class printing_combine extends printing_base {
}
protected void specific_printing() throws Exception {
- logger.trace("Print combine results");
+ logger.info("Print combine results");
this.set_view("Printing protein file results");
msms_output output = new msms_output();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
index 7e44fc0964a4a4a3974b5e6959590b1b73a02b95..8ecb161fa9527be0090a7c473f0ccf4fba9ca420 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
@@ -16,7 +16,7 @@ public class printing_indiv extends printing_base {
}
protected void specific_printing () throws Exception {
- logger.trace("Print individual results");
+ logger.info("Print individual results");
this.set_view("Printing protein file results");
msms_output output = new msms_output();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
index ad6f939309ba223af665d3b18692880936ec2c19..61f9f9394d987ffa384edcce11e8c65ac1240b23 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
@@ -15,7 +15,7 @@ public class printing_phosphopeptide extends printing_base {
}
protected void specific_printing() throws Exception {
- logger.trace("Print phophopeptide results");
+ logger.info("Print phophopeptide results");
this.set_view("Printing protein file results");
msms_output output = new msms_output();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java
index 375b03d93c8815a33b1a52dbcf514347da6a4aa1..9ff24dfc1499d872411a7e3e2c55acc0985219ef 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java
@@ -15,7 +15,7 @@ public class process extends Thread {
private boolean stop;
- private String error;
+ private Exception error;
protected config conf;
@@ -27,7 +27,7 @@ public class process extends Thread {
public process(config conf) {
super();
- this.error = "";
+ this.error = null;
this.setStop(false);
this.view = "";
this.setConf(conf);
@@ -39,27 +39,24 @@ public class process extends Thread {
try {
long start = System.currentTimeMillis();
this.processing();
- System.out.println("Execution time = "+(System.currentTimeMillis()-start)/1000);
+ logger.info("Execution time = "+(System.currentTimeMillis()-start)/1000);
} catch (StopException e) {
+ logger.info("Process were stopping");
} catch (Exception e) {
- e.printStackTrace();
+ this.error = e;
+ logger.error("Process were stopping");
+ logger.error(e.getMessage());
StackTraceElement[] f = e.getStackTrace();
- this.setError(e.getMessage() + "\nat : " + f[0].toString());
- // print error on screen!!!
- // stopping(""+e);
- this.set_view("Error:\n" + this.getError());
+ for(int i = 0;i<f.length;i++){
+ logger.error(f[i]);
+ }
+ this.set_view("Error:\n" + e.getMessage());
this.setStop(true);
}
}
protected void processing() throws Exception {
// Ecrire le process et penser à relever des StopException
-
- }
-
- public void stopping() throws Exception {
-
- throw new StopException("Stopping");
}
public String getView() {
@@ -73,14 +70,10 @@ public class process extends Thread {
this.view = v;
}
- public String getError() {
+ public Exception getError() {
return (this.error);
}
- public void setError(String S) {
- this.error = S;
- }
-
public void setStop(boolean stop) {
this.stop = stop;
this.view = "Stopping...";
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/reinitialise_result_filter_and_create_grouping.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/reinitialise_result_filter_and_create_grouping.java
index 1600978c417ec661f99ede584f9e38dabf876e46..d5c744fef42c20f6196746a6b0f673f8e42bd19f 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/reinitialise_result_filter_and_create_grouping.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/reinitialise_result_filter_and_create_grouping.java
@@ -27,7 +27,7 @@ public class reinitialise_result_filter_and_create_grouping extends process {
}
protected void processing() throws Exception {
- logger.trace("Reinitialise result and performed filter and grouping");
+ logger.info("Reinitialise result and performed filter and grouping");
//reinitilaise les peptides
this.set_view("Reinitialise peptide");
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/save_result_and_filtering.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/save_result_and_filtering.java
index 8a5cc4c15e6738c3892f021846c00195fbb20ace..44ba5e0312167c8eef03cf123e67bf9b439dc136 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/save_result_and_filtering.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/save_result_and_filtering.java
@@ -29,7 +29,7 @@ public class save_result_and_filtering extends process {
}
protected void processing() throws Exception {
- logger.trace("save result and filter");
+ logger.info("save result and filter");
// Invalider les protéines non présents dans les protéines identifiées
this.set_view("Removing redondant proteins");
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java
index 8816f530f2aa0e7bec0762556d73abcf550e5cd0..b0472a9a735a4e54ad58a93a93b700845f1081dc 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java
@@ -8,8 +8,6 @@ import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-
public class xtandem_analysis extends process {
private File[] xtandem;
@@ -25,7 +23,7 @@ public class xtandem_analysis extends process {
}
protected void processing() throws Exception {
- logger.trace("Xtandem analysis start");
+ logger.info("Xtandem analysis start");
//creation du fichier database
File databasexml = new File(this.save_dir.getAbsolutePath()+System.getProperty("file.separator")+"database.xml");
msms_output out = new msms_output();
@@ -42,7 +40,7 @@ public class xtandem_analysis extends process {
File infile = new File(this.save_dir.getAbsolutePath()+System.getProperty("file.separator")+"infile.xml");
for (int i = 0; i < xtandem.length; i++) {
- logger.trace("Xtandem analysis on : "+xtandem[i].getName());
+ logger.info("Xtandem analysis on : "+xtandem[i].getName());
File result_out = new File(this.get_out(xtandem[i]));
// parsing
//creation du fichier infile
@@ -76,12 +74,12 @@ public class xtandem_analysis extends process {
//System.out.println(pipe.getStatus());
}
- if (!pipe.get_error().equals(""))
- throw new MSMSException(pipe.get_error());
+ if (pipe.get_error()!=null)
+ throw pipe.get_error();
if(!result_out.exists())
- throw new MSMSException("Problems durnig analysis of '"+xtandem[i].getName()+"'\n"+pipe.get_Stdout());
+ throw new MSMSException("Analysis of '"+xtandem[i].getName()+" give no result'\n"+pipe.get_Stdout());
- logger.trace("finish");
+ logger.info("finish");
this.add_current_progress();
}
databasexml.delete();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Main_Windows.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Main_Windows.java
index 87fb7f5c6637b555a9f69282e0b8929f43555019..0de50909aafdab1bad68878e713d532a4e8b13eb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Main_Windows.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Main_Windows.java
@@ -18,7 +18,6 @@ import fr.inra.pappso.xtandempipeline.thread.DataType_Combine;
import fr.inra.pappso.xtandempipeline.thread.DataType_individual;
import fr.inra.pappso.xtandempipeline.thread.DataType_phosphopeptide;
import fr.inra.pappso.xtandempipeline.thread.load_result_and_create_grouping;
-import fr.inra.pappso.xtandempipeline.thread.printing_base;
import fr.inra.pappso.xtandempipeline.thread.process;
import fr.inra.pappso.xtandempipeline.thread.reinitialise_result_filter_and_create_grouping;
import fr.inra.pappso.xtandempipeline.thread.save_result_and_filtering;
@@ -70,7 +69,8 @@ public class Main_Windows {
protected Shell shell;
- //protected DataType_Base XtandemPipelineSession.getInstance().getDataTypeBase();
+ // protected DataType_Base
+ // XtandemPipelineSession.getInstance().getDataTypeBase();
private Peptide_Details peptide_details;
@@ -91,21 +91,21 @@ public class Main_Windows {
private Image[] images;
private Vector<Button> buttons;
-
+
private Vector<MenuItem> items;
private Button filter_button;
public Main_Windows() {
logger.debug("Main_Windows begin");
- //ouverture d'une session
+ // ouverture d'une session
boolean oldconfig = false;
- try {
+ try {
conf = XtandemPipelineSession.getInstance().getConfig();
oldconfig = conf.loadPropertiesFromXml();
} catch (Exception e) {
- logger.error("Problem to load old config file"+e);
- e.printStackTrace();
+ logger.error("Problem to load old config file" + e);
+ // e.printStackTrace();
}
buttons = new Vector<Button>();
items = new Vector<MenuItem>();
@@ -134,9 +134,9 @@ public class Main_Windows {
shell.setImages(images);
this.set_window();
-
- shell.setText("X!Tandem results "+XtandemPipelineMain.version);
-
+
+ shell.setText("X!Tandem results " + XtandemPipelineMain.version);
+
if (!oldconfig)
new Path_configuration(this);
@@ -221,7 +221,9 @@ public class Main_Windows {
}
protected void calcul_fdr(Button widget) {
- if ( XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active() && database_list.getSelectionCount() > 0) {
+ if (XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_active()
+ && database_list.getSelectionCount() > 0) {
String[] databases = database_list.getSelection();
calculation_peptide_fdr calc_pep = new calculation_peptide_fdr(
@@ -343,17 +345,23 @@ public class Main_Windows {
item0.setHeight(composite.computeSize(SWT.DEFAULT, SWT.DEFAULT).y);
item0.setControl(composite);
}
-
+
private void update_filter_param() {
- ((Text) filter_button.getData("peptide")).setText(""+XtandemPipelineSession.getInstance().getConfig().get_peptide_evalue());
- ((Text) filter_button.getData("pepnumber")).setText(""+XtandemPipelineSession.getInstance().getConfig().get_peptide_number());
- ((Text) filter_button.getData("protein")).setText(""+XtandemPipelineSession.getInstance().getConfig().get_protein_evalue());
+ ((Text) filter_button.getData("peptide")).setText(""
+ + XtandemPipelineSession.getInstance().getConfig()
+ .get_peptide_evalue());
+ ((Text) filter_button.getData("pepnumber")).setText(""
+ + XtandemPipelineSession.getInstance().getConfig()
+ .get_peptide_number());
+ ((Text) filter_button.getData("protein")).setText(""
+ + XtandemPipelineSession.getInstance().getConfig()
+ .get_protein_evalue());
}
-
protected void filter_results_to(Button widget) {
try {
- if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active())
+ if (!XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_active())
throw new StopException("");
float fl1;
float fl2;
@@ -386,14 +394,20 @@ public class Main_Windows {
process p = new reinitialise_result_filter_and_create_grouping(
conf, identifications.elementAt(identif_select
- .getSelectionIndex()), XtandemPipelineSession.getInstance().getDataTypeBase());
+ .getSelectionIndex()), XtandemPipelineSession
+ .getInstance().getDataTypeBase());
new Running(this, p, false);
+ if (p.isStop())
+ throw new StopException("");
+ if (p.getError() != null)
+ throw p.getError();
+
this.view_result();
} catch (StopException e) {
// TODO Auto-generated catch block
- System.out.println("stop");
+ logger.debug("stop");
} catch (MSMSException e) {
MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
messageBox.setMessage(e.getMessage());
@@ -407,7 +421,8 @@ public class Main_Windows {
boolean type = false;
if (((Combo) widget.getData("type")).getSelectionIndex() == 0)
type = true;
- if ( XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active()) {
+ if (XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_active()) {
calculation_peptide_mh_deviation calc = new calculation_peptide_mh_deviation(
type);
int index = identif_select.getSelectionIndex();
@@ -493,7 +508,7 @@ public class Main_Windows {
MenuItem xtandemitem = new MenuItem(xtandem, SWT.NONE);
xtandemitem.setText("Analysis");
new MenuItem(fileMenu, SWT.SEPARATOR);
-
+
// Create all the items in the File dropdown menu
MenuItem newItem = new MenuItem(fileMenu, SWT.CASCADE);
newItem.setText("Load result");
@@ -604,15 +619,21 @@ public class Main_Windows {
}
private void update_identification_result() {
- logger.debug("Number of identification results : "+identifications.size());
+ logger.debug("Number of identification results : "
+ + identifications.size());
identif_select.removeAll();
- logger.debug("datatype=" + XtandemPipelineSession.getInstance().getDataTypeBase());
- if ( XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active()) {
- if ( XtandemPipelineSession.getInstance().getDataTypeBase().getIs_invididual()) {
+ logger.debug("datatype="
+ + XtandemPipelineSession.getInstance().getDataTypeBase());
+ if (XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_active()) {
+ if (XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_invididual()) {
for (Identification ident : identifications) {
- identif_select.add(ident.get_samples().getMsRunList().get(0).getSampleName());
+ identif_select.add(ident.get_samples().getMsRunList()
+ .get(0).getSampleName());
}
- } else if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_phosphopeptide()) {
+ } else if (!XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_phosphopeptide()) {
identif_select.add("Combine result");
} else {
identif_select.add("Phosphopeptide result");
@@ -620,11 +641,11 @@ public class Main_Windows {
identif_select.select(0);
identif_select.update();
this.view_result();
-
- //on met à jour les valeurs de filtrage
+
+ // on met à jour les valeurs de filtrage
this.update_filter_param();
-
- //on degrise les menus
+
+ // on degrise les menus
for (Button but : buttons)
but.setEnabled(true);
for (MenuItem it : items)
@@ -634,32 +655,37 @@ public class Main_Windows {
}
protected boolean view_result() {
- if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active())
+ if (!XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_active())
return (false);
int index = identif_select.getSelectionIndex();
- System.out.println(index + "");
+ logger.debug(index + "");
Text t = (Text) identif_select.getData("sample");
t.setText("" + identifications.elementAt(index).get_samples().size());
- //shell.setText(identif_select.getItem(index));
+ // shell.setText(identif_select.getItem(index));
Text t2 = (Text) identif_select.getData("group");
- t2.setText("" + identifications.elementAt(index).getGrouping().getGroupList().size());
+ t2.setText(""
+ + identifications.elementAt(index).getGrouping().getGroupList()
+ .size());
t.update();
t2.update();
-
+
// on mets à jour la liste des bases de données
database_list.removeAll();
- for (Database url : identifications.elementAt(index).get_database_list())
+ for (Database url : identifications.elementAt(index)
+ .get_database_list())
database_list.add(url.getDatabasePath());
// envoyer les signaux aux autres fenetres
- this.protein_list
- .load_data(identifications.elementAt(index), XtandemPipelineSession.getInstance().getDataTypeBase());
+ this.protein_list.load_data(identifications.elementAt(index),
+ XtandemPipelineSession.getInstance().getDataTypeBase());
return (true);
}
public void view_protein(Identification ident, SubGroup sg,
HashSampleScanSetProt hashProt) {
- this.peptide_list.load_data(ident, hashProt, XtandemPipelineSession.getInstance().getDataTypeBase());
+ this.peptide_list.load_data(ident, hashProt, XtandemPipelineSession
+ .getInstance().getDataTypeBase());
this.protein_details.view_protein_details(hashProt);
}
@@ -690,7 +716,7 @@ public class Main_Windows {
&& (se.getData("menuitem").equals(menu)))
se.setMinimized(false);
}
-
+
window_base base = (window_base) menu.getData("windows");
if (base.getShell() == null || base.getShell().isDisposed())
base.open_windows();
@@ -723,12 +749,13 @@ public class Main_Windows {
protected void export_identification_results() {
try {
- DataType_Base datatype = XtandemPipelineSession.getInstance().getDataTypeBase();
- if (! datatype.getIs_active())
+ DataType_Base datatype = XtandemPipelineSession.getInstance()
+ .getDataTypeBase();
+ if (!datatype.getIs_active())
throw new StopException("");
- //on recree un nouveau printer sinon erreur si déjà processer
+ // on recree un nouveau printer sinon erreur si déjà processer
datatype.newPrint();
-
+
datatype.getPrint().setIdentifications(identifications);
Export_Windows export = new Export_Windows(this);
@@ -738,10 +765,10 @@ public class Main_Windows {
new Running(this, datatype.getPrint(), false);
- if (! datatype.getPrint().getError().equalsIgnoreCase(""))
- throw new MSMSException( datatype.getPrint().getError());
- if ( datatype.getPrint().isStop())
+ if (datatype.getPrint().isStop())
throw new StopException("");
+ if (datatype.getPrint().getError() != null)
+ throw datatype.getPrint().getError();
MessageBox messageBox = new MessageBox(shell, SWT.OK);
messageBox.setMessage("Export results save as :\n"
@@ -749,7 +776,7 @@ public class Main_Windows {
messageBox.open();
} catch (StopException e) {
// TODO Auto-generated catch block
- System.out.println("stop");
+ logger.debug("stop");
} catch (Exception e) {
this.view_error(e, "Problems trying to export results :");
}
@@ -757,7 +784,7 @@ public class Main_Windows {
protected void analysed(DataType_Base type) {
try {
- //on met à jour le type de datatype
+ // on met à jour le type de datatype
XtandemPipelineSession.getInstance().setDataTypeBase(type);
// configuration des paramètres de filtrage
Filter_Windows filter = new Filter_Windows(this);
@@ -765,12 +792,11 @@ public class Main_Windows {
throw new StopException("Stopping");
new Running(this, type.getPro(), false);
- System.out.println("Finich");
if (type.getPro().isStop())
throw new StopException("Stopping");
- if (!type.getPro().getError().equalsIgnoreCase(""))
- throw new MSMSException(type.getPro().getError());
+ if (type.getPro().getError() != null)
+ throw type.getPro().getError();
identifications = type.getPro().getIdentifications();
if (identifications.size() == 0)
@@ -780,7 +806,7 @@ public class Main_Windows {
} catch (StopException e) {
// TODO Auto-generated catch block
- System.out.println("stop");
+ logger.debug("stop");
} catch (Exception e) {
this.view_error(e, "Problems trying to load results :");
}
@@ -790,7 +816,8 @@ public class Main_Windows {
try {
if (!conf.getXtandem_software_installed())
throw new MSMSException(
- "X!Tandem executable is not installed. Please see :\n\tOptions->Path configuration\n\tAbout->Documentation");
+ "X!Tandem executable is not installed. Please see :"
+ +"\n\tOptions->Path configuration\n\tAbout->Documentation");
xtandem_analysis xtande = new xtandem_analysis(conf);
Xtandem_Analysis_Param params = new Xtandem_Analysis_Param(this,
@@ -800,10 +827,10 @@ public class Main_Windows {
new Running(this, xtande, true);
- if (!xtande.getError().equalsIgnoreCase(""))
- throw new MSMSException(xtande.getError());
if (xtande.isStop())
throw new StopException("");
+ if (xtande.getError() != null)
+ throw xtande.getError();
MessageBox messageBox = new MessageBox(shell, SWT.OK);
messageBox
@@ -812,80 +839,89 @@ public class Main_Windows {
messageBox.open();
} catch (StopException e) {
- System.out.println("stop");
- } catch (MSMSException e) {
- MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
- messageBox.setMessage(e.getMessage());
- messageBox.open();
+ logger.debug("stop");
} catch (Exception e) {
this.view_error(e, "Problems during X!Tandem analysis :");
}
}
protected void view_error(Exception e, String text_error) {
+ logger.error(text_error);
+ logger.error(e.getMessage());
StackTraceElement[] f = e.getStackTrace();
- String error = e.getMessage() + "\nat : " + f[0].toString() + "\n"
- + f[1].toString();
+ String error;
+ if(e.getClass().equals(MSMSException.class)){
+ error = e.getMessage();
+ }else{
+ error = e.getMessage() + "\nat : " + f[0].toString() + "\n"
+ + f[1].toString() + "\n" + f[2].toString();
+ }
MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
messageBox.setMessage(text_error + "\n" + error);
messageBox.open();
- e.printStackTrace();
}
public void load_current_project() {
try {
File out = this.get_file_project("Load project", SWT.OPEN);
- load_result_and_create_grouping loading = new load_result_and_create_grouping(conf,out);
+ load_result_and_create_grouping loading = new load_result_and_create_grouping(
+ conf, out);
new Running(this, loading, false);
-
- if (!loading.getError().equalsIgnoreCase(""))
- throw new MSMSException(loading.getError());
+
if (loading.isStop())
throw new StopException("");
-
+ if (loading.getError() != null)
+ throw loading.getError();
+
this.identifications = loading.getIdentifications();
-
+
this.update_identification_result();
} catch (StopException e) {
- System.out.println("stop");
+ logger.debug("stop");
} catch (Exception e) {
- this.view_error(e, "Problems during X!Tandem analysis :");
+ this.view_error(e, "Problems during loading project :");
}
}
public void save_current_project() {
try {
- if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active())
+ if (!XtandemPipelineSession.getInstance().getDataTypeBase()
+ .getIs_active())
throw new StopException("");
- File out = this.get_file_project("Save current project as", SWT.SAVE);
- save_result_and_filtering save = new save_result_and_filtering(conf, out, identifications, XtandemPipelineSession.getInstance().getDataTypeBase());
- new Running(this,save,false);
-
- if (!save.getError().equalsIgnoreCase(""))
- throw new MSMSException(save.getError());
+ File out = this.get_file_project("Save current project as",
+ SWT.SAVE);
+ save_result_and_filtering save = new save_result_and_filtering(
+ conf, out, identifications, XtandemPipelineSession
+ .getInstance().getDataTypeBase());
+ new Running(this, save, false);
+
if (save.isStop())
throw new StopException("");
+ if (save.getError() != null)
+ throw save.getError();
} catch (StopException e) {
- System.out.println("stop");
+ logger.debug("stop");
} catch (Exception e) {
- this.view_error(e, "Problems during X!Tandem analysis :");
+ this.view_error(e, "Problems during saving project :");
}
}
-
- private File get_file_project(String information,int type) throws StopException {
- FileDialog dlg = new FileDialog(shell, type|SWT.SINGLE);
- dlg.setFilterPath(conf.getXmlresult().getPath());
- dlg.setText(information);
- dlg.setFilterExtensions(new String[]{"*.xpip","*.*"});
- dlg.setFilterNames(new String[]{"X!Tandem pipeline project","All files"});
- String fileName = dlg.open();
- if (fileName == null)
- throw new StopException("No project file selected");
- fileName = fileName.replaceFirst("\\.xpip$", "");
- return (new File(fileName+".xpip"));
+
+ private File get_file_project(String information, int type)
+ throws StopException {
+ FileDialog dlg = new FileDialog(shell, type | SWT.SINGLE);
+ dlg.setFilterPath(conf.getXmlresult().getPath());
+ dlg.setText(information);
+ dlg.setFilterExtensions(new String[] { "*.xpip", "*.*" });
+ dlg.setFilterNames(new String[] { "X!Tandem pipeline project",
+ "All files" });
+ String fileName = dlg.open();
+ if (fileName == null)
+ throw new StopException("No project file selected");
+ fileName = fileName.replaceFirst("\\.xpip$", "");
+ return (new File(fileName + ".xpip"));
}
}
@@ -897,8 +933,8 @@ class ResultSelectionListener implements Listener {
}
public void handleEvent(Event e) {
-// System.out.println("Event: [" + e.toString() + "]");
-// System.out.println(e.widget.getStyle());
+ // System.out.println("Event: [" + e.toString() + "]");
+ // System.out.println(e.widget.getStyle());
// Menu Check
if (e.widget.getStyle() == 32) {
// name.open_closed_shell((MenuItem) e.widget);
@@ -947,7 +983,7 @@ class ResultSelectionListener implements Listener {
MessageBox messageBox = new MessageBox(name.shell, SWT.OK);
messageBox.setMessage(XtandemPipelineMain.warning);
messageBox.open();
- } else if (it.getText().equals("About")) {
+ } else if (it.getText().equals("About")) {
MessageBox messageBox = new MessageBox(name.shell, SWT.OK);
messageBox.setMessage(XtandemPipelineMain.about);
messageBox.open();
@@ -955,7 +991,7 @@ class ResultSelectionListener implements Listener {
MessageBox messageBox = new MessageBox(name.shell, SWT.OK);
messageBox.setMessage(XtandemPipelineMain.news);
messageBox.open();
- } else if (it.getText().equals("Hide window")) {
+ } else if (it.getText().equals("Hide window")) {
name.hide_shell(it.getParent().getParentItem());
} else if (it.getText().equals("Close window")) {
name.close_shell(it.getParent().getParentItem());