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
deleted file mode 100644
index 54e023f90505b83d45120376b77c23859d548181..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar.java
+++ /dev/null
@@ -1,99 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import java.util.ArrayList;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
-import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.GroupSet;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_compar extends print_base {
-
- public print_compar(msms_output out, MsRunSet samp) {
- super(out, samp);
- logger.info("Print Compar file");
- }
-
- public void print_header() throws Exception {
- String S = "Groupe" + "\t" + "Sub-group" + "\t" + "Description" + "\t" + "Redundancy"+ "\t" + "MW" + "\t" + "Evalue";
- for(MsRun sample : samples.getMsRunList()){
- S = S + "\t" + sample.getSampleName();
- }
- S = S + "\tType\n";
- out.write(S);
- }
-
- @Override
- public void execute(GroupSet grouping) throws Exception {
- this.print_header();
- for(Group group : grouping.getGroupList()){
- this.print_group_information(group, "Spectra");
- }
- out.write("\n");
-
- for(Group group : grouping.getGroupList()){
- this.print_group_information(group, "Specific");
- }
- out.write("\n");
-
- for(Group group : grouping.getGroupList()){
- this.print_group_information(group, "Unique");
- }
- out.write("\n");
-
- for(Group group : grouping.getGroupList()){
- this.print_group_information(group, "PAI");
- }
- out.write("\n");
- }
-
- public void print_group_information(Group group, String type)
- throws Exception {
- for(SubGroup sg : group.getSubGroupSet().getSubGroupList()){
- String subgroup = this.get_subgroup_number(group, sg);
- ArrayList<HashSampleScanSetProt> hprotlist = sg.getHashSampleScanSetProtList();
- Match top = (Match) hprotlist.get(0).getGrpProtMatch();
-
- //données des
- StringBuilder S = new StringBuilder();
- S.append(group.getNumber());
- S.append("\t"+subgroup);
- S.append("\t"+ top.get_protein_match().get_description());
- if (hprotlist.size() > 1)
- S.append("\t" + hprotlist.size()+"*");
- else
- S.append("\t" + "\"-\"");
- S.append("\t" + top.get_protein_match().get_mw());
- S.append("\t" + top.get_protein_match().get_evalue());
-
- //On ecris les données pour chaque sample
- float value = 0;
- for(MsRun sample : samples.getMsRunList()){
- if (type.equals("Spectra"))
- value = top.get_valid_peptide_number_to(sample);
-
- if (type.equals("Specific"))
- value = group.getNumberOfSpecificPeptideInSubGroupToSample(hprotlist.get(0),sample);
- if (type.equals("Unique")) {
- value = top.get_unique_valid_peptide_number_to(sample);
- }
- if (type.equals("PAI")) {
- value = (float) top.get_spectra_numbers_to(sample)
- / top.get_protein_match().get_PAI_count();
- }
- if (value > 0)
- S.append("\t" + value);
- else
- S.append("\t");
-
- }
- S.append("\t" + type + "\n");
- out.write(S.toString());
-
- }
- }
-}
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
deleted file mode 100644
index 4626ed984f5a3d90a746cb18a89b46d77efc2aaa..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_compar_phospho.java
+++ /dev/null
@@ -1,98 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import java.util.ArrayList;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
-import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.GroupSet;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_compar_phospho extends print_base {
-
- public print_compar_phospho(msms_output out, MsRunSet samp) {
- super(out, samp);
- logger.info("Print Compar file in phospho mode");
- }
-
- public void print_header() throws Exception {
- String S = "Groupe" + "\t" + "Sub-group" + "\t" + "Description" + "\t"
- + "Redundancy" + "\t" + "Position";
- for (MsRun sample : samples.getMsRunList()) {
- S = S + "\t" + sample.getSampleName();
- }
- S = S + "\tType\n";
- out.write(S);
- }
-
- @Override
- public void execute(GroupSet grouping) throws Exception {
- this.print_header();
- for(Group group : grouping.getGroupList()){
- this.print_group_information(group, "Spectra");
- }
- out.write("\n");
-
-// for(Group group : grouping.getGroupList()){
-// this.print_group_information(group, "Specific");
-// }
-// out.write("\n");
-
- for(Group group : grouping.getGroupList()){
- this.print_group_information(group, "Unique");
- }
- out.write("\n");
-//
-// for(Group group : grouping.getGroupList()){
-// this.print_group_information(group, "PAI");
-// }
-// out.write("\n");
- }
-
- public void print_group_information(Group group, String type)
- throws Exception {
- for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- String subgroup = this.get_subgroup_number(group, sg);
- ArrayList<HashSampleScanSetProt> hprotlist = sg
- .getHashSampleScanSetProtList();
-
- HashSampleScanSetPhospho phospho = (HashSampleScanSetPhospho) hprotlist.get(0);
-
- // données des
- StringBuilder S = new StringBuilder();
- S.append(group.getNumber());
- S.append("\t" + subgroup);
- S.append("\t" + ((Match)phospho.getGrpProtMatch()).get_protein_match().get_description());
- if (hprotlist.size() > 1)
- S.append("\t" + hprotlist.size() + "*");
- else
- S.append("\t" + "\"-\"");
-
- S.append("\t" + phospho.getPhosphoPositionToPrint());
-
- // On ecris les données pour chaque sample
- float value = 0;
- for (MsRun sample : samples.getMsRunList()) {
- if (type.equals("Spectra"))
- value = phospho.getTotalHashSampleScantoMsRun(sample);
-
- if (type.equals("Unique")) {
- value = phospho.getUniqueHashPeptideSampleScantoMsRun(sample);
- }
- if (value > 0)
- S.append("\t" + value);
- else
- S.append("\t");
-
- }
- S.append("\t" + type + "\n");
- out.write(S.toString());
-
- }
- }
-
-}
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
deleted file mode 100644
index a6875273232dec7ea73f11837412b6fd8a7d3741..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import java.util.ArrayList;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_peptide_list extends print_base {
-
- public print_peptide_list(msms_output out) {
- super(out);
- logger.info("Print Peptide liste file in normal mode");
- }
-
- public void print_header() throws Exception {
- String S = "Groupe" + "\t" + "Description" + "\t" + "Sample" + "\t"
- + "Scan" + "\t" + "Rt" + "\t" + "Sequence" + "\t" + "Modifs"
- + "\t" + "Used" + "\t" + "on a total of" + "\t" + "Sub-groups"
- + "\t" + "E-value" + "\t" + "Charge" + "\t" + "MH+ Obs" + "\t"
- + "MH+ theo" + "\t" + "DeltaMH+" + "\t" + "Delta-ppm" + "\n";
- out.write(S);
- }
-
- public void print_group_information(Group group) throws Exception {
- for (HashSampleScan hash : group.getHashSampleScanSet()
- .getHashSampleScanList()) {
- SubGroupSet set = group.getSubGroupContaining(hash);
- ArrayList<SubGroup> sgList = set.getSubGroupList();
- Match top = (Match) sgList.get(0).getHashSampleScanSetProtList()
- .get(0).getGrpProtMatch();
- Peptide pep = (Peptide) top.getBestPeptideToHashSampleScan(hash);
- StringBuilder S = new StringBuilder();
-
- // on rempli
- S.append(group.getNumber() + "\t");
- if (set.size() == 1)
- S.append(top.get_protein_match().get_description());
- S.append("\t" + hash.getGrpMsSample().getSampleName());
- S.append("\t" + hash.getScan());
- S.append("\t" + pep.get_RT());
- S.append("\t" + pep.getSequence());
- S.append("\t" + pep.get_Modifs_formater());
-
- if (set.size() > 1)
- S.append("\t" + set.size() + "\t"
- + group.getSubGroupSet().size());
- else
- S.append("\t" + "\"-\"" + "\t" + "\"-\"");
- S.append("\t");
- // match[] order = m.get_match_order();
- boolean second = false;
- for (SubGroup sub : sgList) {
- if (second) {
- S.append(" ");
- }
- S.append(this.get_subgroup_number(group, sub));
- second = true;
- }
-
- S.append("\t" + pep.get_evalue());
- S.append("\t" + pep.get_charge());
- S.append("\t" + pep.get_mhplus_obser());
- S.append("\t" + pep.get_mhplus_theo());
- S.append("\t" + pep.get_deltamass());
- S
- .append("\t"
- + ((pep.get_deltamass() / pep.get_mhplus_theo()) * 1000000));
- S.append("\n");
- out.write(S.toString());
- }
- out.write("\n");
- }
-
-}
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
deleted file mode 100644
index da2433280bd1b1d6697ee3bcebbfeba597a18b90..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_peptide_list_to_phosphopeptide.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.TreeSet;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.class_msms.MapDb.Peptide;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
-import fr.inra.pappso.xtandempipeline.grouping.interfaces.GrpPhosphoModif;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_peptide_list_to_phosphopeptide extends print_base {
-
- public print_peptide_list_to_phosphopeptide(msms_output out) {
- super(out);
- logger.info("Print Peptide liste file in phospho mode");
- }
-
- public void print_header() throws Exception {
- String S = "Groupe" + "\t" + "Description" + "\t" + "Sample" + "\t"
- + "Scan" + "\t" + "Rt" + "\t" + "Sequence" + "\t" + "Best Position"
- + "\t" + "Phosphopeptide" + "\t" + "All Position" + "\t"+ "Modifs" + "\t"+ "Used" + "\t" + "on a total of"
- + "\t" + "Sub-groups" + "\t" + "E-value" + "\t" + "Charge"
- + "\t" + "MH+ Obs" + "\t" + "MH+ theo" + "\t" + "DeltaMH+"
- + "\t" + "Delta-ppm" + "\n";
- out.write(S);
- }
-
- public void print_group_information(Group group) throws Exception {
- for (HashSampleScan hash : group.getHashSampleScanSet()
- .getHashSampleScanList()) {
- SubGroupSet set = group.getSubGroupContaining(hash);
- ArrayList<SubGroup> sgList = set.getSubGroupList();
- HashSampleScanSetPhospho phospho = (HashSampleScanSetPhospho) sgList.get(0).getHashSampleScanSetProtList().get(0);
- Match top = (Match) phospho.getGrpProtMatch();
- Peptide pep = (Peptide) top.getBestPeptideToHashSampleScan(hash);
- StringBuilder S = new StringBuilder();
-
- // on rempli
- S.append(group.getNumber() + "\t");
- if (set.size() == 1)
- S.append(top.get_protein_match().get_description());
- S.append("\t" + hash.getGrpMsSample().getSampleName());
- S.append("\t" + hash.getScan());
- S.append("\t" + pep.get_RT());
- S.append("\t" + pep.getSequence());
- // position
- S.append("\t" + pep.get_phospho_Modifs_position());
-
- // Comparaison des positions lié à l'incertitude
- TreeSet<Integer> posi = phospho.getAllPositionIncluderedon(hash);
- Collection<GrpPhosphoModif> phosphoModifs = pep.getGrpPhosphoModifs();
-
- // Multi
- if (phosphoModifs.size() >= 1) {
- if (phosphoModifs.size() > 1) {
- S.append("\t" + "Multi" + "\t");
- } else {
- S.append("\t" + "Mono" + "\t");
- }
- S.append("\"");
- for (Integer pos : posi)
- S.append(pos + " ");
- S.append("\"");
- } else {
- S.append("\t" + "No" + "\t" + "\"-\"");
- }
-
- S.append("\t" + pep.get_Modifs_formater());
-
- if (set.size() > 1)
- S.append("\t" + set.size() + "\t"
- + group.getSubGroupSet().size());
- else
- S.append("\t" + "\"-\"" + "\t" + "\"-\"");
- S.append("\t");
-
-
- boolean second = false;
- for (SubGroup sub : sgList) {
- if (second) {
- S.append(" ");
- }
- S.append(this.get_subgroup_number(group, sub));
- second = true;
- }
-
- S.append("\t" + pep.get_evalue());
- S.append("\t" + pep.get_charge());
- S.append("\t" + pep.get_mhplus_obser());
- S.append("\t" + pep.get_mhplus_theo());
- S.append("\t" + pep.get_deltamass());
- S.append("\t"
- + ((pep.get_deltamass() / pep.get_mhplus_theo()) * 1000000));
- S.append("\n");
- out.write(S.toString());
- }
- out.write("\n");
- }
-
-}
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
deleted file mode 100644
index 581e34d877a85d32b8857dc60f0763d6e99bd8e2..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_combined.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_protein_to_combined extends print_base {
-
- public print_protein_to_combined(msms_output out) {
- super(out);
- logger.info("Print Protein liste file in Combined mode");
- }
-
- public void print_header() throws Exception {
- String S = "Group" + "\t" + "Sub-group" + "\t" + "Description" + "\t"
- + "log(E value)" + "\t" + "Coverage" + "\t" + "MW" + "\t"
- + "Spectra" + "\t" + "Specific uniques" + "\t" + "Uniques"
- + "\t" + "PAI" + "\t" + "Redundancy" + "\n";
- out.write(S);
- }
-
- public void print_group_information(Group group) throws Exception {
- for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- for (HashSampleScanSetProt hashProt : sg.getHashSampleScanSetProtList()) {
- StringBuilder S = new StringBuilder();
- Match top = (Match) hashProt.getGrpProtMatch();
-
- S.append(group.getNumber() + "\t" + this.get_subgroup_number(group, sg) + "\t"
- + top.get_protein_match().get_description());
- S.append("\t" + top.get_protein_match().get_evalue());
- S.append("\t" + top.get_coverage());
- S.append("\t" + top.get_protein_match().get_mw());
- S.append("\t" + top.get_valid_peptide_number());
- if(group.getSubGroupSet().size() > 1)
- S.append("\t"
- + group.getNumberOfSpecificUniquePeptideInSubGroup(hashProt));
- else
- S.append("\t" + "\"-\"");
- S.append("\t" + top.get_unique_valid_peptide_number());
- S.append("\t");
- S.append((float) top.get_valid_peptide_number()
- / top.get_protein_match().get_PAI_count() + "\t");
- if (sg.getHashSampleScanSetProtSet().size() > 1)
- S.append("* " + sg.getHashSampleScanSetProtSet().size());
- S.append("\n");
-
- out.write(S.toString());
- }
- }
- out.write("\n");
- }
-}
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
deleted file mode 100644
index 13b2f5f716db797b1593d205e662d8c20559c843..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_indiv.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
-import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_protein_to_indiv extends print_base {
-
- public print_protein_to_indiv(msms_output out, MsRunSet sample) {
- super(out, sample);
- logger.info("Print Protein liste file in Individual mode");
- }
-
- public void print_header(MsRun samp) throws Exception {
- out.write(samp.getSampleName() + "\n");
- String S = "Group" + "\t" + "Sub-group" + "\t" + "Description" + "\t"
- + "log(E value)" + "\t" + "Coverage" + "\t" + "MW" + "\t"
- + "Spectra" + "\t" + "Specifics" + "\t" + "Uniques" + "\t"
- + "PAI" + "\t" + "Redundancy" + "\n";
- out.write(S);
- }
-
- public void print_group_information_to_sample(Group group, MsRun sample)
- throws Exception {
- for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- for (HashSampleScanSetProt hashProt : sg.getHashSampleScanSetProtList()) {
- StringBuilder S = new StringBuilder();
- Match top = (Match) hashProt.getGrpProtMatch();
- S.append(group.getNumber() + "\t" + this.get_subgroup_number(group, sg) + "\t"
- + top.get_protein_match().get_description());
- S.append("\t" + top.get_protein_match().get_evalue(sample));
- S.append("\t" + top.get_coverage_to(sample));
- S.append("\t" + top.get_protein_match().get_mw());
- S.append("\t" + top.get_valid_peptide_number_to(sample));
- if(group.getSubGroupSet().size() > 1)
- S.append("\t"
- + group.getNumberOfSpecificPeptideInSubGroupToSample(hashProt, sample));
- else
- S.append("\t" + "\"-\"");
- S.append("\t" + top.get_unique_valid_peptide_number_to(sample));
- S.append("\t");
- S.append((float) top.get_spectra_numbers_to(sample)
- / top.get_protein_match().get_PAI_count() + "\t");
- if (sg.getHashSampleScanSetProtSet().size() > 1)
- S.append("* " + sg.getHashSampleScanSetProtSet().size());
- S.append("\n");
- out.write(S.toString());
-
- }
- }
- out.write("\n");
- }
-
-}
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
deleted file mode 100644
index bb626d7ef8688dccdd1c39a4654be2d27bcffe2f..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_protein_to_phosphopeptide.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package fr.inra.pappso.xtandempipeline.filter_print;
-
-import fr.inra.pappso.xtandempipeline.class_msms.Match;
-import fr.inra.pappso.xtandempipeline.grouping.Group;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
-
-public class print_protein_to_phosphopeptide extends print_base {
-
- public print_protein_to_phosphopeptide(msms_output out) {
- super(out);
- logger.info("Print Protein liste file in Phospho mode");
- }
-
- public void print_header() throws Exception {
- String S = "Group" + "\t" + "Sub-group" + "\t" + "Description"
- + "\t" + "MW" + "\t" + "Position" + "\t"
- + "Spectra" + "\t" + "Uniques" + "\t"
- + "Redundancy" + "\n";
- out.write(S);
- }
-
- public void print_group_information(Group group) throws Exception {
- for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
- for (HashSampleScanSetProt hashProt : sg.getHashSampleScanSetProtList()) {
- StringBuilder S = new StringBuilder();
- Match top = (Match) hashProt.getGrpProtMatch();
- HashSampleScanSetPhospho phospho = (HashSampleScanSetPhospho) hashProt;
-
- S.append(group.getNumber() + "\t" + this.get_subgroup_number(group, sg) + "\t"
- + top.get_protein_match().get_description());
- S.append("\t" + top.get_protein_match().get_mw());
-
- S.append("\t" + "\""+phospho.getPhosphoPositionToPrint()+"\"");
-
- S.append("\t" + phospho.size());
-
- S.append("\t" + phospho.getUniquePeptideHashSampleScan());
- S.append("\t");
- if (sg.getHashSampleScanSetProtSet().size() > 1)
- S.append("* " + sg.getHashSampleScanSetProtSet().size());
- S.append("\n");
-
- out.write(S.toString());
- }
- }
- out.write("\n");
- }
-
-}
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 9ae88a6e00f9c1c7c02b17d2ebe4dac1b8d033bb..5c48262064e5d714c48cb23f46f950adb0b82309 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java
@@ -1,16 +1,13 @@
package fr.inra.pappso.xtandempipeline.thread;
+import fr.inra.pappso.csv2ods.Ods2Csv;
import fr.inra.pappso.libodsstream.OdsDocWriter;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
-import fr.inra.pappso.xtandempipeline.filter_print.print_compar;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_compar;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_peptide_list;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_protein_to_combined;
-import fr.inra.pappso.xtandempipeline.filter_print.print_peptide_list;
-import fr.inra.pappso.xtandempipeline.filter_print.print_protein_to_combined;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
public class printing_combine extends printing_base {
@@ -71,14 +68,19 @@ public class printing_combine extends printing_base {
logger.info("Print combine results");
this.set_view("Printing protein file results");
- msms_output output = new msms_output();
- output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
+
+ Ods2Csv ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_protein.txt");
+
+ OdsDocWriter odsDoc = ods2csv.getOdsDocPipedOutput();
+ // msms_output output = new msms_output();
+ // output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
- ident.print_result(new print_protein_to_combined(output));
+ ident.print_result(new print_ods_protein_to_combined(odsDoc));
}
-
- output.close();
+ odsDoc.close();
// Verification pas arrete
if (this.isStop())
@@ -86,13 +88,18 @@ public class printing_combine extends printing_base {
this.add_current_progress();
this.set_view("Printing peptide file results");
- output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
+ ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_peptide.txt");
+
+ odsDoc = ods2csv.getOdsDocPipedOutput();
+ // output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
- ident.print_result(new print_peptide_list(output));
+ ident.print_result(new print_ods_peptide_list(odsDoc));
}
- output.close();
+ odsDoc.close();
// Verification pas arrete
if (this.isStop())
@@ -100,11 +107,16 @@ public class printing_combine extends printing_base {
this.add_current_progress();
this.set_view("Printing compar file results");
- output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
+ ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_compar.txt");
+
+ odsDoc = ods2csv.getOdsDocPipedOutput();
+ // output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
for (Identification ident : this.identifications) {
- ident.print_result(new print_compar(output, ident.getMsRunSet()));
+ ident.print_result(new print_ods_compar(odsDoc, ident.getMsRunSet()));
}
- output.close();
+ odsDoc.close();
this.add_current_progress();
}
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 259aabc2ba83a6dd6a9bb14c068aa8165f90db72..8f3c9968f8f6664d2bfa87ad67b72686df0a64a8 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_indiv.java
@@ -1,14 +1,12 @@
package fr.inra.pappso.xtandempipeline.thread;
+import fr.inra.pappso.csv2ods.Ods2Csv;
import fr.inra.pappso.libodsstream.OdsDocWriter;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_peptide_list;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_protein_to_indiv;
-import fr.inra.pappso.xtandempipeline.filter_print.print_peptide_list;
-import fr.inra.pappso.xtandempipeline.filter_print.print_protein_to_indiv;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
public class printing_indiv extends printing_base {
@@ -54,15 +52,20 @@ public class printing_indiv extends printing_base {
logger.info("Print individual results");
this.set_view("Printing protein file results");
- msms_output output = new msms_output();
- output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
+ Ods2Csv ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_protein.txt");
+
+ OdsDocWriter odsDoc = ods2csv.getOdsDocPipedOutput();
+ // msms_output output = new msms_output();
+ // output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
- ident.print_result(new print_protein_to_indiv(output, ident
+ ident.print_result(new print_ods_protein_to_indiv(odsDoc, ident
.getMsRunSet()));
}
- output.close();
+ odsDoc.close();
// Verification pas arrete
if (this.isStop())
@@ -70,12 +73,17 @@ public class printing_indiv extends printing_base {
this.add_current_progress();
this.set_view("Printing peptide file results");
- output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
+ ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_peptide.txt");
+
+ odsDoc = ods2csv.getOdsDocPipedOutput();
+ // output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
- ident.print_result(new print_peptide_list(output));
+ ident.print_result(new print_ods_peptide_list(odsDoc));
}
- output.close();
+ odsDoc.close();
// Verification pas arrete
if (this.isStop())
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 cbae3ca8f2141e871cee575a46625ba4f7400962..15b6ffc2c1aaa56433d3af8809a1581b70d3c4e2 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_phosphopeptide.java
@@ -1,16 +1,13 @@
package fr.inra.pappso.xtandempipeline.thread;
+import fr.inra.pappso.csv2ods.Ods2Csv;
import fr.inra.pappso.libodsstream.OdsDocWriter;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
-import fr.inra.pappso.xtandempipeline.filter_print.print_compar_phospho;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_compar_phospho;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_peptide_list_to_phosphopeptide;
import fr.inra.pappso.xtandempipeline.filter_print.print_ods_protein_to_phosphopeptide;
-import fr.inra.pappso.xtandempipeline.filter_print.print_peptide_list_to_phosphopeptide;
-import fr.inra.pappso.xtandempipeline.filter_print.print_protein_to_phosphopeptide;
-import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
public class printing_phosphopeptide extends printing_base {
@@ -72,14 +69,19 @@ public class printing_phosphopeptide extends printing_base {
logger.info("Print phophopeptide results");
this.set_view("Printing protein file results");
- msms_output output = new msms_output();
- output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
+ // msms_output output = new msms_output();
+ Ods2Csv ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_protein.txt");
+
+ OdsDocWriter odsDoc = ods2csv.getOdsDocPipedOutput();
+ // output.open(this.getfileout().getAbsolutePath() + "_protein.txt");
// protein view
for (Identification ident : this.identifications) {
- ident.print_result(new print_protein_to_phosphopeptide(output));
+ ident.print_result(new print_ods_protein_to_phosphopeptide(odsDoc));
}
- output.close();
+ odsDoc.close();
// Verification pas arrete
if (this.isStop())
@@ -87,12 +89,18 @@ public class printing_phosphopeptide extends printing_base {
this.add_current_progress();
this.set_view("Printing peptide file results");
- output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
+ ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_peptide.txt");
+
+ odsDoc = ods2csv.getOdsDocPipedOutput();
+ // output.open(this.getfileout().getAbsolutePath() + "_peptide.txt");
// peptide list
for (Identification ident : this.identifications) {
- ident.print_result(new print_peptide_list_to_phosphopeptide(output));
+ ident.print_result(new print_ods_peptide_list_to_phosphopeptide(
+ odsDoc));
}
- output.close();
+ odsDoc.close();
// Verification pas arrete
if (this.isStop())
@@ -100,12 +108,17 @@ public class printing_phosphopeptide extends printing_base {
this.add_current_progress();
this.set_view("Printing compar file results");
- output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
+ ods2csv = new Ods2Csv();
+ ods2csv.setSinkFilename(this.getfileout().getAbsolutePath()
+ + "_compar.txt");
+
+ odsDoc = ods2csv.getOdsDocPipedOutput();
+ // output.open(this.getfileout().getAbsolutePath() + "_compar.txt");
for (Identification ident : this.identifications) {
- ident.print_result(new print_compar_phospho(output, ident
+ ident.print_result(new print_ods_compar_phospho(odsDoc, ident
.getMsRunSet()));
}
- output.close();
+ odsDoc.close();
this.add_current_progress();
}