diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineSession.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineSession.java
index 614a6d5a24c83792a4b0e0e10c0dfbaeb5815742..32e2f87fb3d4b0a4903360fff40e5ee9ff826faf 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineSession.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineSession.java
@@ -2,7 +2,10 @@ package fr.inra.pappso.xtandempipeline;
import java.util.ArrayList;
+import org.apache.log4j.Logger;
+
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.Match;
import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.grouping.HashPeptide;
@@ -17,6 +20,8 @@ public class XtandemPipelineSession {
private static XtandemPipelineSession session=null;
+ private static final Logger logger = Logger.getLogger(XtandemPipelineSession.class);
+
private HashSampleScanSet sampleScanSet = new HashSampleScanSet();
private HashPeptideSet peptideSet = new HashPeptideSet();
private HashProteinSet proteinSet = new HashProteinSet();
@@ -28,7 +33,8 @@ public class XtandemPipelineSession {
private DataType_Base dataType;
private XtandemPipelineSession(){
-
+ conf = new config();
+ dataType = new DataType_Base(conf);
}
static public XtandemPipelineSession getInstance(){
@@ -58,4 +64,16 @@ public class XtandemPipelineSession {
public void setIdentificationList(ArrayList<Identification> identifis) {
this.identificationList = identifis;
}
+
+ public config getConfig() {
+ return this.conf;
+ }
+ public DataType_Base getDataTypeBase() {
+ return this.dataType;
+ }
+
+ public void setDataTypeBase(DataType_Base type) {
+ this.dataType = type;
+ }
+
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
index 371dd66591c5b0cd1a5d5e4b7f7d5c0148295982..92e7e40ce009e80eba7be1b78af765074204573f 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Match.java
@@ -163,21 +163,21 @@ public class Match implements Comparable<Match> {
}
public int get_coverage_to(MsRun samp) {
- HashMap<String, String> seq = new HashMap<String, String>();
+ HashMap<Integer, Boolean> seq = new HashMap<Integer, Boolean>();
for (int i = 0; i < this.protein_match.get_sequence().length(); i++) {
int i_po = i + 1;
- seq.put(new String("" + i_po), "");
+ seq.put(i_po, false);
}
for (Peptide pep : peptides_match.values()) {
if (pep.getMsRun().equals(samp)) {
for (int j = pep.get_start(); j <= pep.get_stop(); j++) {
- seq.put(new String("" + j), "ok");
+ seq.put(j, true);
}
}
}
int k = 0;
- for (String ST : seq.values()) {
- if (seq.get(ST).equals("ok"))
+ for (boolean ST : seq.values()) {
+ if (ST)
k++;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Peptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Peptide.java
index 14a006c4ee632c604226970ff8d7322c4f44a81a..69662ce344ea1417ea8657972c67479345d0b194 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Peptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Peptide.java
@@ -44,7 +44,7 @@ public class Peptide implements Comparable<Peptide> {
private float hypercorr;
- private ArrayList<Modifs> Modifs;
+ private ArrayList<Modifs> modifList;
private boolean validate;
@@ -53,24 +53,15 @@ public class Peptide implements Comparable<Peptide> {
private ArrayList<Double> intensity_values;
public int compareTo(Peptide p) {
- // int j = this.get_sample().compareTo(p.get_sample());
- // if (j != 0)
- // return (j);
- // int i = this.scan - p.get_scan();
int i = this.hashSampleScan.compareTo(p.getSampleScan());
if (i != 0)
return (i);
return (int) (this.evalue - p.get_evalue());
-
- // if (this.sample.equals(p.get_sample())) {
- // return (this.scan - p.get_scan());
- // }
- // return this.sample.compareTo(p.get_sample());
}
// constructeur
public Peptide() {
- this.Modifs = new ArrayList<Modifs>();
+ this.modifList = new ArrayList<Modifs>();
this.RT = 0;
this.validate = true;
this.scan_in_xtandem = 0;
@@ -180,7 +171,7 @@ public class Peptide implements Comparable<Peptide> {
int posi_corrected = posi - this.start + 1;
Modifs mod = new Modifs(AA, posi_corrected, modvalue);
mod.setPosi_in_prot(posi);
- this.Modifs.add(mod);
+ this.modifList.add(mod);
}
public void set_sequence(String S) {
@@ -246,18 +237,18 @@ public class Peptide implements Comparable<Peptide> {
}
public ArrayList<Modifs> get_Modifs() {
- return (this.Modifs);
+ return (this.modifList);
}
public String get_Modifs_formater() {
StringBuilder format = new StringBuilder();
- if (Modifs.size() >= 1) {
- Modifs mod = Modifs.get(0);
+ if (modifList.size() >= 1) {
+ Modifs mod = modifList.get(0);
format.append(mod.get_formater_value());
}
- if (Modifs.size() >= 2) {
- for (int i = 1; i < Modifs.size(); i++) {
- Modifs mod = Modifs.get(i);
+ if (modifList.size() >= 2) {
+ for (int i = 1; i < modifList.size(); i++) {
+ Modifs mod = modifList.get(i);
format.append(" - " + mod.get_formater_value());
}
}
@@ -267,7 +258,7 @@ public class Peptide implements Comparable<Peptide> {
public Float get_mass_Modifs_without_isotope(boolean removeMS3) {
Float f = (float) 0;
- for (Modifs mod : Modifs) {
+ for (Modifs mod : modifList) {
if (!mod.isIsotopic()) {
if (mod.is_phopho_modifs() && removeMS3)
f += Peptide.phospho_mass;
@@ -280,7 +271,7 @@ public class Peptide implements Comparable<Peptide> {
public Float get_mh_theo_without_isotope(boolean correctedMS3) {
Float f = this.mhplus_theo;
- for (Modifs mod : Modifs) {
+ for (Modifs mod : modifList) {
if (mod.isIsotopic()) {
f -= mod.get_modvalue();
} else if (mod.is_phopho_modifs() && correctedMS3) {
@@ -293,7 +284,7 @@ public class Peptide implements Comparable<Peptide> {
public boolean is_phopho_peptide() {
boolean phospho = false;
- for (Modifs mod : Modifs) {
+ for (Modifs mod : modifList) {
if (mod.is_phopho_modifs())
phospho = true;
}
@@ -302,7 +293,7 @@ public class Peptide implements Comparable<Peptide> {
public ArrayList<Modifs> get_phospho_Modifs() {
ArrayList<Modifs> phospho = new ArrayList<Modifs>();
- for (Modifs mod : Modifs) {
+ for (Modifs mod : modifList) {
if (mod.is_phopho_modifs())
phospho.add(mod);
}
@@ -431,4 +422,15 @@ public class Peptide implements Comparable<Peptide> {
return this.hashSampleScan;
}
+ public String get_Modifs_formater_without_isotope() {
+ StringBuilder format = new StringBuilder();
+ for(Modifs mod : modifList){
+ if(!mod.isIsotopic()){
+ format.append(" " + mod.get_formater_value());
+ }
+ }
+ format.append(" ");
+ return (format.toString());
+ }
+
}
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 004064622ea8b24416d0b6086e480b33f3e67a23..d7a2572810415653eb5b4544195940580d4c361d 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
@@ -1,128 +1,104 @@
package fr.inra.pappso.xtandempipeline.class_msms;
import java.io.File;
-import java.io.Serializable;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
import java.util.Arrays;
+import java.util.Properties;
import java.util.Vector;
-import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import org.apache.log4j.Logger;
-
-public class config implements Serializable {
+public class config {
private static final long serialVersionUID = 123L;
+ private static final Logger logger = Logger.getLogger(config.class);
- private File database_filter;
+ private static String database_filter = "database_filter";
// le fichier de la base de donnee pour laquelle on veux retirer les
// protéines
- private float protein_evalue;
+ private static String protein_evalue = "protein_evalue";
// log(evalue) maximun pour valider une protein
- private float peptide_evalue;
+ private static String peptide_evalue = "peptide_evalue";
// evalue maximun pour valider une protéine ou une isofome et pour combiner
// les proteines
- private int peptide_number;
+ private static String peptide_number = "peptide_number";
// minimum de peptides differents permettant l'identification
- private boolean export_fasta;
+ private static String export_fasta = "export_fasta";
// indique si l'on veux esporter les protéines identifiées en fichier Fasta
- private boolean export_proticdbml;
+ private static String export_proticdbml = "export_proticdbml";
// indique si l'on veux esporter les identification en fichier xml
// compatible Protic
- private boolean export_quantimscpp;
+ private static String export_masschroq = "export_quantimscpp";
// indique si l'on veux esporter les identification en fichier xml
// compatible quantimscpp
- private boolean remove_non_phopho_peptide;
- // indique si l'on veux ne garder que les peptides phosphorylés
-
- private boolean protein_filter_to_complete;
+ private static String protein_filter_to_complete = "protein_filter_to_complete";
// indique si l'on veux appliquer les filtres au niveau proteique sur
// l'ensemble des echantillons
- private boolean export_fdr;
+ private static String export_fdr = "export_fdr";
// indique si on veux exporter la répartition des peptides dans les banques
// pour des evalue croissants
- private boolean export_pepnovo;
+ private static String export_pepnovo = "export_pepnovo";
// indique si on veux exporter les identifications pour une analyse en
// pepnovo
- private File xtandem_link;
+ private static String xtandem_link = "xtandem_link";
// lien vers le fichier X!tandem
- private File xtandem_model;
+ private static String xtandem_model = "xtandem_model";
// lien vers les model xtandem
- private File raw_data;
+ private static String raw_data = "raw_data";
// dossier contenant les raw_data
- private File xmlresult;
+ private static String xmlresult = "xmlresult";
// dossier contenant les fichiers resultats
- private File protein_database;
+ private static String protein_database = "protein_database";
// dossier contenant les fichiers fasta
+ private Properties properties;
+
public config() {
- this.protein_evalue = -4;
- this.peptide_evalue = Float.parseFloat("" + 0.05);
- this.peptide_number = 2;
- this.database_filter = new File("no selected");
- this.export_fasta = false;
- this.export_quantimscpp = false;
- this.export_quantimscpp = false;
- this.remove_non_phopho_peptide = false;
- this.protein_filter_to_complete = false;
- this.export_fdr = false;
- this.export_pepnovo = false;
- this.xmlresult = new File(System.getProperty("user.home"));
- this.raw_data = new File(System.getProperty("user.home"));
- this.protein_database = new File(System.getProperty("user.home"));
- this.xtandem_model = new File(System.getProperty("user.home")
- + System.getProperty("file.separator") + "xtandem_models");
-
+ properties = new Properties();
+ }
+
+ public File getXtandem_link() {
+ File xtandem;
if (System.getProperty("os.name").contains("Windows")) {
- File model = new File("C:/Benperl/Xtandem");
- if (model.exists())
- this.xtandem_model = model;
- this.xtandem_link = new File("C:/Benperl/Xtandem/tandem.exe");
+ xtandem = new File("C:/Benperl/Xtandem/tandem.exe");
} else if (System.getProperty("os.name").contains("Linux")) {
- this.xtandem_link = new File("/usr/bin/tandem");
+ xtandem = new File("/usr/bin/tandem");
} else {
- this.xtandem_link = new File("Not defined");
+ xtandem = new File("Not defined");
}
-
- //si le dossier model n'existe pas on le crée
- if(!this.xtandem_model.exists())
- this.xtandem_model.mkdir();
+ File file = new File(properties.getProperty(xtandem_link,xtandem.getPath()));
+ return file;
}
- public File getXtandem_link() {
- return xtandem_link;
- }
-
- public File getXtandem_software() throws Exception {
- if (!this.xtandem_link.exists())
- throw new MSMSException("The X!Tandem software : "
- + xtandem_link.getAbsolutePath()
- + " is not present on your system");
- return xtandem_link;
- }
-
- public void setXtandem_link(File xtandem_link) {
- this.xtandem_link = xtandem_link;
+ public void setXtandem_link(File F) {
+ properties.setProperty(xtandem_link, F.getPath());
}
public File getXtandem_model() {
- return xtandem_model;
+ File file = new File(properties.getProperty(
+ xtandem_model,this.getRacinePath()+System.getProperty("file.separator")+"xtandem_models"));
+ if(!file.exists())
+ file.mkdirs();
+ return (file);
}
public Vector<File> getXtandem_models() {
- File[] files = this.xtandem_model.listFiles();
+ File[] files = this.getXtandem_model().listFiles();
Vector<File> fi = new Vector<File>();
if (files == null)
return fi;
@@ -135,7 +111,7 @@ public class config implements Serializable {
}
public Vector<File> getprotein_databases() {
- File[] files = this.protein_database.listFiles();
+ File[] files = this.getProtein_database().listFiles();
Vector<File> fi = new Vector<File>();
if (files == null)
return fi;
@@ -147,131 +123,191 @@ public class config implements Serializable {
return (fi);
}
- public void setXtandem_model(File xtandem_model) {
- this.xtandem_model = xtandem_model;
+ public void setXtandem_model(File F) {
+ properties.setProperty(xtandem_model, F.getPath());
}
public File getRaw_data() {
- return raw_data;
+ File file = new File(properties.getProperty(raw_data,
+ System.getProperty("user.home")));
+ return (file);
}
- public void setRaw_data(File raw_data) {
- this.raw_data = raw_data;
+ public void setRaw_data(File F) {
+ properties.setProperty(raw_data, F.getPath());
}
public File getXmlresult() {
- return xmlresult;
+ File file = new File(properties.getProperty(xmlresult,
+ System.getProperty("user.home")));
+ return (file);
}
- public void setXmlresult(File xmlresult) {
- this.xmlresult = xmlresult;
+ public void setXmlresult(File F) {
+ properties.setProperty(xmlresult, F.getPath());
}
public File getProtein_database() {
- return protein_database;
+ File file = new File(properties.getProperty(protein_database,
+ System.getProperty("user.home")));
+ return (file);
}
- public void setProtein_database(File protein_database) {
- this.protein_database = protein_database;
+ public void setProtein_database(File F) {
+ properties.setProperty(protein_database, F.getPath());
}
public void set_database_filter(File F) {
- this.database_filter = F;
+ properties.setProperty(database_filter, F.getName());
}
public void set_protein_evalue(float F) {
- this.protein_evalue = F;
+ properties.setProperty(protein_evalue, "" + F);
}
public void set_peptide_evalue(float F) {
- this.peptide_evalue = F;
+ properties.setProperty(peptide_evalue, "" + F);
}
public void set_peptide_number(int F) {
- this.peptide_number = F;
+ properties.setProperty(peptide_number, "" + F);
}
public void set_export_fasta(boolean F) {
- this.export_fasta = F;
+ properties.setProperty(export_fasta, "" + F);
}
public void set_export_proticdbml(boolean F) {
- this.export_proticdbml = F;
+ properties.setProperty(export_proticdbml, "" + F);
}
- public void set_export_quantimscpp(boolean F) {
- this.export_quantimscpp = F;
+ public void set_export_masschroq(boolean F) {
+ properties.setProperty(export_masschroq, "" + F);
}
public void set_export_pepnovo(boolean F) {
- this.export_pepnovo = F;
- }
-
- public void set_remove_non_phoshopeptide(boolean F) {
- this.remove_non_phopho_peptide = F;
+ properties.setProperty(export_pepnovo, "" + F);
}
public void set_protein_filter_to_complete(boolean F) {
- this.protein_filter_to_complete = F;
+ properties.setProperty(protein_filter_to_complete, "" + F);
}
public File get_database_filter() {
- return (this.database_filter);
+ File file = new File(properties.getProperty(database_filter,
+ "no selected"));
+ return (file);
}
public float get_protein_evalue() {
- return (this.protein_evalue);
+ float value = Float.parseFloat(properties.getProperty(protein_evalue,
+ "-4"));
+ return (value);
}
public float get_peptide_evalue() {
- return (this.peptide_evalue);
+ float value = Float.parseFloat(properties.getProperty(peptide_evalue,
+ "0.05"));
+ return (value);
}
public int get_peptide_number() {
- return (this.peptide_number);
+ int value = Integer.parseInt(properties
+ .getProperty(peptide_number, "2"));
+ return (value);
}
public boolean get_export_fasta() {
- return (this.export_fasta);
+ String value = properties.getProperty(export_fasta, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
}
public boolean get_export_proticdbml() {
- return (this.export_proticdbml);
+ String value = properties.getProperty(export_proticdbml, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
}
- public boolean get_export_quantimscpp() {
- return (this.export_quantimscpp);
+ public boolean get_export_masschroq() {
+ String value = properties.getProperty(export_masschroq, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
}
public boolean get_export_pepnovo() {
- return (this.export_pepnovo);
- }
-
- public boolean get_remove_non_phopsho_peptide() {
- return (this.remove_non_phopho_peptide);
+ String value = properties.getProperty(export_pepnovo, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
}
public boolean get_protein_filter_to_complete() {
- return (this.protein_filter_to_complete);
+ String value = properties.getProperty(protein_filter_to_complete,
+ "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
}
- public void set_Export_fdr(boolean export_fdr) {
- this.export_fdr = export_fdr;
+ public void set_Export_fdr(boolean export) {
+ properties.setProperty(export_fdr, "" + export);
}
public boolean get_Export_fdr() {
- return export_fdr;
+ String value = properties.getProperty(export_fdr, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
}
public boolean getXtandem_software_installed() {
- if (!this.xtandem_link.exists())
+ File file = this.getXtandem_link();
+ if (!file.exists())
return false;
- else if (!this.xtandem_link.isFile())
+ else if (!file.isFile())
return false;
- else if (!this.xtandem_link.canExecute())
+ else if (!file.canExecute())
return false;
else
return true;
}
+ public boolean loadPropertiesFromXml() throws Exception {
+ File xml = new File(this.getRacinePath()
+ + System.getProperty("file.separator") + "xtandempipeline.conf");
+ if (!xml.exists()){
+ logger.trace("New configuration file");
+ return (false);
+ }
+ logger.trace("Load properties configuration from : "+xml.getPath());
+ properties.loadFromXML(new FileInputStream(xml));
+ return (true);
+ }
+
+ 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());
+ properties.storeToXML(new FileOutputStream(xml),
+ "Xtandem pipeline configuration file");
+ }
+
+ private File getRacinePath() {
+ File path;
+ if (System.getProperty("os.name").contains("Linux")) {
+ path = new File(System.getProperty("user.home")
+ + "/.config/xtandempipeline");
+ } else {
+ path = new File(System.getProperty("user.home")
+ + System.getProperty("file.separator") + "xtandempipeline");
+ }
+ if (!path.exists()) {
+ path.mkdirs();
+ }
+ return (path);
+ }
}
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 f1ff31057573cc168723ff0856a77831be5ecc08..8b721bd6b05df063c5796ca18d3c29f73fd1c5d5 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
@@ -72,7 +72,7 @@ public class print_compar extends print_base {
//On ecris les données pour chaque sample
float value = 0;
- for(MsRun sample : samples){
+ for(MsRun sample : samples.getMsRunList()){
if (type.equals("Spectra"))
value = top.get_valid_peptide_number_to(sample);
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 0c00dd18c5d2e702227a9cd4c6c237bb26e008c3..71929f1236d2d27830c4aad4d73ed668cac9405c 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
@@ -75,7 +75,7 @@ public class print_compar_phospho extends print_base {
// On ecris les données pour chaque sample
float value = 0;
- for (MsRun sample : samples) {
+ for (MsRun sample : samples.getMsRunList()) {
if (type.equals("Spectra"))
value = phospho.getTotalHashSampleScantoMsRun(sample);
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 f3e91739d9540272402dbe07a0aed5addf990a3b..b93db8b734cfcd0b5b7c3898a08fef63bd014039 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
@@ -62,8 +62,10 @@ public class print_peptide_list_to_phosphopeptide extends print_base {
} else {
S.append("\t" + "Mono" + "\t");
}
+ S.append("\"");
for (Integer pos : posi)
S.append(pos + " ");
+ S.append("\"");
} else {
S.append("\t" + "No" + "\t" + "\"-\"");
}
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 eb7298eec0c00028ce5363b753866bba26f4f91c..e5fe1e1fa74e6851982fa714572bfeb9f57758a1 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
@@ -15,8 +15,8 @@ public class print_protein_to_indiv extends print_base {
logger.trace("Print Protein liste file in Individual mode");
}
- public void print_header(String samp) throws Exception {
- out.write(samp + "\n");
+ 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"
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 094fd4ffcd65fd1285c955445353c11475666fd5..50ff38f6e6e3e1512451e164c1a9c6caf6d207fe 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
@@ -15,9 +15,9 @@ public class print_protein_to_phosphopeptide extends print_base {
}
public void print_header() throws Exception {
- String S = "Group" + "\t" + "Sub-group" + "\t" + "Description" + "\t"
+ String S = "Group" + "\t" + "Sub-group" + "\t" + "Description"
+ "\t" + "MW" + "\t" + "Position" + "\t"
- + "Spectra" + "\t" + "Specific" + "\t" + "Uniques" + "\t"
+ + "Spectra" + "\t" + "Uniques" + "\t"
+ "Redundancy" + "\n";
out.write(S);
}
@@ -33,14 +33,10 @@ public class print_protein_to_phosphopeptide extends print_base {
+ top.get_protein_match().get_description());
S.append("\t" + top.get_protein_match().get_mw());
- S.append("\t" + phospho.getPhosphoPositionToPrint());
+ S.append("\t" + "\""+phospho.getPhosphoPositionToPrint()+"\"");
S.append("\t" + phospho.size());
- if(group.getSubGroupSet().size() > 1)
- S.append("\t"
- + group.getNumberOfSpecificPeptideInSubGroup(hashProt));
- else
- S.append("\t" + "\"-\"");
+
S.append("\t" + phospho.getUniquePeptideHashSampleScan());
S.append("\t");
if (sg.getHashSampleScanSetProtSet().size() > 1)
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java
index 5d670cfd4bfed818e1ca50e1f4043f8cc245a0ff..8a542e9d922e4c4f8ccde918ff216d044085609e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java
@@ -119,7 +119,7 @@ public class HashSampleScanSetProt extends HashSampleScanSet {
if (hash.getMsRun().equals(sample))
count++;
}
- return (this.size());
+ return (count);
}
public int getUniqueHashPeptideSampleScantoMsRun(MsRun sample) {
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 cacd335da2e192de380595a2af2850f8d3208f3b..34c6f66351eca744f5b67eeae638ba0e4d787738 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQML.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/MassChroQML.java
@@ -6,8 +6,10 @@ import org.w3c.dom.*;
import javax.xml.parsers.*;
import java.io.*;
import java.util.ArrayList;
-import java.util.Enumeration;
+import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
+
import javax.xml.transform.*;
import javax.xml.transform.dom.*;
import javax.xml.transform.stream.*;
@@ -337,12 +339,9 @@ public class MassChroQML {
for(Group group : ident.getGrouping().getGroupList()){
for(SubGroup sg : group.getSubGroupSet().getSubGroupList()){
Protein top = sg.getHashSampleScanSetProtList().get(0).getMatch().get_protein_match();
+
// balise proteines
- String prot_id = "P"+group.getNumber()+ ".";
- if(sg.getNumber()<10)
- prot_id += "0"+sg.getNumber();
- else
- prot_id += sg.getNumber();
+ String prot_id = this.getSubGroupGroupNumber(group, sg);
Element protein = doc.createElement("protein");
protein.setAttribute("id", prot_id);
@@ -354,7 +353,7 @@ public class MassChroQML {
}
private void add_peptides() throws Exception {
- Hashtable<String, Hashtable<String, String>> pep_sequence_to_prot = new Hashtable<String, Hashtable<String, String>>();
+ Hashtable<String, HashSet<String>> pep_sequence_to_prot = new Hashtable<String, HashSet<String>>();
for(Group group : ident.getGrouping().getGroupList()){
for(HashSampleScan hash : group.getHashSampleScanSet().getHashSampleScanList()){
SubGroupSet set = group.getSubGroupContaining(hash);
@@ -372,16 +371,16 @@ public class MassChroQML {
peptide.setAttribute("id", pep_id);
this.seq_to_element.put(seqMod,
peptide);
- peptide.setAttribute("seq", pep.get_LI_sequence());
+ peptide.setAttribute("seq", pep.get_sequence());
peptide.setAttribute("mh", ""
+ pep.get_mh_theo_without_isotope(true));
peptide.setAttribute("mods", ""
- + pep.get_Modifs_formater());
+ + pep.get_Modifs_formater_without_isotope());
this.peptide_list.appendChild(peptide);
// table temporaire pour prot_id
- Hashtable<String, String> temp = new Hashtable<String, String>();
- pep_sequence_to_prot.put(seqMod,
- temp);
+ HashSet<String> temp = new HashSet<String>();
+ //Hashtable<String, String> temp = new Hashtable<String, String>();
+ pep_sequence_to_prot.put(seqMod,temp);
}
//On ajoute une observation
Element observed = doc.createElement("observed_in");
@@ -394,14 +393,8 @@ public class MassChroQML {
peptide.appendChild(observed);
for(SubGroup sgTemp : sgList){
- Match matchTemp = sgTemp.getHashSampleScanSetProtList().get(0).getMatch();
- Hashtable<String, String> temp = pep_sequence_to_prot
- .get(seqMod);
- if (!temp.containsKey(matchTemp.get_protein_match()
- .get_cle_accession()))
- temp.put(matchTemp.get_protein_match().get_cle_accession(),
- this.prot_to_id.get(matchTemp
- .get_protein_match().get_cle_accession()));
+ HashSet<String> temp = pep_sequence_to_prot.get(seqMod);
+ temp.add(this.getSubGroupGroupNumber(group, sgTemp));
}
@@ -410,11 +403,11 @@ public class MassChroQML {
// on reparcourt la liste pour ajouter les prots id
for(String seq : pep_sequence_to_prot.keySet()){
Element peptide = this.seq_to_element.get(seq);
- Hashtable<String, String> temp = pep_sequence_to_prot.get(seq);
- Enumeration<String> prots = temp.elements();
- String ids = prots.nextElement();
- while (prots.hasMoreElements())
- ids = ids + " " + prots.nextElement();
+ HashSet<String> temp = pep_sequence_to_prot.get(seq);
+ Iterator<String> prots = temp.iterator();
+ String ids = prots.next();
+ while (prots.hasNext())
+ ids = ids + " " + prots.next();
peptide.setAttribute("prot_ids", ids);
}
@@ -442,5 +435,14 @@ public class MassChroQML {
public void set_isotopes_mods(ModifsList mods) {
this.mods = mods;
}
+
+ private String getSubGroupGroupNumber(Group group,SubGroup sg){
+ String prot_id = "P"+group.getNumber()+ ".";
+ if(sg.getNumber()<10)
+ prot_id += "0"+sg.getNumber();
+ else
+ prot_id += sg.getNumber();
+ return(prot_id);
+ }
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Serialising.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Serialising.java
deleted file mode 100644
index 7bc2a413347ffe2d31de2a6c7978f14de92e9c89..0000000000000000000000000000000000000000
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Serialising.java
+++ /dev/null
@@ -1,66 +0,0 @@
-package fr.inra.pappso.xtandempipeline.sax_parse;
-
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-
-import org.apache.log4j.Logger;
-
-import fr.inra.pappso.xtandempipeline.class_msms.config;
-
-public class Serialising {
-
- private static final Logger logger = Logger.getLogger(Serialising.class);
-
- public Serialising() {
-
- }
-
- public void serialise_xtandem_conf(config conf) throws Exception {
- logger.trace("save conf files");
- FileOutputStream fos = null;
- ObjectOutputStream out_ser = null;
- String file_out = this.get_conf_save("xtandem_parser.conf");
- fos = new FileOutputStream(file_out);
- out_ser = new ObjectOutputStream(fos);
- out_ser.writeObject(conf);
- out_ser.close();
- }
-
- public config unserialise_xtandem_conf() throws Exception {
- logger.trace("load conf files");
- FileInputStream fis = null;
- ObjectInputStream in = null;
- String file_in = this.get_conf_save("xtandem_parser.conf");
- // if (!new File (file_in).exists())
- // return(new config());
- fis = new FileInputStream(file_in);
- in = new ObjectInputStream(fis);
- config conf = (config) in.readObject();
- in.close();
-
- // try {
- //test si dernière version, si erreur
- conf.get_export_quantimscpp();
- conf.get_protein_filter_to_complete();
- conf.get_remove_non_phopsho_peptide();
- conf.get_Export_fdr();
- conf.get_export_pepnovo();
- conf.getXtandem_link();
- conf.getXtandem_link().getAbsolutePath();
- // }catch (Exception e) {
- // conf = new config();
- // System.out.println("update config file");
- // }
-
- return (conf);
- }
-
- private String get_conf_save(String name) {
- String S = System.getProperty("user.home")
- + System.getProperty("file.separator") + name;
- return S;
- }
-
-}
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 0fb04e4ec6a6b24506032b17fcc93a4216c93118..021ec2a1c26255317f3b9947985288909d379e3d 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
@@ -9,6 +9,7 @@ import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
import fr.inra.pappso.xtandempipeline.class_msms.Match;
@@ -75,6 +76,7 @@ public class load_project extends org.xml.sax.helpers.DefaultHandler {
// System.out.println("Start= "+Start_element_);
if (Start_element_.equals("information")) {
datatype = datatype.getType(attrs.getValue("Data_Type"));
+ XtandemPipelineSession.getInstance().setDataTypeBase(datatype);
this.pro.set_max_progress(Integer.parseInt(attrs.getValue("match_number")));
}
if (Start_element_.equals("filter_params")) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Base.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Base.java
index 234ad4a069b120b942703e1e269c242087a32372..cbfea7ff9957f7c6e27ddd0fc4b88c7078518e8e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Base.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Base.java
@@ -19,7 +19,7 @@ public class DataType_Base {
protected config conf;
public DataType_Base(config conf){
- this.setConf(conf);
+ this.conf=conf;
this.defined_variable();
}
@@ -33,82 +33,34 @@ public class DataType_Base {
}
-
- public void setPrint(printing_base print) {
- this.print = print;
- }
-
-
-
public printing_base getPrint() {
return print;
}
-
- public void setPro(process pro) {
- this.pro = pro;
+
+ public void newPrint() {
}
-
-
public process getPro() {
return pro;
}
-
- public void setIs_phosphopeptide(Boolean is_phosphopeptide) {
- this.is_phosphopeptide = is_phosphopeptide;
- }
-
-
-
public Boolean getIs_phosphopeptide() {
return is_phosphopeptide;
}
-
- public void setIs_invididual(Boolean is_invididual) {
- this.is_invididual = is_invididual;
- }
-
-
public Boolean getIs_invididual() {
return is_invididual;
}
-
-
-
- public void setInformation(String information) {
- this.information = information;
- }
-
-
-
public String getInformation() {
return information;
}
-
-
- public void setIs_active(Boolean is_active) {
- this.is_active = is_active;
- }
-
-
-
public Boolean getIs_active() {
return is_active;
}
-
-
- public void setConf(config conf) {
- this.conf = conf;
- }
-
-
-
public config getConf() {
return conf;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Combine.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Combine.java
index c751e3a895586b8b549a4c2caabebb4a4b3853ce..dcbffe0bf3c77c58f2ef67389ec49c5d9958d8ec 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Combine.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_Combine.java
@@ -11,13 +11,17 @@ public class DataType_Combine extends DataType_Base{
protected void defined_variable() {
is_active = true;
is_invididual = false;
- print = new printing_combine(conf);
information = "Combine : </b>All sample analysis are combined, then filtered to obtained an unique result.";
pro = new combined(conf);
is_phosphopeptide = false;
+ print = new printing_combine(conf);
}
public String getType() {
// TODO Auto-generated method stub
return "combi";
}
+
+ public void newPrint() {
+ print = new printing_combine(conf);
+ }
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_individual.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_individual.java
index 071a7987a21bd694332ada2c17eec5c5ee2d3eaa..f00f9a9b1b3f3e73275687f8acf8ab98189a9308 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_individual.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_individual.java
@@ -12,13 +12,17 @@ public class DataType_individual extends DataType_Base{
is_active = true;
is_invididual = true;
is_phosphopeptide = false;
- print = new printing_indiv(conf);
information = "Individual : Each sample is filtered separately.";
pro = new individual(conf);
+ print = new printing_indiv(conf);
}
public String getType() {
// TODO Auto-generated method stub
return "indiv";
}
+
+ public void newPrint() {
+ print = new printing_indiv(conf);
+ }
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_phosphopeptide.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_phosphopeptide.java
index 77a76f850fc3619bc6c75e86770e0549a229af3d..096ab2775bfb0c175f2e03f0b7bb714d9f901ae5 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_phosphopeptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/DataType_phosphopeptide.java
@@ -12,14 +12,18 @@ public class DataType_phosphopeptide extends DataType_Base{
is_active = true;
is_invididual = false;
is_phosphopeptide = true;
- print = new printing_phosphopeptide(conf);
information = "Phosphopeptide : </b>Only phosphopeptide are conserved. All sample analysis are combined, then filtered to obtained an non-redondant list of phosphosite.";
pro = new phosphosite(conf);
+ print = new printing_phosphopeptide(conf);
}
public String getType() {
// TODO Auto-generated method stub
return "phospho";
}
+
+ public void newPrint() {
+ print = new printing_phosphopeptide(conf);
+ }
}
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 b468cc3c0c2702a4af2129295f7b72e2fd4183f1..49403166309f045c9db12e78ac2bdb295e517f39 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
@@ -131,14 +131,14 @@ public class printing_base extends process {
throw new StopException("");
this.add_current_progress();
- if ((conf.get_export_quantimscpp()) & (this.getIdentifications().size() == 1)) {
+ if ((conf.get_export_masschroq()) & (this.getIdentifications().size() == 1)) {
this.set_view("Printing MassChroQ xml file results");
Identification ident = this.getIdentifications().firstElement();
//modification isotopic
ident.filtered_match(new filter_isotopic_modifs(this.isotopic_mods));
MassChroQML xml = new MassChroQML(new File(this.getfileout()
.getAbsolutePath()
- + "_masschroq.xml"));
+ + ".masschroqML"));
//transfert des isotopes
xml.set_isotopes_mods(this.isotopic_mods);
xml.set_identification(ident);
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_Details.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_Details.java
index 1bae8ea10cfd96d9184a4d8e15b2752cbc781c70..7b062bcd3038455f84dcf0d8296f62fdb1e10c9b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_Details.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_Details.java
@@ -1,7 +1,6 @@
package fr.inra.pappso.xtandempipeline.ui.results;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
-import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Peptide;
import fr.inra.pappso.xtandempipeline.ui.swt.Main_Windows;
@@ -11,8 +10,8 @@ import org.eclipse.swt.graphics.Point;
public class Peptide_Details extends window_base {
- public Peptide_Details(Main_Windows global, config conf) {
- super(global, conf);
+ public Peptide_Details(Main_Windows global) {
+ super(global);
}
protected void move_CTabItem(CTabItem item, int index) {
@@ -29,7 +28,7 @@ public class Peptide_Details extends window_base {
protected void view_CTab_Item_in_independant_windows(CTabItem dragItem,
Point point) {
Peptide_Details_item dragitem = (Peptide_Details_item) dragItem;
- Peptide_Details win = new Peptide_Details(controlleur, conf);
+ Peptide_Details win = new Peptide_Details(controlleur);
win.setLinked_to_main(false);
win.set_menu_item(menuitem);
win.open_windows();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_List.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_List.java
index 6150f7ffb94fb3522b4f6f37f662a3976ac4a75c..c73f87aec122e46acfea9712e6fbd3bdfae37f72 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_List.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Peptide_List.java
@@ -1,7 +1,6 @@
package fr.inra.pappso.xtandempipeline.ui.results;
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.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
@@ -12,8 +11,8 @@ import org.eclipse.swt.graphics.Point;
public class Peptide_List extends window_base {
- public Peptide_List(Main_Windows global, config conf) {
- super(global, conf);
+ public Peptide_List(Main_Windows global) {
+ super(global);
}
protected void initialise() {
@@ -45,7 +44,7 @@ public class Peptide_List extends window_base {
protected void view_CTab_Item_in_independant_windows(CTabItem dragItem,
Point point) {
Peptide_List_item dragitem = (Peptide_List_item) dragItem;
- Peptide_List win = new Peptide_List(controlleur, conf);
+ Peptide_List win = new Peptide_List(controlleur);
win.setLinked_to_main(false);
win.set_menu_item(menuitem);
win.open_windows();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_Details.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_Details.java
index c83fe48b9584d9accc6a171f2bbdfae48c1312c8..25f3884bef30727d06c74a4494ee6b47c8d3454d 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_Details.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_Details.java
@@ -1,19 +1,16 @@
package fr.inra.pappso.xtandempipeline.ui.results;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
-import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.ui.swt.Main_Windows;
import org.eclipse.swt.custom.CTabItem;
import org.eclipse.swt.graphics.Point;
-
-
public class Protein_Details extends window_base {
- public Protein_Details(Main_Windows global, config conf) {
- super(global,conf);
+ public Protein_Details(Main_Windows global) {
+ super(global);
// TODO Auto-generated constructor stub
}
@@ -47,7 +44,7 @@ public class Protein_Details extends window_base {
protected void view_CTab_Item_in_independant_windows(CTabItem dragItem,
Point point) {
Protein_Details_item dragitem = (Protein_Details_item) dragItem;
- Protein_Details win = new Protein_Details(controlleur, conf);
+ Protein_Details win = new Protein_Details(controlleur);
win.setLinked_to_main(false);
win.set_menu_item(menuitem);
win.open_windows();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_List.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_List.java
index c89a0e83e537f2f82599ec5084cba0553ebeda98..177f2ec7eb999e69186cdb10f1b3beffae37d905 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_List.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/Protein_List.java
@@ -1,7 +1,6 @@
package fr.inra.pappso.xtandempipeline.ui.results;
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.thread.DataType_Base;
import fr.inra.pappso.xtandempipeline.ui.swt.Main_Windows;
@@ -9,13 +8,10 @@ import fr.inra.pappso.xtandempipeline.ui.swt.Main_Windows;
import org.eclipse.swt.custom.CTabItem;
import org.eclipse.swt.graphics.Point;
-
-
-
public class Protein_List extends window_base {
- public Protein_List(Main_Windows global, config conf) {
- super(global, conf);
+ public Protein_List(Main_Windows global) {
+ super(global);
}
protected void initialise() {
@@ -52,7 +48,7 @@ public class Protein_List extends window_base {
protected void view_CTab_Item_in_independant_windows(CTabItem dragItem,
Point point) {
Protein_List_item dragitem = (Protein_List_item) dragItem;
- Protein_List win = new Protein_List(controlleur, conf);
+ Protein_List win = new Protein_List(controlleur);
win.setLinked_to_main(false);
win.set_menu_item(menuitem);
win.open_windows();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/window_base.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/window_base.java
index ae4d7f3f4f413cb1ce66ca914e22e3931fc6a493..d3c7186ce9a727ddf7a41835dd08eca7555cd353 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/window_base.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/results/window_base.java
@@ -1,5 +1,6 @@
package fr.inra.pappso.xtandempipeline.ui.results;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.ui.swt.Main_Windows;
@@ -38,9 +39,9 @@ public class window_base {
protected static final Logger logger = Logger.getLogger(window_base.class);
- public window_base(Main_Windows global, config conf) {
+ public window_base(Main_Windows global) {
this.controlleur = global;
- this.conf = conf;
+ this.conf = XtandemPipelineSession.getInstance().getConfig();
this.linked_to_main = true;
}
@@ -125,7 +126,7 @@ public class window_base {
protected void view_CTab_Item_in_independant_windows(CTabItem dragItem,
Point point) {
- window_base win = new window_base(controlleur, conf);
+ window_base win = new window_base(controlleur);
win.setLinked_to_main(false);
win.set_menu_item(menuitem);
win.open_windows();
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Export_Windows.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Export_Windows.java
index 450fa1980b3ff0f0748405106dd94f4e887e4be0..630e918d6f9e0b0a6de28acbb3187e261cf421af 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Export_Windows.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Export_Windows.java
@@ -19,6 +19,7 @@ import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Text;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
@@ -26,7 +27,6 @@ import fr.inra.pappso.xtandempipeline.class_msms.ModifsList;
import fr.inra.pappso.xtandempipeline.filter_print.print_fasta;
import fr.inra.pappso.xtandempipeline.filter_print.print_fasta_to_group;
import fr.inra.pappso.xtandempipeline.filter_print.print_fasta_to_subgroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.Serialising;
import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
public class Export_Windows {
@@ -57,9 +57,9 @@ public class Export_Windows {
protected Button setisotopelabel;
- public Export_Windows(Main_Windows controlleur, config X, DataType_Base datatype) {
- this.conf = X;
- this.datatype = datatype;
+ public Export_Windows(Main_Windows controlleur) {
+ this.conf = XtandemPipelineSession.getInstance().getConfig();
+ this.datatype = XtandemPipelineSession.getInstance().getDataTypeBase();
this.Cancelled = true;
// initialise la fenetre
shell = new Shell(controlleur.getDisplay(), SWT.DIALOG_TRIM | SWT.APPLICATION_MODAL);
@@ -143,13 +143,13 @@ public class Export_Windows {
choice_quantimscpp_export = new Button(group, SWT.CHECK);
choice_quantimscpp_export
.setText("Results for further quantification by MassChroQ");
- choice_quantimscpp_export.setSelection(conf.get_export_quantimscpp());
+ choice_quantimscpp_export.setSelection(conf.get_export_masschroq());
this.setisotopelabel = new Button(group, SWT.PUSH);
setisotopelabel.setLayoutData(new GridData(
GridData.HORIZONTAL_ALIGN_CENTER));
setisotopelabel.setText("Defined isotope labelling");
- setisotopelabel.setEnabled(conf.get_export_quantimscpp());
+ setisotopelabel.setEnabled(conf.get_export_masschroq());
setisotopelabel.addSelectionListener(new SelectionAdapter() {
public void widgetSelected(SelectionEvent e) {
Export_Windows.this.defined_isotope_label();
@@ -257,10 +257,10 @@ public class Export_Windows {
conf.set_export_fasta(this.choice_fasta_export.getSelection());
conf.set_export_pepnovo(this.choice_pepnovo_export.getSelection());
conf.set_export_proticdbml(this.choice_protic_export.getSelection());
- conf.set_export_quantimscpp(this.choice_quantimscpp_export
+ conf.set_export_masschroq(this.choice_quantimscpp_export
.getSelection());
// on sauve
- new Serialising().serialise_xtandem_conf(conf);
+ conf.savePropertiestoXml();
datatype.getPrint().setfileout(out);
int index = fasta_type.getSelectionIndex();
if (index >= 0)
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Filter_Windows.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Filter_Windows.java
index 0ac6f531f2492a1d23fde3c31a0eb15a79ba97e0..b208718d6ff6b55458112892b87a6781d740339e 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Filter_Windows.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Filter_Windows.java
@@ -18,10 +18,10 @@ import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Text;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
-import fr.inra.pappso.xtandempipeline.sax_parse.Serialising;
import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
public class Filter_Windows {
@@ -36,10 +36,10 @@ public class Filter_Windows {
private Boolean Cancelled;
private DataType_Base type;
- public Filter_Windows(Main_Windows controlleur, config X, DataType_Base type) {
+ public Filter_Windows(Main_Windows controlleur) {
Cancelled = true;
- this.type = type;
- this.conf = X;
+ this.conf = XtandemPipelineSession.getInstance().getConfig();
+ this.type = XtandemPipelineSession.getInstance().getDataTypeBase();
this.add_xml = new Vector<File>();
current_directory = conf.getXmlresult().getAbsolutePath();
shell = new Shell(controlleur.getDisplay(),SWT.DIALOG_TRIM|SWT.APPLICATION_MODAL);
@@ -205,7 +205,7 @@ public class Filter_Windows {
private void next_clic() {
try {
this.modified_conf();
- new Serialising().serialise_xtandem_conf(conf);
+ conf.savePropertiestoXml();
type.getPro().setXtandem(add_xml);
Cancelled = false;
shell.dispose();
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 4d5c0a900e5e279a95becda577d80a64461b66f4..87fb7f5c6637b555a9f69282e0b8929f43555019 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
@@ -1,6 +1,7 @@
package fr.inra.pappso.xtandempipeline.ui.swt;
import fr.inra.pappso.xtandempipeline.XtandemPipelineMain;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.Database;
@@ -12,15 +13,12 @@ import fr.inra.pappso.xtandempipeline.filter_print.calculation_peptide_mh_deviat
import fr.inra.pappso.xtandempipeline.filter_print.calculation_protein_fdr;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.sax_parse.Serialising;
import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
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_combine;
-import fr.inra.pappso.xtandempipeline.thread.printing_indiv;
-import fr.inra.pappso.xtandempipeline.thread.printing_phosphopeptide;
+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;
@@ -72,7 +70,7 @@ public class Main_Windows {
protected Shell shell;
- protected DataType_Base data_type;
+ //protected DataType_Base XtandemPipelineSession.getInstance().getDataTypeBase();
private Peptide_Details peptide_details;
@@ -100,21 +98,21 @@ public class Main_Windows {
public Main_Windows() {
logger.debug("Main_Windows begin");
- boolean newconfig = false;
- try {
- conf = new Serialising().unserialise_xtandem_conf();
+ //ouverture d'une session
+ boolean oldconfig = false;
+ try {
+ conf = XtandemPipelineSession.getInstance().getConfig();
+ oldconfig = conf.loadPropertiesFromXml();
} catch (Exception e) {
- conf = new config();
- System.out.println("" + e);
- newconfig = true;
+ logger.error("Problem to load old config file"+e);
+ e.printStackTrace();
}
buttons = new Vector<Button>();
items = new Vector<MenuItem>();
- data_type = new DataType_Base(conf);
- peptide_details = new Peptide_Details(this, conf);
- protein_details = new Protein_Details(this, conf);
- peptide_list = new Peptide_List(this, conf);
- protein_list = new Protein_List(this, conf);
+ peptide_details = new Peptide_Details(this);
+ protein_details = new Protein_Details(this);
+ peptide_list = new Peptide_List(this);
+ protein_list = new Protein_List(this);
identifications = new Vector<Identification>();
@@ -139,8 +137,8 @@ public class Main_Windows {
shell.setText("X!Tandem results "+XtandemPipelineMain.version);
- if (newconfig)
- new Path_configuration(this, conf);
+ if (!oldconfig)
+ new Path_configuration(this);
while (!shell.isDisposed()) {
if (!display.readAndDispatch()) {
@@ -223,7 +221,7 @@ public class Main_Windows {
}
protected void calcul_fdr(Button widget) {
- if (data_type.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(
@@ -347,15 +345,15 @@ public class Main_Windows {
}
private void update_filter_param() {
- ((Text) filter_button.getData("peptide")).setText(""+this.data_type.getConf().get_peptide_evalue());
- ((Text) filter_button.getData("pepnumber")).setText(""+this.data_type.getConf().get_peptide_number());
- ((Text) filter_button.getData("protein")).setText(""+this.data_type.getConf().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 (!data_type.getIs_active())
+ if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active())
throw new StopException("");
float fl1;
float fl2;
@@ -388,7 +386,7 @@ public class Main_Windows {
process p = new reinitialise_result_filter_and_create_grouping(
conf, identifications.elementAt(identif_select
- .getSelectionIndex()), data_type);
+ .getSelectionIndex()), XtandemPipelineSession.getInstance().getDataTypeBase());
new Running(this, p, false);
this.view_result();
@@ -409,7 +407,7 @@ public class Main_Windows {
boolean type = false;
if (((Combo) widget.getData("type")).getSelectionIndex() == 0)
type = true;
- if (data_type.getIs_active()) {
+ if ( XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active()) {
calculation_peptide_mh_deviation calc = new calculation_peptide_mh_deviation(
type);
int index = identif_select.getSelectionIndex();
@@ -608,13 +606,13 @@ public class Main_Windows {
private void update_identification_result() {
logger.debug("Number of identification results : "+identifications.size());
identif_select.removeAll();
- System.out.println("datatype=" + data_type);
- if (data_type.getIs_active()) {
- if (data_type.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());
}
- } else if (!data_type.getIs_phosphopeptide()) {
+ } else if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_phosphopeptide()) {
identif_select.add("Combine result");
} else {
identif_select.add("Phosphopeptide result");
@@ -636,7 +634,7 @@ public class Main_Windows {
}
protected boolean view_result() {
- if (!data_type.getIs_active())
+ if (! XtandemPipelineSession.getInstance().getDataTypeBase().getIs_active())
return (false);
int index = identif_select.getSelectionIndex();
System.out.println(index + "");
@@ -655,13 +653,13 @@ public class Main_Windows {
// envoyer les signaux aux autres fenetres
this.protein_list
- .load_data(identifications.elementAt(index), data_type);
+ .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, data_type);
+ this.peptide_list.load_data(ident, hashProt, XtandemPipelineSession.getInstance().getDataTypeBase());
this.protein_details.view_protein_details(hashProt);
}
@@ -725,29 +723,24 @@ public class Main_Windows {
protected void export_identification_results() {
try {
- if (!data_type.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
+ datatype.newPrint();
+
+ datatype.getPrint().setIdentifications(identifications);
- // ATTENTION si le process a déjà été tourné, il y aura une erreur,
- // remise à jour
- if (data_type.getIs_invididual())
- data_type.setPrint(new printing_indiv(conf));
- else if (data_type.getIs_phosphopeptide())
- data_type.setPrint(new printing_phosphopeptide(conf));
- else
- data_type.setPrint(new printing_combine(conf));
- data_type.getPrint().setIdentifications(identifications);
-
- Export_Windows export = new Export_Windows(this, conf, data_type);
+ Export_Windows export = new Export_Windows(this);
File S_out = export.getFileOut();
if (export.isCancelled())
throw new StopException("Stopping");
- new Running(this, data_type.getPrint(), false);
+ new Running(this, datatype.getPrint(), false);
- if (!data_type.getPrint().getError().equalsIgnoreCase(""))
- throw new MSMSException(data_type.getPrint().getError());
- if (data_type.getPrint().isStop())
+ if (! datatype.getPrint().getError().equalsIgnoreCase(""))
+ throw new MSMSException( datatype.getPrint().getError());
+ if ( datatype.getPrint().isStop())
throw new StopException("");
MessageBox messageBox = new MessageBox(shell, SWT.OK);
@@ -764,8 +757,10 @@ public class Main_Windows {
protected void analysed(DataType_Base type) {
try {
+ //on met à jour le type de datatype
+ XtandemPipelineSession.getInstance().setDataTypeBase(type);
// configuration des paramètres de filtrage
- Filter_Windows filter = new Filter_Windows(this, conf, type);
+ Filter_Windows filter = new Filter_Windows(this);
if (filter.isCancelled())
throw new StopException("Stopping");
@@ -780,7 +775,7 @@ public class Main_Windows {
identifications = type.getPro().getIdentifications();
if (identifications.size() == 0)
throw new MSMSException("No valide identification");
- this.data_type = type;
+
this.update_identification_result();
} catch (StopException e) {
@@ -849,8 +844,8 @@ public class Main_Windows {
if (loading.isStop())
throw new StopException("");
- this.data_type = loading.getData_type();
this.identifications = loading.getIdentifications();
+
this.update_identification_result();
} catch (StopException e) {
System.out.println("stop");
@@ -861,11 +856,11 @@ public class Main_Windows {
public void save_current_project() {
try {
- if (!data_type.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, data_type);
+ 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(""))
@@ -931,7 +926,7 @@ class ResultSelectionListener implements Listener {
else if (it.getText().equals("Phosphopeptide"))
name.analysed(new DataType_phosphopeptide(name.conf));
else if (it.getText().equals("Path preference"))
- new Path_configuration(name, name.conf);
+ new Path_configuration(name);
else if (it.getText().equals("X!Tandem preset"))
new Xtandem_preset(name, name.conf);
else if (it.getText().equals("Documentation")) {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Path_configuration.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Path_configuration.java
index 5f9e7d1bdb91089344c6172ea23eec4174244fff..921602f6a2a450ace65b60b1e9a23f1eb89fedfb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Path_configuration.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Path_configuration.java
@@ -20,17 +20,17 @@ import org.eclipse.swt.widgets.Text;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
-import fr.inra.pappso.xtandempipeline.sax_parse.Serialising;
public class Path_configuration {
protected Shell shell;
private config conf;
- public Path_configuration(Main_Windows controlleur, config X) {
- this.conf = X;
+ public Path_configuration(Main_Windows controlleur) {
+ this.conf = XtandemPipelineSession.getInstance().getConfig();
shell = new Shell(controlleur.getDisplay(), SWT.DIALOG_TRIM | SWT.APPLICATION_MODAL);
shell.setImages(controlleur.getImages());
shell.setText("Path configuration");
@@ -188,7 +188,7 @@ public class Path_configuration {
public void save_configuration_to_disque() {
try {
- new Serialising().serialise_xtandem_conf(conf);
+ conf.savePropertiestoXml();
} catch (MSMSException e) {
MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
messageBox