From 28590df0b280aa9420d590c378a40a7fa7868c4f Mon Sep 17 00:00:00 2001
From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Mon, 6 Feb 2012 16:28:54 +0000
Subject: [PATCH] introducing IdentificationDataFile
git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@188 b8ef2a07-7df7-436f-90b9-41648038564b
---
.../IdentificationDataFile.java | 36 ++++
.../IdentificationXtandemFile.java | 10 +
.../xtandempipeline/class_msms/MsRun.java | 9 +-
.../xtandempipeline/class_msms/Peptide.java | 8 +-
.../sax_parse/XtandemPhospho.java | 10 +-
.../sax_parse/load_project.java | 4 +-
.../xtandempipeline/sax_parse/parse_file.java | 6 +-
.../xtandempipeline/sax_parse/xtandem.java | 10 +-
.../sax_parse/xtandem_params.java | 33 ++--
.../xtandempipeline/thread/combined.java | 40 ++--
.../xtandempipeline/thread/individual.java | 41 ++--
.../xtandempipeline/thread/phosphosite.java | 10 +-
.../xtandempipeline/thread/process.java | 28 +--
.../thread/xtandem_analysis.java | 106 +++++-----
.../ui/swt/Filter_Windows.java | 185 +++++++++---------
.../ui/swt/Xtandem_Analysis_Param.java | 12 +-
.../ui/swt/Xtandem_preset.java | 51 +++--
17 files changed, 332 insertions(+), 267 deletions(-)
create mode 100644 xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationDataFile.java
create mode 100644 xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationXtandemFile.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationDataFile.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationDataFile.java
new file mode 100644
index 000000000..4fbaecd42
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationDataFile.java
@@ -0,0 +1,36 @@
+package fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile;
+
+import java.io.File;
+
+public class IdentificationDataFile implements
+ Comparable<IdentificationDataFile> {
+
+ protected File file = null;
+
+ public static IdentificationDataFile newIdentificationDataFile(String value) {
+ File file = new File(value);
+ return new IdentificationXtandemFile(file);
+ }
+
+ public String getName() {
+ return this.file.getName();
+ }
+
+ public String getAbsolutePath() {
+ return this.file.getAbsolutePath();
+ }
+
+ public File getFile() {
+ return this.file;
+ }
+
+ public boolean exists() {
+ return this.file.exists();
+ }
+
+ @Override
+ public int compareTo(IdentificationDataFile toCompare) {
+ return this.file.compareTo(toCompare.file);
+ }
+
+}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationXtandemFile.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationXtandemFile.java
new file mode 100644
index 000000000..3d8603bf9
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/IdentificationDataFile/IdentificationXtandemFile.java
@@ -0,0 +1,10 @@
+package fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile;
+
+import java.io.File;
+
+public class IdentificationXtandemFile extends IdentificationDataFile {
+
+ public IdentificationXtandemFile (File xtandemFile) {
+ this.file = xtandemFile;
+ }
+}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
index 606dc0fb1..be5ac5818 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/MsRun.java
@@ -1,26 +1,27 @@
package fr.inra.pappso.xtandempipeline.class_msms;
-import java.io.File;
import java.util.HashSet;
import org.apache.log4j.Logger;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
+
public class MsRun implements Comparable<MsRun>{
private static final Logger logger = Logger.getLogger(MsRun.class);
private String sample;
- private HashSet<File> files = new HashSet<File>(0);
+ private HashSet<IdentificationDataFile> files = new HashSet<IdentificationDataFile>(0);
public MsRun(String sample_name) {
logger.debug("MsRun begin");
sample = sample_name;
}
- public File addFile(File file) {
+ public IdentificationDataFile addFile(IdentificationDataFile file) {
if(files.add(file)) {
return file;
}
- for (File otherFile:this.files) {
+ for (IdentificationDataFile otherFile:this.files) {
if (file.equals(otherFile)) {
return otherFile;
}
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 bdf1f2941..9bd0ee916 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Peptide.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Peptide.java
@@ -1,11 +1,11 @@
package fr.inra.pappso.xtandempipeline.class_msms;
-import java.io.File;
import java.util.ArrayList;
import org.apache.log4j.Logger;
import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
import fr.inra.pappso.xtandempipeline.grouping.HashPeptide;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScan;
@@ -14,7 +14,7 @@ public class Peptide implements Comparable<Peptide> {
final static float phospho_mass = (float) 79.96633;
- private File sample_file;
+ private IdentificationDataFile sample_file;
private int scan_in_xtandem;
@@ -100,7 +100,7 @@ public class Peptide implements Comparable<Peptide> {
return (cle);
}
- public void set_sample_id(MsRun msRun, File origin) {
+ public void set_sample_id(MsRun msRun, IdentificationDataFile origin) {
this.sample_file = msRun.addFile(origin);
if (this.hashSampleScan == null) {
hashSampleScan = XtandemPipelineSession.getInstance()
@@ -350,7 +350,7 @@ public class Peptide implements Comparable<Peptide> {
return S;
}
- public File getSample_file() {
+ public IdentificationDataFile getSample_file() {
return sample_file;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
index 4466b7700..bcfd00391 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
@@ -2,17 +2,17 @@ package fr.inra.pappso.xtandempipeline.sax_parse;
import org.apache.log4j.Logger;
import org.xml.sax.*;
-import java.io.File;
import java.util.Hashtable;
import java.util.Vector;
import fr.inra.pappso.xtandempipeline.class_msms.*;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
private static final Logger logger = Logger.getLogger(XtandemPhospho.class);
- private File sample_;
+ private IdentificationDataFile sample_;
private Protein prot_;
@@ -55,19 +55,19 @@ public class XtandemPhospho extends org.xml.sax.helpers.DefaultHandler {
identification_ = new Identification();
}
- public XtandemPhospho(File S) {
+ public XtandemPhospho(IdentificationDataFile S) {
super();
identification_ = new Identification();
sample_ = S;
}
- public XtandemPhospho(Identification L, File S) {
+ public XtandemPhospho(Identification L, IdentificationDataFile S) {
super();
identification_ = L;
sample_ = S;
}
- public void set_sample(File S) {
+ public void set_sample(IdentificationDataFile S) {
sample_ = 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 9353d5314..aa677a1b4 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
@@ -16,6 +16,7 @@ import fr.inra.pappso.xtandempipeline.class_msms.Match;
import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
import fr.inra.pappso.xtandempipeline.class_msms.Peptide;
import fr.inra.pappso.xtandempipeline.class_msms.Protein;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
import fr.inra.pappso.xtandempipeline.thread.process;
@@ -219,7 +220,8 @@ public class load_project extends org.xml.sax.helpers.DefaultHandler {
if (attrs.getValue("sample_file") == null) {
throw new MSMSException("sample_file is null");
}
- File sample_file = new File(attrs.getValue("sample_file"));
+ IdentificationDataFile sample_file = IdentificationDataFile
+ .newIdentificationDataFile(attrs.getValue("sample_file"));
pep_.set_sample_id(
this.identification_.getMsRunSet().getInstance(
sample_file.getName()), sample_file);
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
index eaf3bb969..9aa73debb 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
@@ -10,6 +10,7 @@ import org.apache.log4j.Logger;
import org.apache.xerces.impl.io.MalformedByteSequenceException;
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
import javax.xml.parsers.SAXParserFactory;
import javax.xml.parsers.SAXParser;
@@ -25,11 +26,12 @@ public class parse_file {
// private File file_to_parse;
- public parse_file(DefaultHandler h, File f) throws Exception {
+ public parse_file(DefaultHandler h, IdentificationDataFile f)
+ throws Exception {
logger.debug("parse_file begin");
// on recupere le handler et le fichier à parser
this.handler = h;
- File file_to_parse = f;
+ File file_to_parse = f.getFile();
logger.info("Parsing xml file : " + f.getName());
if (!file_to_parse.exists())
throw new MSMSException("The file "
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
index 2f459f5ac..f484d10cd 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
@@ -2,16 +2,16 @@ package fr.inra.pappso.xtandempipeline.sax_parse;
import org.apache.log4j.Logger;
import org.xml.sax.*;
-import java.io.File;
import java.util.Hashtable;
import java.util.Vector;
import fr.inra.pappso.xtandempipeline.class_msms.*;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
public class xtandem extends org.xml.sax.helpers.DefaultHandler {
private static final Logger logger = Logger.getLogger(xtandem.class);
- private File sample_;
+ private IdentificationDataFile sample_;
private Protein prot_;
@@ -54,19 +54,19 @@ public class xtandem extends org.xml.sax.helpers.DefaultHandler {
identification_ = new Identification();
}
- public xtandem(File S) {
+ public xtandem(IdentificationDataFile S) {
super();
identification_ = new Identification();
sample_ = S;
}
- public xtandem(Identification L, File S) {
+ public xtandem(Identification L, IdentificationDataFile S) {
super();
identification_ = L;
sample_ = S;
}
- public void set_sample(File S) {
+ public void set_sample(IdentificationDataFile S) {
sample_ = S;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java
index f710feb73..e98d0237d 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_params.java
@@ -1,38 +1,39 @@
package fr.inra.pappso.xtandempipeline.sax_parse;
-import java.io.File;
import java.io.InputStream;
import java.util.Vector;
import org.apache.log4j.Logger;
-
import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
import fr.inra.pappso.xtandempipeline.class_msms.xtandem_param;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationXtandemFile;
public class xtandem_params {
private static final Logger logger = Logger.getLogger(xtandem_params.class);
-
+
private Vector<xtandem_param> params;
private Vector<String> groups;
- private InputStream template = this.getClass().getResourceAsStream("/resources/xtandem_model.xml");
+ private InputStream template = this.getClass().getResourceAsStream(
+ "/resources/xtandem_model.xml");
public xtandem_params() {
this.params = new Vector<xtandem_param>();
this.groups = new Vector<String>();
}
- public void load_xml(File xml) throws Exception {
- logger.info("Load xtandem param from : "+xml.getName());
- new parse_file(new xml_xtandem_param(this),xml);
+ public void load_xml(IdentificationXtandemFile xml) throws Exception {
+ logger.info("Load xtandem param from : " + xml.getName());
+ new parse_file(new xml_xtandem_param(this), xml);
}
public void load_new_param() throws Exception {
- if (template==null)
- throw new MSMSException("Problem accessing resource : xtandem_model.xml");
+ if (template == null)
+ throw new MSMSException(
+ "Problem accessing resource : xtandem_model.xml");
new_xtandem_param handler = new new_xtandem_param(this);
new parse_file(handler, template);
logger.debug(this.groups.size());
@@ -64,16 +65,16 @@ public class xtandem_params {
return (groups);
}
- public void save_to_xml(File xml) throws Exception{
+ public void save_to_xml(IdentificationXtandemFile xml) throws Exception {
msms_output out = new msms_output();
out.open(xml.getAbsolutePath());
- out.write("<?xml version=\"1.0\"?>"+"\n");
- out.write("<bioml label=\"example api document\">"+"\n");
- for(int i=0;i<this.params.size();i++){
- out.write(params.elementAt(i).write_to_xml()+"\n");
+ out.write("<?xml version=\"1.0\"?>" + "\n");
+ out.write("<bioml label=\"example api document\">" + "\n");
+ for (int i = 0; i < this.params.size(); i++) {
+ out.write(params.elementAt(i).write_to_xml() + "\n");
}
- out.write("</bioml>"+"\n");
+ out.write("</bioml>" + "\n");
out.close();
}
-
+
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java
index 6ced58b89..1f4459739 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/combined.java
@@ -1,13 +1,12 @@
package fr.inra.pappso.xtandempipeline.thread;
-import java.io.File;
import java.util.Vector;
-
import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
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.class_msms.IdentificationDataFile.IdentificationDataFile;
import fr.inra.pappso.xtandempipeline.filter_print.filter_index_and_order_match_scan;
import fr.inra.pappso.xtandempipeline.filter_print.filter_protein_evalue;
import fr.inra.pappso.xtandempipeline.filter_print.filter_protein_evalue_to;
@@ -18,13 +17,13 @@ import fr.inra.pappso.xtandempipeline.filter_print.filter_peptide_evalue;
import fr.inra.pappso.xtandempipeline.sax_parse.parse_file;
import fr.inra.pappso.xtandempipeline.sax_parse.xtandem;
-
public class combined extends process {
- private Vector<File> xtandem;
+ private Vector<IdentificationDataFile> xtandem;
-// private ArrayList<Identification> identifications = XtandemPipelineSession
-// .getInstance().getIdentificationList();
+ // private ArrayList<Identification> identifications =
+ // XtandemPipelineSession
+ // .getInstance().getIdentificationList();
public combined(config conf) {
super(conf);
@@ -32,7 +31,7 @@ public class combined extends process {
protected void processing() throws Exception {
logger.info("Process result in Combine mode");
-
+
// Ecrire le process et penser à relever des StopException
xtandem handler = new xtandem();
for (int i = 0; i < xtandem.size(); i++) {
@@ -51,22 +50,22 @@ public class combined extends process {
// filtering
this.set_view("Parsing finished\n" + "Filtering peptides");
Identification ident = handler.get_identifications();
-
- //on mets à jour les liens
+
+ // on mets à jour les liens
ident.filtered_match(new filter_index_and_order_match_scan());
- //filtre evalue peptide
+ // filtre evalue peptide
ident.filtered_match(new filter_peptide_evalue((conf
.get_peptide_evalue())));
-
+
// verification pas arreté
if (this.isStop())
throw new StopException("");
this.add_current_progress();
-
+
// calcul de la evalue globale et modification evalue sample
ident.filtered_match(new filter_recalcul_protein_evalue());
-
+
// verification pas arreté
if (this.isStop())
throw new StopException("");
@@ -91,10 +90,9 @@ public class combined extends process {
this.add_current_progress();
// creation des submatchs
- this.set_view("Grouping\n"
- + "Be patient, this step can take some time");
+ this.set_view("Grouping\n" + "Be patient, this step can take some time");
ident.performedGroupSet();
-
+
// verification pas arreté
if (this.isStop())
throw new StopException("");
@@ -103,7 +101,8 @@ public class combined extends process {
// elimination des protéines contaminantes
ident.remove_contaminant_submatch(conf.get_database_filter());
- //ArrayList<Identification> identifications = XtandemPipelineSession.getInstance().getIdentificationList();
+ // ArrayList<Identification> identifications =
+ // XtandemPipelineSession.getInstance().getIdentificationList();
XtandemPipelineSession.getInstance().getIdentificationList().add(ident);
// Verification pas arrete
@@ -113,12 +112,13 @@ public class combined extends process {
}
- public void setXtandem(Vector<File> xtandem) {
+ @Override
+ public void setXtandem(Vector<IdentificationDataFile> xtandem) {
this.xtandem = xtandem;
- this.set_max_progress(xtandem.size()+5);
+ this.set_max_progress(xtandem.size() + 5);
}
- public Vector<File> getXtandem() {
+ public Vector<IdentificationDataFile> getXtandem() {
return xtandem;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
index 7c63c5752..63578377b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/individual.java
@@ -1,6 +1,5 @@
package fr.inra.pappso.xtandempipeline.thread;
-import java.io.File;
import java.util.ArrayList;
import java.util.Vector;
@@ -10,6 +9,7 @@ import fr.inra.pappso.xtandempipeline.class_msms.MsRun;
import fr.inra.pappso.xtandempipeline.class_msms.MsRunSet;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
import fr.inra.pappso.xtandempipeline.filter_print.filter_index_and_order_match_scan;
import fr.inra.pappso.xtandempipeline.filter_print.filter_protein_evalue_to;
import fr.inra.pappso.xtandempipeline.filter_print.filter_recalcul_protein_evalue;
@@ -20,10 +20,11 @@ import fr.inra.pappso.xtandempipeline.sax_parse.xtandem;
public class individual extends process {
- private Vector<File> xtandem;
-
-// private ArrayList<Identification> identifications = XtandemPipelineSession
-// .getInstance().getIdentificationList();
+ private Vector<IdentificationDataFile> xtandem;
+
+ // private ArrayList<Identification> identifications =
+ // XtandemPipelineSession
+ // .getInstance().getIdentificationList();
public individual(config conf) {
super(conf);
@@ -31,9 +32,10 @@ public class individual extends process {
protected void processing() throws Exception {
logger.info("Process result in Individual mode");
-
- ArrayList<Identification> identifications = XtandemPipelineSession.getInstance().getIdentificationList();
-
+
+ ArrayList<Identification> identifications = XtandemPipelineSession
+ .getInstance().getIdentificationList();
+
// Ecrire le process et penser à relever des StopException
for (int i = 0; i < xtandem.size(); i++) {
// parsing
@@ -53,7 +55,7 @@ public class individual extends process {
else
handler = new xtandem(xtandem.get(i));
new parse_file(handler, xtandem.get(i));
-
+
if (identtemp == null)
identifications.add(handler.get_identifications());
@@ -67,16 +69,11 @@ public class individual extends process {
for (int j = 0; j < identifications.size(); j++) {
Identification ident = identifications.get(j);
// filtering
- this.set_view("Analysing file : "
- + (j + 1)
- + "/"
- + identifications.size()
- + "\n"
- + "Filtering file : "
- + ident.get_samples().getMsRunList()
- .get(0).getSampleName());
-
- //on mets à jour les liens
+ this.set_view("Analysing file : " + (j + 1) + "/"
+ + identifications.size() + "\n" + "Filtering file : "
+ + ident.get_samples().getMsRunList().get(0).getSampleName());
+
+ // on mets à jour les liens
ident.filtered_match(new filter_index_and_order_match_scan());
ident.filtered_match(new filter_peptide_evalue((conf
@@ -104,14 +101,14 @@ public class individual extends process {
}
- public void setXtandem(Vector<File> xtandem) {
+ @Override
+ public void setXtandem(Vector<IdentificationDataFile> xtandem) {
this.xtandem = xtandem;
this.set_max_progress(xtandem.size() * 2);
}
- public Vector<File> getXtandem() {
+ public Vector<IdentificationDataFile> getXtandem() {
return xtandem;
}
-
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java
index 6bf587aae..22a6685a9 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/phosphosite.java
@@ -1,6 +1,5 @@
package fr.inra.pappso.xtandempipeline.thread;
-import java.io.File;
import java.util.ArrayList;
import java.util.Vector;
@@ -8,6 +7,7 @@ import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
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.class_msms.IdentificationDataFile.IdentificationDataFile;
import fr.inra.pappso.xtandempipeline.filter_print.filter_index_and_order_match_scan;
import fr.inra.pappso.xtandempipeline.filter_print.filter_peptide_redondancy;
import fr.inra.pappso.xtandempipeline.filter_print.filter_protein_evalue;
@@ -21,7 +21,7 @@ import fr.inra.pappso.xtandempipeline.sax_parse.parse_file;
public class phosphosite extends process {
- private Vector<File> xtandem;
+ private Vector<IdentificationDataFile> xtandem;
private ArrayList<Identification> identifications = XtandemPipelineSession
.getInstance().getIdentificationList();
@@ -58,7 +58,6 @@ public class phosphosite extends process {
ident.filtered_match(new filter_peptide_evalue((conf
.get_peptide_evalue())));
ident.filtered_match(new filter_peptide_redondancy());
-
// verification pas arreté
if (this.isStop())
@@ -112,12 +111,13 @@ public class phosphosite extends process {
}
- public void setXtandem(Vector<File> xtandem) {
+ @Override
+ public void setXtandem(Vector<IdentificationDataFile> xtandem) {
this.xtandem = xtandem;
this.set_max_progress(xtandem.size() + 7);
}
- public Vector<File> getXtandem() {
+ public Vector<IdentificationDataFile> getXtandem() {
return xtandem;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java
index 9ed1ddbe6..9815f2436 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/process.java
@@ -1,12 +1,12 @@
package fr.inra.pappso.xtandempipeline.thread;
-import java.io.File;
import java.util.Vector;
import org.apache.log4j.Logger;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationDataFile;
public class process extends Thread {
@@ -17,11 +17,11 @@ public class process extends Thread {
private Exception error;
protected config conf;
-
+
private int maxprogress;
-
+
private int currentprogress;
-
+
protected static final Logger logger = Logger.getLogger(process.class);
public process(config conf) {
@@ -30,7 +30,7 @@ public class process extends Thread {
this.setStop(false);
this.view = "";
this.setConf(conf);
- this.currentprogress=0;
+ this.currentprogress = 0;
this.maxprogress = 1;
}
@@ -43,7 +43,8 @@ public class process extends Thread {
try {
long start = System.currentTimeMillis();
this.processing();
- logger.info("Execution time = "+(System.currentTimeMillis()-start)/1000);
+ logger.info("Execution time = "
+ + (System.currentTimeMillis() - start) / 1000);
} catch (StopException e) {
logger.info("Process were stopping");
} catch (Exception e) {
@@ -51,11 +52,11 @@ public class process extends Thread {
logger.error("Process were stopping");
logger.error(e.getMessage());
StackTraceElement[] f = e.getStackTrace();
- for(int i = 0;i<f.length;i++){
+ for (int i = 0; i < f.length; i++) {
logger.error(f[i]);
}
this.set_view("Error:\n" + e.getMessage());
- //this.setStop(true);
+ // this.setStop(true);
}
}
@@ -69,7 +70,7 @@ public class process extends Thread {
public void set_view(String v) {
if (v.length() > 1000)
- this.view = v.substring(v.length()-999);
+ this.view = v.substring(v.length() - 999);
else
this.view = v;
}
@@ -95,25 +96,26 @@ public class process extends Thread {
return conf;
}
- public void setXtandem(Vector<File> xtandem) {
+ public void setXtandem(Vector<IdentificationDataFile> xtandem) {
}
synchronized public int get_max_progress() {
return this.maxprogress;
}
-
+
public void set_max_progress(int max) {
this.maxprogress = max;
}
-
+
synchronized public int get_current_progress() {
return this.currentprogress;
}
-
+
public void add_current_progress() {
this.currentprogress++;
}
+
public void set_current_progress(int p) {
this.currentprogress = p;
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java
index 8d853e75e..25c51b1fe 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/xtandem_analysis.java
@@ -2,22 +2,22 @@ package fr.inra.pappso.xtandempipeline.thread;
import java.io.File;
-
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.class_msms.IdentificationDataFile.IdentificationXtandemFile;
import fr.inra.pappso.xtandempipeline.sax_parse.msms_output;
import fr.inra.pappso.xtandempipeline.sax_parse.xtandem_params;
public class xtandem_analysis extends process {
private File[] xtandem;
-
+
private File[] databases;
-
+
private File save_dir;
-
- private File model;
+
+ private IdentificationXtandemFile model;
public xtandem_analysis(config conf) {
super(conf);
@@ -25,67 +25,79 @@ public class xtandem_analysis extends process {
protected void processing() throws Exception {
logger.info("Xtandem analysis start");
- //creation du fichier database
- File databasexml = new File(this.save_dir.getAbsolutePath()+System.getProperty("file.separator")+"database.xml");
+ // creation du fichier database
+ File databasexml = new File(this.save_dir.getAbsolutePath()
+ + System.getProperty("file.separator") + "database.xml");
msms_output out = new msms_output();
out.open(databasexml.getAbsolutePath());
- out.write("<?xml version=\"1.0\"?>"+"\n");
- out.write("<bioml label=\"x! taxon-to-file matching list\">"+"\n");
- out.write("<taxon label=\"usedefined\">"+"\n");
- for(int j = 0;j<databases.length;j++){
- out.write("<file format=\"peptide\" URL=\""+databases[j].getAbsolutePath()+"\" />"+"\n");
+ out.write("<?xml version=\"1.0\"?>" + "\n");
+ out.write("<bioml label=\"x! taxon-to-file matching list\">" + "\n");
+ out.write("<taxon label=\"usedefined\">" + "\n");
+ for (int j = 0; j < databases.length; j++) {
+ out.write("<file format=\"peptide\" URL=\""
+ + databases[j].getAbsolutePath() + "\" />" + "\n");
}
- out.write("</taxon>"+"\n");
- out.write("</bioml>"+"\n");
+ out.write("</taxon>" + "\n");
+ out.write("</bioml>" + "\n");
out.close();
- File infile = new File(this.save_dir.getAbsolutePath()+System.getProperty("file.separator")+"infile.xml");
-
- //Correction du fichier de parametres
+ File infile = new File(this.save_dir.getAbsolutePath()
+ + System.getProperty("file.separator") + "infile.xml");
+
+ // Correction du fichier de parametres
logger.info("Corrected xtandem preset error");
xtandem_params params = new xtandem_params();
params.load_new_param();
params.load_xml(model);
params.save_to_xml(model);
-
+
for (int i = 0; i < xtandem.length; i++) {
- logger.info("Xtandem analysis on : "+xtandem[i].getName());
+ logger.info("Xtandem analysis on : " + xtandem[i].getName());
File result_out = new File(this.get_out(xtandem[i]));
// parsing
- //creation du fichier infile
+ // creation du fichier infile
out.open(infile.getAbsolutePath());
- out.write("<?xml version=\"1.0\"?>"+"\n");
- out.write("<bioml label=\""+xtandem[i].getName()+"\">"+"\n");
- out.write("<note type=\"heading\">Paths</note>"+"\n");
- out.write("<note type=\"input\" label=\"list path, default parameters\">"+model.getAbsolutePath()+"</note>"+"\n");
- out.write("<note type=\"input\" label=\"list path, taxonomy information\">"+databasexml.getAbsolutePath()+"</note>"+"\n");
- out.write("<note type=\"input\" label=\"spectrum, path\">"+xtandem[i].getAbsolutePath()+"</note>"+"\n");
- out.write("<note type=\"heading\">Protein general</note>"+"\n");
- out.write("<note type=\"input\" label=\"protein, taxon\">usedefined</note>"+"\n");
- out.write("<note type=\"heading\">Output</note>"+"\n");
- out.write("<note type=\"input\" label=\"output, path\">"+result_out.getAbsolutePath()+"</note>"+"\n");
- out.write("</bioml>"+"\n");
+ out.write("<?xml version=\"1.0\"?>" + "\n");
+ out.write("<bioml label=\"" + xtandem[i].getName() + "\">" + "\n");
+ out.write("<note type=\"heading\">Paths</note>" + "\n");
+ out.write("<note type=\"input\" label=\"list path, default parameters\">"
+ + model.getAbsolutePath() + "</note>" + "\n");
+ out.write("<note type=\"input\" label=\"list path, taxonomy information\">"
+ + databasexml.getAbsolutePath() + "</note>" + "\n");
+ out.write("<note type=\"input\" label=\"spectrum, path\">"
+ + xtandem[i].getAbsolutePath() + "</note>" + "\n");
+ out.write("<note type=\"heading\">Protein general</note>" + "\n");
+ out.write("<note type=\"input\" label=\"protein, taxon\">usedefined</note>"
+ + "\n");
+ out.write("<note type=\"heading\">Output</note>" + "\n");
+ out.write("<note type=\"input\" label=\"output, path\">"
+ + result_out.getAbsolutePath() + "</note>" + "\n");
+ out.write("</bioml>" + "\n");
out.close();
-
- //creation des fichiers
+
+ // creation des fichiers
base_shell pipe = new base_shell();
- pipe.set_commande(new String[]{conf.getXtandem_link().getAbsolutePath(),infile.getAbsolutePath()});
+ pipe.set_commande(new String[] {
+ conf.getXtandem_link().getAbsolutePath(),
+ infile.getAbsolutePath() });
pipe.start_process();
while (pipe.status()) {
Thread.currentThread();
Thread.sleep(100);
- if (this.isStop()){
+ if (this.isStop()) {
pipe.stop_process();
throw new StopException("");
}
- this.set_view("Analyse file : " + (i+1) + "/" + xtandem.length
- + "\n" + xtandem[i].getName()+"\n"+pipe.get_Stdout());
- //System.out.println(pipe.getStatus());
-
+ this.set_view("Analyse file : " + (i + 1) + "/"
+ + xtandem.length + "\n" + xtandem[i].getName() + "\n"
+ + pipe.get_Stdout());
+ // System.out.println(pipe.getStatus());
+
}
- if (pipe.get_error()!=null)
+ if (pipe.get_error() != null)
throw pipe.get_error();
- if(!result_out.exists())
- throw new MSMSException("Analysis of '"+xtandem[i].getName()+" give no result'\n"+pipe.get_Stdout());
+ if (!result_out.exists())
+ throw new MSMSException("Analysis of '" + xtandem[i].getName()
+ + " give no result'\n" + pipe.get_Stdout());
logger.info("finish");
this.add_current_progress();
@@ -93,7 +105,6 @@ public class xtandem_analysis extends process {
databasexml.delete();
infile.delete();
-
}
public void setXtandem(File[] xtandem) {
@@ -121,22 +132,23 @@ public class xtandem_analysis extends process {
return save_dir;
}
- public void setModel(File model) {
+ public void setModel(IdentificationXtandemFile model) {
this.model = model;
}
- public File getModel() {
+ public IdentificationXtandemFile getModel() {
return model;
}
+
private String get_out(File out) {
String basename = out.getName();
basename = basename.replaceFirst(".mzXML$", "");
basename = basename.replaceFirst(".mgf$", "");
basename = basename.replaceFirst(".mzData$", "");
basename = basename.replaceFirst(".mzML$", "");
- basename = basename.replaceFirst(".pkl$", "");
+ basename = basename.replaceFirst(".pkl$", "");
basename = basename.replaceFirst(".xml$", "");
-
+
return (this.getSave_dir().getAbsolutePath()
+ System.getProperty("file.separator") + basename + "." + "xml");
}
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 b208718d6..5c94389fc 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
@@ -17,16 +17,16 @@ import org.eclipse.swt.widgets.MessageBox;
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.class_msms.IdentificationDataFile.IdentificationDataFile;
import fr.inra.pappso.xtandempipeline.thread.DataType_Base;
public class Filter_Windows {
protected config conf;
- private Vector<File> add_xml;
+ private Vector<IdentificationDataFile> add_xml;
private String current_directory;
private Shell shell;
private Text pep_evalue;
@@ -35,14 +35,15 @@ public class Filter_Windows {
private Button filter_to_all;
private Boolean Cancelled;
private DataType_Base type;
-
+
public Filter_Windows(Main_Windows controlleur) {
Cancelled = true;
this.conf = XtandemPipelineSession.getInstance().getConfig();
- this.type = XtandemPipelineSession.getInstance().getDataTypeBase();
- this.add_xml = new Vector<File>();
+ this.type = XtandemPipelineSession.getInstance().getDataTypeBase();
+ this.add_xml = new Vector<IdentificationDataFile>();
current_directory = conf.getXmlresult().getAbsolutePath();
- shell = new Shell(controlleur.getDisplay(),SWT.DIALOG_TRIM|SWT.APPLICATION_MODAL);
+ shell = new Shell(controlleur.getDisplay(), SWT.DIALOG_TRIM
+ | SWT.APPLICATION_MODAL);
shell.setImages(controlleur.getImages());
// initialise la fenetre
init();
@@ -51,7 +52,7 @@ public class Filter_Windows {
// regle et affiche la fenetre
shell.pack();
- //shell.setSize(500, 600);
+ // shell.setSize(500, 600);
shell.open();
while (!shell.isDisposed()) {
if (!controlleur.getDisplay().readAndDispatch()) {
@@ -60,23 +61,23 @@ public class Filter_Windows {
}
}
- private void init() {
+ private void init() {
shell.setText("Configuration of the filtering parameters");
- GridLayout layout = new GridLayout(1,false);
+ GridLayout layout = new GridLayout(1, false);
layout.marginLeft = layout.marginTop = layout.marginRight = layout.marginBottom = 10;
layout.verticalSpacing = 10;
shell.setLayout(layout);
- //AJout des filtres
-
+ // AJout des filtres
+
Group add_xtandem = new Group(shell, SWT.SHADOW_IN);
add_xtandem.setText("Set X!Tandem result files");
add_xtandem.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
- add_xtandem.setLayout(new GridLayout(2,false));
-
- Text add_result = new Text(add_xtandem, SWT.SINGLE|SWT.READ_ONLY);
+ add_xtandem.setLayout(new GridLayout(2, false));
+
+ Text add_result = new Text(add_xtandem, SWT.SINGLE | SWT.READ_ONLY);
add_result.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
add_result.setText("No selected");
- Button add = new Button(add_xtandem,SWT.PUSH);
+ Button add = new Button(add_xtandem, SWT.PUSH);
add.setText("Add files");
add.setData("text", add_result);
add.addSelectionListener(new SelectionAdapter() {
@@ -84,12 +85,12 @@ public class Filter_Windows {
Filter_Windows.this.add_clic((Button) e.widget);
}
});
-
+
Group filter = new Group(shell, SWT.SHADOW_IN);
filter.setText("Filter result to");
filter.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
- filter.setLayout(new GridLayout(2,false));
-
+ filter.setLayout(new GridLayout(2, false));
+
pep_evalue = new Text(filter, SWT.SINGLE);
pep_evalue.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
Label l = new Label(filter, SWT.NONE);
@@ -105,30 +106,29 @@ public class Filter_Windows {
l = new Label(filter, SWT.NONE);
l.setText("Maximal protein log(E value) to conserve a protein");
-
- Label separator = new Label(filter,SWT.SEPARATOR|SWT.HORIZONTAL);
+ Label separator = new Label(filter, SWT.SEPARATOR | SWT.HORIZONTAL);
GridData data = new GridData(GridData.FILL_HORIZONTAL);
- data.horizontalSpan=2;
+ data.horizontalSpan = 2;
separator.setLayoutData(data);
-
+
filter_to_all = new Button(filter, SWT.CHECK);
filter_to_all.setText(" ");
filter_to_all.setEnabled(!type.getIs_invididual());
l = new Label(filter, SWT.NONE);
- l.setText("Apply protein filter to sum of all samples");
-
+ l.setText("Apply protein filter to sum of all samples");
+
Group database = new Group(shell, SWT.SHADOW_IN);
database.setText("Remove result from contaminants database");
- //data = new GridData(GridData.FILL_HORIZONTAL);
- //data.horizontalSpan=2;
- //database.setLayoutData(data);
+ // data = new GridData(GridData.FILL_HORIZONTAL);
+ // data.horizontalSpan=2;
+ // database.setLayoutData(data);
database.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
- database.setLayout(new GridLayout(2,false));
-
- Text data_conta = new Text(database, SWT.SINGLE|SWT.READ_ONLY);
+ database.setLayout(new GridLayout(2, false));
+
+ Text data_conta = new Text(database, SWT.SINGLE | SWT.READ_ONLY);
data_conta.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
data_conta.setText(conf.get_database_filter().getName());
- Button select = new Button(database,SWT.PUSH);
+ Button select = new Button(database, SWT.PUSH);
select.setText("Select");
select.setData("text", data_conta);
select.addSelectionListener(new SelectionAdapter() {
@@ -136,15 +136,15 @@ public class Filter_Windows {
Filter_Windows.this.select_clic((Button) e.widget);
}
});
-
- separator = new Label(shell,SWT.SEPARATOR|SWT.HORIZONTAL);
-// data = (new GridData(GridData.FILL_HORIZONTAL));
-// data.horizontalSpan=2;
+
+ separator = new Label(shell, SWT.SEPARATOR | SWT.HORIZONTAL);
+ // data = (new GridData(GridData.FILL_HORIZONTAL));
+ // data.horizontalSpan=2;
separator.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
-
-// l = new Label(shell,SWT.NONE);
-// l.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
- Button next = new Button(shell,SWT.PUSH);
+
+ // l = new Label(shell,SWT.NONE);
+ // l.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
+ Button next = new Button(shell, SWT.PUSH);
next.setLayoutData(new GridData(GridData.HORIZONTAL_ALIGN_END));
next.setText("Next");
next.setEnabled(false);
@@ -154,9 +154,8 @@ public class Filter_Windows {
}
});
add.setData("next", next);
-
+
}
-
private void add_data() {
// TODO Auto-generated method stub
@@ -164,13 +163,12 @@ public class Filter_Windows {
pep_evalue.setText(("" + conf.get_peptide_evalue()));
pep_number.setText(("" + conf.get_peptide_number()));
filter_to_all.setSelection(conf.get_protein_filter_to_complete());
-// if (conf.get_protein_filter_to_complete())
-// filter_to_all.setSelection(true);
-// else
-// filter_to_all.setSelection(false);
+ // if (conf.get_protein_filter_to_complete())
+ // filter_to_all.setSelection(true);
+ // else
+ // filter_to_all.setSelection(false);
}
-
-
+
private void modified_conf() throws MSMSException {
float fl1;
float fl2;
@@ -178,14 +176,12 @@ public class Filter_Windows {
try {
fl1 = Float.valueOf(prot_evalue.getText()).floatValue();
} catch (Exception e) {
- throw new MSMSException(
- "Log(E value) protein must be like '-8'");
+ throw new MSMSException("Log(E value) protein must be like '-8'");
}
try {
fl2 = Float.valueOf(pep_evalue.getText()).floatValue();
} catch (Exception e) {
- throw new MSMSException(
- "Peptide E value must be like '0.05'");
+ throw new MSMSException("Peptide E value must be like '0.05'");
}
try {
it = Integer.parseInt(pep_number.getText());
@@ -210,15 +206,19 @@ public class Filter_Windows {
Cancelled = false;
shell.dispose();
} catch (MSMSException e) {
- MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
- messageBox.setMessage("Problems trying to save the configuration :\n" + e.getMessage());
- messageBox.open();
- } catch (Exception e) {
+ MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
+ messageBox
+ .setMessage("Problems trying to save the configuration :\n"
+ + e.getMessage());
+ messageBox.open();
+ } catch (Exception e) {
StackTraceElement[] f = e.getStackTrace();
String error = e.getMessage() + "\nat : " + f[0].toString();
- MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
- messageBox.setMessage("Problems trying to save the configuration :\n" + error);
- messageBox.open();
+ MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
+ messageBox
+ .setMessage("Problems trying to save the configuration :\n"
+ + error);
+ messageBox.open();
e.printStackTrace();
}
}
@@ -230,13 +230,14 @@ public class Filter_Windows {
conf.set_database_filter(files);
} catch (StopException S) {
-
+
} catch (Exception e) {
StackTraceElement[] f = e.getStackTrace();
String error = e.getMessage() + "\nat : " + f[0].toString();
- MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
- messageBox.setMessage("Problems during database selection :\n" + error);
- messageBox.open();
+ MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
+ messageBox.setMessage("Problems during database selection :\n"
+ + error);
+ messageBox.open();
e.printStackTrace();
} finally {
database_filter.setText(conf.get_database_filter().getName());
@@ -246,75 +247,77 @@ public class Filter_Windows {
private void add_clic(Button but) {
try {
- File[] files = this.get_file_xml();
- for (int m = 0 ; m < files.length; m++) {
+ IdentificationDataFile[] files = this.get_file_xml();
+ for (int m = 0; m < files.length; m++) {
if (!add_xml.contains(files[m]))
add_xml.add(files[m]);
}
-// for (int i = 0; i < files.length; i++)
-// add_xml.add(files[i]);
+ // for (int i = 0; i < files.length; i++)
+ // add_xml.add(files[i]);
Text t = (Text) but.getData("text");
t.setText(add_xml.size() + " files selected");
t.update();
-
- if(add_xml.size()>0)
+
+ if (add_xml.size() > 0)
((Button) but.getData("next")).setEnabled(true);
} catch (StopException S) {
-
+
} catch (Exception e) {
StackTraceElement[] f = e.getStackTrace();
String error = e.getMessage() + "\nat : " + f[0].toString();
- MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
- messageBox.setMessage("Problems during xml files selection :\n" + error);
- messageBox.open();
+ MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
+ messageBox.setMessage("Problems during xml files selection :\n"
+ + error);
+ messageBox.open();
e.printStackTrace();
} finally {
// database_filter.setText(conf.get_database_filter().getName());
}
}
-
+
private File get_file_fasta() throws StopException {
- FileDialog dlg = new FileDialog(shell, SWT.OPEN|SWT.SINGLE);
- dlg.setFilterPath(conf.getProtein_database().getPath());
- dlg.setText("Select the contaminants database");
- dlg.setFilterExtensions(new String[]{"*.fasta","*.*"});
- dlg.setFilterNames(new String[]{"Fasta file","All files"});
- String fileName = dlg.open();
- if (fileName == null)
- throw new StopException("No fasta selected");
+ FileDialog dlg = new FileDialog(shell, SWT.OPEN | SWT.SINGLE);
+ dlg.setFilterPath(conf.getProtein_database().getPath());
+ dlg.setText("Select the contaminants database");
+ dlg.setFilterExtensions(new String[] { "*.fasta", "*.*" });
+ dlg.setFilterNames(new String[] { "Fasta file", "All files" });
+ String fileName = dlg.open();
+ if (fileName == null)
+ throw new StopException("No fasta selected");
return (new File(fileName));
}
- private File[] get_file_xml() throws Exception {
+ private IdentificationDataFile[] get_file_xml() throws Exception {
FileDialog dlg = new FileDialog(shell, SWT.OPEN | SWT.MULTI);
dlg.setFilterExtensions(new String[] { "*.xml", "*.*" });
- dlg.setFilterNames(new String[] { "X!Tandem result files",
- "All files" });
+ dlg.setFilterNames(new String[] { "X!Tandem result files", "All files" });
dlg.setFilterPath(current_directory);
dlg.setText("Add new xml result files to analyse");
String fileName = dlg.open();
if (fileName == null)
throw new StopException("No xml file selected");
String[] f = dlg.getFileNames();
- File[] files = new File[f.length];
- for (int i =0;i<f.length;i++) {
- files[i] = (new File(dlg.getFilterPath()
- + System.getProperty("file.separator") + f[i]));
+ IdentificationDataFile[] files = new IdentificationDataFile[f.length];
+ for (int i = 0; i < f.length; i++) {
+ files[i] = (IdentificationDataFile.newIdentificationDataFile(dlg
+ .getFilterPath()
+ + System.getProperty("file.separator")
+ + f[i]));
}
Arrays.sort(files);
current_directory = dlg.getFilterPath();
return (files);
}
-
- public Vector<File> get_Add_xml() {
+
+ public Vector<IdentificationDataFile> get_Add_xml() {
return add_xml;
}
public boolean isCancelled() {
return Cancelled;
}
-
+
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_Analysis_Param.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_Analysis_Param.java
index 302f7a4cb..4a4cdb7d5 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_Analysis_Param.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_Analysis_Param.java
@@ -22,6 +22,7 @@ import org.eclipse.swt.widgets.Text;
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationXtandemFile;
import fr.inra.pappso.xtandempipeline.thread.xtandem_analysis;
public class Xtandem_Analysis_Param {
@@ -86,7 +87,7 @@ public class Xtandem_Analysis_Param {
else
comboPresetList.select(0);
- this.bEditPreset.setEnabled(true);
+ this.bEditPreset.setEnabled(true);
if (models.size() == 0) {
this.bEditPreset.setEnabled(false);
}
@@ -321,10 +322,11 @@ public class Xtandem_Analysis_Param {
this.xtandem.setDatabases(fasta);
// Vector<File> all_models = (Vector<File>) this.params.getData();
- this.xtandem.setModel(new File(this.comboPresetList.getData("path")
- + System.getProperty("file.separator")
- + this.comboPresetList.getItem(this.comboPresetList
- .getSelectionIndex())));
+ this.xtandem.setModel(new IdentificationXtandemFile(new File(
+ this.comboPresetList.getData("path")
+ + System.getProperty("file.separator")
+ + this.comboPresetList.getItem(this.comboPresetList
+ .getSelectionIndex()))));
this.xtandem.setSave_dir(out_dir);
// on indique que la fenetre n'a pas ete cancel
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_preset.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_preset.java
index 41aa18c1c..c6542647b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_preset.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/ui/swt/Xtandem_preset.java
@@ -24,11 +24,10 @@ import org.eclipse.swt.widgets.TabFolder;
import org.eclipse.swt.widgets.TabItem;
import org.eclipse.swt.widgets.Text;
-
-
import fr.inra.pappso.xtandempipeline.MsException.StopException;
import fr.inra.pappso.xtandempipeline.class_msms.config;
import fr.inra.pappso.xtandempipeline.class_msms.xtandem_param;
+import fr.inra.pappso.xtandempipeline.class_msms.IdentificationDataFile.IdentificationXtandemFile;
import fr.inra.pappso.xtandempipeline.sax_parse.xtandem_params;
public class Xtandem_preset {
@@ -50,7 +49,7 @@ public class Xtandem_preset {
private Vector<Text> text_field;
private Vector<Combo> combo_field;
-
+
private boolean is_full;
public Xtandem_preset(Main_Windows controlleur, config conf) {
@@ -67,13 +66,12 @@ public class Xtandem_preset {
shell.pack();
shell.open();
}
-
public Xtandem_preset(Shell modal, config conf, String xmlfilename) {
- is_full=false;
+ is_full = false;
System.out.println("edit param xtandem");
this.conf = conf;
- shell = new Shell(modal, SWT.SHELL_TRIM| SWT.APPLICATION_MODAL);
+ shell = new Shell(modal, SWT.SHELL_TRIM | SWT.APPLICATION_MODAL);
shell.setImages(modal.getImages());
this.defined_interface();
// on rempli les données avec un nouveau model
@@ -82,15 +80,14 @@ public class Xtandem_preset {
shell.pack();
shell.open();
-
- if(xmlfilename==null){
+
+ if (xmlfilename == null) {
this.restore_default_value();
- }
- else{
+ } else {
this.set_model_list(xmlfilename);
this.load_value_to_xml();
}
-
+
while (!shell.isDisposed()) {
if (!modal.getDisplay().readAndDispatch()) {
modal.getDisplay().sleep();
@@ -168,14 +165,13 @@ public class Xtandem_preset {
open.setEnabled(is_full);
save_and_select.pack();
- }
+ }
protected void close_on_non_full() {
- if(!is_full)
+ if (!is_full)
shell.dispose();
}
-
private void set_model_list(String name) {
try {
Vector<File> xmls = conf.getXtandem_models();
@@ -268,23 +264,23 @@ public class Xtandem_preset {
}
private void delete_xml_file() {
- File xml = this.get_current_xml(model_list.getItem(model_list
- .getSelectionIndex()));
+ IdentificationXtandemFile xml = this.get_current_xml(model_list
+ .getItem(model_list.getSelectionIndex()));
if (xml.exists()) {
MessageBox messageBox = new MessageBox(shell, SWT.YES | SWT.NO);
messageBox.setMessage("Deleted the model file :\n" + xml.getName());
int response = messageBox.open();
- if(response==SWT.YES){
- xml.delete();
- this.set_model_list(xml.getName());
+ if (response == SWT.YES) {
+ xml.getFile().delete();
+ this.set_model_list(xml.getName());
}
}
}
private void load_value_to_xml() {
try {
- File xml = this.get_current_xml(model_list.getItem(model_list
- .getSelectionIndex()));
+ IdentificationXtandemFile xml = this.get_current_xml(model_list
+ .getItem(model_list.getSelectionIndex()));
this.params.load_xml(xml);
for (Combo com : combo_field) {
xtandem_param param = (xtandem_param) com.getData("param");
@@ -304,16 +300,16 @@ public class Xtandem_preset {
}
- private File get_current_xml(String filename) {
+ private IdentificationXtandemFile get_current_xml(String filename) {
File c = new File(conf.getXtandem_model()
+ System.getProperty("file.separator") + filename);
- return c;
+ return new IdentificationXtandemFile(c);
}
private void save_value_to_xml() {
try {
String name = modelname.getText().replaceFirst("\\.xml$", "");
- File xml = this.get_current_xml(name + ".xml");
+ IdentificationXtandemFile xml = this.get_current_xml(name + ".xml");
System.out.println(xml.getAbsolutePath());
int count = 0;
@@ -337,14 +333,15 @@ public class Xtandem_preset {
throw new StopException(count + " values are wrong");
if (xml.exists()) {
MessageBox messageBox = new MessageBox(shell, SWT.YES | SWT.NO);
- messageBox.setMessage("The model file : " + xml.getName()+" exist.\n Do you want to overwrite?");
+ messageBox.setMessage("The model file : " + xml.getName()
+ + " exist.\n Do you want to overwrite?");
int reponse = messageBox.open();
- if(reponse==SWT.YES)
+ if (reponse == SWT.YES)
params.save_to_xml(xml);
} else
params.save_to_xml(xml);
System.out.println("save");
-
+
this.set_model_list(xml.getName());
} catch (StopException e) {
MessageBox messageBox = new MessageBox(shell, SWT.ERROR);
--
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