From cbe66a3b87a0bb05837a4c52262d0767f7e95640 Mon Sep 17 00:00:00 2001
From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Tue, 30 Apr 2013 15:17:35 +0000
Subject: [PATCH] new checkbox to export redundant peptide list
git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@368 b8ef2a07-7df7-436f-90b9-41648038564b
---
.../xtandempipeline/class_msms/config.java | 27 +++++++++++++++++++
.../output/OdsRedundantPeptideOutput.java | 2 +-
.../xtandempipeline/thread/printing_base.java | 5 ++--
.../ui/swt/Export_Windows.java | 10 +++++++
4 files changed, 41 insertions(+), 3 deletions(-)
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 01b803e55..a89d2ed24 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
@@ -33,6 +33,11 @@ public class config {
private static String mascot_evalue = "mascot_evalue";
// Type of evalue stocked for mascot search theoritical or experimental
+ // indicates that we want an export redundant peptide in ODS
+ private static String export_redundant_ods = "export_redundant_ods";
+ // indicates that we want an export redundant peptide in CSV
+ private static String export_redundant_csv = "export_redundant_csv";
+
// indicates that we want an export in ODS
private static String export_ods = "export_ods";
// indicates that we want an export in TXT
@@ -258,6 +263,14 @@ public class config {
properties.setProperty(export_proticdbml, "" + F);
}
+ public void set_export_redundant_ods(boolean F) {
+ properties.setProperty(export_redundant_ods, "" + F);
+ }
+
+ public void set_export_redundant_csv(boolean F) {
+ properties.setProperty(export_redundant_csv, "" + F);
+ }
+
public void set_export_masschroq(boolean F) {
properties.setProperty(export_masschroq, "" + F);
}
@@ -336,6 +349,20 @@ public class config {
return (true);
}
+ public boolean get_export_redundant_ods() {
+ String value = properties.getProperty(export_redundant_ods, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
+ }
+
+ public boolean get_export_redundant_csv() {
+ String value = properties.getProperty(export_redundant_csv, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
+ }
+
public boolean get_export_txt() {
String value = properties.getProperty(export_txt, "false");
if (value.equals("false"))
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
index e9d41ba65..bdbb44234 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
@@ -55,6 +55,7 @@ public class OdsRedundantPeptideOutput {
throws MSMSException {
try {
odsTable = new OdsDocWriter(outputStream);
+ odsTable.writeSheet("peptides");
} catch (IOException e) {
String message = "IOException " + e.getMessage();
logger.error(message);
@@ -83,7 +84,6 @@ public class OdsRedundantPeptideOutput {
public void write(Identification ident) throws MSMSException {
try {
- odsTable.writeSheet("peptides");
this.writeHeaders();
for (Group group : ident.getGrouping().getGroupList()) {
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 907552a86..40d53c396 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java
@@ -158,7 +158,7 @@ public class printing_base extends process {
// redundant peptide output (containing start and stop positions on
// proteins)
- if (true) {
+ if (conf.get_export_redundant_ods()) {
FileOutputStream outputStream = new FileOutputStream(new File(this
.getfileout().getAbsolutePath() + "_pep_redundant.ods"));
OdsRedundantPeptideOutput odsRedOutput = new OdsRedundantPeptideOutput(
@@ -167,7 +167,8 @@ public class printing_base extends process {
odsRedOutput.write(ident);
}
odsRedOutput.close();
-
+ }
+ if (conf.get_export_redundant_csv()) {
FileOutputStream csvStream = new FileOutputStream(new File(this
.getfileout().getAbsolutePath() + "_pep_redundant.csv"));
CsvRedundantPeptideOutput csvRedOutput = new CsvRedundantPeptideOutput(
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 4f2f1fa12..f5b3a7085 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
@@ -38,6 +38,8 @@ public class Export_Windows {
private Button choice_spreadsheet_export;
+ private Button choice_redundant_ods_export;
+
private Button choice_fasta_export;
private Button choice_protic_export;
@@ -144,6 +146,12 @@ public class Export_Windows {
}
});
+ choice_redundant_ods_export = new Button(group, SWT.CHECK);
+ choice_redundant_ods_export
+ .setText("Redundant peptide list (containing start and stop on protein sequence)");
+ choice_redundant_ods_export.setSelection(conf
+ .get_export_redundant_ods());
+
choice_fasta_export = new Button(group, SWT.CHECK);
choice_fasta_export.setText("Identified proteins to a fasta file");
choice_fasta_export.setSelection(conf.get_export_fasta());
@@ -326,6 +334,8 @@ public class Export_Windows {
conf.set_export_proticdbml(this.choice_protic_export.getSelection());
conf.set_export_masschroq(this.choice_quantimscpp_export
.getSelection());
+ conf.set_export_redundant_ods(this.choice_redundant_ods_export
+ .getSelection());
// on sauve
conf.savePropertiestoXml();
datatype.getPrint().setfileout(out);
--
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