From c3d2da50e0bebc9fcc0ee788cdc2f964af586459 Mon Sep 17 00:00:00 2001
From: valot <valot@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Tue, 14 Feb 2012 10:10:20 +0000
Subject: [PATCH] Add 2 modes of calculation of the mascot evalue
(theoritical/experimental)
git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@208 b8ef2a07-7df7-436f-90b9-41648038564b
---
.../xtandempipeline/class_msms/config.java | 15 +++++++++++--
.../xtandempipeline/sax_parse/Mascot.java | 13 ++++++++++-
.../ui/swt/Filter_Windows.java | 22 ++++++++++++++-----
3 files changed, 41 insertions(+), 9 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 84b577d20..d2562309d 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/config.java
@@ -13,7 +13,6 @@ import fr.inra.pappso.xtandempipeline.XtandemPipelineMain;
public class config {
- private static final long serialVersionUID = 123L;
private static final Logger logger = Logger.getLogger(config.class);
private static String database_filter = "database_filter";
@@ -30,6 +29,8 @@ public class config {
private static String peptide_number = "peptide_number";
// minimum de peptides differents permettant l'identification
+ private static String mascot_evalue = "mascot_evalue";
+ // Type of evalue stocked for mascot search theoritical or experimental
//indicates that we want an export in ODS
private static String export_ods = "export_ods";
@@ -193,7 +194,10 @@ public class config {
properties.setProperty(peptide_number, "" + F);
}
-
+ public void set_mascot_evalue_theoritical(boolean F) {
+ properties.setProperty(mascot_evalue, "" + F);
+ }
+
public void set_export_ods(boolean F) {
logger.debug("set export_ods " +F);
properties.setProperty(export_ods, "" + F);
@@ -246,6 +250,13 @@ public class config {
.getProperty(peptide_number, "2"));
return (value);
}
+
+ public boolean get_mascot_evalue_theoritical() {
+ String value = properties.getProperty(mascot_evalue, "false");
+ if (value.equals("false"))
+ return (false);
+ return (true);
+ }
public boolean get_export_fasta() {
String value = properties.getProperty(export_fasta, "false");
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
index 7e681d404..322476470 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
@@ -11,6 +11,7 @@ import com.compomics.mascotdatfile.util.mascot.ProteinHit;
import com.compomics.mascotdatfile.util.mascot.Query;
import com.compomics.mascotdatfile.util.mascot.QueryToPeptideMap;
+import fr.inra.pappso.xtandempipeline.XtandemPipelineSession;
import fr.inra.pappso.xtandempipeline.class_msms.Identification;
import fr.inra.pappso.xtandempipeline.class_msms.Match;
import fr.inra.pappso.xtandempipeline.class_msms.Modifs;
@@ -113,12 +114,22 @@ public class Mascot {
pep_.set_charge((int) round(
(pep.getPeptideMr() / query.getPrecursorMZ()), 0));
pep_.set_deltamass((float) pep.getDeltaMass());
- pep_.set_evalue((float) pep.getExpectancy());
pep_.set_hypercorr((float) pep.getIonsScore());
pep_.set_mhplus_obser((float) (pep.getPeptideMr()
+ pep.getDeltaMass() + 1.007825));
pep_.set_mhplus_theo((float) (pep.getPeptideMr() + 1.007825));
pep_.set_sequence(pep.getSequence());
+
+
+ if(XtandemPipelineSession.getInstance().getConfig().get_mascot_evalue_theoritical()){
+ //Evalue theoritical
+ pep_.set_evalue((float) pep.getExpectancy());
+ }else{
+ //Evalue experimental
+ double eval = (pep.getIonsScore()-pep.getHomologyThreshold())/10;
+ eval = 0.05 / Math.pow(10, eval);
+ pep_.set_evalue((float) eval);
+ }
// Add first query
pep_.set_scan(query.getQueryNumber());
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 6b1014960..f13dafc30 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
@@ -33,6 +33,7 @@ public class Filter_Windows {
private Text prot_evalue;
private Text pep_number;
private Button filter_to_all;
+ private Button theoriticalButton;
private Boolean Cancelled;
private DataType_Base type;
@@ -116,6 +117,18 @@ public class Filter_Windows {
filter_to_all.setEnabled(!type.getIs_invididual());
l = new Label(filter, SWT.NONE);
l.setText("Apply protein filter to sum of all samples");
+
+ Group mascotEvalue = new Group(shell, SWT.SHADOW_IN);
+ mascotEvalue.setText("Mascot Evalue calculation");
+ mascotEvalue.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
+ mascotEvalue.setLayout(new GridLayout(1, false));
+
+ theoriticalButton = new Button(mascotEvalue, SWT.RADIO);
+ theoriticalButton.setText("Theoritical (The ion score threshold is the same for all spectra)");
+ theoriticalButton.setSelection(conf.get_mascot_evalue_theoritical());
+ Button experimentalButton = new Button(mascotEvalue, SWT.RADIO);
+ experimentalButton.setText("Experimental (The ion score threshold depend of the spectra)");
+ experimentalButton.setSelection(!conf.get_mascot_evalue_theoritical());
Group database = new Group(shell, SWT.SHADOW_IN);
database.setText("Remove result from contaminants database");
@@ -158,15 +171,10 @@ public class Filter_Windows {
}
private void add_data() {
- // TODO Auto-generated method stub
prot_evalue.setText(("" + conf.get_protein_evalue()));
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);
+ filter_to_all.setSelection(conf.get_protein_filter_to_complete());
}
private void modified_conf() throws MSMSException {
@@ -196,6 +204,8 @@ public class Filter_Windows {
conf.set_protein_filter_to_complete(true);
else
conf.set_protein_filter_to_complete(false);
+
+ conf.set_mascot_evalue_theoritical(theoriticalButton.getSelection());
}
private void next_clic() {
--
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