From 0a6dce3ed8e52dee6bd7a52b96f3afa128c6f18f Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 19 Apr 2017 14:26:41 +0200
Subject: [PATCH] remove translation stop reading xtandem results
---
src/input/xpipsaxhandler.cpp | 6 +++++-
src/input/xtandemsaxhandler.cpp | 3 ++-
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index c3ead7438..71ae62ab5 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -180,7 +180,7 @@ bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
qDebug() << "startElement_sample ";
-
+
MsRunSp ms_run = _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
ms_run.get()->setFilename(attributes.value("value").simplified());
_current_identification_group_p->addMsRunSp(ms_run);
@@ -277,6 +277,8 @@ bool XpipSaxHandler::endElement_peptide() {
bool XpipSaxHandler::endElement_sequence() {
//if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
+
+ //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
_current_protein.setSequence(_current_text);
//}
//else {
@@ -285,6 +287,7 @@ bool XpipSaxHandler::endElement_sequence() {
return true;
}
bool XpipSaxHandler::endElement_protein() {
+
ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
_p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
@@ -392,3 +395,4 @@ pappso::AaModificationP XpipSaxHandler::getAaModificationP(pappso::mz mass) cons
throw pappso::ExceptionNotFound(QObject::tr("XpipSaxHandler::getAaModificationP => modification not found for mass %1").arg(mass));
}
+
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 5647756b3..c616abcf6 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -189,7 +189,8 @@ bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
bool is_ok = true;
_current_text = _current_text.simplified().replace(" ", "");
if (!_current_text.isEmpty()) {
- _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text);
+ //._sequence.replace(QRegExp("\\*"), "")).removeTranslationStop()
+ _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text.replace(QRegExp("\\*"), ""));
}
// <domain id="4017.1.1" start="21" end="31" expect="2.0e-06"
--
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