From 2d0b5e34f41905569f0f8d268e2c16c9bdd8bc2e Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 29 May 2020 11:02:21 +0200
Subject: [PATCH] first fix for issue #23
---
.../identificationdatasource.h | 2 +-
src/utils/identificationdatasourcestore.cpp | 16 ++++++++++------
src/utils/identificationdatasourcestore.h | 5 +----
3 files changed, 12 insertions(+), 11 deletions(-)
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 1fe886ec..21d65ed4 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -42,7 +42,7 @@ class IdentificationDataSource
public:
IdentificationDataSource(const QString resource_name);
IdentificationDataSource(const IdentificationDataSource &other);
- ~IdentificationDataSource();
+ virtual ~IdentificationDataSource();
PeptideEvidenceStore &getPeptideEvidenceStore();
const PeptideEvidenceStore &getPeptideEvidenceStore() const;
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index 7ba69ddc..c539aaf5 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -50,6 +50,7 @@ IdentificationDataSourceSp
IdentificationDataSourceStore::getInstance(const QString &location,
IdentificationEngine engine)
{
+ //TODO file format read needs a fix
qDebug() << "IdentificationDataSourceStore::getInstance begin " << location;
std::map<QString, IdentificationDataSourceSp>::iterator it =
_map_identification_data_sources.find(location);
@@ -75,11 +76,13 @@ IdentificationDataSourceStore::getInstance(const QString &location,
else if(ext.toLower() == "pep")
{
// pep xml file
- p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ // p_identfile =
+ // std::make_shared<IdentificationPwizFile>(location_file);
}
else
{
- //p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ // p_identfile =
+ // std::make_shared<IdentificationPwizFile>(location_file);
}
if(p_identfile == nullptr)
{
@@ -123,7 +126,7 @@ IdentificationDataSourceStore::getInstance(const QString &location)
QString ext = location_file.completeSuffix();
// QString sample_name = location_file.baseName();
IdentificationDataSourceSp p_identfile = nullptr;
- if(ext.toLower() == "xml")
+ if((ext.toLower() == "xml") || (ext.toLower() == ".d.xml"))
{
// X!Tandem result file
p_identfile =
@@ -144,8 +147,8 @@ IdentificationDataSourceStore::getInstance(const QString &location)
else if(ext.toLower() == "pepxml")
{
// pep xml file
- p_identfile =
- std::make_shared<IdentificationPepXmlFile>(location_file);
+ // p_identfile =
+ // std::make_shared<IdentificationPepXmlFile>(location_file);
}
else if(ext.toLower() == "dat")
{
@@ -155,7 +158,8 @@ IdentificationDataSourceStore::getInstance(const QString &location)
}
else
{
- p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ // p_identfile =
+ // std::make_shared<IdentificationPwizFile>(location_file);
}
if(p_identfile == nullptr)
{
diff --git a/src/utils/identificationdatasourcestore.h b/src/utils/identificationdatasourcestore.h
index b59e667a..a6091e91 100644
--- a/src/utils/identificationdatasourcestore.h
+++ b/src/utils/identificationdatasourcestore.h
@@ -30,8 +30,7 @@
*implementation
******************************************************************************/
-#ifndef IDENTIFICATIONDATASOURCESTORE_H
-#define IDENTIFICATIONDATASOURCESTORE_H
+#pragma once
#include <map>
#include <set>
@@ -54,5 +53,3 @@ class IdentificationDataSourceStore
std::map<QString, IdentificationDataSourceSp>
_map_identification_data_sources;
};
-
-#endif // IDENTIFICATIONDATASOURCESTORE_H
--
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