From 3252eb6b6985e15fb789a7b1e7f0240723c88f45 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 13 Dec 2018 09:36:48 +0100
Subject: [PATCH] accept empty labels for unmodified peptides
---
src/core/labeling/label.cpp | 11 ++++++++++-
src/core/labeling/label.h | 1 +
src/core/labeling/labelingmethod.cpp | 19 ++++++++++++++++++-
src/core/labeling/labelingmethod.h | 4 +++-
src/core/peptidextp.cpp | 2 +-
src/core/peptidextp.h | 2 +-
src/resources/catalog_label.xml | 2 ++
7 files changed, 36 insertions(+), 5 deletions(-)
diff --git a/src/core/labeling/label.cpp b/src/core/labeling/label.cpp
index 4eb7b7b2..85b89639 100644
--- a/src/core/labeling/label.cpp
+++ b/src/core/labeling/label.cpp
@@ -85,7 +85,8 @@ Label::containsAaModificationP(
{
for(LabelModification label_modification : _modification_list)
{
- if(std::find(modification_set.begin(), modification_set.end(),
+ if(std::find(modification_set.begin(),
+ modification_set.end(),
label_modification.modification) != modification_set.end())
{
return true;
@@ -142,3 +143,11 @@ Label::writeMassChroqMl(QXmlStreamWriter *output_stream) const
// </isotope_label>
output_stream->writeEndElement();
}
+
+bool
+Label::isEmpty() const
+{
+ if(_modification_list.size() == 0)
+ return true;
+ return false;
+}
diff --git a/src/core/labeling/label.h b/src/core/labeling/label.h
index ed21b41c..3adec8ca 100644
--- a/src/core/labeling/label.h
+++ b/src/core/labeling/label.h
@@ -57,6 +57,7 @@ class Label
const QString &getXmlId() const;
const std::vector<LabelModification> &getLabelModifictionList() const;
+ bool isEmpty() const;
private:
QString _xml_id;
diff --git a/src/core/labeling/labelingmethod.cpp b/src/core/labeling/labelingmethod.cpp
index aed64bb8..aa0bb6ec 100644
--- a/src/core/labeling/labelingmethod.cpp
+++ b/src/core/labeling/labelingmethod.cpp
@@ -70,17 +70,23 @@ LabelingMethod::LabelingMethod(const QString &method_id) : _xml_id(method_id)
}
-Label *
+const Label *
LabelingMethod::getLabel(
const std::list<pappso::AaModificationP> &modification_set) const
{
for(Label *p_label : _label_list)
{
+
if(p_label->containsAaModificationP(modification_set))
{
return p_label;
}
}
+ auto p_empty_label = getEmptyLabel();
+ if(p_empty_label != nullptr)
+ {
+ return p_empty_label;
+ }
return nullptr;
}
@@ -152,3 +158,14 @@ LabelingMethod::getLabelList() const
{
return _label_list;
}
+
+const Label *
+LabelingMethod::getEmptyLabel() const
+{
+ for(const Label *p_label : _label_list)
+ {
+ if(p_label->isEmpty())
+ return p_label;
+ }
+ return nullptr;
+}
diff --git a/src/core/labeling/labelingmethod.h b/src/core/labeling/labelingmethod.h
index e0b03080..abd8f4c6 100644
--- a/src/core/labeling/labelingmethod.h
+++ b/src/core/labeling/labelingmethod.h
@@ -47,12 +47,14 @@ class LabelingMethod
LabelingMethod(const LabelingMethod &other);
~LabelingMethod();
LabelingMethodSp makeLabelingMethodSp() const;
- Label *
+ const Label *
getLabel(const std::list<pappso::AaModificationP> &modification_set) const;
const QString &getXmlId() const;
void writeMassChroqMl(QXmlStreamWriter *output_stream) const;
const std::vector<Label *> &getLabelList() const;
+ const Label *getEmptyLabel() const;
+
private:
void parseMethod(QDomNode &method_node);
void parseLabel(QDomNode &method_node);
diff --git a/src/core/peptidextp.cpp b/src/core/peptidextp.cpp
index d4dd5d93..598a1222 100644
--- a/src/core/peptidextp.cpp
+++ b/src/core/peptidextp.cpp
@@ -127,7 +127,7 @@ PeptideXtp::applyLabelingMethod(LabelingMethodSp labeling_method_sp)
modification_set.unique();
_p_label = nullptr;
- Label *p_label = labeling_method_sp.get()->getLabel(modification_set);
+ const Label *p_label = labeling_method_sp.get()->getLabel(modification_set);
if(p_label != nullptr)
{
_p_label = p_label;
diff --git a/src/core/peptidextp.h b/src/core/peptidextp.h
index a1539d67..dc545559 100644
--- a/src/core/peptidextp.h
+++ b/src/core/peptidextp.h
@@ -77,7 +77,7 @@ class PeptideXtp : public pappso::Peptide
*/
pappso::PeptideSp _sp_native_peptide = nullptr;
- Label *_p_label = nullptr;
+ const Label *_p_label = nullptr;
};
#endif // PEPTIDEXTP_H
diff --git a/src/resources/catalog_label.xml b/src/resources/catalog_label.xml
index 99efc420..7adf2ad3 100644
--- a/src/resources/catalog_label.xml
+++ b/src/resources/catalog_label.xml
@@ -22,5 +22,7 @@
<mod at="R" value="6.02" acc="MOD:01331"/>
<mod at="K" value="4.01" acc="MOD:00942"/>
</isotope_label>
+ <isotope_label id="light">
+ </isotope_label>
</isotope_label_list>
</catalog>
--
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