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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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PAPPSO
MassChroQ
Commits
84e6eebf
Commit
84e6eebf
authored
Sep 01, 2016
by
Olivier Langella
Browse files
fix problem getting peptide traces on labeled peptides
parent
ca63d566
Changes
5
Hide whitespace changes
Inline
Side-by-side
src/lib/peptides/peptide.h
View file @
84e6eebf
...
...
@@ -166,6 +166,12 @@ public:
getCharges
(
const
msRunHashGroup
&
group
)
const
;
const
QString
getSequence
()
const
;
virtual
const
Peptide
*
getOriginalPeptidePointer
()
const
{
return
this
;
};
protected:
...
...
src/lib/peptides/peptide_isotope.h
View file @
84e6eebf
...
...
@@ -76,6 +76,10 @@ public:
virtual
const
PeptideRtSp
&
getPeptideRtSp
()
const
override
;
virtual
const
Peptide
*
getOriginalPeptidePointer
()
const
{
return
_p_peptide_original
;
};
private:
const
Peptide
*
_p_peptide_original
;
...
...
src/lib/quanti_items/quantiItemPeptide.cpp
View file @
84e6eebf
...
...
@@ -156,11 +156,19 @@ CalcWriterInterface * QuantiItemPeptide::newCalcWriterInterface(const Quantifica
QDir
trace_dir
(
QString
(
"%1/%2/%3"
).
arg
(
quantificator
->
getTracesDirectory
().
absolutePath
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
p_msrun
->
getXmlId
()));
trace_dir
.
mkpath
(
trace_dir
.
absolutePath
());
CalcWriterInterface
*
_p_writer
=
nullptr
;
const
IsotopeLabel
*
p_label
=
this
->
getPeptide
()
->
getIsotopeLabel
();
QString
begin_path
;
if
(
p_label
==
nullptr
)
{
begin_path
=
QString
(
"%1/%2_%3-%4-z%5"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
this
->
_z
);
}
else
{
begin_path
=
QString
(
"%1/%2_%3-%4-%5-z%6"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
p_label
->
getXmlId
()).
arg
(
this
->
_z
);
}
if
(
quantificator
->
getTracesFormat
()
==
McqTsvFormat
::
tsv
)
{
_p_writer
=
new
TsvDirectoryWriter
(
QString
(
"%1/%2_%3-%4-z%5.d"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
this
->
_z
));
_p_writer
=
new
TsvDirectoryWriter
(
begin_path
.
append
(
".d"
));
}
else
{
_p_writer
=
new
OdsDocWriter
(
QString
(
"%1/%2_%3-%4-z%5.ods"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
this
->
_z
));
_p_writer
=
new
OdsDocWriter
(
begin_path
.
append
(
".ods"
));
}
return
_p_writer
;
...
...
src/lib/quanti_items/quantiitempeptidenaturalisotope.cpp
View file @
84e6eebf
...
...
@@ -120,11 +120,20 @@ CalcWriterInterface * QuantiItemPeptideNaturalIsotope::newCalcWriterInterface(co
QDir
trace_dir
(
QString
(
"%1/%2/%3"
).
arg
(
quantificator
->
getTracesDirectory
().
absolutePath
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
p_msrun
->
getXmlId
()));
trace_dir
.
mkpath
(
trace_dir
.
absolutePath
());
CalcWriterInterface
*
_p_writer
=
nullptr
;
const
IsotopeLabel
*
p_label
=
this
->
getPeptide
()
->
getIsotopeLabel
();
QString
begin_path
;
if
(
p_label
==
nullptr
)
{
begin_path
=
QString
(
"%1/%2_%3-%4-z%5-%6-%7"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
this
->
_z
).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeNumber
()).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeRank
());
}
else
{
begin_path
=
QString
(
"%1/%2_%3-%4-%5-z%6-%7-%8"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
p_label
->
getXmlId
()).
arg
(
this
->
_z
).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeNumber
()).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeRank
());
}
if
(
quantificator
->
getTracesFormat
()
==
McqTsvFormat
::
tsv
)
{
_p_writer
=
new
TsvDirectoryWriter
(
QString
(
"%1/%2_%3-%4-z%5-%6-%7.d"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
this
->
_z
).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeNumber
()).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeRank
()
));
_p_writer
=
new
TsvDirectoryWriter
(
begin_path
.
append
(
".d"
));
}
else
{
_p_writer
=
new
OdsDocWriter
(
QString
(
"%1/%2_%3-%4-z%5-%6-%7.ods"
).
arg
(
trace_dir
.
absolutePath
()).
arg
(
prefix
).
arg
(
quantificator
->
getXmlId
()).
arg
(
this
->
getPeptide
()
->
getXmlId
()).
arg
(
this
->
_z
).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeNumber
()).
arg
(
this
->
getPeptideNaturalIsotopeAverageSp
()
->
getIsotopeRank
()
));
_p_writer
=
new
OdsDocWriter
(
begin_path
.
append
(
".ods"
));
}
return
_p_writer
;
...
...
src/lib/quantificator.cpp
View file @
84e6eebf
...
...
@@ -162,7 +162,8 @@ void Quantificator::add_peptide_quanti_items(
++
itpep
,
debug_i
++
)
{
mcqout
()
<<
"Quantificator::add_peptide_quanti_items for "
<<
debug_i
<<
" "
<<
isotope_peptides
.
size
()
<<
endl
;
bool
trace_peptide
=
false
;
if
(
std
::
find
(
trace_peptide_list
.
begin
(),
trace_peptide_list
.
end
(),
*
itpep
)
!=
trace_peptide_list
.
end
())
{
const
Peptide
*
original_peptide_p
=
(
*
itpep
)
->
getOriginalPeptidePointer
();
if
(
std
::
find
(
trace_peptide_list
.
begin
(),
trace_peptide_list
.
end
(),
original_peptide_p
)
!=
trace_peptide_list
.
end
())
{
trace_peptide
=
true
;
}
...
...
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