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PAPPSO
xtpcpp
Commits
d3d09069
Commit
d3d09069
authored
Jun 13, 2019
by
Langella Olivier
Browse files
tpp tandem version compliant
parent
08a7e39e
Changes
2
Hide whitespace changes
Inline
Side-by-side
src/core/tandem_run/tandemparameters.cpp
View file @
d3d09069
...
...
@@ -33,6 +33,25 @@
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/exception/exceptionnotpossible.h>
/*
*
specific parameters for the modified TPP tandem version :
http://tools.proteomecenter.org/wiki/index.php?title=TPP:X%21Tandem_and_the_TPP
<note label="scoring, algorithm" type="input">k-score</note>
<note label="spectrum, use conditioning" type="input">no</note>
<note label="scoring, minimum ion count" type="input">1</note>
new labels :
"protein, taxon" https://www.thegpm.org/TANDEM/api/pt.html
"protein, homolog management"
"refine, sequence path" https://www.thegpm.org/TANDEM/api/rsp.html
"refine, tic percent" https://www.thegpm.org/TANDEM/api/rtp.html
"output, log path" https://www.thegpm.org/TANDEM/api/olp.html
"output, message" https://www.thegpm.org/TANDEM/api/om.html
"output, sequence path" https://www.thegpm.org/TANDEM/api/osp.html
"output, path" https://www.thegpm.org/TANDEM/api/opath.html
*/
TandemParameters
::
TandemParameters
()
{
}
...
...
@@ -159,7 +178,9 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(
label
==
"output, parameters"
)
||
(
label
==
"output, performance"
)
||
(
label
==
"output, histograms"
)
||
(
label
==
"output, path hashing"
)
||
(
label
==
"spectrum, use noise suppression"
))
(
label
==
"spectrum, use noise suppression"
)
||
(
label
==
"spectrum, use conditioning"
)
||
(
label
==
"protein, homolog management"
))
{
if
((
value
!=
"yes"
)
&&
(
value
!=
"no"
))
{
...
...
@@ -168,12 +189,6 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
.
arg
(
label
)
.
arg
(
value
));
}
/*
<note label="scoring, algorithm" type="input">k-score</note>
<note label="spectrum, use conditioning" type="input">no</note>
<note label="scoring, minimum ion count" type="input">1</note>
*/
}
else
if
((
label
==
"spectrum, parent monoisotopic mass error minus"
)
||
...
...
@@ -190,7 +205,8 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(
label
==
"spectrum, neutral loss window"
)
||
(
label
==
"spectrum, minimum fragment mz"
)
||
(
label
==
"output, maximum valid expectation value"
)
||
(
label
==
"output, maximum valid protein expectation value"
)
(
label
==
"output, maximum valid protein expectation value"
)
||
(
label
==
"refine, tic percent"
)
)
...
...
@@ -235,8 +251,11 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(
label
==
"refine, potential modification motif 1"
)
||
(
label
==
"refine, potential modification motif 2"
)
||
(
label
==
"output, sort results by"
)
||
(
label
==
"output, xsl path"
)
||
(
label
==
"spectrum, path"
))
(
label
==
"output, xsl path"
)
||
(
label
==
"spectrum, path"
)
||
(
label
==
"scoring, algorithm"
)
||
(
label
==
"protein, taxon"
)
||
(
label
==
"refine, sequence path"
)
||
(
label
==
"output, log path"
)
||
(
label
==
"output, message"
)
||
(
label
==
"output, sequence path"
)
||
(
label
==
"output, path"
))
{
// string
}
...
...
@@ -246,7 +265,7 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(
label
==
"spectrum, sequence batch size"
)
||
(
label
==
"spectrum, threads"
)
||
(
label
==
"scoring, minimum ion count"
)
||
(
label
==
"scoring, maximum missed cleavage sites"
)
||
(
label
==
"scoring, maximum missed cleavage sites"
)
||
(
label
==
"output, histogram column width"
))
{
...
...
src/gui/edit/edit_tandem_preset_dialog/edittandempresetdialog.cpp
View file @
d3d09069
...
...
@@ -1016,14 +1016,31 @@ EditTandemPresetDialog::populate()
}
//<note type="input" label="protein, cleavage C-terminal mass
// change">+17.00305</note>
ui
->
pcctmc_edit
->
setText
(
_tandem_params
.
getValue
(
"protein, cleavage C-terminal mass change"
));
//<note type="input" label="protein, cleavage N-terminal mass
// change">+1.00794</note>
ui
->
pcntmc_edit
->
setText
(
_tandem_params
.
getValue
(
"protein, cleavage N-terminal mass change"
));
try
{
//<note type="input" label="protein, cleavage C-terminal mass
// change">+17.00305</note>
ui
->
pcctmc_edit
->
setText
(
_tandem_params
.
getValue
(
"protein, cleavage C-terminal mass change"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
pcctmc_edit
->
setText
(
"+17.00305"
);
}
try
{
//<note type="input" label="protein, cleavage N-terminal mass
// change">+1.00794</note>
ui
->
pcntmc_edit
->
setText
(
_tandem_params
.
getValue
(
"protein, cleavage N-terminal mass change"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
pcntmc_edit
->
setText
(
"+1.00794"
);
}
//<note type="input" label="protein, C-terminal residue modification
// mass">0.0</note>
...
...
@@ -1056,10 +1073,16 @@ EditTandemPresetDialog::populate()
//<note type="input" label="protein, stP bias">yes</note>
ui
->
pstpb_yes_radio_button
->
setChecked
(
true
);
ui
->
pstpb_no_radio_button
->
setChecked
(
false
);
if
(
_tandem_params
.
getValue
(
"protein, stP bias"
)
==
"no"
)
{
// -1 for not found
ui
->
pstpb_yes_radio_button
->
setChecked
(
false
);
ui
->
pstpb_no_radio_button
->
setChecked
(
true
);
try
{
if
(
_tandem_params
.
getValue
(
"protein, stP bias"
)
==
"no"
)
{
// -1 for not found
ui
->
pstpb_yes_radio_button
->
setChecked
(
false
);
ui
->
pstpb_no_radio_button
->
setChecked
(
true
);
}
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
}
//<note type="input" label="protein, modified residue mass file"></note>
...
...
@@ -1070,37 +1093,80 @@ EditTandemPresetDialog::populate()
ui
->
rmm_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, modification mass"
));
//<note type="input" label="residue, modification mass 1"></note>
ui
->
rmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, modification mass 1"
));
//<note type="input" label="residue, modification mass 2"></note>
ui
->
rmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, modification mass 2"
));
try
{
//<note type="input" label="residue, modification mass 1"></note>
ui
->
rmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, modification mass 1"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
rmm1_edit
->
setText
(
""
);
}
try
{
//<note type="input" label="residue, modification mass 2"></note>
ui
->
rmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, modification mass 2"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
rmm2_edit
->
setText
(
""
);
}
//<note type="input" label="residue, potential modification
// mass">15.99491@M</note>
ui
->
rpmm_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification mass"
));
//<note type="input" label="residue, potential modification mass
// 1"></note>
ui
->
rpmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification mass 1"
));
//<note type="input" label="residue, potential modification mass
// 2"></note>
ui
->
rpmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification mass 2"
));
try
{
//<note type="input" label="residue, potential modification mass
// 1"></note>
ui
->
rpmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification mass 1"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
rpmm1_edit
->
setText
(
""
);
}
try
{
//<note type="input" label="residue, potential modification mass
// 2"></note>
ui
->
rpmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification mass 2"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
rpmm2_edit
->
setText
(
""
);
}
//<note type="input" label="residue, potential modification motif"></note>
ui
->
rpmmotif_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification motif"
));
//<note type="input" label="residue, potential modification motif
// 1"></note>
ui
->
rpmmotif1_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification motif 1"
));
//<note type="input" label="residue, potential modification motif
// 2"></note>
ui
->
rpmmotif2_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification motif 2"
));
try
{
//<note type="input" label="residue, potential modification motif
// 1"></note>
ui
->
rpmmotif1_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification motif 1"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
rpmmotif1_edit
->
setText
(
""
);
}
try
{
//<note type="input" label="residue, potential modification motif
// 2"></note>
ui
->
rpmmotif2_edit
->
setText
(
_tandem_params
.
getValue
(
"residue, potential modification motif 2"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
rpmmotif2_edit
->
setText
(
""
);
}
//<note type="input" label="scoring, minimum ion count">4</note>
ui
->
smic_edit
->
setText
(
...
...
@@ -1199,33 +1265,78 @@ EditTandemPresetDialog::populate()
//<note type="input" label="refine, modification mass">57.02146@C</note>
ui
->
refmm_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, modification mass"
));
//<note type="input" label="refine, modification mass 1"></note>
ui
->
refmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, modification mass 1"
));
//<note type="input" label="refine, modification mass 2"></note>
ui
->
refmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, modification mass 2"
));
try
{
//<note type="input" label="refine, modification mass 1"></note>
ui
->
refmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, modification mass 1"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
refmm1_edit
->
setText
(
""
);
}
try
{
//<note type="input" label="refine, modification mass 2"></note>
ui
->
refmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, modification mass 2"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
refmm2_edit
->
setText
(
""
);
}
//<note type="input" label="refine, potential modification
// mass">15.99491@M</note>
ui
->
refpmm_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification mass"
));
//<note type="input" label="refine, potential modification mass 1"></note>
ui
->
refpmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification mass 1"
));
//<note type="input" label="refine, potential modification mass 2"></note>
ui
->
refpmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification mass 2"
));
try
{
//<note type="input" label="refine, potential modification mass
// 1"></note>
ui
->
refpmm1_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification mass 1"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
refpmm1_edit
->
setText
(
""
);
}
try
{
//<note type="input" label="refine, potential modification mass
// 2"></note>
ui
->
refpmm2_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification mass 2"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
refpmm2_edit
->
setText
(
""
);
}
//<note type="input" label="refine, potential modification motif"></note>
ui
->
refpmmotif_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification motif"
));
//<note type="input" label="refine, potential modification motif
// 1"></note>
ui
->
refpmmotif1_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification motif 1"
));
//<note type="input" label="refine, potential modification motif
// 2"></note>
ui
->
refpmmotif2_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification motif 2"
));
try
{
//<note type="input" label="refine, potential modification motif
// 1"></note>
ui
->
refpmmotif1_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification motif 1"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
refpmmotif1_edit
->
setText
(
""
);
}
try
{
//<note type="input" label="refine, potential modification motif
// 2"></note>
ui
->
refpmmotif2_edit
->
setText
(
_tandem_params
.
getValue
(
"refine, potential modification motif 2"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
refpmmotif2_edit
->
setText
(
""
);
}
//<note type="input" label="refine, use potential modifications for full
// refinement">yes</note>
ui
->
rupmffr_yes_radio_button
->
setChecked
(
true
);
...
...
@@ -1239,10 +1350,16 @@ EditTandemPresetDialog::populate()
//<note type="input" label="refine, cleavage semi">no</note>
ui
->
rcsemi_yes_radio_button
->
setChecked
(
true
);
ui
->
rcsemi_no_radio_button
->
setChecked
(
false
);
if
(
_tandem_params
.
getValue
(
"refine, cleavage semi"
)
==
"no"
)
{
// -1 for not found
ui
->
rcsemi_yes_radio_button
->
setChecked
(
false
);
ui
->
rcsemi_no_radio_button
->
setChecked
(
true
);
try
{
if
(
_tandem_params
.
getValue
(
"refine, cleavage semi"
)
==
"no"
)
{
// -1 for not found
ui
->
rcsemi_yes_radio_button
->
setChecked
(
false
);
ui
->
rcsemi_no_radio_button
->
setChecked
(
true
);
}
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
}
//<note type="input" label="refine, unanticipated cleavage">no</note>
ui
->
ruc_yes_radio_button
->
setChecked
(
true
);
...
...
@@ -1270,14 +1387,31 @@ EditTandemPresetDialog::populate()
}
//<note type="input" label="output, maximum valid expectation
// value">0.05</note>
ui
->
omvev_edit
->
setText
(
_tandem_params
.
getValue
(
"output, maximum valid expectation value"
));
//<note type="input" label="output, maximum valid protein expectation
// value">0.05</note>
ui
->
omvpev_edit
->
setText
(
_tandem_params
.
getValue
(
"output, maximum valid protein expectation value"
));
try
{
//<note type="input" label="output, maximum valid expectation
// value">0.05</note>
ui
->
omvev_edit
->
setText
(
_tandem_params
.
getValue
(
"output, maximum valid expectation value"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
omvev_edit
->
setText
(
"0.01"
);
}
try
{
//<note type="input" label="output, maximum valid protein expectation
// value">0.05</note>
ui
->
omvpev_edit
->
setText
(
_tandem_params
.
getValue
(
"output, maximum valid protein expectation value"
));
}
catch
(
pappso
::
ExceptionNotFound
&
error
)
{
ui
->
omvpev_edit
->
setText
(
"0.01"
);
}
//<note type="input" label="output, results">valid</note>
ui
->
oresu_all_radio_button
->
setChecked
(
false
);
ui
->
oresu_valid_radio_button
->
setChecked
(
true
);
...
...
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