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vidjil
vidjil
Commits
4a87b4eb
Commit
4a87b4eb
authored
Apr 03, 2015
by
Mathieu Giraud
1
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core/segment.{cpp,h}: remembers the evalue when it is computed, and output in .json
parent
7113617c
Changes
3
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3 changed files
with
15 additions
and
4 deletions
+15
-4
algo/core/segment.cpp
algo/core/segment.cpp
+12
-2
algo/core/segment.h
algo/core/segment.h
+1
-0
algo/vidjil.cpp
algo/vidjil.cpp
+2
-2
No files found.
algo/core/segment.cpp
View file @
4a87b4eb
...
...
@@ -194,6 +194,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline)
Dend
=
0
;
because
=
0
;
// Cause of unsegmentation
score
=
0
;
evalue
=
NO_LIMIT_VALUE
;
int
s
=
(
size_t
)
germline
->
index
->
getS
()
;
int
length
=
sequence
.
length
()
;
...
...
@@ -348,9 +349,15 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
}
}
// end for (Germlines)
// E-value threshold
if
(
threshold_nb_expected
>
NO_LIMIT_VALUE
)
if
(
the_kseg
->
isSegmented
()
&&
getNbExpected
()
>
threshold_nb_expected
)
the_kseg
->
setSegmentationStatus
(
UNSEG_NOISY
);
if
(
the_kseg
->
isSegmented
())
{
// the_kseg->evalue also depends on the number of germlines from the *Multi*KmerSegmenter
the_kseg
->
evalue
=
getNbExpected
();
if
(
the_kseg
->
evalue
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_NOISY
);
}
}
}
double
KmerSegmenter
::
getProbabilityAtLeastOrAbove
(
int
at_least
)
const
{
...
...
@@ -936,6 +943,9 @@ void KmerSegmenter::toJsonList(JsonList *seg)
{
int
sequenceSize
=
sequence
.
size
();
if
(
evalue
>
NO_LIMIT_VALUE
)
seg
->
add
(
"evalue"
,
evalue
);
JsonList
*
json_affectValues
;
json_affectValues
=
new
JsonList
();
json_affectValues
->
add
(
"start"
,
0
);
...
...
algo/core/segment.h
View file @
4a87b4eb
...
...
@@ -76,6 +76,7 @@ protected:
string
seg_V
,
seg_N
,
seg_J
,
system
;
int
best_D
;
int
evalue
;
string
seg_N1
,
seg_D
,
seg_N2
;
Cost
segment_cost
;
...
...
algo/vidjil.cpp
View file @
4a87b4eb
...
...
@@ -1233,8 +1233,8 @@ int main (int argc, char **argv)
seg
.
toJsonList
(
&
json_seg
);
// Re-launch also a KmerMultiSegmenter, for
debug purposes
KmerMultiSegmenter
kmseg
(
seg
.
getSequence
(),
multigermline
,
0
);
// Re-launch also a KmerMultiSegmenter, for
control purposes (affectations, evalue)
KmerMultiSegmenter
kmseg
(
seg
.
getSequence
(),
multigermline
,
0
,
expected_value
);
KmerSegmenter
*
kseg
=
kmseg
.
the_kseg
;
kseg
->
toJsonList
(
&
json_seg
);
...
...
Mathieu Giraud
@magiraud
mentioned in issue
#4108
·
Dec 16, 2019
mentioned in issue
#4108
mentioned in issue #4108
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