Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
metexplore
met4j
Commits
79e4783c
Commit
79e4783c
authored
Mar 16, 2022
by
cfrainay
Browse files
Use 'merged degree' for percentile filter
parent
241b672b
Changes
1
Hide whitespace changes
Inline
Side-by-side
met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/networkAnalysis/SideCompoundsScan.java
View file @
79e4783c
...
...
@@ -92,12 +92,28 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
//perform scan
//------------
System
.
err
.
println
(
"Scaning..."
);
//if merging compartment
Map
<
String
,
Integer
>
mergedDegree
=
new
HashMap
<>();
if
(
merge
){
mergedDegree
=
graph
.
vertexSet
().
stream
().
collect
(
Collectors
.
groupingBy
(
BioMetabolite:
:
getName
,
Collectors
.
summingInt
(
v
->
graph
.
degreeOf
(
v
))
)
);
}
//degree statistics
DescriptiveStatistics
degreeStats
=
new
DescriptiveStatistics
();
double
dt
=
degree
;
if
(!
Double
.
isNaN
(
degreePrecentile
))
{
for
(
BioMetabolite
v
:
graph
.
vertexSet
())
{
degreeStats
.
addValue
(
graph
.
degreeOf
(
v
));
if
(
merge
){
degreeStats
.
addValue
(
mergedDegree
.
get
(
v
.
getName
()));
}
else
{
degreeStats
.
addValue
(
graph
.
degreeOf
(
v
));
}
}
dt
=
degreeStats
.
getPercentile
(
degreePrecentile
);
}
...
...
@@ -117,17 +133,6 @@ public class SideCompoundsScan extends AbstractMet4jApplication {
//if ids only, report side only
if
(
noReportValue
)
sideOnly
=
true
;
//if merging compartment
Map
<
String
,
Integer
>
mergedDegree
=
new
HashMap
<>();
if
(
merge
){
mergedDegree
=
graph
.
vertexSet
().
stream
().
collect
(
Collectors
.
groupingBy
(
BioMetabolite:
:
getName
,
Collectors
.
summingInt
(
v
->
graph
.
degreeOf
(
v
))
)
);
}
int
count
=
0
;
for
(
BioMetabolite
v
:
graph
.
vertexSet
())
{
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment