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metexplore
met4j
Commits
781cbe56
Commit
781cbe56
authored
May 12, 2022
by
lcottret
Browse files
Finish tag 0.10
parents
d925056a
1d26a07f
Changes
50
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
781cbe56
...
...
@@ -18,4 +18,5 @@ met4j-core/src/main/java/fr/inra/toulouse/metexplore/met4j_core/Test\.java
/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/sandbox/
dependency-reduced-pom.xml
\ No newline at end of file
dependency-reduced-pom.xml
/met4j.sif
.gitlab-ci.yml
View file @
781cbe56
image
:
maven:3.6-adoptopenjdk-14
stages
:
-
build
-
test
-
deploy
-
build-containers
.template_docker
:
stage
:
build-containers
image
:
docker:latest
services
:
-
docker:dind
variables
:
MAVEN_CLI_OPTS
:
"
-s
.m2/settings.xml
--batch-mode"
...
...
@@ -9,19 +21,20 @@ cache:
-
.m2/repository/
build
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
build
script
:
-
mvn compile
test
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
test
script
:
-
mvn clean test
-
cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
deploySnapshot
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
deploy
script
:
-
mvn $MAVEN_CLI_OPTS deploy -Dmaven.test.skip=true
...
...
@@ -29,6 +42,7 @@ deploySnapshot:
-
develop
deployCentral
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
deploy
before_script
:
-
'
which
ssh-agent
||
(
apt-get
update
-qy
&&
apt-get
install
openssh-client
-qqy
)'
...
...
@@ -49,3 +63,47 @@ deployCentral:
-
mvn $MAVEN_CLI_OPTS release:perform -Darguments=-Dgpg.passphrase=${GPG_PASSPHRASE} -DlocalCheckout=true
only
:
-
master
buildSingularity
:
stage
:
build-containers
image
:
name
:
quay.io/singularity/singularity:v3.4.0
entrypoint
:
[
"
"
]
script
:
-
singularity build met4j-toolbox.sif met4j.singularity
-
singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_TAG"
rules
:
-
if
:
$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when
:
manual
-
if
:
$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
when
:
manual
buildDockerProdGitlab
:
extends
:
.template_docker
before_script
:
-
docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
script
:
-
docker build -t "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest" .
-
docker push "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest"
rules
:
-
if
:
$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when
:
manual
-
if
:
$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
when
:
manual
buildDockerProdDockerhub
:
extends
:
.template_docker
before_script
:
-
docker login -u "$DOCKERHUB_USER" -p "$DOCKERHUB_PASSWORD" $DOCKERHUB_REGISTRY
script
:
-
docker build --pull -t "$DOCKERHUB_IMAGE:latest" .
-
docker push "$DOCKERHUB_IMAGE:latest"
rules
:
-
if
:
$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
when
:
manual
-
if
:
$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
when
:
manual
CHANGELOG.md
View file @
781cbe56
...
...
@@ -4,6 +4,18 @@ All notable changes to this project will be documented in this file.
The format is based on
[
Keep a Changelog
](
https://keepachangelog.com/en/1.0.0/
)
,
and this project adheres to
[
Semantic Versioning
](
https://semver.org/spec/v2.0.0.html
)
.
## 0.10.0
### Features
[met4j-toolbox] New app: networkAnalysis.CompoundNet: Advanced compound graph building
[met4j-toolbox] New app: attributes.ExtractPathways: SBML sub network creation from a list of pathways
[met4j-toolbox] New app: attributes.ExtractSbmlAnnot: Extract sbml annotations
[met4j-toolbox] App improvements: networkAnalysis.SideCompoundsScan: Handle multiple compartments
## 0.9.1
### Fixed
...
...
Dockerfile
0 → 100644
View file @
781cbe56
FROM
debian:stable-slim
RUN
export
DEBIAN_FRONTEND
=
noninteractive
RUN
apt-get update
\
&&
apt-get upgrade
-y
\
&&
apt-get
install
-y
openjdk-11-jre git maven
\
&&
apt-get clean
\
&&
apt-get purge
RUN
mkdir
-p
/opt
&&
cd
/opt
\
&&
git clone https://forgemia.inra.fr/metexplore/met4j.git
\
&&
cd
met4j
\
&&
mvn
install
\
&&
cd
met4j-toolbox
\
&&
mvn package
RUN
mkdir
-p
/opt/bin
\
&&
cd
/opt/met4j/met4j-toolbox
\
&&
cp
target/met4j
*
.jar /opt/bin/met4j.jar
\
&&
cd
/opt
\
&&
rm
-rf
met4j ~/.m2
\
&&
apt-get remove
-y
git
&&
apt-get autoremove
-y
COPY
./docker_files/met4j.sh /opt/bin
ENTRYPOINT
["/opt/bin/met4j.sh"]
README.md
View file @
781cbe56
...
...
@@ -62,7 +62,7 @@ mv ./target/*-jar-with-dependencies.jar ../../../
## Usage
Documentation for the library modules can be found in each module's own README.
Detailed code examples can be found at
[
https://forgemia.inra.fr/metexplore/tutorialmet4j
](
https://cecill.info/licences/Licence_CeCILL_V2.1-en.html
)
.
Detailed code examples can be found at
[
here
](
https://forgemia.inra.fr/metexplore/tutorialmet4j
)
.
The toolbox can be launched using
```
...
...
@@ -74,6 +74,14 @@ which will list all the contained applications that can be called using
java -cp met4j-toolbox-0.8.0-jar-with-dependencies.jar <App full name> -h
```
### With singularity
You need at least
[
singularity
](
https://sylabs.io/guides/3.5/user-guide/quick_start.html
)
v3.5.
```
console
singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:latest
```
## Contributing
Pull requests are welcome
**on the gitlab repo**
(
[
https://forgemia.inra.fr/metexplore/met4j
](
https://forgemia.inra.fr/metexplore/met4j
)
). For major changes, please open an issue first to discuss what you would like to change.
...
...
coverage/pom.xml
View file @
781cbe56
...
...
@@ -44,7 +44,7 @@
<parent>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
<relativePath>
../pom.xml
</relativePath>
</parent>
...
...
docker_files/met4j.sh
0 → 100644
View file @
781cbe56
#!bin/bash
#
# Copyright INRAE (2022)
#
# contact-metexplore@inrae.fr
#
# This software is a computer program whose purpose is to [describe
# functionalities and technical features of your software].
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
#
#
path_jar
=
/opt/bin/met4j.jar
# path_jar=../met4j-toolbox/target/met4j-toolbox-0.9.1-SNAPSHOT.jar
if
[
$#
-lt
1
]
then
echo
"display Help"
exec
java
-jar
$path_jar
else
echo
"Lauch met4j-toolbox"
exec
java
-Dlog4j
.configuration
=
-cp
$path_jar
fr.inrae.toulouse.metexplore.met4j_toolbox.
"
$@
"
fi
\ No newline at end of file
met4j-chemUtils/pom.xml
View file @
781cbe56
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</parent>
<properties>
...
...
@@ -35,7 +35,7 @@
<dependency>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j-core
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
<dependency>
...
...
met4j-core/pom.xml
View file @
781cbe56
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</parent>
<scm>
...
...
met4j-graph/pom.xml
View file @
781cbe56
...
...
@@ -5,7 +5,7 @@
<parent>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</parent>
<artifactId>
met4j-graph
</artifactId>
...
...
@@ -40,7 +40,7 @@
<dependency>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j-core
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</dependency>
<dependency>
<groupId>
org.apache.commons
</groupId>
...
...
@@ -50,12 +50,12 @@
<dependency>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j-mathUtils
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</dependency>
<dependency>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j-chemUtils
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</dependency>
</dependencies>
...
...
met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/AtomMappingWeightPolicy.java
View file @
781cbe56
...
...
@@ -4,11 +4,13 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import
fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy
;
import
fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph
;
import
fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge
;
import
org.apache.commons.lang3.StringUtils
;
import
java.util.ArrayList
;
import
java.util.Collection
;
import
java.util.HashMap
;
import
java.util.Map
;
import
java.util.function.Function
;
import
java.util.regex.Matcher
;
import
java.util.regex.Pattern
;
import
java.util.stream.Collectors
;
...
...
@@ -101,6 +103,23 @@ public class AtomMappingWeightPolicy extends WeightingPolicy<BioMetabolite, Reac
.
sep
(
"\t"
));
}
public
AtomMappingWeightPolicy
fromConservedCarbonIndexes
(
String
GSAMoutputFile
){
String
sep
=
","
;
return
this
.
fromNumberOfConservedCarbons
(
new
WeightsFromFile
(
GSAMoutputFile
,
false
)
.
weightCol
(
8
)
.
edgeLabelCol
(
6
)
.
sourceCol
(
0
)
.
targetCol
(
3
)
.
processWeigthCol
(
new
Function
<
String
,
Double
>()
{
@Override
public
Double
apply
(
String
s
)
{
return
Double
.
valueOf
(
s
.
split
(
sep
).
length
);
}
})
.
sep
(
"\t"
))
;
}
@Override
public
void
setWeight
(
CompoundGraph
compoundGraph
)
{
if
(
conservedCarbons
==
null
)
throw
new
IllegalArgumentException
(
"an atom mapping must be provided"
);
...
...
@@ -110,7 +129,8 @@ public class AtomMappingWeightPolicy extends WeightingPolicy<BioMetabolite, Reac
for
(
ReactionEdge
e
:
compoundGraph
.
edgeSet
()){
Integer
cc
=
null
;
if
(
importer
!=
null
){
cc
=(
int
)
compoundGraph
.
getEdgeWeight
(
e
);
Double
w
=
compoundGraph
.
getEdgeWeight
(
e
);
if
(!
Double
.
isNaN
(
w
))
cc
=
Integer
.
valueOf
((
int
)
compoundGraph
.
getEdgeWeight
(
e
));
}
else
{
Map
<
BioMetabolite
,
Integer
>
mapping
=
conservedCarbons
.
get
(
e
.
getV1
());
if
(
mapping
!=
null
)
cc
=
conservedCarbons
.
get
(
e
.
getV1
()).
get
(
e
.
getV2
());
...
...
met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/WeightsFromFile.java
View file @
781cbe56
...
...
@@ -42,6 +42,7 @@ import java.util.Arrays;
import
java.util.Collections
;
import
java.util.HashSet
;
import
java.util.Set
;
import
java.util.function.Function
;
import
fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph
;
import
fr.inrae.toulouse.metexplore.met4j_graph.core.Edge
;
...
...
@@ -71,7 +72,12 @@ public class WeightsFromFile<V extends BioEntity, E extends Edge<V>,G extends Bi
private
int
weightCol
=
3
;
private
boolean
skipHeader
=
false
;
private
boolean
missingAsNaN
=
true
;
private
Function
<
String
,
Double
>
process
=
Double:
:
parseDouble
;
public
WeightsFromFile
<
V
,
E
,
G
>
processWeigthCol
(
Function
<
String
,
Double
>
process
)
{
this
.
process
=
process
;
return
this
;
}
public
WeightsFromFile
<
V
,
E
,
G
>
removeEdgeNotInFile
()
{
this
.
removeEdgeNotInFile
=
true
;
return
this
;
...
...
@@ -151,7 +157,7 @@ public class WeightsFromFile<V extends BioEntity, E extends Edge<V>,G extends Bi
if
(
e
!=
null
){
if
(!
seenEdges
.
contains
(
e
)){
try
{
double
w
=
Double
.
parseDouble
(
lineParts
[
weightCol
]);
double
w
=
process
.
apply
(
lineParts
[
weightCol
]);
if
(!
Double
.
isNaN
(
w
)){
g
.
setEdgeWeight
(
e
,
w
);
seenEdges
.
add
(
e
);
...
...
met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestWeightingPolicy.java
View file @
781cbe56
...
...
@@ -416,6 +416,94 @@ public class TestWeightingPolicy {
}
/**
* Test the weights Import
*/
@Test
public
void
testWeightsFromFileImportIII
()
{
Path
tmpPath
=
null
;
try
{
tmpPath
=
Files
.
createTempFile
(
"test_edgeWeightmport"
,
".tmp"
);
}
catch
(
IOException
e1
)
{
e1
.
printStackTrace
();
Assert
.
fail
(
"Creation of the temporary directory"
);
}
String
filePath
=
"EdgeWeightTestFileII.tab"
;
try
{
filePath
=
TestUtils
.
copyProjectResource
(
filePath
,
tmpPath
.
toFile
());
}
catch
(
IOException
e
)
{
e
.
printStackTrace
();
fail
(
"problem while reading edge weight file"
);
}
double
abWeight
,
bcWeight
,
adWeight
,
efWeight
,
bxWeight
,
ebWeight
,
deWeight
,
fcWeight
,
ycWeight
;
abWeight
=
0.2
;
bcWeight
=
0.4
;
adWeight
=
0.6
;
efWeight
=
0.8
;
bxWeight
=
1.0
;
ebWeight
=
1.2
;
deWeight
=
1.4
;
fcWeight
=
1.6
;
ycWeight
=
1.8
;
WeightsFromFile
<
BioMetabolite
,
ReactionEdge
,
CompoundGraph
>
wp
=
new
WeightsFromFile
<
BioMetabolite
,
ReactionEdge
,
CompoundGraph
>(
filePath
)
.
sep
(
","
)
.
sourceCol
(
0
)
.
targetCol
(
1
)
.
edgeLabelCol
(
2
)
.
weightCol
(
4
)
.
processWeigthCol
(
s
->
{
return
Double
.
parseDouble
(
s
)*
2
;});
wp
.
setWeight
(
g
);
assertEquals
(
"wrong weight after import"
,
abWeight
,
g
.
getEdgeWeight
(
ab
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
adWeight
,
g
.
getEdgeWeight
(
ad
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
bcWeight
,
g
.
getEdgeWeight
(
bc
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
bxWeight
,
g
.
getEdgeWeight
(
bx
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
deWeight
,
g
.
getEdgeWeight
(
de
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
ebWeight
,
g
.
getEdgeWeight
(
eb
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
efWeight
,
g
.
getEdgeWeight
(
ef
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
fcWeight
,
g
.
getEdgeWeight
(
fc
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight after import"
,
ycWeight
,
g
.
getEdgeWeight
(
yc
),
Double
.
MIN_VALUE
);
}
@Test
public
void
testAtomMappingWeightPolicy
()
{
Path
tmpPath
=
null
;
try
{
tmpPath
=
Files
.
createTempFile
(
"test_edgeWeightmport"
,
".tmp"
);
}
catch
(
IOException
e1
)
{
e1
.
printStackTrace
();
Assert
.
fail
(
"Creation of the temporary directory"
);
}
String
filePath
=
"AAMTestFile.tab"
;
try
{
filePath
=
TestUtils
.
copyProjectResource
(
filePath
,
tmpPath
.
toFile
());
}
catch
(
IOException
e
)
{
e
.
printStackTrace
();
fail
(
"problem while reading edge weight file"
);
}
int
CCnb1
=
21
;
int
CCnb5
=
5
;
int
CCnb6
=
1
;
AtomMappingWeightPolicy
wp1
=
new
AtomMappingWeightPolicy
().
fromConservedCarbonIndexes
(
filePath
);
wp1
.
setWeight
(
g
);
assertEquals
(
"wrong weight for AAM weight"
,
CCnb1
,
g
.
getEdgeWeight
(
ad
),
Double
.
MIN_VALUE
);
assertTrue
(
"wrong weight for AAM weight"
,
Double
.
isNaN
(
g
.
getEdgeWeight
(
ab
)));
assertTrue
(
"wrong weight for AAM weight"
,
Double
.
isNaN
(
g
.
getEdgeWeight
(
bc
)));
assertTrue
(
"wrong weight for AAM weight"
,
Double
.
isNaN
(
g
.
getEdgeWeight
(
bx
)));
assertEquals
(
"wrong weight for AAM weight"
,
CCnb5
,
g
.
getEdgeWeight
(
eb
),
Double
.
MIN_VALUE
);
assertEquals
(
"wrong weight for AAM weight"
,
CCnb6
,
g
.
getEdgeWeight
(
ef
),
Double
.
MIN_VALUE
);
assertTrue
(
"wrong weight for AAM weight"
,
Double
.
isNaN
(
g
.
getEdgeWeight
(
yc
)));
}
@Test
public
void
testAtomMappingWeightPolicyI
()
{
...
...
met4j-graph/src/test/resources/AAMTestFile.tab
0 → 100644
View file @
781cbe56
a 60.021129368 4-2 d 60.021129368 4-2 abd 0.0 2,4,5,6,7,9,10,12,13,23,24,26,28,30,31,33,35,37,43,45,47
e 60.021129368 35-33 b 139.98745989 35-33 efb 79.96633052199999 50,52,53,57,59
e 169.998024574 49-47-46 f 265.959269716 49-47-46 efb 95.961245142 54
\ No newline at end of file
met4j-io/pom.xml
View file @
781cbe56
...
...
@@ -6,7 +6,7 @@
<parent>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</parent>
<artifactId>
met4j-io
</artifactId>
...
...
@@ -25,7 +25,7 @@
<dependency>
<groupId>
fr.inrae.toulouse.metexplore
</groupId>
<artifactId>
met4j-core
</artifactId>
<version>
0.
9.1
-SNAPSHOT
</version>
<version>
0.
10.0
-SNAPSHOT
</version>
</dependency>
<dependency>
<groupId>
org.sbml.jsbml
</groupId>
...
...
met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributes.java
View file @
781cbe56
...
...
@@ -55,27 +55,49 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
*/
public
class
GenericAttributes
{
/** Constant <code>SBML_UNIT_DEFINITIONS="unit_definitions"</code> */
/**
* Constant <code>SBML_UNIT_DEFINITIONS="unit_definitions"</code>
*/
public
static
final
String
SBML_UNIT_DEFINITIONS
=
"unit_definitions"
;
/** Constant <code>SBML_NOTES="notes"</code> */
/**
* Constant <code>SBML_NOTES="notes"</code>
*/
public
static
final
String
SBML_NOTES
=
"notes"
;
/** Constant <code>PMIDS="pmids"</code> */
/**
* Constant <code>PMIDS="pmids"</code>
*/
public
static
final
String
PMIDS
=
"pmids"
;
/** Constant <code>COMMENT="comment"</code> */
/**
* Constant <code>COMMENT="comment"</code>
*/
public
static
final
String
COMMENT
=
"comment"
;
/** Constant <code>SBO_TERM="sbo_term"</code> */
/**
* Constant <code>SBO_TERM="sbo_term"</code>
*/
public
static
final
String
SBO_TERM
=
"sbo_term"
;
/** Constant <code>CONSTANT="constant"</code> */
/**
* Constant <code>CONSTANT="constant"</code>
*/
public
static
final
String
CONSTANT
=
"constant"
;
/** Constant <code>SBML_ANNOTATION="annotation"</code> */
/**
* Constant <code>SBML_ANNOTATION="annotation"</code>
*/
public
static
final
String
SBML_ANNOTATION
=
"annotation"
;
/** Constant <code>GENERIC="generic"</code> */
/**
* Constant <code>GENERIC="generic"</code>
*/
public
static
final
String
GENERIC
=
"generic"
;
/** Constant <code>TYPE="type"</code> */
/**
* Constant <code>TYPE="type"</code>
*/
public
static
final
String
TYPE
=
"type"
;
/** Constant <code>ANNOTATOR_COMMENTS="annotator_comments"</code> */
/**
* Constant <code>ANNOTATOR_COMMENTS="annotator_comments"</code>
*/
public
static
final
String
ANNOTATOR_COMMENTS
=
"annotator_comments"
;
/** Constant <code>AUTHORS="AUTHORS"</code> */
/**
* Constant <code>AUTHORS="AUTHORS"</code>
*/
public
static
final
String
AUTHORS
=
"AUTHORS"
;
...
...
@@ -103,7 +125,7 @@ public class GenericAttributes {
/**
* Set constant condition
*
* @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param e
a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param flag a {@link java.lang.Boolean} object.
*/
public
static
void
setConstant
(
BioEntity
e
,
Boolean
flag
)
{
...
...
@@ -131,7 +153,7 @@ public class GenericAttributes {
/**
* set notes
*
* @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param e
a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param notes a {@link fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes} object.
*/
public
static
void
setNotes
(
BioEntity
e
,
Notes
notes
)
{
...
...
@@ -145,7 +167,7 @@ public class GenericAttributes {
* <p>
* TODO : see if it useful since there is BioRef...
*
* @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param e
a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param pmids a {@link java.util.Set} object.
*/
public
static
void
setPmids
(
BioEntity
e
,
Set
<
Integer
>
pmids
)
{
...
...
@@ -157,7 +179,7 @@ public class GenericAttributes {
/**
* add pmid
*
* @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param e
a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param pmid a {@link java.lang.Integer} object.
*/
public
static
void
addPmid
(
BioEntity
e
,
Integer
pmid
)
{
...
...
@@ -196,7 +218,7 @@ public class GenericAttributes {
/**
* set comment
*
* @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param e
a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param comment a {@link java.lang.String} object.
*/
public
static
void
setComment
(
BioEntity
e
,
String
comment
)
{
...
...
@@ -206,13 +228,14 @@ public class GenericAttributes {
/**
* set Sbo term
*
* @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
* @param e