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metexplore
met4j
Commits
bf25b558
Commit
bf25b558
authored
Apr 01, 2022
by
lcottret
Browse files
Merge branch 'testsAndPerfs' into develop
parents
46b5faf2
093ceca4
Changes
26
Hide whitespace changes
Inline
Side-by-side
.gitlab-ci.yml
View file @
bf25b558
...
@@ -19,8 +19,6 @@ test:
...
@@ -19,8 +19,6 @@ test:
-
mvn clean test
-
mvn clean test
-
cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
-
cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
deploySnapshot
:
deploySnapshot
:
stage
:
deploy
stage
:
deploy
script
:
script
:
...
...
met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributes.java
View file @
bf25b558
...
@@ -55,27 +55,49 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
...
@@ -55,27 +55,49 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
*/
*/
public
class
GenericAttributes
{
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"
;
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"
;
public
static
final
String
SBML_NOTES
=
"notes"
;
/** Constant <code>PMIDS="pmids"</code> */
/**
* Constant <code>PMIDS="pmids"</code>
*/
public
static
final
String
PMIDS
=
"pmids"
;
public
static
final
String
PMIDS
=
"pmids"
;
/** Constant <code>COMMENT="comment"</code> */
/**
* Constant <code>COMMENT="comment"</code>
*/
public
static
final
String
COMMENT
=
"comment"
;
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"
;
public
static
final
String
SBO_TERM
=
"sbo_term"
;
/** Constant <code>CONSTANT="constant"</code> */
/**
* Constant <code>CONSTANT="constant"</code>
*/
public
static
final
String
CONSTANT
=
"constant"
;
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"
;
public
static
final
String
SBML_ANNOTATION
=
"annotation"
;
/** Constant <code>GENERIC="generic"</code> */
/**
* Constant <code>GENERIC="generic"</code>
*/
public
static
final
String
GENERIC
=
"generic"
;
public
static
final
String
GENERIC
=
"generic"
;
/** Constant <code>TYPE="type"</code> */
/**
* Constant <code>TYPE="type"</code>
*/
public
static
final
String
TYPE
=
"type"
;
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"
;
public
static
final
String
ANNOTATOR_COMMENTS
=
"annotator_comments"
;
/** Constant <code>AUTHORS="AUTHORS"</code> */
/**
* Constant <code>AUTHORS="AUTHORS"</code>
*/
public
static
final
String
AUTHORS
=
"AUTHORS"
;
public
static
final
String
AUTHORS
=
"AUTHORS"
;
...
@@ -103,7 +125,7 @@ public class GenericAttributes {
...
@@ -103,7 +125,7 @@ public class GenericAttributes {
/**
/**
* Set constant condition
* 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.
* @param flag a {@link java.lang.Boolean} object.
*/
*/
public
static
void
setConstant
(
BioEntity
e
,
Boolean
flag
)
{
public
static
void
setConstant
(
BioEntity
e
,
Boolean
flag
)
{
...
@@ -131,7 +153,7 @@ public class GenericAttributes {
...
@@ -131,7 +153,7 @@ public class GenericAttributes {
/**
/**
* set notes
* 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.
* @param notes a {@link fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes} object.
*/
*/
public
static
void
setNotes
(
BioEntity
e
,
Notes
notes
)
{
public
static
void
setNotes
(
BioEntity
e
,
Notes
notes
)
{
...
@@ -145,7 +167,7 @@ public class GenericAttributes {
...
@@ -145,7 +167,7 @@ public class GenericAttributes {
* <p>
* <p>
* TODO : see if it useful since there is BioRef...
* 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.
* @param pmids a {@link java.util.Set} object.
*/
*/
public
static
void
setPmids
(
BioEntity
e
,
Set
<
Integer
>
pmids
)
{
public
static
void
setPmids
(
BioEntity
e
,
Set
<
Integer
>
pmids
)
{
...
@@ -157,7 +179,7 @@ public class GenericAttributes {
...
@@ -157,7 +179,7 @@ public class GenericAttributes {
/**
/**
* add pmid
* 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.
* @param pmid a {@link java.lang.Integer} object.
*/
*/
public
static
void
addPmid
(
BioEntity
e
,
Integer
pmid
)
{
public
static
void
addPmid
(
BioEntity
e
,
Integer
pmid
)
{
...
@@ -196,7 +218,7 @@ public class GenericAttributes {
...
@@ -196,7 +218,7 @@ public class GenericAttributes {
/**
/**
* set comment
* 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.
* @param comment a {@link java.lang.String} object.
*/
*/
public
static
void
setComment
(
BioEntity
e
,
String
comment
)
{
public
static
void
setComment
(
BioEntity
e
,
String
comment
)
{
...
@@ -206,13 +228,14 @@ public class GenericAttributes {
...
@@ -206,13 +228,14 @@ public class GenericAttributes {
/**
/**
* set Sbo term
* set Sbo term
*
*
* @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 sboTerm a {@link java.lang.String} object.
* @param sboTerm a {@link java.lang.String} object.
*/
*/
public
static
void
setSboTerm
(
BioEntity
e
,
String
sboTerm
)
{
public
static
void
setSboTerm
(
BioEntity
e
,
String
sboTerm
)
{
if
(!
StringUtils
.
isValidSboTerm
(
sboTerm
))
{
if
(!
StringUtils
.
isValidSboTerm
(
sboTerm
))
{
System
.
err
.
println
(
"[Warning] SBO term badly formatted for "
+
e
.
getId
()
System
.
err
.
println
(
"[Warning] SBO term badly formatted for "
+
e
.
getId
()
+
" ("
+
sboTerm
+
", must be in the format SBO:1234567). It has not been set."
);
+
" ("
+
sboTerm
+
", must be in the format SBO:1234567). It has been set to null."
);
e
.
getAttributes
().
remove
(
SBO_TERM
);
}
else
{
}
else
{
e
.
setAttribute
(
SBO_TERM
,
sboTerm
);
e
.
setAttribute
(
SBO_TERM
,
sboTerm
);
}
}
...
@@ -241,7 +264,7 @@ public class GenericAttributes {
...
@@ -241,7 +264,7 @@ public class GenericAttributes {
/**
/**
* set annotation
* set annotation
*
*
* @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 val a {@link fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.SbmlAnnotation} object.
* @param val a {@link fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.SbmlAnnotation} object.
*/
*/
public
static
void
setAnnotation
(
BioEntity
e
,
SbmlAnnotation
val
)
{
public
static
void
setAnnotation
(
BioEntity
e
,
SbmlAnnotation
val
)
{
...
@@ -269,7 +292,7 @@ public class GenericAttributes {
...
@@ -269,7 +292,7 @@ public class GenericAttributes {
/**
/**
* Set generic attribute
* Set generic attribute
*
*
* @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.
* @param flag a {@link java.lang.Boolean} object.
*/
*/
public
static
void
setGeneric
(
BioEntity
e
,
Boolean
flag
)
{
public
static
void
setGeneric
(
BioEntity
e
,
Boolean
flag
)
{
...
@@ -289,7 +312,7 @@ public class GenericAttributes {
...
@@ -289,7 +312,7 @@ public class GenericAttributes {
/**
/**
* set comment
* 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 type a {@link java.lang.String} object.
* @param type a {@link java.lang.String} object.
*/
*/
public
static
void
setType
(
BioEntity
e
,
String
type
)
{
public
static
void
setType
(
BioEntity
e
,
String
type
)
{
...
@@ -299,7 +322,7 @@ public class GenericAttributes {
...
@@ -299,7 +322,7 @@ public class GenericAttributes {
/**
/**
* set annotator comments
* set annotator comments
*
*
* @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 comments a {@link java.util.Set} object.
* @param comments a {@link java.util.Set} object.
*/
*/
public
static
void
setAnnotatorComments
(
BioEntity
e
,
Set
<
AnnotatorComment
>
comments
)
{
public
static
void
setAnnotatorComments
(
BioEntity
e
,
Set
<
AnnotatorComment
>
comments
)
{
...
@@ -311,7 +334,7 @@ public class GenericAttributes {
...
@@ -311,7 +334,7 @@ public class GenericAttributes {
/**
/**
* add comment
* add 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 fr.inrae.toulouse.metexplore.met4j_io.annotations.AnnotatorComment} object.
* @param comment a {@link fr.inrae.toulouse.metexplore.met4j_io.annotations.AnnotatorComment} object.
*/
*/
public
static
void
addAnnotatorComment
(
BioEntity
e
,
AnnotatorComment
comment
)
{
public
static
void
addAnnotatorComment
(
BioEntity
e
,
AnnotatorComment
comment
)
{
...
...
met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/errors/GeneSetException.java
View file @
bf25b558
...
@@ -37,10 +37,6 @@ package fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors;
...
@@ -37,10 +37,6 @@ package fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors;
public
class
GeneSetException
extends
Exception
{
public
class
GeneSetException
extends
Exception
{
public
GeneSetException
(
String
message
)
{
super
(
message
);
}
public
GeneSetException
()
{
public
GeneSetException
()
{
super
(
"Not possible to transform gene set since it has been added in a gene association"
);
super
(
"Not possible to transform gene set since it has been added in a gene association"
);
}
}
...
...
met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/fbc/FluxReaction.java
View file @
bf25b558
...
@@ -64,7 +64,7 @@ public class FluxReaction extends BioEntity {
...
@@ -64,7 +64,7 @@ public class FluxReaction extends BioEntity {
* The actual {@link BioReaction} that is behind this
* The actual {@link BioReaction} that is behind this
* {@link FluxReaction}
* {@link FluxReaction}
*/
*/
private
BioReaction
underlyingReaction
;
private
final
BioReaction
underlyingReaction
;
/**
/**
* The object holding the Gene Association
* The object holding the Gene Association
*
*
...
@@ -151,16 +151,6 @@ public class FluxReaction extends BioEntity {
...
@@ -151,16 +151,6 @@ public class FluxReaction extends BioEntity {
bn
.
affectEnzyme
(
rxn
,
enz
);
bn
.
affectEnzyme
(
rxn
,
enz
);
}
}
/**
* <p>createIdFromProteins.</p>
*
* @param proteins a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} object.
* @return a {@link java.lang.String} object.
*/
public
static
String
createIdFromProteins
(
BioCollection
<
BioProtein
>
proteins
)
{
return
proteins
.
getIds
().
stream
().
sorted
().
collect
(
Collectors
.
joining
(
"_AND_"
));
}
/**
/**
* Get the {@link #underlyingReaction}
* Get the {@link #underlyingReaction}
*
*
...
...
met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlReader.java
View file @
bf25b558
...
@@ -39,18 +39,15 @@ package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader;
...
@@ -39,18 +39,15 @@ package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader;
import
java.io.*
;
import
java.io.*
;
import
java.util.ArrayList
;
import
java.util.ArrayList
;
import
java.util.Arrays
;
import
java.util.Arrays
;
import
java.util.Date
;
import
java.util.HashMap
;
import
java.util.HashMap
;
import
java.util.Set
;
import
java.util.stream.Collectors
;
import
javax.xml.stream.XMLStreamException
;
import
javax.xml.stream.XMLStreamException
;
import
fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.JSBMLPackageReaderException
;
import
org.sbml.jsbml.Model
;
import
org.sbml.jsbml.Model
;
import
org.sbml.jsbml.SBMLDocument
;
import
org.sbml.jsbml.SBMLDocument
;
import
org.sbml.jsbml.SBMLError
;
import
org.sbml.jsbml.SBMLError.SEVERITY
;
import
org.sbml.jsbml.SBMLReader
;
import
org.sbml.jsbml.SBMLReader
;
import
org.sbml.jsbml.validator.SBMLValidator
;
import
fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork
;
import
fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork
;
import
fr.inrae.toulouse.metexplore.met4j_io.jsbml.dataTags.AdditionalDataTag
;
import
fr.inrae.toulouse.metexplore.met4j_io.jsbml.dataTags.AdditionalDataTag
;
...
@@ -66,8 +63,8 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
...
@@ -66,8 +63,8 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
* depending on the SBML level defined in the file
* depending on the SBML level defined in the file
*
*
* @author Benjamin Merlet
* @author Benjamin Merlet
* @since 3.0
* @version $Id: $Id
* @version $Id: $Id
* @since 3.0
*/
*/
public
class
JsbmlReader
{
public
class
JsbmlReader
{
...
@@ -80,7 +77,7 @@ public class JsbmlReader {
...
@@ -80,7 +77,7 @@ public class JsbmlReader {
* The list of errors and/or warnings found by jsbml while parsing the SBML
* The list of errors and/or warnings found by jsbml while parsing the SBML
* File
* File
*/
*/
public
ArrayList
<
String
>
errorsAndWarnings
=
new
ArrayList
<
String
>();
public
ArrayList
<
String
>
errorsAndWarnings
=
new
ArrayList
<>();
/**
/**
* The SBML filename
* The SBML filename
*/
*/
...
@@ -89,16 +86,8 @@ public class JsbmlReader {
...
@@ -89,16 +86,8 @@ public class JsbmlReader {
* The SBML Model retrieved through jsbml's
* The SBML Model retrieved through jsbml's
*/
*/
private
Model
model
;
private
Model
model
;
/**
* Attribute that specifies if the input sbml is valid or not
*/
private
boolean
validSBML
=
true
;
/**
* Set to true to use SBML online validator
*/
private
boolean
useValidator
=
true
;
private
String
xml
=
null
;
private
String
xml
String
=
null
;
/**
/**
* Constructor
* Constructor
...
@@ -108,19 +97,6 @@ public class JsbmlReader {
...
@@ -108,19 +97,6 @@ public class JsbmlReader {
*/
*/
public
JsbmlReader
(
String
filename
)
throws
IOException
{
public
JsbmlReader
(
String
filename
)
throws
IOException
{
this
.
filename
=
filename
;
this
.
filename
=
filename
;
this
.
useValidator
=
false
;
}
/**
* Constructor
*
* @param filename the filename
* @param useValidator set the {@link #useValidator} attribute
* @throws java.io.IOException if any.
*/
public
JsbmlReader
(
String
filename
,
boolean
useValidator
)
throws
IOException
{
this
.
filename
=
filename
;
this
.
useValidator
=
useValidator
;
}
}
/**
/**
...
@@ -130,21 +106,8 @@ public class JsbmlReader {
...
@@ -130,21 +106,8 @@ public class JsbmlReader {
* @throws java.io.IOException if any.
* @throws java.io.IOException if any.
*/
*/
public
JsbmlReader
(
InputStream
inputStream
)
throws
IOException
{
public
JsbmlReader
(
InputStream
inputStream
)
throws
IOException
{
this
.
xml
=
this
.
inputStreamToString
(
inputStream
);
this
.
xmlString
=
this
.
inputStreamToString
(
inputStream
);
this
.
useValidator
=
false
;
}
/**
* <p>Constructor for JsbmlReader.</p>
*
* @param inputStream a {@link java.io.InputStream} object.
* @param useValidator a boolean.
* @throws java.io.IOException if any.
*/
public
JsbmlReader
(
InputStream
inputStream
,
boolean
useValidator
)
throws
IOException
{
this
.
xml
=
this
.
inputStreamToString
(
inputStream
);
this
.
useValidator
=
useValidator
;
}
}
private
String
inputStreamToString
(
InputStream
inputStream
)
throws
IOException
{
private
String
inputStreamToString
(
InputStream
inputStream
)
throws
IOException
{
...
@@ -152,21 +115,19 @@ public class JsbmlReader {
...
@@ -152,21 +115,19 @@ public class JsbmlReader {
StringBuilder
sb
=
new
StringBuilder
();
StringBuilder
sb
=
new
StringBuilder
();
String
line
;
String
line
;
while
((
line
=
br
.
readLine
())
!=
null
)
{
while
((
line
=
br
.
readLine
())
!=
null
)
{
sb
.
append
(
line
+
System
.
lineSeparator
());
sb
.
append
(
line
).
append
(
System
.
lineSeparator
());
}
}
return
sb
.
toString
();
return
sb
.
toString
();
}
}
/*
*
/*
* A test main method
* A test main method
*
*
* @param args the arguments
* @param args the arguments
* @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
* @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
* @throws java.io.IOException if any.
* @throws java.io.IOException if any.
*/
*/
public
static
void
main
(
String
[]
args
)
throws
Met4jSbmlReaderException
,
IOException
,
JSBMLPackageReaderException
{
/*
public static void main(String[] args) throws Met4jSbmlReaderException, IOException, JSBMLPackageReaderException {
// String
// String
String inputFile = args[0];
String inputFile = args[0];
...
@@ -205,7 +166,7 @@ public class JsbmlReader {
...
@@ -205,7 +166,7 @@ public class JsbmlReader {
System.err.println("End :" + new Date());
System.err.println("End :" + new Date());
}
}
*/
/**
/**
* <p>read.</p>
* <p>read.</p>
...
@@ -218,43 +179,41 @@ public class JsbmlReader {
...
@@ -218,43 +179,41 @@ public class JsbmlReader {
* @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
* @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
*/
*/
public
BioNetwork
read
(
ArrayList
<
PackageParser
>
userEnabledPackages
)
throws
Met4jSbmlReaderException
{
public
BioNetwork
read
(
ArrayList
<
PackageParser
>
userEnabledPackages
)
throws
Met4jSbmlReaderException
{
try
{
try
{
this
.
initiateModel
();
this
.
initiateModel
();
}
catch
(
IOException
|
XMLStreamException
e
)
{
}
catch
(
IOException
|
XMLStreamException
e
)
{
e
.
printStackTrace
();
e
.
printStackTrace
();
this
.
setValidSBML
(
false
);
}
}
if
(
this
.
isValidSBML
())
{
System
.
err
.
println
(
"Verifying enabled Plugins..."
);
System
.
err
.
println
(
"Verifying enabled Plugins..."
);
ArrayList
<
PackageParser
>
verifiedPkgs
=
this
ArrayList
<
PackageParser
>
verifiedPkgs
=
this
.
verifyPackages
(
userEnabledPackages
);
.
verifyPackages
(
userEnabledPackages
);
JsbmlToBioNetwork
converter
=
new
JsbmlToBioNetwork
(
this
.
getModel
());
JsbmlToBioNetwork
converter
=
new
JsbmlToBioNetwork
(
this
.
getModel
());
this
.
setConverter
(
converter
);
this
.
setConverter
(
converter
);
try
{
try
{
converter
.
setPackages
(
verifiedPkgs
);
converter
.
setPackages
(
verifiedPkgs
);
}
catch
(
Exception
e
)
{
}
catch
(
Exception
e
)
{
e
.
printStackTrace
();
e
.
printStackTrace
();
System
.
exit
(
1
);
throw
new
Met4jSbmlReaderException
(
"Problem while setting the JSBML packages"
);
}
}
System
.
err
.
println
(
"Parsing model "
+
this
.
getModel
().
getId
());
return
parseModel
();
}
this
.
getConverter
().
parseModel
();
protected
BioNetwork
parseModel
()
throws
Met4jSbmlReaderException
{
System
.
err
.
println
(
"Parsing model "
+
this
.
getModel
().
getId
());
System
.
err
.
println
(
"End Parsing model "
+
this
.
getModel
().
getId
()
);
this
.
getConverter
().
parseModel
(
);
this
.
errorsAndW
ar
n
ing
s
.
addAll
(
PackageParser
.
errorsAndWarnings
);
System
.
err
.
println
(
"End P
ar
s
ing
model "
+
this
.
getModel
().
getId
()
);
return
this
.
getConverter
().
getNetwork
();
this
.
errorsAndWarnings
.
addAll
(
PackageParser
.
errorsAndWarnings
);
}
else
{
return
null
;
return
this
.
getConverter
().
getNetwork
();
}
}
}
/**
/**
...
@@ -264,9 +223,7 @@ public class JsbmlReader {
...
@@ -264,9 +223,7 @@ public class JsbmlReader {
* @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
* @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
*/
*/
public
BioNetwork
read
()
throws
Met4jSbmlReaderException
{
public
BioNetwork
read
()
throws
Met4jSbmlReaderException
{
ArrayList
<
PackageParser
>
pkgs
=
new
ArrayList
<
PackageParser
>(
Arrays
.
asList
(
ArrayList
<
PackageParser
>
pkgs
=
new
ArrayList
<>(
Arrays
.
asList
(
new
NotesParser
(
true
),
new
FBCParser
(),
new
GroupPathwayParser
(),
new
AnnotationParser
(
true
)));
new
NotesParser
(
true
),
new
FBCParser
(),
new
GroupPathwayParser
(),
new
AnnotationParser
(
true
)));
return
this
.
read
(
pkgs
);
return
this
.
read
(
pkgs
);
}
}