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minerva
core
Commits
1d423443
Commit
1d423443
authored
Apr 19, 2021
by
Piotr Gawron
Browse files
separate sink/source for each reaction
parent
74f87ef3
Pipeline
#40043
passed with stage
in 39 minutes and 26 seconds
Changes
2
Pipelines
1
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CHANGELOG
View file @
1d423443
minerva
(
16.0.0
~
alpha
.2
)
stable
;
urgency
=
medium
*
Backward
incompatibility
:
debian
package
cannot
be
upgraded
from
version
prior
to
12.1.0
(#
1464
)
*
Small
improvement
:
artifitial
source
and
sink
is
created
separately
for
each
uncomplete
reaction
(#
1475
)
*
Small
improvement
:
homomultimer
information
is
provided
in
API
(#
1468
)
--
Piotr
Gawron
<
piotr
.
gawron
@
uni
.
lu
>
Fri
,
26
Mar
2021
10
:
00
:
00
+
0200
...
...
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
View file @
1d423443
...
...
@@ -26,8 +26,7 @@ import lcsb.mapviewer.model.map.species.field.*;
import
lcsb.mapviewer.modelutils.map.ElementUtils
;
public
class
SbmlSpeciesParser
extends
SbmlElementParser
<
org
.
sbml
.
jsbml
.
Species
>
{
private
static
String
ARTIFITIAL_SINK_ID
=
"sbml_artifitial_sink"
;
private
static
String
ARTIFITIAL_SOURCE_ID
=
"sbml_artifitial_source"
;
private
static
String
ARTIFITIAL_ID
=
"sbml_artifitial_"
;
Logger
logger
=
LogManager
.
getLogger
();
Map
<
String
,
String
>
structuralStateIdMap
=
new
HashMap
<>();
...
...
@@ -433,8 +432,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
speciesId
=
((
org
.
sbml
.
jsbml
.
Species
)
getLayout
().
getSpeciesGlyph
(
element
.
getElementId
()).
getSpeciesInstance
())
.
getId
();
}
else
{
if
(!
element
.
getElementId
().
equals
(
ARTIFITIAL_SINK_ID
)
&&
!
element
.
getElementId
().
equals
(
ARTIFITIAL_SOURCE_ID
))
{
if
(!
element
.
getElementId
().
startsWith
(
ARTIFITIAL_ID
))
{
compartmentId
=
getSbmlModel
().
getSpecies
(
element
.
getElementId
()).
getCompartment
();
}
}
...
...
@@ -547,22 +545,16 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
public
Species
getArtifitialInput
()
{
Species
result
=
getMinervaModel
().
getElementByElementId
(
ARTIFITIAL_SOURCE_ID
);
if
(
result
==
null
)
{
result
=
new
Unknown
(
ARTIFITIAL_SOURCE_ID
);
result
.
setName
(
"Artifitial source"
);
getMinervaModel
().
addElement
(
result
);
}
Species
result
=
new
Unknown
(
ARTIFITIAL_ID
+
getNextId
());
result
.
setName
(
"Artifitial source"
);
getMinervaModel
().
addElement
(
result
);
return
result
;
}
public
Species
getArtifitialOutput
()
{
Species
result
=
getMinervaModel
().
getElementByElementId
(
ARTIFITIAL_SINK_ID
);
if
(
result
==
null
)
{
result
=
new
Degraded
(
ARTIFITIAL_SINK_ID
);
result
.
setName
(
"Artifitial sink"
);
getMinervaModel
().
addElement
(
result
);
}
Species
result
=
new
Degraded
(
ARTIFITIAL_ID
+
getNextId
());
result
.
setName
(
"Artifitial sink"
);
getMinervaModel
().
addElement
(
result
);
return
result
;
}
...
...
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