There are some deprecated methods which should be replaced
// fluxBounds
for (FluxBound fluxBound : fbcModel.getListOfFluxBounds()) {
Reaction reaction = fluxBound.getReactionInstance();
CyNode n = metaId2Node.get(reaction.getMetaId());
String operation = fluxBound.getOperation().toString();
Double value = fluxBound.getValue();
if (operation.equals(Operation.EQUAL)) {
AttributeUtil.set(network, n, SBML.ATTR_FBC_LOWER_FLUX_BOUND, value.toString(), String.class);
AttributeUtil.set(network, n, SBML.ATTR_FBC_UPPER_FLUX_BOUND, value.toString(), String.class);
} else if (operation.equals(Operation.GREATER_EQUAL)) {
AttributeUtil.set(network, n, SBML.ATTR_FBC_LOWER_FLUX_BOUND, value.toString(), String.class);
} else if (operation.equals(Operation.LESS_EQUAL)) {
AttributeUtil.set(network, n, SBML.ATTR_FBC_UPPER_FLUX_BOUND, value.toString(), String.class);
}
}
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[53,30] org.sbml.jsbml.ext.fbc.FluxBound in org.sbml.jsbml.ext.fbc has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[54,30] org.sbml.jsbml.ext.fbc.FluxBound in org.sbml.jsbml.ext.fbc has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[54,30] org.sbml.jsbml.ext.fbc.FluxBound in org.sbml.jsbml.ext.fbc has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[54,40] org.sbml.jsbml.ext.fbc.FluxBound.Operation in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/util/GUIUtil.java:[128,22] writeStringToFile(java.io.File,java.lang.String) in org.apache.commons.io.FileUtils has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/util/SBMLUtil.java:[358,46] getCharge() in org.sbml.jsbml.Species has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/util/SBMLUtil.java:[393,71] getFast() in org.sbml.jsbml.Reaction has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[668,72] getCharge() in org.sbml.jsbml.Species has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[696,71] getFast() in org.sbml.jsbml.Reaction has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1176,48] getListOfFluxBounds() in org.sbml.jsbml.ext.fbc.FBCModelPlugin has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1176,18] org.sbml.jsbml.ext.fbc.FluxBound in org.sbml.jsbml.ext.fbc has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1177,46] getReactionInstance() in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1179,45] getOperation() in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1180,41] getValue() in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1181,38] org.sbml.jsbml.ext.fbc.FluxBound.Operation in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1184,45] org.sbml.jsbml.ext.fbc.FluxBound.Operation in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
[WARNING] /home/mkoenig/git/cy3sbml/src/main/java/org/cy3sbml/SBMLReaderTask.java:[1186,45] org.sbml.jsbml.ext.fbc.FluxBound.Operation in org.sbml.jsbml.ext.fbc.FluxBound has been deprecated
There are some deprecated methods which should be replaced