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matthiaskoenig / cy3sbml

cy3sbml: SBML for Cytoscape 3
GNU Lesser General Public License v3.0
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Fix deprecated fbc methods #247

Closed matthiaskoenig closed 6 years ago

matthiaskoenig commented 7 years ago

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
matthiaskoenig commented 6 years ago

Nothing to fix here. If this becomes an issue will revisit.