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Identifier Index

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C

calc_bimatrix (in libModelSimilarity)	cluster() (in DatabaseAnnotation)	consolewriter (in libTI2.results.consolewriter)
calculate_posteriori() (in Parameter_balancing)	cluster() (in DatabaseAnnotation)	Constraint (in libSBtab.Validator)
call() (in abstract_fortran_solver)	cofactorlist (in libTI2.add_new_kinetics)	construct_aid_distances() (in SingleAnnotation)
CannotSave (in libSBAnnotation.xmlobject)	colormap (in semanticSBML.sbml2dot)	construct_aid_distances() (in SingleAnnotation)
CannotSave (in semanticSBML.xmlobject)	Column (in libSBtab)	construct_aid_distances() (in SingleAnnotation)
canonical_table_name() (in libSBtab.Document)	Column (in libSBtab.Column)	contains_formula() (in pre_defined_formulas)
castCopyAndTranspose() (in MathArrayFunc)	Column (in libSBtab.Row)	ContentTooShortError (in libSBAnnotation.database_new)
cfg (in semanticSBML.annotate)	columnGet() (in Row)	convert (in libSBtab)
chain_count (in libModelSimilarity.wolfscluster)	ColumnName() (in libSBtab.Column)	convert() (in Model)
change() (in Constraint)	ColumnNotFoundException (in libSBAnnotation.indexedTables)	Convert2SBML (in libSBtab.convert)
change_MergeElement_parent() (in Merge_view)	ColumnNotFoundException (in libSBAnnotation.tables)	Convert2SBTab (in libSBtab.convert)
changeAndActivateColumns() (in Table)	ColumnParserWarning (in libSBtab.Warning)	copasiestimator (in libTI2.solvers.copasisolver)
changeColumns() (in Table)	ColumnProxy (in libSBtab.Column)	copasisolve() (in solver)
changeParserDict() (in Column)	ColumnTable (in libSBtab.Table)	copasisolver (in libTI2.solvers)
changeRequiredColumns() (in Table)	ColumnWarning (in libSBtab.Warning)	copasisolver (in libTI2.solvers.copasisolver)
changeToBeKnown() (in Table)	commonType() (in MathArrayFunc)	copasititrator (in libTI2.solvers.copasisolver)
characters() (in InterproHandler)	ComparableModel (in libModelSimilarity.compareModels)	copy() (in simulation_data_handler)
Charge() (in libSBtab.Column)	compare() (in odeCompare)	copy_aim() (in Model)
ChebiRead (in libSBAnnotation.buildDB)	compare() (in parameter_identifier)	copy_from_to() (in libTI2.model.rre_generator)
check() (in Model)	compare_clean_formulas() (in libTI2.model.function_manipulation)	copy_params() (in Model)
check() (in SemanticSbmlGui_doc)	compare_model_annotation_object() (in DatabaseAnnotation)	copy_signalling_params() (in Model)
check_consistency() (in Model)	compare_model_annotation_object() (in DatabaseAnnotation)	copyAnnotations() (in Annotation_view)
Check_view (in semanticSBMLgui.gui_view_check)	compare_models() (in CompareModels)	copyAttributes() (in Merger)
Check_view (in semanticSBMLui.console_views)	compare_to_annotation_information_object() (in DatabaseAnnotation)	cos() (in DerivVar)
checkAndGetXml() (in libSBAnnotation.annotate)	compare_to_file() (in DatabaseAnnotation)	cosh() (in DerivVar)
checkAnnotations() (in MergedElement)	compare_to_file() (in DatabaseAnnotation)	count_degree_of_annotation() (in libModelSimilarity.stats)
checkboxes() (in consolewriter)	compare_to_file() (in DatabaseAnnotation)	count_qualifiers() (in libModelSimilarity.stats)
checkConnection() (in Local)	compare_to_file() (in DatabaseAnnotation)	count_resources() (in libModelSimilarity.stats)
checkConsistency() (in FastSBMLCreator)	CompareAnnotations (in libModelSimilarity.calc_bimatrix)	countAnnotations() (in DatabaseAnnotation)
Checker (in semanticSBML.sbmlcheck)	compareElements() (in libSBtab.IDMerge)	countAnnotations() (in DatabaseAnnotation)
checkForBlanks() (in Balance_view)	compareElements() (in Local)	countAnnotations() (in DatabaseAnnotation)
checkIdPattern() (in Annotation)	compareLocation() (in Local)	cpsfile (in libTI2.solvers.copasisolver)
checkMeOut() (in SboElement)	compareModels (in libModelSimilarity)	create_cpsf() (in copasiestimator)
checkMeOut() (in ElementAnnotations)	CompareModels (in libModelSimilarity.compareModels)	create_cpsf() (in copasisolver)
CheckResult (in semanticSBML.sbmlcheck)	Compartment (in libSBtab.Row)	create_cpsf() (in copasititrator)
children_linker (in libTI2.model.sboreader)	Compartment() (in libSBtab.Column)	create_MergeElement_view() (in Merge_view)
chooseBestTuple() (in Local)	CompartmentID_DB() (in libSBtab.Column)	create_model_ec() (in fastSBMLCreator.fastSBMLCreator)
chooseCompartment() (in Id2Sbml_view)	compartmentIds() (in Model)	create_model_plt() (in fastSBMLCreator.fastSBMLCreator)
circleMenu() (in Merge_view)	compartmentIds() (in SemanticSbmlGui_doc)	create_model_pmn() (in fastSBMLCreator.fastSBMLCreator)
class2size (in libSBAnnotation.buildDB)	CompartmentName() (in libSBtab.Column)	create_orthogonal() (in model_reduction)
className() (in Row)	CompartmentSBMLid() (in libSBtab.Column)	create_orthogonal2() (in model_reduction)
className() (in Table)	compartmentstyle (in semanticSBML.sbml2dot)	create_solver() (in abstract_fortran_titrator)
clean_up_formula() (in libTI2.model.function_manipulation)	CompartmentTable (in libSBtab.Table)	create_solver() (in dopri5titrator)
cleanequationstring() (in csolver)	compile() (in abstract_fortran_solver)	create_solver() (in eulsimtitrator)
clear() (in Table)	Compound (in libSBtab.Row)	create_solver() (in limextitrator)
clearNicknames() (in Document)	Compound() (in libSBtab.Column)	create_solver() (in lsodatitrator)
close() (in CustomFile)	CompoundID_KEGG_Compound() (in libSBtab.Column)	create_solver() (in lsodetitrator)
close() (in Annotation_view)	CompoundName() (in libSBtab.Column)	create_solver() (in radautitrator)
close() (in Balance_view)	CompoundSBMLid() (in libSBtab.Column)	create_solver() (in seulextitrator)
close() (in Check_view)	CompoundTable (in libSBtab.Table)	create_Tuple_view() (in Merge_view)
close() (in GraphSVG_view)	compute_aim_fulfillment() (in Model)	createCompartment() (in FastSBMLCreator)
close() (in SemanticSbmlGui_view)	compute_elasticities() (in Model)	createGeneric() (in FastSBMLCreator)
close() (in Merge_view)	compute_matrix() (in DatabaseAnnotation)	createGlobalGeneric() (in FastSBMLCreator)
close() (in Tuple_widget)	compute_matrix() (in EuklideanDistance)	createParameter() (in FastSBMLCreator)
close() (in SemanticSbmlGui_view)	compute_signal_characteristics() (in Model)	createReaction() (in FastSBMLCreator)
close() (in Console_view)	compute_time_mean() (in model_reduction)	createSBMLmodel() (in Merger)
close() (in Merge_view)	condprint() (in global_options)	createSpecies() (in FastSBMLCreator)
closeAllDocuments() (in SemanticSbmlGui_docmgr)	config (in libSBAnnotation)	csolve() (in solver)
closeDocument() (in SemanticSbmlGui_docmgr)	Config (in libSBAnnotation.config)	csolver (in libTI2.solvers)
cluster (in libModelSimilarity.bicluster.interpret_bicluster)	connect_view_functions() (in MergeTuple)	csolver (in libTI2.solvers.csolver)
cluster (in libModelSimilarity)	connect_view_functions() (in OriginElement)	CustomConsole (in semanticSBMLui.CustomInteractiveConsole)
Cluster	conservation_constraint_check() (in Checker)	CustomFile (in libSBAnnotation.file)
Cluster (in libModelSimilarity.okapicluster)	Console_view (in semanticSBMLui.console_views)	CustomInteractiveConsole (in semanticSBMLui)
Cluster (in libModelSimilarity.wolfscluster)	console_views (in semanticSBMLui)	cut_long_lines() (in libTI2.solvers.abstract_fortran_solver)
cluster() (in DatabaseAnnotation)	consolewriter (in libTI2.results)