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C

CELLML - Static variable in class de.unirostock.sems.bives.tools.DocumentClassifier
The Constant CELLML.
classify(InputStream, URI) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Classify.
classify(TreeDocument) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Classify.
classify(String) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Classify.
classify(File) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Classify.

D

de.unirostock.sems.bives - package de.unirostock.sems.bives
 
de.unirostock.sems.bives.tools - package de.unirostock.sems.bives.tools
 
DocumentClassifier - Class in de.unirostock.sems.bives.tools
The Class DocumentClassifier.
DocumentClassifier() - Constructor for class de.unirostock.sems.bives.tools.DocumentClassifier
 

E

executeCompare(String, String, HashMap<String, String>, CommandLine, List<Exception>) - Method in class de.unirostock.sems.bives.Executer
Execute compare.
Executer - Class in de.unirostock.sems.bives
The Class Executer.
Executer() - Constructor for class de.unirostock.sems.bives.Executer
Instantiates a new executer.
executeSingle(String, HashMap<String, String>, CommandLine, List<Exception>) - Method in class de.unirostock.sems.bives.Executer
Execute single.
exit - Static variable in class de.unirostock.sems.bives.Main
Should we exit?.

G

getCellMlDocument() - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Gets the cell ml document.
getExceptions() - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Gets the exceptions.
getOptions() - Method in class de.unirostock.sems.bives.Executer
 
getSbmlDocument() - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Gets the sbml document.
getXmlDocument() - Method in class de.unirostock.sems.bives.tools.DocumentClassifier
Gets the xml document.

H

htmlPageEnd() - Static method in class de.unirostock.sems.bives.Executer
 
htmlPageStart() - Static method in class de.unirostock.sems.bives.Executer
 
humanReadable(int) - Static method in class de.unirostock.sems.bives.tools.DocumentClassifier
Human readable.

M

Main - Class in de.unirostock.sems.bives
 
Main() - Constructor for class de.unirostock.sems.bives.Main
Instantiates a new main.
main(String[]) - Static method in class de.unirostock.sems.bives.Main
 
Main.ExecutionException - Exception in de.unirostock.sems.bives
The Class ExecutionException.
Main.ExecutionException(String) - Constructor for exception de.unirostock.sems.bives.Main.ExecutionException
Instantiates a new execution exception.

R

REQ_DEBUG - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_DEBUGG - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_FILES - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_FILES.
REQ_HELP - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_JSON - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_OUT - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT.
REQ_WANT_CELLML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_CELLML.
REQ_WANT_COMP_HIERARCHY_DOT - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_COMP_HIERARCHY_DOT.
REQ_WANT_COMP_HIERARCHY_GRAPHML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_COMP_HIERARCHY_GRAPHML.
REQ_WANT_COMP_HIERARCHY_JSON - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_COMP_HIERARCHY_JSON.
REQ_WANT_DIFF - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_DIFF.
REQ_WANT_DOCUMENTTYPE - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_DOCUMENTTYPE.
REQ_WANT_MATCHING_IDS - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_META - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_META.
REQ_WANT_NEGLECT_NAMES - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_REACTIONS_DOT - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REACTIONS_DOT.
REQ_WANT_REACTIONS_DOT2 - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_REACTIONS_GRAPHML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REACTIONS_GRAPHML.
REQ_WANT_REACTIONS_GRAPHML2 - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_REACTIONS_JSON - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REACTIONS_JSON.
REQ_WANT_REACTIONS_JSON2 - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_REGULAR - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REGULAR.
REQ_WANT_REPORT_HTML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REPORT_HTML.
REQ_WANT_REPORT_HTML_FP - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REPORT_HTML_FP.
REQ_WANT_REPORT_MD - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REPORT_MD.
REQ_WANT_REPORT_RST - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_REPORT_RST.
REQ_WANT_SBML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SBML.
REQ_WANT_SINGLE_COMP_HIERARCHY_DOT - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_DOT.
REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML.
REQ_WANT_SINGLE_COMP_HIERARCHY_JSON - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_JSON.
REQ_WANT_SINGLE_FLATTEN - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_FLATTEN.
REQ_WANT_SINGLE_REACTIONS_DOT - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_REACTIONS_DOT.
REQ_WANT_SINGLE_REACTIONS_DOT2 - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_SINGLE_REACTIONS_GRAPHML - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_REACTIONS_GRAPHML.
REQ_WANT_SINGLE_REACTIONS_GRAPHML2 - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_SINGLE_REACTIONS_JSON - Static variable in class de.unirostock.sems.bives.Executer
The Constant REQ_WANT_SINGLE_REACTIONS_JSON.
REQ_WANT_SINGLE_REACTIONS_JSON2 - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_WANT_STRICT_NAMES - Static variable in class de.unirostock.sems.bives.Executer
 
REQ_XML - Static variable in class de.unirostock.sems.bives.Executer
 
result(String) - Static method in class de.unirostock.sems.bives.Executer
Result.
run(String[]) - Method in class de.unirostock.sems.bives.Main
Run.

S

SBML - Static variable in class de.unirostock.sems.bives.tools.DocumentClassifier
The Constant SBML.

U

UNKNOWN - Static variable in class de.unirostock.sems.bives.tools.DocumentClassifier
The Constant UNKNOWN.
usage(String) - Method in class de.unirostock.sems.bives.Main
Usage.

X

XML - Static variable in class de.unirostock.sems.bives.tools.DocumentClassifier
The Constant XML.
XML_PATTERN - Static variable in class de.unirostock.sems.bives.Executer
Pattern to distinguish xml files from URLs.
C D E G H M R S U X 

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