A C D E G H M P R S U X
All Classes All Packages

A

asJson(int) - Static method in class de.unirostock.sems.bives.tools.DocumentClassifier

Human readable.

C

CELLML - Static variable in class de.unirostock.sems.bives.tools.DocumentClassifier

The Constant CELLML.

classify(TreeDocument) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier

Classify.

classify(File) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier

Classify.

classify(InputStream, URI) - Method in class de.unirostock.sems.bives.tools.DocumentClassifier

Classify.

classify(String) - 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, JSONObject, 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, JSONObject, CommandLine, List<Exception>) - Method in class de.unirostock.sems.bives.Executer

Execute single.

ExecutionException(String) - Constructor for exception de.unirostock.sems.bives.Main.ExecutionException

Instantiates a new execution exception.

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

Get available (command-line) options.

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

HelpException() - Constructor for exception de.unirostock.sems.bives.Main.HelpException

htmlPageEnd() - Static method in class de.unirostock.sems.bives.Executer

Static string to close an HTML page.

htmlPageStart() - Static method in class de.unirostock.sems.bives.Executer

Static string to start an HTML page.

humanReadable(int) - Static method in class de.unirostock.sems.bives.tools.DocumentClassifier

Human readable.

M

main(String[]) - Static method in class de.unirostock.sems.bives.Main

The main method.

Main - Class in de.unirostock.sems.bives

Main() - Constructor for class de.unirostock.sems.bives.Main

Instantiates a new main.

Main.ExecutionException - Exception in de.unirostock.sems.bives

The Class ExecutionException.

Main.HelpException - Exception in de.unirostock.sems.bives

The Class HelpException.

P

parseCommandLine(String[], Executer) - Static method in class de.unirostock.sems.bives.Main

Parses the command line.

R

REQ_CA - Static variable in class de.unirostock.sems.bives.Executer

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_INC_ANNO - 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_SEP_ANNO - 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_MERGE - Static variable in class de.unirostock.sems.bives.Executer

The Constant REQ_WANT_MERGE.

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_REACTIONS_SBGN_JSON - Static variable in class de.unirostock.sems.bives.Executer

The Constant REQ_WANT_REACTIONS_SBGN_JSON.

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.

A C D E G H M P R S U X
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