java.lang.Object
- de.unirostock.sems.bives.Executer

```
public class Executer
extends Object
```
The Class Executer.

Author:

Martin Scharm

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`REQ_CA`
`static String`	`REQ_DEBUG`
`static String`	`REQ_DEBUGG`
`static String`	`REQ_FILES`	The Constant REQ_FILES.
`static String`	`REQ_HELP`
`static String`	`REQ_INC_ANNO`
`static String`	`REQ_JSON`
`static String`	`REQ_OUT`
`static String`	`REQ_SEP_ANNO`
`static String`	`REQ_WANT`	The Constant REQ_WANT.
`static String`	`REQ_WANT_CELLML`	The Constant REQ_WANT_CELLML.
`static String`	`REQ_WANT_COMP_HIERARCHY_DOT`	The Constant REQ_WANT_COMP_HIERARCHY_DOT.
`static String`	`REQ_WANT_COMP_HIERARCHY_GRAPHML`	The Constant REQ_WANT_COMP_HIERARCHY_GRAPHML.
`static String`	`REQ_WANT_COMP_HIERARCHY_JSON`	The Constant REQ_WANT_COMP_HIERARCHY_JSON.
`static String`	`REQ_WANT_DIFF`	The Constant REQ_WANT_DIFF.
`static String`	`REQ_WANT_DOCUMENTTYPE`	The Constant REQ_WANT_DOCUMENTTYPE.
`static String`	`REQ_WANT_MATCHING_IDS`
`static String`	`REQ_WANT_MERGE`	The Constant REQ_WANT_MERGE.
`static String`	`REQ_WANT_META`	The Constant REQ_WANT_META.
`static String`	`REQ_WANT_NEGLECT_NAMES`
`static String`	`REQ_WANT_REACTIONS_DOT`	The Constant REQ_WANT_REACTIONS_DOT.
`static String`	`REQ_WANT_REACTIONS_DOT2`
`static String`	`REQ_WANT_REACTIONS_GRAPHML`	The Constant REQ_WANT_REACTIONS_GRAPHML.
`static String`	`REQ_WANT_REACTIONS_GRAPHML2`
`static String`	`REQ_WANT_REACTIONS_JSON`	The Constant REQ_WANT_REACTIONS_JSON.
`static String`	`REQ_WANT_REACTIONS_JSON2`
`static String`	`REQ_WANT_REACTIONS_SBGN_JSON`	The Constant REQ_WANT_REACTIONS_SBGN_JSON.
`static String`	`REQ_WANT_REGULAR`	The Constant REQ_WANT_REGULAR.
`static String`	`REQ_WANT_REPORT_HTML`	The Constant REQ_WANT_REPORT_HTML.
`static String`	`REQ_WANT_REPORT_HTML_FP`	The Constant REQ_WANT_REPORT_HTML_FP.
`static String`	`REQ_WANT_REPORT_MD`	The Constant REQ_WANT_REPORT_MD.
`static String`	`REQ_WANT_REPORT_RST`	The Constant REQ_WANT_REPORT_RST.
`static String`	`REQ_WANT_SBML`	The Constant REQ_WANT_SBML.
`static String`	`REQ_WANT_SINGLE_COMP_HIERARCHY_DOT`	The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_DOT.
`static String`	`REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML`	The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML.
`static String`	`REQ_WANT_SINGLE_COMP_HIERARCHY_JSON`	The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_JSON.
`static String`	`REQ_WANT_SINGLE_FLATTEN`	The Constant REQ_WANT_SINGLE_FLATTEN.
`static String`	`REQ_WANT_SINGLE_REACTIONS_DOT`	The Constant REQ_WANT_SINGLE_REACTIONS_DOT.
`static String`	`REQ_WANT_SINGLE_REACTIONS_DOT2`
`static String`	`REQ_WANT_SINGLE_REACTIONS_GRAPHML`	The Constant REQ_WANT_SINGLE_REACTIONS_GRAPHML.
`static String`	`REQ_WANT_SINGLE_REACTIONS_GRAPHML2`
`static String`	`REQ_WANT_SINGLE_REACTIONS_JSON`	The Constant REQ_WANT_SINGLE_REACTIONS_JSON.
`static String`	`REQ_WANT_SINGLE_REACTIONS_JSON2`
`static String`	`REQ_WANT_STRICT_NAMES`
`static String`	`REQ_XML`
`static Pattern`	`XML_PATTERN`	Pattern to distinguish xml files from URLs.

Constructor Summary

Constructors
Constructor Description

Executer()
Instantiates a new executer.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`executeCompare(String document1, String document2, org.json.simple.JSONObject toReturn, org.apache.commons.cli.CommandLine line, List<Exception> errors)`	Execute compare.
`void`	`executeSingle(String document, org.json.simple.JSONObject toReturn, org.apache.commons.cli.CommandLine line, List<Exception> errors)`	Execute single.
`org.apache.commons.cli.Options`	`getOptions()`	Get available (command-line) options.
`static String`	`htmlPageEnd()`	Static string to close an HTML page.
`static String`	`htmlPageStart()`	Static string to start an HTML page.
`static String`	`result(String s)`	Result.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - XML_PATTERN
```
public static final Pattern XML_PATTERN
```
    Pattern to distinguish xml files from URLs.
  - REQ_FILES
```
public static final String REQ_FILES
```
    The Constant REQ_FILES.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT
```
public static final String REQ_WANT
```
    The Constant REQ_WANT.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_META
```
public static final String REQ_WANT_META
```
    The Constant REQ_WANT_META.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_DOCUMENTTYPE
```
public static final String REQ_WANT_DOCUMENTTYPE
```
    The Constant REQ_WANT_DOCUMENTTYPE.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_DIFF
```
public static final String REQ_WANT_DIFF
```
    The Constant REQ_WANT_DIFF.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_MATCHING_IDS
```
public static final String REQ_WANT_MATCHING_IDS
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_NEGLECT_NAMES
```
public static final String REQ_WANT_NEGLECT_NAMES
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_STRICT_NAMES
```
public static final String REQ_WANT_STRICT_NAMES
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_MERGE
```
public static final String REQ_WANT_MERGE
```
    The Constant REQ_WANT_MERGE.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REPORT_MD
```
public static final String REQ_WANT_REPORT_MD
```
    The Constant REQ_WANT_REPORT_MD.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REPORT_RST
```
public static final String REQ_WANT_REPORT_RST
```
    The Constant REQ_WANT_REPORT_RST.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REPORT_HTML
```
public static final String REQ_WANT_REPORT_HTML
```
    The Constant REQ_WANT_REPORT_HTML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REPORT_HTML_FP
```
public static final String REQ_WANT_REPORT_HTML_FP
```
    The Constant REQ_WANT_REPORT_HTML_FP.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_GRAPHML
```
public static final String REQ_WANT_REACTIONS_GRAPHML
```
    The Constant REQ_WANT_REACTIONS_GRAPHML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_GRAPHML2
```
public static final String REQ_WANT_REACTIONS_GRAPHML2
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_DOT
```
public static final String REQ_WANT_REACTIONS_DOT
```
    The Constant REQ_WANT_REACTIONS_DOT.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_DOT2
```
public static final String REQ_WANT_REACTIONS_DOT2
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_SBGN_JSON
```
public static final String REQ_WANT_REACTIONS_SBGN_JSON
```
    The Constant REQ_WANT_REACTIONS_SBGN_JSON.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_JSON
```
public static final String REQ_WANT_REACTIONS_JSON
```
    The Constant REQ_WANT_REACTIONS_JSON.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REACTIONS_JSON2
```
public static final String REQ_WANT_REACTIONS_JSON2
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_COMP_HIERARCHY_GRAPHML
```
public static final String REQ_WANT_COMP_HIERARCHY_GRAPHML
```
    The Constant REQ_WANT_COMP_HIERARCHY_GRAPHML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_COMP_HIERARCHY_DOT
```
public static final String REQ_WANT_COMP_HIERARCHY_DOT
```
    The Constant REQ_WANT_COMP_HIERARCHY_DOT.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_COMP_HIERARCHY_JSON
```
public static final String REQ_WANT_COMP_HIERARCHY_JSON
```
    The Constant REQ_WANT_COMP_HIERARCHY_JSON.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SBML
```
public static final String REQ_WANT_SBML
```
    The Constant REQ_WANT_SBML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_CELLML
```
public static final String REQ_WANT_CELLML
```
    The Constant REQ_WANT_CELLML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_REGULAR
```
public static final String REQ_WANT_REGULAR
```
    The Constant REQ_WANT_REGULAR.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_REACTIONS_GRAPHML
```
public static final String REQ_WANT_SINGLE_REACTIONS_GRAPHML
```
    The Constant REQ_WANT_SINGLE_REACTIONS_GRAPHML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_REACTIONS_GRAPHML2
```
public static final String REQ_WANT_SINGLE_REACTIONS_GRAPHML2
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_REACTIONS_DOT
```
public static final String REQ_WANT_SINGLE_REACTIONS_DOT
```
    The Constant REQ_WANT_SINGLE_REACTIONS_DOT.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_REACTIONS_DOT2
```
public static final String REQ_WANT_SINGLE_REACTIONS_DOT2
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_REACTIONS_JSON
```
public static final String REQ_WANT_SINGLE_REACTIONS_JSON
```
    The Constant REQ_WANT_SINGLE_REACTIONS_JSON.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_REACTIONS_JSON2
```
public static final String REQ_WANT_SINGLE_REACTIONS_JSON2
```
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML
```
public static final String REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML
```
    The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_COMP_HIERARCHY_DOT
```
public static final String REQ_WANT_SINGLE_COMP_HIERARCHY_DOT
```
    The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_DOT.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_COMP_HIERARCHY_JSON
```
public static final String REQ_WANT_SINGLE_COMP_HIERARCHY_JSON
```
    The Constant REQ_WANT_SINGLE_COMP_HIERARCHY_JSON.
    
    See Also:
    
    Constant Field Values
  - REQ_WANT_SINGLE_FLATTEN
```
public static final String REQ_WANT_SINGLE_FLATTEN
```
    The Constant REQ_WANT_SINGLE_FLATTEN.
    
    See Also:
    
    Constant Field Values
  - REQ_DEBUG
```
public static final String REQ_DEBUG
```
    See Also:
    
    Constant Field Values
  - REQ_DEBUGG
```
public static final String REQ_DEBUGG
```
    See Also:
    
    Constant Field Values
  - REQ_XML
```
public static final String REQ_XML
```
    See Also:
    
    Constant Field Values
  - REQ_INC_ANNO
```
public static final String REQ_INC_ANNO
```
    See Also:
    
    Constant Field Values
  - REQ_SEP_ANNO
```
public static final String REQ_SEP_ANNO
```
    See Also:
    
    Constant Field Values
  - REQ_JSON
```
public static final String REQ_JSON
```
    See Also:
    
    Constant Field Values
  - REQ_CA
```
public static final String REQ_CA
```
    See Also:
    
    Constant Field Values
  - REQ_OUT
```
public static final String REQ_OUT
```
    See Also:
    
    Constant Field Values
  - REQ_HELP
```
public static final String REQ_HELP
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Executer
```
public Executer()
```
    Instantiates a new executer.
- Method Detail
  - getOptions
```
public org.apache.commons.cli.Options getOptions()
```
    Get available (command-line) options.
    
    Returns:
    
    the options
  - executeSingle
```
public void executeSingle(String document,
                          org.json.simple.JSONObject toReturn,
                          org.apache.commons.cli.CommandLine line,
                          List<Exception> errors)
                   throws Exception
```
    Execute single.
    
    Parameters:
    
    document - the document
    
    toReturn - the to return
    
    line - the line
    
    errors - the errors
    
    Throws:
    
    Exception - the exception
  - executeCompare
```
public void executeCompare(String document1,
                           String document2,
                           org.json.simple.JSONObject toReturn,
                           org.apache.commons.cli.CommandLine line,
                           List<Exception> errors)
                    throws Exception
```
    Execute compare.
    
    Parameters:
    
    document1 - the document1
    
    document2 - the document2
    
    toReturn - the to return
    
    line - the line
    
    errors - the errors
    
    Throws:
    
    Exception - the exception
  - result
```
public static String result(String s)
```
    Result.
    
    Parameters:
    
    s - the s
    
    Returns:
    
    the string
  - htmlPageStart
```
public static String htmlPageStart()
```
    Static string to start an HTML page.
    
    Returns:
    
    the string
  - htmlPageEnd
```
public static String htmlPageEnd()
```
    Static string to close an HTML page.
    
    Returns:
    
    the string

Class Executer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

XML_PATTERN

REQ_FILES

REQ_WANT

REQ_WANT_META

REQ_WANT_DOCUMENTTYPE

REQ_WANT_DIFF

REQ_WANT_MATCHING_IDS

REQ_WANT_NEGLECT_NAMES

REQ_WANT_STRICT_NAMES

REQ_WANT_MERGE

REQ_WANT_REPORT_MD

REQ_WANT_REPORT_RST

REQ_WANT_REPORT_HTML

REQ_WANT_REPORT_HTML_FP

REQ_WANT_REACTIONS_GRAPHML

REQ_WANT_REACTIONS_GRAPHML2

REQ_WANT_REACTIONS_DOT

REQ_WANT_REACTIONS_DOT2

REQ_WANT_REACTIONS_SBGN_JSON

REQ_WANT_REACTIONS_JSON

REQ_WANT_REACTIONS_JSON2

REQ_WANT_COMP_HIERARCHY_GRAPHML

REQ_WANT_COMP_HIERARCHY_DOT

REQ_WANT_COMP_HIERARCHY_JSON

REQ_WANT_SBML

REQ_WANT_CELLML

REQ_WANT_REGULAR

REQ_WANT_SINGLE_REACTIONS_GRAPHML

REQ_WANT_SINGLE_REACTIONS_GRAPHML2

REQ_WANT_SINGLE_REACTIONS_DOT

REQ_WANT_SINGLE_REACTIONS_DOT2

REQ_WANT_SINGLE_REACTIONS_JSON

REQ_WANT_SINGLE_REACTIONS_JSON2

REQ_WANT_SINGLE_COMP_HIERARCHY_GRAPHML

REQ_WANT_SINGLE_COMP_HIERARCHY_DOT

REQ_WANT_SINGLE_COMP_HIERARCHY_JSON

REQ_WANT_SINGLE_FLATTEN

REQ_DEBUG

REQ_DEBUGG

REQ_XML

REQ_INC_ANNO

REQ_SEP_ANNO

REQ_JSON

REQ_CA

REQ_OUT

REQ_HELP

Constructor Detail

Executer

Method Detail

getOptions

executeSingle

executeCompare

result

htmlPageStart

htmlPageEnd