Class RLO

java.lang.Object
  |
  +--RLO

class RLO

extends java.lang.Object

This class is used to specify the .R script LayOuts (RLO) analyses. In addition to the name of the .R script file and menu name, it also encodes the environment required for data input (output) to (from) R as well as actions to be taken after the .R script has been evaluated by R. Such actions may include bringing data back into the client or displaying plots generated by R.

Field Summary

(package private) java.lang.String	date RLO creation date
(package private) int	genRbits GenR Bits is a bit pattern of selected (R_GENR_xxxx) options used during .R script generation.
(package private) int	id sequence # of description
(package private) java.lang.String[]	inputDataFileNames Name of input file if any (if not null)
(package private) int[]	inputDataTypes R_DATA_TYPE_xxxx type of input file if any
(package private) java.lang.String	menuName Analysis menu name
(package private) java.lang.String	menuStubName Desired client menu stub.
(package private) int	nInputFiles # of input files if any, 0 if none
(package private) int	nOutputFiles # of output files if any, 0 if none
(package private) int	nSetR2ClientFiles # of output files used to set R to Client data if any, 0 if none
(package private) java.lang.String[]	outputDataFileNames List of output files if any, null if none
(package private) int[]	outputDataTypes List of R_FILE_TYPE_xxxx types of output files if any, null if none.
(package private) int	processBits Process Bits is a bit pattern of selected (R_PB_xxxx) options used during processing
private static RevalBase	rEvalBase
(package private) java.lang.String	RscriptName Name of .R script file
(package private) java.lang.String	scriptSpecificRoptions Optional script Specific R startup options.
(package private) java.lang.String[]	setR2ClientFileNames List of output file names used to set R to Client data if any, null if none
(package private) java.lang.String[]	setR2ClientObjNames List of client object names used to set R to Client data if any, null if none.
(package private) int[]	setR2ClientObjTypes List of R_SET_R2CLIENT__xxxx types of output files if any, null if none.

Constructor Summary

(package private)	RLO() RLO() - constructor instance to create empty RLO
(package private)	RLO(RevalBase rEvalBase, int maxAnalyses) RLO() - constructor for initial database allocation

Method Summary

(package private) int	addRLO(java.lang.String menuName, java.lang.String menuStubName, java.lang.String RscriptName, java.lang.String[] inputDataFileNames, int[] inputDataTypes, int processBits, int genRbits, java.lang.String[] outputDataFileNames, int[] outputDataTypes, java.lang.String[] setR2ClientFileNames, java.lang.String[] setR2ClientObjNames, int[] setR2ClientObjTypes, java.lang.String scriptSpecificRoptions) addRLO() - add new R LayOut (RLO) instance to the RLO database.
(package private) void	clearRLOdb() clearRLOdb() - clear list of R LayOuts analyses in the database
(package private) RLO	getCurrentRLO() getCurrentRLO() - return current RLO
(package private) int[]	getListofRLOids() getListofRLOids() - get list of all IDs
(package private) java.lang.String[]	getListofRLOmenuNames() getListofRLOmenuNames() - get list of all menuNames
(package private) java.lang.String[]	getListofRLOscriptNames() getListofRLOscriptNames() - get list of all R script names
(package private) RLO	getRLObyID(int id) getRLObyID() - get the RLO by id
(package private) RLO	getRLObyMenuName(java.lang.String menuName) getRLObyMenuName() - get the RLO by menuName
(package private) RLO	getRLObyRscriptName(java.lang.String RscriptName) getRLObyRscriptName() - get the RLO by RscriptName
(package private) int	getRLOidByRscriptName(java.lang.String rsName) getRLOidByRscriptName() - get the current RLO analysis method id by RscriptName
(package private) java.lang.String	getRLOinputFile(int lookForFileType, int nth) getRLOinputFile() get the nth Input Data file by input file type.
(package private) java.lang.String	getRLOoutFile(int lookForFileType, int nth) getRLOoutFile() get the nth Output Data file by out file type.
(package private) int	newRLO() newRLO() - create new empty R LayOut (RLO) instance to RLO database.
(package private) void	regrowRLOdbIfNeeded() regrowRLOdbIfNeeded() - grow RLO database if need more space
(package private) boolean	rmvRLO(int rloIdToRemove) rmvRLO() - remove the RLO from the analyses database This removes the .rlo file from the RLO/ directory and the .R script file from the R/ directory.
(package private) void	setCurrentRLO(int id) setCurrentRLO() - set the current RLO analysis by id
(package private) boolean	setRLO(int rloID, java.lang.String menuName, java.lang.String menuStubName, java.lang.String RscriptName, java.lang.String[] inputDataFileNames, int[] inputDataTypes, int processBits, int genRbits, java.lang.String[] outputDataFileNames, int[] outputDataTypes, java.lang.String[] setR2ClientFileNames, java.lang.String[] setR2ClientObjNames, int[] setR2ClientObjTypes, java.lang.String scriptSpecificRoptions) setRLO() - set R LayOut (RLO) instance to the RLO database.

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait

Field Detail

rEvalBase

private static RevalBase rEvalBase

id

int id

sequence # of description

menuName

java.lang.String menuName

Analysis menu name

menuStubName

java.lang.String menuStubName

Desired client menu stub. If null or "", then put in (Plugins | RLO methods submenu)

RscriptName

java.lang.String RscriptName

Name of .R script file

date

java.lang.String date

RLO creation date

nInputFiles

int nInputFiles

# of input files if any, 0 if none

inputDataFileNames

java.lang.String[] inputDataFileNames

Name of input file if any (if not null)

inputDataTypes

int[] inputDataTypes

R_DATA_TYPE_xxxx type of input file if any

processBits

int processBits

Process Bits is a bit pattern of selected (R_PB_xxxx) options used during processing

genRbits

int genRbits

GenR Bits is a bit pattern of selected (R_GENR_xxxx) options used during .R script generation.

nOutputFiles

int nOutputFiles

# of output files if any, 0 if none

outputDataFileNames

java.lang.String[] outputDataFileNames

List of output files if any, null if none

outputDataTypes

int[] outputDataTypes

List of R_FILE_TYPE_xxxx types of output files if any, null if none.

nSetR2ClientFiles

int nSetR2ClientFiles

# of output files used to set R to Client data if any, 0 if none

setR2ClientFileNames

java.lang.String[] setR2ClientFileNames

List of output file names used to set R to Client data if any, null if none

setR2ClientObjNames

java.lang.String[] setR2ClientObjNames

List of client object names used to set R to Client data if any, null if none. E.g., If the object is a gene set (condition list), then this is the gene set (condition list) name

setR2ClientObjTypes

int[] setR2ClientObjTypes

List of R_SET_R2CLIENT__xxxx types of output files if any, null if none.

scriptSpecificRoptions

java.lang.String scriptSpecificRoptions

Optional script Specific R startup options. These can include things like "--min-vsize=20M", or "--min-nsize=200k", etc. See Appendix B the "Introduction to R" reference manual for specific options.

Constructor Detail

RLO

RLO(RevalBase rEvalBase,
    int maxAnalyses)

RLO() - constructor for initial database allocation

Parameters:

rtst - (while debugging for access display)

rEvalBase -

maxAnalyses - to set up the database

RLO

RLO()

RLO() - constructor instance to create empty RLO

Method Detail

newRLO

int newRLO()

newRLO() - create new empty R LayOut (RLO) instance to RLO database.

Returns:

the id number

regrowRLOdbIfNeeded

void regrowRLOdbIfNeeded()

regrowRLOdbIfNeeded() - grow RLO database if need more space

addRLO

int addRLO(java.lang.String menuName,
           java.lang.String menuStubName,
           java.lang.String RscriptName,
           java.lang.String[] inputDataFileNames,
           int[] inputDataTypes,
           int processBits,
           int genRbits,
           java.lang.String[] outputDataFileNames,
           int[] outputDataTypes,
           java.lang.String[] setR2ClientFileNames,
           java.lang.String[] setR2ClientObjNames,
           int[] setR2ClientObjTypes,
           java.lang.String scriptSpecificRoptions)

addRLO() - add new R LayOut (RLO) instance to the RLO database. The RLO is a meta-language for specifying the processing interaction between R and client.

E.g., the following is an example that exports various types (4) of client data, generates 4 types of output files, and sets the client state from 2 of those files.

Parameters:

menuName - text description of the RLO entry

menuStubName - used by client to put RLO menu entry in a particular menu.

RscriptName - is the name of the .R file

inputDataFileNames - opt. list of R input data file names

inputDataTypes - corresponding list of R input data file types values

processBits - set for use during eval

genRbits - set and used during edit by R script GUI

outputDataFileNames - opt. list of R output data file names

outputDataTypes - corresponding list of R output data file types values

setR2ClientFileNames - opt. list of action file names to set R output data to client state objects

setR2ClientObjNames - opt. list of client action object names to set R output data to client state objects

setR2ClientObjType - opt. list of client object type values to set R output data to client state objects

scriptSpecificRoptions -

Returns:

the id number

setRLO

boolean setRLO(int rloID,
               java.lang.String menuName,
               java.lang.String menuStubName,
               java.lang.String RscriptName,
               java.lang.String[] inputDataFileNames,
               int[] inputDataTypes,
               int processBits,
               int genRbits,
               java.lang.String[] outputDataFileNames,
               int[] outputDataTypes,
               java.lang.String[] setR2ClientFileNames,
               java.lang.String[] setR2ClientObjNames,
               int[] setR2ClientObjTypes,
               java.lang.String scriptSpecificRoptions)

setRLO() - set R LayOut (RLO) instance to the RLO database. The RLO is a meta-language for specifying the processing interaction between R and client.

E.g., the following is an example that exports various types (4) of client data, generates 4 types of output files, and sets the client state from 2 of those files.

Parameters:

menuName - text description of the RLO entry

menuStubName - used by client to put RLO menu entry in a particular menu.

RscriptName - is the name of the .R file

inputDataFileNames - opt. list of R input data file names

inputDataTypes - corresponding list of R input data file types values

processBits - used during eval

genRbits - set and used used during edit by R script GUI

outputDataFileNames - opt. list of R output data file names

outputDataTypes - corresponding list of R output data file types values

setR2ClientFileNames - opt. list of action file names to set R output data to client state objects

setR2ClientObjNames - opt. list of client action object names to set R output data to client state objects

setR2ClientObjType - opt. list of client object type values to set R output data to client state objects

scriptSpecificRoptions -

Returns:

the id number

rmvRLO

boolean rmvRLO(int rloIdToRemove)

rmvRLO() - remove the RLO from the analyses database This removes the .rlo file from the RLO/ directory and the .R script file from the R/ directory.

Parameters:

rloIdToRemove - to remove

Returns:

true if removed

clearRLOdb

void clearRLOdb()

clearRLOdb() - clear list of R LayOuts analyses in the database

getRLOidByRscriptName

int getRLOidByRscriptName(java.lang.String rsName)

getRLOidByRscriptName() - get the current RLO analysis method id by RscriptName

Parameters:

rsName - is the RscriptName to lookup in the database

Returns:

current RLO object id, -1 if not found

setCurrentRLO

void setCurrentRLO(int id)

setCurrentRLO() - set the current RLO analysis by id

getCurrentRLO

RLO getCurrentRLO()

getCurrentRLO() - return current RLO

getListofRLOscriptNames

java.lang.String[] getListofRLOscriptNames()

getListofRLOscriptNames() - get list of all R script names

Returns:

list of RLO R script names

getListofRLOmenuNames

java.lang.String[] getListofRLOmenuNames()

getListofRLOmenuNames() - get list of all menuNames

Returns:

list of RLO menu names

getListofRLOids

int[] getListofRLOids()

getListofRLOids() - get list of all IDs

Returns:

list of RLO ids

getRLObyMenuName

RLO getRLObyMenuName(java.lang.String menuName)

getRLObyMenuName() - get the RLO by menuName

getRLObyRscriptName

RLO getRLObyRscriptName(java.lang.String RscriptName)

getRLObyRscriptName() - get the RLO by RscriptName

getRLObyID

RLO getRLObyID(int id)

getRLObyID() - get the RLO by id

Parameters:

id - to use in searching analyses database

Returns:

getRLOoutFile

java.lang.String getRLOoutFile(int lookForFileType,
                               int nth)

getRLOoutFile() get the nth Output Data file by out file type. Search outputDataTypes[] entries in the current RLO analyses[curAnalysis] instance.

Parameters:

lookForFileType - is one of R_FILE_TYPE_xxxx values

nth - is the nth instance to return (counting from 1 - not 0!)

Returns:

file name if found, else null if failed.

See Also:

getCurrentRLO()

getRLOinputFile

java.lang.String getRLOinputFile(int lookForFileType,
                                 int nth)

getRLOinputFile() get the nth Input Data file by input file type. Search inputDataTypes[] entries in the current RLO analyses[curAnalysis] instance.

Parameters:

lookForFileType - is one of R_FILE_TYPE_xxxx values

nth - is the nth instance to return (counting from 1 - not 0!)

Returns:

file name if found, else null if failed.

See Also:

getCurrentRLO()