A B C D E F G H I J K L M N O P Q R S T U V W X
A
- ABSENT -
Static variable in interface org.genepattern.data.expr.IResExpressionData
-
- ACCESS_PRIVATE -
Static variable in interface org.genepattern.util.IGPConstants
- access_id values for database
- ACCESS_PUBLIC -
Static variable in interface org.genepattern.util.IGPConstants
-
- ANALYSISJOBINFO - class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO.
-
- ANALYSISJOBINFO() -
Constructor for class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- ANALYSISPARAMETERS - class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS.
-
- ANALYSISPARAMETERS() -
Constructor for class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- ANALYSISTASKINFO - class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO.
-
- ANALYSISTASKINFO() -
Constructor for class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- ANT -
Static variable in interface org.genepattern.util.IGPConstants
-
- ANY -
Static variable in interface org.genepattern.util.IGPConstants
- any
- ANY -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- ATTRIBUTE - class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE.
-
- ATTRIBUTE() -
Constructor for class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- AUTHOR -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes author key
- AUTHORITY_BROAD -
Static variable in class org.genepattern.util.LSIDUtil
-
- AUTHORITY_FOREIGN -
Static variable in class org.genepattern.util.LSIDUtil
-
- AUTHORITY_MINE -
Static variable in class org.genepattern.util.LSIDUtil
-
- AbstractReader - class org.genepattern.io.AbstractReader.
- An abstract class for reading documents.
- AdminProxy - class org.genepattern.webservice.AdminProxy.
-
- AdminProxy(String, String) -
Constructor for class org.genepattern.webservice.AdminProxy
-
- AdminProxy(String, String, boolean) -
Constructor for class org.genepattern.webservice.AdminProxy
-
- AdminSoapBindingStub - class org.genepattern.webservice.AdminSoapBindingStub.
-
- AdminSoapBindingStub() -
Constructor for class org.genepattern.webservice.AdminSoapBindingStub
-
- AdminSoapBindingStub(URL, Service) -
Constructor for class org.genepattern.webservice.AdminSoapBindingStub
-
- AdminSoapBindingStub(Service) -
Constructor for class org.genepattern.webservice.AdminSoapBindingStub
-
- AnalysisJob - class org.genepattern.webservice.AnalysisJob.
- Client side job information - includes server and JobInfo.
- AnalysisJob() -
Constructor for class org.genepattern.webservice.AnalysisJob
- Constructs a new AnalysisJob .
- AnalysisJob(String, JobInfo) -
Constructor for class org.genepattern.webservice.AnalysisJob
- Constructs a new AnalysisJob
- AnalysisJob(String, JobInfo, boolean) -
Constructor for class org.genepattern.webservice.AnalysisJob
- Constructs a new AnalysisJob
- AnalysisService - class org.genepattern.webservice.AnalysisService.
- Holds a TaskInfo object and the server on which the task is
located.
- AnalysisService(String, TaskInfo) -
Constructor for class org.genepattern.webservice.AnalysisService
- Creates a new AnalysisService instance
- AnalysisSoapBindingStub - class org.genepattern.webservice.AnalysisSoapBindingStub.
-
- AnalysisSoapBindingStub() -
Constructor for class org.genepattern.webservice.AnalysisSoapBindingStub
-
- AnalysisSoapBindingStub(URL, Service) -
Constructor for class org.genepattern.webservice.AnalysisSoapBindingStub
-
- AnalysisSoapBindingStub(Service) -
Constructor for class org.genepattern.webservice.AnalysisSoapBindingStub
-
- AnalysisWebServiceProxy - class org.genepattern.webservice.AnalysisWebServiceProxy.
-
- AnalysisWebServiceProxy(String, String) -
Constructor for class org.genepattern.webservice.AnalysisWebServiceProxy
-
- AnalysisWebServiceProxy(String, String, boolean) -
Constructor for class org.genepattern.webservice.AnalysisWebServiceProxy
-
- accept(File, String) -
Method in class org.genepattern.util.PropertyFactory
- used to filter the resources dir for files ending with .props or
.properties
- addColumn(int, String, String, Object[]) -
Method in class org.genepattern.io.OdfObject
-
- addHeader(String, String) -
Method in class org.genepattern.io.OdfWriter
-
- addHeader(String, int) -
Method in class org.genepattern.io.OdfWriter
-
- addHeader(String, double) -
Method in class org.genepattern.io.OdfWriter
-
- addHeader(String, String[]) -
Method in class org.genepattern.io.OdfWriter
-
- addInputParameter(String, ParameterInfo) -
Method in class org.genepattern.data.pipeline.PipelineModel
- Adds a runtime prompt parameter
- addParameter(String, String) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- addParameter(ParameterInfo) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- addParameterInfo(ParameterInfo) -
Method in class org.genepattern.webservice.JobInfo
- Add new ParameterInfo into the JobInfo
- addTableModelListener(TableModelListener) -
Method in class org.genepattern.io.OdfObject
-
- addTask(JobSubmission) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- addTask(JobSubmission, int) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- appendExecutionLog(PrintWriter) -
Static method in class org.genepattern.io.OdfWriter
-
- asExpressionData(int, int, String[], String[], String[], String[], double[][]) -
Method in class org.genepattern.util.MatlabUtil
-
- assignments(String[]) -
Method in interface org.genepattern.io.expr.cls.IClsHandler
-
B
- BROAD_AUTHORITY -
Static variable in class org.genepattern.util.LSIDUtil
-
- BrowserLauncher - class org.genepattern.util.BrowserLauncher.
- BrowserLauncher is a class that provides one static method, openURL, which
opens the default web browser for the current user of the system to the given
URL.
- beforeExec() -
Method in class org.genepattern.webservice.LocalTaskExecutor
-
- beforeExec() -
Method in class org.genepattern.webservice.TaskExecutor
-
- beginProgress(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- bpog(String[]) -
Static method in class org.genepattern.util.RunGenePatternTaskMain
-
- build -
Variable in class org.genepattern.util.Version
- this is a number that represents the build
C
- CACHED_INPUT_MODE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- COMMAND_LINE -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes command line key
- COMMAND_PREFIX -
Static variable in interface org.genepattern.util.IGPConstants
-
- CPU_TYPE -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes CPU type key
- CdtParser - class org.genepattern.io.expr.stanford.CdtParser.
-
- CdtParser() -
Constructor for class org.genepattern.io.expr.stanford.CdtParser
-
- CdtReader - class org.genepattern.io.expr.stanford.CdtReader.
- Reader for cdt documents.
- CdtReader() -
Constructor for class org.genepattern.io.expr.stanford.CdtReader
-
- ClassVector - class org.genepattern.data.matrix.ClassVector.
- A one-dimensional matrix used to hold class assignment information.
- ClassVector(String[]) -
Constructor for class org.genepattern.data.matrix.ClassVector
- Constructs a new class vector from the array of class assignments
- ClassVector(String[], String[]) -
Constructor for class org.genepattern.data.matrix.ClassVector
- Constructs a new class vector from the array of class assignments
- ClsParser - class org.genepattern.io.expr.cls.ClsParser.
- Class for reading cls files using callbacks.
- ClsParser() -
Constructor for class org.genepattern.io.expr.cls.ClsParser
-
- ClsReader - class org.genepattern.io.expr.cls.ClsReader.
- Class for reading cls documents.
- ClsReader() -
Constructor for class org.genepattern.io.expr.cls.ClsReader
-
- ClsWriter - class org.genepattern.io.expr.cls.ClsWriter.
-
Writer for cls files.
- ClsWriter() -
Constructor for class org.genepattern.io.expr.cls.ClsWriter
-
- call(int, int, int) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- call(int, int, int) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- canDecode(InputStream) -
Method in class org.genepattern.io.OdfParser
- Returns
true if this parser can claims to be able to
decode the given stream upon brief examination, false
otherwise
- canDecode(InputStream) -
Method in interface org.genepattern.io.expr.IExpressionDataParser
- Returns
true if this parser can claims to be able to
decode the given stream upon brief examination, false
otherwise
- canDecode(InputStream) -
Method in class org.genepattern.io.expr.cls.ClsParser
-
- canDecode(InputStream) -
Method in class org.genepattern.io.expr.gct.GctParser
-
- canDecode(InputStream) -
Method in class org.genepattern.io.expr.res.ResParser
-
- canDecode(InputStream) -
Method in class org.genepattern.io.expr.stanford.CdtParser
-
- canRead(InputStream) -
Method in interface org.genepattern.io.expr.IExpressionDataReader
-
- canRead(InputStream) -
Method in class org.genepattern.io.expr.cls.ClsReader
-
- canRead(InputStream) -
Method in class org.genepattern.io.expr.gct.GctReader
-
- canRead(InputStream) -
Method in class org.genepattern.io.expr.odf.OdfDatasetReader
-
- canRead(InputStream) -
Method in class org.genepattern.io.expr.res.ResReader
-
- canRead(InputStream) -
Method in class org.genepattern.io.expr.stanford.CdtReader
-
- capitalize(String) -
Static method in class org.genepattern.util.StringUtils
- returns the String with the first character capitalized so wisconsin =>
Wisconsin
- checkFileExtension(String) -
Method in interface org.genepattern.io.expr.IExpressionDataWriter
- Appends the correct file extension to the pathname if it does not exist.
- checkFileExtension(String) -
Method in class org.genepattern.io.expr.cls.ClsWriter
-
- checkFileExtension(String) -
Method in class org.genepattern.io.expr.gct.GctWriter
-
- checkFileExtension(String) -
Method in class org.genepattern.io.expr.mage.MAGEMLWriter
-
- checkFileExtension(String) -
Method in class org.genepattern.io.expr.odf.OdfDatasetWriter
-
- checkFileExtension(String) -
Method in class org.genepattern.io.expr.res.ResWriter
-
- checkFileExtension(String) -
Method in class org.genepattern.io.expr.stanford.StanfordTxtWriter
-
- checkStatus(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- checkStatus(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
- Checks the status of a job.
- checkStatus(int) -
Method in class org.genepattern.webservice.RequestHandler
- Deprecated.
- classes(String[]) -
Method in interface org.genepattern.io.expr.cls.IClsHandler
-
- clone(String, String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- cloneTask(String, String) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- cloneTask(String, String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- columnDescription(int, String) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- columnDescription(int, String) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- columnName(int, String) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- columnName(int, String) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- compareAuthorities(LSID, LSID) -
Method in class org.genepattern.util.LSIDUtil
-
- compareTo(Object) -
Method in class org.genepattern.util.LSID
-
- containsInputFileParam() -
Method in class org.genepattern.webservice.JobInfo
- Checks to see if the JobInfo contains a input file parameter field
- containsInputFileParam() -
Method in class org.genepattern.webservice.TaskInfo
- Checks to see if the TaslInfo contains a input file parameter field
- containsOutputFileParam() -
Method in class org.genepattern.webservice.JobInfo
- Checks to see if the JobInfo contains a output file parameter field
- continueProgress(int) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- copy() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Make a deep copy of this matrix
- copy() -
Method in class org.genepattern.util.LSID
-
- countNonEmpty(String[]) -
Static method in class org.genepattern.util.StringUtils
- counts the number of non-null elements that have a trimed length of at
least 1
- create() -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- create() -
Method in interface org.genepattern.io.expr.IExpressionDataCreator
-
- createProvenancePipeline(JobInfo[], String) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- createProvenancePipeline(String, String) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- createProvenancePipeline(JobInfo[], String) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- createProvenancePipeline(String, String) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
D
- DEFAULT_PATCH_REPOSITORY_URL -
Static variable in interface org.genepattern.util.IGPConstants
-
- DEFAULT_PATCH_URL -
Static variable in interface org.genepattern.util.IGPConstants
-
- DELIMITER -
Static variable in class org.genepattern.util.LSID
-
- DESC -
Static variable in class org.genepattern.data.pipeline.PipelineModel
-
- DESCRIPTION -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfo.description
- DOMAIN -
Static variable in interface org.genepattern.util.IGPConstants
-
- DoubleMatrix2D - class org.genepattern.data.matrix.DoubleMatrix2D.
- A labelled dense 2-dimensional matrix holding double elements.
- DoubleMatrix2D(double[][]) -
Constructor for class org.genepattern.data.matrix.DoubleMatrix2D
- Creates a new matrix
- DoubleMatrix2D(double[][], String[], String[]) -
Constructor for class org.genepattern.data.matrix.DoubleMatrix2D
- Creates a new matrix
- DoubleMatrix2D(int, int) -
Constructor for class org.genepattern.data.matrix.DoubleMatrix2D
- Creates a new matrix
- data(int, int, String) -
Method in interface org.genepattern.io.IOdfHandler
-
- data(int, int, double) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- data(int, int, double) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- date -
Variable in class org.genepattern.util.Version
- the date of the build
- decode(String) -
Static method in class org.genepattern.webservice.TaskInfoAttributes
- factory method to create a TaskInfoAttributes object from an encoded XML
stream of one that was previously saved
- delete(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- deleteATTRIBUTE() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- deleteFiles(String, String[]) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- deleteFiles(String, String[]) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- deleteJOB() -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- deleteJob(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- deleteJob(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- deleteJobResultFile(int, String) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- deleteJobResultFile(int, String) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- deletePARAMETER() -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- deleteTASK() -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- deleteTask(String) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- deleteTask(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- deserialize(String) -
Static method in class org.genepattern.data.pipeline.PipelineModel
-
- det() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Matrix determinant
- downloadFile(String, String) -
Method in class org.genepattern.webservice.JobResult
- Downloads the result file from the server to the given download
directory.
- downloadFile(String, String, boolean) -
Method in class org.genepattern.webservice.JobResult
- Downloads the result file from the server to the given download
directory.
- downloadFiles(String) -
Method in class org.genepattern.webservice.JobResult
- Downloads all the available result files from the server to the given
download directory.
- downloadFiles(String, boolean) -
Method in class org.genepattern.webservice.JobResult
- Downloads all the available result files from the server to the given
download directory.
E
- ERROR -
Static variable in class org.genepattern.webservice.JobStatus
-
- E_OMNIBUS_BUSY -
Static variable in class org.genepattern.webservice.OmnigeneErrorCode
- Server busy error in Omnibus
- E_OMNIBUS_FATAL_ERROR -
Static variable in class org.genepattern.webservice.OmnigeneErrorCode
- Fatal Error in Omnibus
- E_OMNIBUS_UNRECOGNIZED_VERSION -
Static variable in class org.genepattern.webservice.OmnigeneErrorCode
-
- E_PROPERTY_NOT_FOUND -
Static variable in class org.genepattern.webservice.OmnigeneErrorCode
- Property value not found
- E_SERVER_NOT_STARTED -
Static variable in class org.genepattern.webservice.OmnigeneErrorCode
- App server not started
- ExpressionData - class org.genepattern.data.expr.ExpressionData.
- Implementation of IExpressionData interface
- ExpressionData(DoubleMatrix2D, String[], String[]) -
Constructor for class org.genepattern.data.expr.ExpressionData
-
- ExpressionDataCreator - class org.genepattern.io.expr.ExpressionDataCreator.
- Expression data creator that creates an instance of
org.genepattern.data.expr.ExpressionData
- ExpressionDataCreator() -
Constructor for class org.genepattern.io.expr.ExpressionDataCreator
-
- ExpressionDataCreator(boolean, boolean) -
Constructor for class org.genepattern.io.expr.ExpressionDataCreator
- Creates a new ExpressionDataCreator instance
- emptyATTRIBUTE() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- emptyJOB() -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- emptyPARAMETER() -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- emptyTASK() -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- encode() -
Method in class org.genepattern.webservice.TaskInfoAttributes
- method to encode a TaskInfoAttributes object into a serializable form for
persisting in the database
- endHeader() -
Method in interface org.genepattern.io.IOdfHandler
-
- endProgress() -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- equals(Object) -
Method in class org.genepattern.util.LSID
-
- equals(Object) -
Method in class org.genepattern.util.Version
- determines if another object is the same as this one
- equals(Version) -
Method in class org.genepattern.util.Version
- determines if another version is the same as this one
- equals(Object) -
Method in class org.genepattern.webservice.SuiteInfo
-
- equals(Object) -
Method in class org.genepattern.webservice.TaskInfo
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- equals(Object) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- errorMessage(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- exec() -
Method in class org.genepattern.webservice.TaskExecutor
-
- exportSuiteToZip(String, File) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- exportSuiteToZip(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- exportToZip(String, File) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- exportToZip(String, boolean, File) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- exportToZip(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- exportToZip(String, boolean) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
F
- FILE_FORMAT -
Static variable in interface org.genepattern.util.IGPConstants
-
- FILE_TYPE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- FINISHED -
Static variable in class org.genepattern.webservice.JobStatus
-
- FORMER_NAME -
Static variable in interface org.genepattern.util.IGPConstants
- when a task is being renamed, this well known parameter describes the
former task name
- FeatureListReader - class org.genepattern.io.FeatureListReader.
- Feature list reader.
- FeatureListReader() -
Constructor for class org.genepattern.io.FeatureListReader
-
- FileWrapper - class org.genepattern.webservice.FileWrapper.
- A utility class to help maintain filenames when files are passed as
attachements to web services.
- FileWrapper() -
Constructor for class org.genepattern.webservice.FileWrapper
-
- FileWrapper(String, DataHandler, long, long) -
Constructor for class org.genepattern.webservice.FileWrapper
-
- findJobsThatCreatedFile(String) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- findJobsThatCreatedFile(String) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
G
- GPConstants - class org.genepattern.util.GPConstants.
-
- GPConstants() -
Constructor for class org.genepattern.util.GPConstants
-
- GPServer - class org.genepattern.client.GPServer.
- This class is used to communicate with a GenePattern server.
- GPServer(String, String) -
Constructor for class org.genepattern.client.GPServer
- Creates a new GPServer instance.
- GP_HOME -
Static variable in class org.genepattern.util.GPpropertiesManager
- the GenePattern home dir (~/gp/)
- GPpropertiesManager - class org.genepattern.util.GPpropertiesManager.
- Handles GenePattern properties such as loading, saving, interpreting, etc.
- GctParser - class org.genepattern.io.expr.gct.GctParser.
- Class for reading a gct document using callbacks.
- GctParser() -
Constructor for class org.genepattern.io.expr.gct.GctParser
-
- GctReader - class org.genepattern.io.expr.gct.GctReader.
- Writer for gct documents.
- GctReader() -
Constructor for class org.genepattern.io.expr.gct.GctReader
-
- GctWriter - class org.genepattern.io.expr.gct.GctWriter.
- Writes gct files.
- GctWriter() -
Constructor for class org.genepattern.io.expr.gct.GctWriter
-
- get(int, int) -
Method in class org.genepattern.data.expr.ExpressionData
- Gets a single element
- get(int, int) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets a single element
- get(int, int) -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Gets a single element
- get(String) -
Method in class org.genepattern.webservice.TaskInfoAttributes
-
- getANALYSISPARAMETERS() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getANALYSISPARAMETERS() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- getATTRIBUTE() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- getAccessId() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getAccessId() -
Method in class org.genepattern.webservice.TaskInfo
-
- getAllPairs() -
Method in class org.genepattern.data.matrix.ClassVector
- Creates a array containing all pairwise class vectors.
- getAllServices() -
Method in class org.genepattern.util.RequestHandlerFactory
- Deprecated. Gets all available analysis service tasks
- getAllSuites() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getAllTasks() -
Method in class org.genepattern.webservice.AdminProxy
-
- getAllTasks() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getAnalysisServices() -
Method in class org.genepattern.webservice.RequestHandler
- Deprecated.
- getArray() -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the underlying double[][] array
- getArray() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the underlying double[][] array
- getArray() -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Gets the underlying int[][] array
- getArray(String) -
Method in class org.genepattern.io.OdfObject
-
- getArrayIds() -
Method in class org.genepattern.io.expr.stanford.CdtParser
-
- getAssignment(int) -
Method in class org.genepattern.data.matrix.ClassVector
- Gets the class assignment
- getAssignments() -
Method in class org.genepattern.data.matrix.ClassVector
- Allocates a new array containing the class assignments
- getAttributes() -
Method in class org.genepattern.webservice.ParameterInfo
- Gets HashMap attributes
- getAuthor() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getAuthor() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getAuthority() -
Method in class org.genepattern.util.LSID
-
- getAuthority() -
Method in class org.genepattern.util.LSIDUtil
-
- getAuthorityType(LSID) -
Method in class org.genepattern.util.LSIDUtil
-
- getBooleanArray(String) -
Method in class org.genepattern.io.OdfObject
-
- getBooleanHeader(String) -
Method in class org.genepattern.io.OdfObject
-
- getBooleanProperty(String) -
Static method in class org.genepattern.util.GPpropertiesManager
- returns a true if the property is set to "true" (case insensitive) false
if the property is null, "" (empty String), or "false"
- getBooleanProperty(String, boolean) -
Static method in class org.genepattern.util.GPpropertiesManager
- returns a true if the property is set to "true" (case insensitive) false
if the property is "false" if the Property is not defined ("", the empty
String; or null) returns the default_value
- getCall(int, int) -
Method in interface org.genepattern.data.expr.IResExpressionData
- Gets the Affymetrix call at the given row and column.
- getCall(int, int) -
Method in class org.genepattern.data.expr.ResExpressionData
-
- getCallAsString(int, int) -
Method in interface org.genepattern.data.expr.IResExpressionData
- Gets the Affymetrix call at the given row and column.
- getCallAsString(int, int) -
Method in class org.genepattern.data.expr.ResExpressionData
-
- getCallMatrix() -
Method in class org.genepattern.data.expr.ResExpressionData
- Gets the 2-dimensional matrix that holds the absent-present calls
- getChildren(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getChildren(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- getChoices(String) -
Method in class org.genepattern.webservice.ParameterInfo
-
- getClassCount() -
Method in class org.genepattern.data.matrix.ClassVector
- Gets the number of different possible values taken by the class
assignments.
- getClassName(int) -
Method in class org.genepattern.data.matrix.ClassVector
- Gets the class name for the specified class number
- getColumnClass(int) -
Method in class org.genepattern.io.OdfObject
-
- getColumnCount() -
Method in class org.genepattern.data.expr.ExpressionData
-
- getColumnCount() -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the number of column in the expression data matrix
- getColumnCount() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the column dimension.
- getColumnCount() -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Gets the column dimension.
- getColumnCount() -
Method in class org.genepattern.io.OdfObject
-
- getColumnDescription(int) -
Method in class org.genepattern.data.expr.ExpressionData
-
- getColumnDescription(int) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the column description at the given column or null if no
column description exists.
- getColumnDescriptions() -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the array containing the column descriptions or null if
no column descriptions are set
- getColumnIndex(String) -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the column index for the column name .
- getColumnIndex(String) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the column index for the column name .
- getColumnIndex(String) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the column index for the column name .
- getColumnIndex(String) -
Method in class org.genepattern.io.OdfObject
-
- getColumnName(int) -
Method in class org.genepattern.data.expr.ExpressionData
-
- getColumnName(int) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the column name at the given column
- getColumnName(int) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the column name at the specified index
- getColumnName(int) -
Method in class org.genepattern.io.OdfObject
-
- getColumnNames() -
Method in class org.genepattern.data.expr.ExpressionData
- Allocates a new array contains the column names
- getColumnNames() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Allocates a new array contains the column names
- getColumnNames() -
Method in class org.genepattern.io.OdfObject
- Gets the column names
- getContent() -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- getDESCRIPTION() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- getDESCRIPTION() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- getDataHandler() -
Method in class org.genepattern.webservice.FileWrapper
-
- getDateCompleted() -
Method in class org.genepattern.webservice.JobInfo
-
- getDateCompleted() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getDateSubmitted() -
Method in class org.genepattern.webservice.JobInfo
-
- getDateSubmitted() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getDescription() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- getDescription() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getDescription() -
Method in class org.genepattern.webservice.ParameterInfo
-
- getDescription() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getDescription() -
Method in class org.genepattern.webservice.TaskInfo
-
- getDocFileNames(String) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- getDocFileNames(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getDocFiles() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getDocFiles(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getDocumentationFiles() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getDoubleArray(String) -
Method in class org.genepattern.io.OdfObject
-
- getDoubleHeader(String) -
Method in class org.genepattern.io.OdfObject
-
- getEncodingScheme() -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getEncodingScheme() -
Method in interface org.genepattern.webservice.WebService
- Returns the encoding scheme name of the web service.
- getEncodingSchemeVersion() -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getEncodingSchemeVersion() -
Method in interface org.genepattern.webservice.WebService
- Returns the encoding scheme version.
- getErrors() -
Method in class org.genepattern.webservice.WebServiceErrorMessageException
-
- getExpressionData() -
Method in class org.genepattern.io.expr.stanford.CdtParser
-
- getExpressionMatrix() -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the 2-dimensional matrix that holds the expression values
- getExpressionReader(String) -
Static method in class org.genepattern.io.IOUtil
- Gets an expression data reader that can read the document at the given
pathname or
null if no reader is found.
- getExpressionWriterByFormatName(String) -
Static method in class org.genepattern.io.IOUtil
- Returns a IExpressionDataWriter that can encode the named format
- getFileSuffixes() -
Method in class org.genepattern.io.AbstractReader
-
- getFileSuffixes() -
Method in interface org.genepattern.io.expr.IExpressionDataReader
-
- getFileSuffixes() -
Method in class org.genepattern.io.expr.cls.ClsParser
-
- getFilename() -
Method in class org.genepattern.webservice.FileWrapper
-
- getFloatProperty(String) -
Static method in class org.genepattern.util.GPpropertiesManager
- returns the float value of the property if the Property is not defined
("", the empty String; or null) returns zero 0.0
- getFloatProperty(String, float) -
Static method in class org.genepattern.util.GPpropertiesManager
- returns the float value of the property if the Property is not defined
("", the empty String; or null) returns the default_value
- getFormatName() -
Method in class org.genepattern.io.AbstractReader
-
- getFormatName() -
Method in interface org.genepattern.io.expr.IExpressionDataReader
-
- getFormatName() -
Method in interface org.genepattern.io.expr.IExpressionDataWriter
- Returns a String identifying the format that this writer encodes.
- getFormatName() -
Method in class org.genepattern.io.expr.cls.ClsParser
-
- getFormatName() -
Method in class org.genepattern.io.expr.gct.GctWriter
-
- getFormatName() -
Method in class org.genepattern.io.expr.mage.MAGEMLWriter
-
- getFormatName() -
Method in class org.genepattern.io.expr.odf.OdfDatasetWriter
-
- getFormatName() -
Method in class org.genepattern.io.expr.res.ResWriter
-
- getFormatName() -
Method in class org.genepattern.io.expr.stanford.StanfordTxtWriter
-
- getGeneIds() -
Method in class org.genepattern.io.expr.stanford.CdtParser
-
- getGenePatternLog() -
Method in class org.genepattern.webservice.AdminProxy
-
- getGenePatternLog() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getHeader(String) -
Method in class org.genepattern.io.OdfObject
-
- getHeaders() -
Method in class org.genepattern.io.OdfObject
-
- getID() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getID() -
Method in class org.genepattern.webservice.TaskInfo
-
- getId() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getId() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- getIdentifier() -
Method in class org.genepattern.util.LSID
-
- getIncrementedMinorVersion() -
Method in class org.genepattern.util.LSID
-
- getIndices(int) -
Method in class org.genepattern.data.matrix.ClassVector
- Gets the indices in the assignments array that have the specified class
number.
- getInputFilename() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getInputParameters() -
Method in class org.genepattern.data.pipeline.PipelineModel
- Gets a map that maps the parameter name as a String to a ParameterInfo object
- getInstance() -
Static method in class org.genepattern.util.LSIDUtil
-
- getInstance() -
Static method in class org.genepattern.util.PropertyFactory
-
- getInstance() -
Static method in class org.genepattern.util.RequestHandlerFactory
- Deprecated.
- getInstance(String, String) -
Static method in class org.genepattern.util.RequestHandlerFactory
- Deprecated.
- getIntHeader(String) -
Method in class org.genepattern.io.OdfObject
-
- getIntProperty(String) -
Static method in class org.genepattern.util.GPpropertiesManager
- returns the int value of the property if the Property is not defined ("",
the empty String; or null) returns integer zero
- getIntProperty(String, int) -
Static method in class org.genepattern.util.GPpropertiesManager
- returns the int value of the property if the Property is not defined ("",
the empty String; or null) returns the default_value
- getIntegerArray(String) -
Method in class org.genepattern.io.OdfObject
-
- getJOB() -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- getJaxbString(ParameterInfo[]) -
Static method in class org.genepattern.webservice.ParameterFormatConverter
- Converts
ParameterInfo to parameter jaxb string
- getJob(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getJobInfo() -
Method in class org.genepattern.webservice.AnalysisJob
- Gets the JobInfo for this analysis job
- getJobNumber() -
Method in class org.genepattern.webservice.JobInfo
-
- getJobNumber() -
Method in class org.genepattern.webservice.JobResult
- Gets the job number for this job.
- getJobs(String, int, int, boolean) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getJobs(String, boolean) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- getKey() -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- getLSID() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- getLSID() -
Method in class org.genepattern.webservice.AnalysisJob
- Gets the LSID of the task that produced this analysis job.
- getLSID() -
Method in class org.genepattern.webservice.JobResult
- Gets the LSID of the task that produced this job result.
- getLSID() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getLSIDToVersionsMap() -
Method in class org.genepattern.webservice.AdminProxy
-
- getLSIDToVersionsMap() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getLabel() -
Method in class org.genepattern.webservice.ParameterInfo
- Gets the parameter displaying label.
- getLastModificationTimes(String, String[]) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- getLastModificationTimes(String, String[]) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getLastModified() -
Method in class org.genepattern.webservice.FileWrapper
-
- getLatestServices() -
Method in class org.genepattern.client.MatlabGPClient
- Contacts this GenePattern server and retrieves a map of task ids to
analysis services
- getLatestSuites() -
Method in class org.genepattern.webservice.AdminProxy
-
- getLatestSuites() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getLatestTasks() -
Method in class org.genepattern.webservice.AdminProxy
-
- getLatestTasks() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getLatestTasksByName() -
Method in class org.genepattern.webservice.AdminProxy
-
- getLatestTasksByName() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getLength() -
Method in class org.genepattern.webservice.FileWrapper
-
- getLsid() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getLsid() -
Method in class org.genepattern.webservice.AnalysisService
- Gets the LSID for this AnalysisService instance
- getLsid() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getLsidDependencies() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getMain(String) -
Method in class org.genepattern.util.RunGenePatternTaskMain
-
- getMaxLineCount(String) -
Static method in class org.genepattern.util.StringUtils
- finds the longest string and returns the number of characters
- getMessage(int) -
Static method in class org.genepattern.webservice.OmnigeneErrorCode
- Returns a text message describing the errno code passed in.
- getMessage() -
Method in class org.genepattern.webservice.WebServiceErrorMessageException
-
- getModuleLSIDs() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getModuleLsids() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getNAME() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- getName() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- getName() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getName() -
Method in class org.genepattern.webservice.AnalysisService
- Gets the name of this AnalysisService instance
- getName() -
Method in class org.genepattern.webservice.Parameter
- Gets the name of this parameter.
- getName() -
Method in class org.genepattern.webservice.ParameterInfo
-
- getName() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getName() -
Method in class org.genepattern.webservice.TaskInfo
-
- getName() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- getNamespace() -
Method in class org.genepattern.util.LSID
-
- getNearerLSID(LSID, LSID) -
Method in class org.genepattern.util.LSIDUtil
-
- getNumOccurances(String, char) -
Static method in class org.genepattern.util.StringUtils
- gets the number of times the delimiter is present in the String
- getNumOccurances(String, String) -
Static method in class org.genepattern.util.StringUtils
- gets the number of times the delimiter is present in the String
- getOmnigeneErrno() -
Method in class org.genepattern.webservice.OmnigeneException
- Return the Omnigene errno
- getOmnigeneMessage() -
Method in class org.genepattern.webservice.OmnigeneException
- Return the Omnigene error message that corresponds to the errno passed
in.
- getOneVersusAll() -
Method in class org.genepattern.data.matrix.ClassVector
- Creates a array containing all one versus all class vectors.
- getOutputFileNames() -
Method in class org.genepattern.webservice.JobResult
- Allocates a new array containing the file names of the output files that
this job created excluding the standard output file and the standard
error file.
- getOwner() -
Method in class org.genepattern.webservice.SuiteInfo
-
- getPARAMETER() -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- getParameterInfo() -
Method in class org.genepattern.webservice.JobInfo
- get parameter info jaxb string
- getParameterInfo() -
Method in class org.genepattern.webservice.TaskInfo
- get parameter info jaxb string
- getParameterInfoArray() -
Method in class org.genepattern.webservice.JobInfo
- get
ParameterInfo array
- getParameterInfoArray(String) -
Static method in class org.genepattern.webservice.ParameterFormatConverter
- Converts Jxb parameter string to
ParameterInfo
- getParameterInfoArray() -
Method in class org.genepattern.webservice.TaskInfo
- get
ParameterInfo array
- getParameters() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- getParameters() -
Method in class org.genepattern.webservice.JobResult
- Allocates a new array containing the input parameters that this job was
invoked with
- getProperties(String) -
Method in class org.genepattern.util.PropertyFactory
- Gets Properties object given a filename
- getPropertiesOnClasspath(String) -
Method in class org.genepattern.util.PropertyFactory
- get properties from classpath
- getProperty(String) -
Static method in class org.genepattern.util.GPpropertiesManager
- gets the property if it exists otherwise sets the property to null
- getProperty(String, String) -
Static method in class org.genepattern.util.GPpropertiesManager
- gets the property if it exists otherwise sets the property to the
specified default value and returns the default value
- getRequestHandler(String) -
Static method in class org.genepattern.util.RequestHandlerFactory
- Deprecated. Gets the RequestHandler based on the siteName which is unique and stored
in omnigene loopup service.
- getResultFilename() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getResultFiles(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getResultFiles(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
- Returns the filenames that were generated by a completed job.
- getResultFiles(int) -
Method in class org.genepattern.webservice.RequestHandler
- Deprecated.
- getRootCause() -
Method in class org.genepattern.webservice.WebServiceException
- Returns the exception that caused this web service exception.
- getRow(int) -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the underlying array at the given row
- getRow(int) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the underlying array at the given row
- getRow(int) -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Gets the underlying array at the given row
- getRowCount() -
Method in class org.genepattern.data.expr.ExpressionData
-
- getRowCount() -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the number of rows in the expression data matrix
- getRowCount() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the row dimension.
- getRowCount() -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Gets the row dimension.
- getRowCount() -
Method in class org.genepattern.io.OdfObject
-
- getRowDescription(int) -
Method in class org.genepattern.data.expr.ExpressionData
-
- getRowDescription(int) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the row description at the given row or null if no row
description exists.
- getRowDescriptions() -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the array containing the row descriptions or null if no
row descriptions are set
- getRowIndex(String) -
Method in class org.genepattern.data.expr.ExpressionData
- Gets the row index for the row name .
- getRowIndex(String) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the row index for the row name .
- getRowIndex(String) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the row index for the row name .
- getRowName(int) -
Method in class org.genepattern.data.expr.ExpressionData
-
- getRowName(int) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the row name at the given row
- getRowName(int) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Gets the row name at the specified index
- getRowNames() -
Method in class org.genepattern.data.expr.ExpressionData
- Allocates a new array contains the row names
- getRowNames() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Allocates a new array contains the row names
- getRuntimePrompt() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- getServer() -
Method in class org.genepattern.webservice.AnalysisJob
- Gets the server on which this analysis job was run
- getServer() -
Method in class org.genepattern.webservice.AnalysisService
- Gets the server on which this AnalysisService instance is
located.
- getServerLog() -
Method in class org.genepattern.webservice.AdminProxy
-
- getServerLog() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getServerURL() -
Method in class org.genepattern.webservice.JobResult
- Gets the url of the server that this job was run on.
- getServiceInfo() -
Method in class org.genepattern.webservice.AdminProxy
-
- getServiceInfo() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getServices() -
Method in class org.genepattern.client.MatlabGPClient
- Contacts this GenePattern server and retrieves a map of task ids to
analysis services
- getStatus() -
Method in class org.genepattern.webservice.JobInfo
-
- getStatus() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getSuite(String) -
Method in class org.genepattern.webservice.AdminProxy
-
- getSuite(String) -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getSuiteLsidToVersionsMap() -
Method in class org.genepattern.webservice.AdminProxy
-
- getSuiteLsidToVersionsMap() -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getSuiteMembership(String) -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getSuiteNamespace() -
Method in class org.genepattern.util.LSIDUtil
-
- getSupportFile(String, String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getSupportFileNames(String) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- getSupportFileNames(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getSupportFiles(String, String[], File) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- getSupportFiles(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getSupportFiles(String, String[]) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- getTASK() -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- getTask(int) -
Method in class org.genepattern.data.pipeline.PipelineModel
- Gets the JobSubmission at the given index
- getTask(String) -
Method in class org.genepattern.webservice.AdminProxy
-
- getTask(String) -
Method in class org.genepattern.webservice.AdminSoapBindingStub
-
- getTaskFileURL(String, String) -
Method in class org.genepattern.client.GPServer
- Returns the url to retrieve the given file as part of the given task.
- getTaskID() -
Method in class org.genepattern.webservice.JobInfo
-
- getTaskId() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- getTaskInfo() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- getTaskInfo() -
Method in class org.genepattern.webservice.AnalysisService
- Gets the TaskInfo object for this AnalysisService
instance
- getTaskInfoAttributes() -
Method in class org.genepattern.webservice.TaskInfo
-
- getTaskLSID() -
Method in class org.genepattern.webservice.JobInfo
-
- getTaskName() -
Method in class org.genepattern.webservice.AnalysisJob
- Gets the task name of the task that produced this analysis job.
- getTaskName() -
Method in class org.genepattern.webservice.JobInfo
-
- getTaskNamespace() -
Method in class org.genepattern.util.LSIDUtil
-
- getTasks() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getTasks() -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getTasks() -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
- Returns all the available tasks that can be used.
- getTasks() -
Method in class org.genepattern.webservice.RequestHandler
- Deprecated.
- getUIValue(ParameterInfo) -
Method in class org.genepattern.webservice.ParameterInfo
-
- getURL(int) -
Method in class org.genepattern.webservice.JobResult
- Returns the url to download the file that was created in the given
creation order
- getURL(String) -
Method in class org.genepattern.webservice.JobResult
- Returns the url to download the given file name.
- getURL() -
Method in class org.genepattern.webservice.RequestHandler
- Deprecated.
- getUnavailableTime() -
Method in class org.genepattern.webservice.UnavailableException
- Returns the time in seconds that the web service is temporarily
unavailable.
- getUserID() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getUserId() -
Method in class org.genepattern.webservice.JobInfo
-
- getUserId() -
Method in class org.genepattern.webservice.TaskInfo
-
- getUserid() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getValue(int, int) -
Method in class org.genepattern.data.expr.ExpressionData
-
- getValue(int, int) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the expression value at the given row and column.
- getValue() -
Method in class org.genepattern.webservice.Parameter
- Gets the value of this parameter.
- getValue() -
Method in class org.genepattern.webservice.ParameterInfo
-
- getValue() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- getValueAsString(int, int) -
Method in class org.genepattern.data.expr.ExpressionData
-
- getValueAsString(int, int) -
Method in interface org.genepattern.data.expr.IExpressionData
- Gets the value at the given row and column as a string.
- getValueAt(int, int) -
Method in class org.genepattern.io.OdfObject
-
- getVersion() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- getVersion() -
Method in class org.genepattern.util.LSID
-
- getWebService() -
Method in class org.genepattern.webservice.UnavailableException
- Returns the web service that is unavailable.
- getWebServiceInfo() -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getWebServiceInfo() -
Method in interface org.genepattern.webservice.WebService
- Returns information about the web service such as description, version,
and author.
- getWebServiceName() -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- getWebServiceName() -
Method in interface org.genepattern.webservice.WebService
- Returns the name of the web service.
- giveParameterInfoArray() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- giveTaskInfoAttributes() -
Method in class org.genepattern.webservice.TaskInfo
-
H
- hasChoices(String) -
Method in class org.genepattern.webservice.ParameterInfo
-
- hasStandardError() -
Method in class org.genepattern.webservice.JobResult
- Tests whether this job wrote to the standard error stream.
- hasStandardOut() -
Method in class org.genepattern.webservice.JobResult
- Tests whether this job wrote to the standard output stream.
- hasVersion() -
Method in class org.genepattern.util.LSID
-
- hashCode() -
Method in class org.genepattern.util.LSID
-
- hashCode() -
Method in class org.genepattern.webservice.SuiteInfo
-
- hashCode() -
Method in class org.genepattern.webservice.TaskInfo
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- hashCode() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- header(String, String[]) -
Method in interface org.genepattern.io.IOdfHandler
-
- header(String, String) -
Method in interface org.genepattern.io.IOdfHandler
-
- helloWorld(String[]) -
Static method in class org.genepattern.util.RunGenePatternTaskMain
-
- htmlEncode(String) -
Static method in class org.genepattern.util.StringUtils
- escapes characters that have an HTML entity representation.
I
- IClsHandler - interface org.genepattern.io.expr.cls.IClsHandler.
- An interface for receiving notification of the content of a cls document
- IExpressionData - interface org.genepattern.data.expr.IExpressionData.
- An interface for expression data.
- IExpressionDataCreator - interface org.genepattern.io.expr.IExpressionDataCreator.
- An interface for creating new instances of expression data objects
- IExpressionDataHandler - interface org.genepattern.io.expr.IExpressionDataHandler.
- An interface for receiving notification of the content of a expression data
document
- IExpressionDataParser - interface org.genepattern.io.expr.IExpressionDataParser.
- Interface for reading expression data documents using callbacks.
- IExpressionDataReader - interface org.genepattern.io.expr.IExpressionDataReader.
- Interface for expression data readers.
- IExpressionDataWriter - interface org.genepattern.io.expr.IExpressionDataWriter.
- Interface for expression data writers.
- IGPConstants - interface org.genepattern.util.IGPConstants.
-
- INHERIT_FILENAME -
Static variable in class org.genepattern.data.pipeline.PipelineModel
-
- INHERIT_TASKNAME -
Static variable in class org.genepattern.data.pipeline.PipelineModel
-
- INPUT_BASENAME -
Static variable in interface org.genepattern.util.IGPConstants
- input filename without directory or extension
- INPUT_EXTENSION -
Static variable in interface org.genepattern.util.IGPConstants
- input filename extension only
- INPUT_FILE -
Static variable in interface org.genepattern.util.IGPConstants
- input filename without directory
- INPUT_MODE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- INPUT_PATH -
Static variable in interface org.genepattern.util.IGPConstants
- input directory
- INSTALLED_PATCH_LSIDS -
Static variable in interface org.genepattern.util.IGPConstants
-
- INVOKE -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes pipeline invocation key (prefixed by language, eg.
- IOUtil - class org.genepattern.io.IOUtil.
- A class containing static convenience methods for reading and writing data
- IOdfHandler - interface org.genepattern.io.IOdfHandler.
- An interface for receiving notification of the content of an odf document
- IResExpressionData - interface org.genepattern.data.expr.IResExpressionData.
- An interface for expression data that includes Affymetrix absent, present,
and marginal calls.
- IntMatrix2D - class org.genepattern.data.matrix.IntMatrix2D.
- A dense 2-dimensional matrix holding int elements.
- IntMatrix2D(int, int) -
Constructor for class org.genepattern.data.matrix.IntMatrix2D
- Creates a new matrix
- IntMatrix2D(int[][]) -
Constructor for class org.genepattern.data.matrix.IntMatrix2D
- Creates a new matrix
- importZip(File, int) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- importZip(DataHandler, int) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- importZip(DataHandler, int, boolean) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- importZipFromURL(String, int) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- importZipFromURL(String, int, boolean) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- importZipFromURL(String, int) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- init() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- init(int, int, boolean, boolean, boolean) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- init(int, int, boolean, boolean, boolean) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- install(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- installSuite(SuiteInfo, DataHandler[], String[]) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- installTask(String) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- installTask(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- isCellEditable(int, int) -
Method in class org.genepattern.io.OdfObject
-
- isClientJob() -
Method in class org.genepattern.webservice.AnalysisJob
- Returns true if this job was executed on the client,
false if this job was executed on the server.
- isEquivalent(LSID) -
Method in class org.genepattern.util.LSID
-
- isInputFile() -
Method in class org.genepattern.webservice.ParameterInfo
- Checks to see if this parameter is used to specify uploaded file from
client.
- isLSID(String) -
Static method in class org.genepattern.util.LSID
-
- isOutputFile() -
Method in class org.genepattern.webservice.ParameterInfo
- Checks to see if this parameter is used to specify output file from
server
- isPermanent() -
Method in class org.genepattern.webservice.UnavailableException
- Returns a
boolean indicating whether this web service is
permanently unavailable.
- isPrivate() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- isSameAuthority(LSID) -
Method in class org.genepattern.util.LSID
-
- isSameIdentifier(LSID) -
Method in class org.genepattern.util.LSID
-
- isSameNamespace(LSID) -
Method in class org.genepattern.util.LSID
-
- isSimilar(LSID) -
Method in class org.genepattern.util.LSID
-
- isSuiteLSID(String) -
Static method in class org.genepattern.util.LSIDUtil
-
- isSuiteLSID(LSID) -
Static method in class org.genepattern.util.LSIDUtil
-
- isVisualizer() -
Method in class org.genepattern.data.pipeline.JobSubmission
-
J
- JAVA -
Static variable in interface org.genepattern.util.IGPConstants
- well known name for command that invoked JVM for Omnigene
- JOB - class org.genepattern.webservice.jaxb.job.JOB.
-
- JOB() -
Constructor for class org.genepattern.webservice.jaxb.job.JOB
-
- JOB_ERROR -
Static variable in class org.genepattern.webservice.JobStatus
-
- JOB_FINISHED -
Static variable in class org.genepattern.webservice.JobStatus
-
- JOB_ID -
Static variable in interface org.genepattern.util.IGPConstants
- job ID (analysis_job ID) of running job
- JOB_NOT_STARTED -
Static variable in class org.genepattern.webservice.JobStatus
-
- JOB_PROCESSING -
Static variable in class org.genepattern.webservice.JobStatus
-
- JVM_LEVEL -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes JVM version number key
- JobInfo - class org.genepattern.webservice.JobInfo.
- Used to hold information about particular job
- JobInfo() -
Constructor for class org.genepattern.webservice.JobInfo
-
- JobInfo(int, int, String, Date, Date, ParameterInfo[], String, String, String) -
Constructor for class org.genepattern.webservice.JobInfo
-
- JobResult - class org.genepattern.webservice.JobResult.
- Encapsulates information about a job run on a GenePattern server.
- JobResult(URL, int, String[], boolean, boolean, Parameter[], String) -
Constructor for class org.genepattern.webservice.JobResult
- Creates a new JobResult instance.
- JobStatus - class org.genepattern.webservice.JobStatus.
- Gets the parameters about Job status
- JobStatus() -
Constructor for class org.genepattern.webservice.JobStatus
-
- JobSubmission - class org.genepattern.data.pipeline.JobSubmission.
-
- JobSubmission(String, String, String, ParameterInfo[], boolean[], boolean, TaskInfo) -
Constructor for class org.genepattern.data.pipeline.JobSubmission
-
- JobSubmission() -
Constructor for class org.genepattern.data.pipeline.JobSubmission
-
K
- KeySortedProperties - class org.genepattern.util.KeySortedProperties.
-
- KeySortedProperties() -
Constructor for class org.genepattern.util.KeySortedProperties
-
- KeySortedProperties(Properties) -
Constructor for class org.genepattern.util.KeySortedProperties
-
- key -
Variable in class org.genepattern.io.OdfObject.Entry
-
L
- LANGUAGE -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes language key
- LEFT_DELIMITER -
Static variable in interface org.genepattern.util.IGPConstants
- parameter delimiters for commandLine and output_filename contents
- LIBDIR -
Static variable in interface org.genepattern.util.IGPConstants
- Location where scripts, DLLs, etc are stored
- LSID -
Static variable in interface org.genepattern.util.IGPConstants
-
- LSID - class org.genepattern.util.LSID.
-
- LSID(String) -
Constructor for class org.genepattern.util.LSID
-
- LSID(String, String, String, String) -
Constructor for class org.genepattern.util.LSID
-
- LSIDUtil - class org.genepattern.util.LSIDUtil.
-
- LSID_PROVENANCE -
Static variable in interface org.genepattern.util.IGPConstants
-
- LocalTaskExecutor - class org.genepattern.webservice.LocalTaskExecutor.
-
- LocalTaskExecutor(TaskInfo, Map, String, String) -
Constructor for class org.genepattern.webservice.LocalTaskExecutor
-
- leftDelimiter -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- log() -
Method in class org.genepattern.webservice.OmnigeneException
- Writes the exception message and a timestamp to the System.out file.
M
- MAGEMLWriter - class org.genepattern.io.expr.mage.MAGEMLWriter.
- Writes MAGE-ML documents.
- MAGEMLWriter() -
Constructor for class org.genepattern.io.expr.mage.MAGEMLWriter
-
- MANIFEST_FILENAME -
Static variable in interface org.genepattern.util.IGPConstants
- well-known name of manifest file within zip file containing
GenePatternAnalysisTask descriptors and support files
- MARGINAL -
Static variable in interface org.genepattern.data.expr.IResExpressionData
-
- MAX_PARAMETERS -
Static variable in interface org.genepattern.util.IGPConstants
-
- MODE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- MULTIPLE -
Static variable in interface org.genepattern.util.IGPConstants
-
- MatlabGPClient - class org.genepattern.client.MatlabGPClient.
- This class is used to communicate with a GenePattern server.
- MatlabGPClient(String, String) -
Constructor for class org.genepattern.client.MatlabGPClient
- Creates a new MatlabGPClient instance.
- MatlabUtil - class org.genepattern.util.MatlabUtil.
-
- MatlabUtil() -
Constructor for class org.genepattern.util.MatlabUtil
-
- main(String[]) -
Static method in class org.genepattern.util.BrowserLauncher
-
- main(String[]) -
Static method in class org.genepattern.util.RunGenePatternTaskMain
-
- main(String[]) -
Static method in class org.genepattern.webservice.ParameterFormatConverter
-
- major -
Variable in class org.genepattern.util.Version
- the major release number - change here indicating major changes in
functionality or internal design
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- marshal(Marshaller) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- matchingVersion(LSID) -
Method in class org.genepattern.util.LSID
-
- minor -
Variable in class org.genepattern.util.Version
- the minor release number - change here indicates new features as well as
bug fixes and possibly some changes in internal design and implementation
- minus(DoubleMatrix2D) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- C = A - B
- modifySuite(SuiteInfo, File[], String[]) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- modifySuite(int, String, String, String, String, String, String[], DataHandler[], String[]) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- modifyTask(int, String, String, ParameterInfo[], HashMap, File[], String[]) -
Method in class org.genepattern.webservice.TaskIntegratorProxy
-
- modifyTask(int, String, String, ParameterInfo[], HashMap, DataHandler[], String[]) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
N
- NAME -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfo.name
- NOT_STARTED -
Static variable in class org.genepattern.webservice.JobStatus
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.job.JOB
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- newDispatcher() -
Static method in class org.genepattern.webservice.jaxb.task.TASK
-
O
- ODF -
Static variable in interface org.genepattern.util.IGPConstants
- fileextension of ODF
- OS -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes OS key
- OUTPUT_MODE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- OdfDatasetReader - class org.genepattern.io.expr.odf.OdfDatasetReader.
- Reader for odf datasets
- OdfDatasetReader() -
Constructor for class org.genepattern.io.expr.odf.OdfDatasetReader
-
- OdfDatasetWriter - class org.genepattern.io.expr.odf.OdfDatasetWriter.
- Writer for odf datasets
- OdfDatasetWriter() -
Constructor for class org.genepattern.io.expr.odf.OdfDatasetWriter
-
- OdfObject - class org.genepattern.io.OdfObject.
- Generic odf representation
- OdfObject(String) -
Constructor for class org.genepattern.io.OdfObject
-
- OdfObject.Entry - class org.genepattern.io.OdfObject.Entry.
-
- OdfParser - class org.genepattern.io.OdfParser.
- Class for reading an ODF document using callbacks.
- OdfParser() -
Constructor for class org.genepattern.io.OdfParser
-
- OdfWriter - class org.genepattern.io.OdfWriter.
-
- OdfWriter(String, String[], String, int, boolean) -
Constructor for class org.genepattern.io.OdfWriter
-
- OmnigeneErrorCode - class org.genepattern.webservice.OmnigeneErrorCode.
- OmnigeneErrorCodes Used in referencing error number with messages.
- OmnigeneErrorCode() -
Constructor for class org.genepattern.webservice.OmnigeneErrorCode
-
- OmnigeneException - exception org.genepattern.webservice.OmnigeneException.
OmnigeneException is the superclass of all Omnigene exceptions
that can be thrown during normal operation of the Omnigene system.- OmnigeneException() -
Constructor for class org.genepattern.webservice.OmnigeneException
- Constructs a
OmnigeneException with no detail message.
- OmnigeneException(String) -
Constructor for class org.genepattern.webservice.OmnigeneException
- Constructs a
OmnigeneException with the specified detail
message.
- OmnigeneException(int) -
Constructor for class org.genepattern.webservice.OmnigeneException
- Constructs an
OmnigeneException class with the specified
detail message.
- OmnigeneException(int, String) -
Constructor for class org.genepattern.webservice.OmnigeneException
- Constructs an
OmnigeneException class with the specified
detail message.
- openURL(String) -
Static method in class org.genepattern.util.BrowserLauncher
- Attempts to open the default web browser to the given URL.
- org.genepattern.client - package org.genepattern.client
- Provides facilities for running GenePattern modules.
- org.genepattern.data.expr - package org.genepattern.data.expr
- Provides facilities for the representation of expression data.
- org.genepattern.data.matrix - package org.genepattern.data.matrix
- Provides matrix facilites.
- org.genepattern.data.pipeline - package org.genepattern.data.pipeline
-
- org.genepattern.io - package org.genepattern.io
- Provides facilities for reading and writing data files.
- org.genepattern.io.expr - package org.genepattern.io.expr
- Provides facilities for reading and writing expression data files.
- org.genepattern.io.expr.cls - package org.genepattern.io.expr.cls
- Provides facilities for reading and writing cls files.
- org.genepattern.io.expr.gct - package org.genepattern.io.expr.gct
- Provides facilities for reading and writing gct files.
- org.genepattern.io.expr.mage - package org.genepattern.io.expr.mage
- Provides facilities for writing MAGE-ML files.
- org.genepattern.io.expr.odf - package org.genepattern.io.expr.odf
- Provides facilities for reading and writing odf files.
- org.genepattern.io.expr.res - package org.genepattern.io.expr.res
- Provides facilities for reading and writing res files.
- org.genepattern.io.expr.stanford - package org.genepattern.io.expr.stanford
-
- org.genepattern.util - package org.genepattern.util
-
- org.genepattern.webservice - package org.genepattern.webservice
-
- org.genepattern.webservice.jaxb.job - package org.genepattern.webservice.jaxb.job
-
- org.genepattern.webservice.jaxb.parameter - package org.genepattern.webservice.jaxb.parameter
-
- org.genepattern.webservice.jaxb.task - package org.genepattern.webservice.jaxb.task
-
P
- PARAMETER - class org.genepattern.webservice.jaxb.parameter.PARAMETER.
-
- PARAMETER() -
Constructor for class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- PARAM_INFO_ATTRIBUTES -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_CHECKBOX -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_CHECKBOX -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- PARAM_INFO_CHOICE -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_CHOICE_DELIMITER -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_CHOICE_TYPES_MULTIPLE_OFFSET -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_CHOICE_TYPES_OFFSET -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_CLIENT_FILENAME -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_DEFAULT_VALUE -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_DEFAULT_VALUE -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- PARAM_INFO_DOMAIN -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_FILE_FORMAT -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_NAME_OFFSET -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_OPTIONAL -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_OPTIONAL -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- PARAM_INFO_PREFIX -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_SPACER -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_STRING -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_STRING -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- PARAM_INFO_TYPE -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPES -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_CLASS_OFFSET -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_FLOAT -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_INPUT_FILE -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_INTEGER -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_NAME_OFFSET -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_OFFSET -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_SEPARATOR -
Static variable in interface org.genepattern.util.IGPConstants
-
- PARAM_INFO_TYPE_TEXT -
Static variable in interface org.genepattern.util.IGPConstants
-
- PATCH_ERROR_EXIT_VALUE -
Static variable in interface org.genepattern.util.IGPConstants
-
- PATCH_SUCCESS_EXIT_VALUE -
Static variable in interface org.genepattern.util.IGPConstants
-
- PERL -
Static variable in interface org.genepattern.util.IGPConstants
-
- PIPELINE_MODEL -
Static variable in class org.genepattern.data.pipeline.PipelineModel
-
- PIPELINE_SCRIPT -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes pipeline code key
- PREFIX -
Static variable in interface org.genepattern.util.IGPConstants
- ParameterInfo attribute for prefix string for command line generation
- PRESENT -
Static variable in interface org.genepattern.data.expr.IResExpressionData
-
- PRIVACY -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes privacy key
- PRIVACY_LEVELS -
Static variable in interface org.genepattern.util.IGPConstants
- array of privacy levels for user choices
- PRIVATE -
Static variable in interface org.genepattern.util.IGPConstants
- two levels of privacy defined: public, private.
- PROCESSING -
Static variable in class org.genepattern.webservice.JobStatus
-
- PUBLIC -
Static variable in interface org.genepattern.util.IGPConstants
- two levels of privacy defined: public, private.
- Parameter - class org.genepattern.webservice.Parameter.
- A job input parameter name-value pair.
- Parameter(String, String) -
Constructor for class org.genepattern.webservice.Parameter
- Creates a new Parameter instance.
- Parameter(String, double) -
Constructor for class org.genepattern.webservice.Parameter
- Creates a new Parameter instance.
- Parameter(String, int) -
Constructor for class org.genepattern.webservice.Parameter
- Creates a new Parameter instance.
- Parameter(String, File) -
Constructor for class org.genepattern.webservice.Parameter
- Creates a new Parameter instance.
- ParameterFormatConverter - class org.genepattern.webservice.ParameterFormatConverter.
- Utility class to convert between jxb string and
ParameterInfo - ParameterFormatConverter() -
Constructor for class org.genepattern.webservice.ParameterFormatConverter
- Creates new ParameterFormatConverter
- ParameterInfo - class org.genepattern.webservice.ParameterInfo.
-
- ParameterInfo() -
Constructor for class org.genepattern.webservice.ParameterInfo
- Creates new ParameterInfo
- ParameterInfo(String, String, String) -
Constructor for class org.genepattern.webservice.ParameterInfo
-
- ParseException - exception org.genepattern.io.ParseException.
- Encapsulate a general error or warning from parsing a file.
- ParseException(String) -
Constructor for class org.genepattern.io.ParseException
- Create a new ParseException.
- ParseException(Exception) -
Constructor for class org.genepattern.io.ParseException
- Create a new ParseException wrapping an existing exception.
- ParseException(String, Exception) -
Constructor for class org.genepattern.io.ParseException
- Create a new ParseException from an existing exception.
- PipelineModel - class org.genepattern.data.pipeline.PipelineModel.
-
- PipelineModel() -
Constructor for class org.genepattern.data.pipeline.PipelineModel
-
- PropertyFactory - class org.genepattern.util.PropertyFactory.
- Class which loads properties files and returns values found in the Property
file of interest This is a singleton
- PropertyNotFoundException - exception org.genepattern.webservice.PropertyNotFoundException.
- To throw property could not be located
- PropertyNotFoundException() -
Constructor for class org.genepattern.webservice.PropertyNotFoundException
- Default Constructor
- PropertyNotFoundException(String) -
Constructor for class org.genepattern.webservice.PropertyNotFoundException
- Constructs PropertyNotFoundException with the specified detail message.
- parse(InputStream) -
Method in class org.genepattern.io.OdfParser
- Parse an ODF document.
- parse(InputStream) -
Method in interface org.genepattern.io.expr.IExpressionDataParser
- Parse a document.
- parse(InputStream) -
Method in class org.genepattern.io.expr.cls.ClsParser
- Parses the
InputStream to create a ClassVector
instance
- parse(InputStream) -
Method in class org.genepattern.io.expr.gct.GctParser
- Parse a gct document.
- parse(InputStream) -
Method in class org.genepattern.io.expr.res.ResParser
- Parse a res document.
- parse(InputStream) -
Method in class org.genepattern.io.expr.stanford.CdtParser
-
- ping() -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- ping() -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
- Pings the service to see if it's alive.
- ping() -
Method in interface org.genepattern.webservice.WebService
- Pings the webservice.
- plus(DoubleMatrix2D) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- C = A + B
- print(PrintStream, String) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Prints this matrix in delimitted format using the default number format.
- print(PrintStream, String, NumberFormat) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Prints this matrix in delimitted format.
- printHeader() -
Method in class org.genepattern.io.OdfWriter
-
- printStackTrace() -
Method in class org.genepattern.webservice.WebServiceException
-
- prompt(String) -
Static method in class org.genepattern.client.Util
- Prompts the user for input from the console.
- purgeJob(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- purgeJob(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
Q
- QUALITY -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes quality key
- QUALITY_DEVELOPMENT -
Static variable in interface org.genepattern.util.IGPConstants
- three levels of quality defined: development, preproduction, production
- QUALITY_LEVELS -
Static variable in interface org.genepattern.util.IGPConstants
- array of quality levels for user choices
- QUALITY_PREPRODUCTION -
Static variable in interface org.genepattern.util.IGPConstants
- three levels of quality defined: development, preproduction, production
- QUALITY_PRODUCTION -
Static variable in interface org.genepattern.util.IGPConstants
- three levels of quality defined: development, preproduction, production
R
- R -
Static variable in interface org.genepattern.util.IGPConstants
-
- REQUIRED_PATCH_LSIDS -
Static variable in interface org.genepattern.util.IGPConstants
-
- REQUIRED_PATCH_URLS -
Static variable in interface org.genepattern.util.IGPConstants
-
- RESERVED_PARAMETER_NAMES -
Static variable in interface org.genepattern.util.IGPConstants
-
- RIGHT_DELIMITER -
Static variable in interface org.genepattern.util.IGPConstants
- parameter delimiters for commandLine and output_filename contents
- RUNTIME_PARAM -
Static variable in class org.genepattern.data.pipeline.PipelineModel
-
- R_HOME -
Static variable in interface org.genepattern.util.IGPConstants
-
- ReaderUtil - class org.genepattern.io.expr.ReaderUtil.
- Utility class for expression data readers.
- RequestHandler - class org.genepattern.webservice.RequestHandler.
- Deprecated. use AnalysisWebServiceProxy instead
- RequestHandler(String, String) -
Constructor for class org.genepattern.webservice.RequestHandler
- Deprecated.
- RequestHandlerFactory - class org.genepattern.util.RequestHandlerFactory.
- Deprecated. use AnalysisWebServiceProxy instead
- ResExpressionData - class org.genepattern.data.expr.ResExpressionData.
- Implementation of IResExpressionData interface
- ResExpressionData(DoubleMatrix2D, IntMatrix2D, String[], String[]) -
Constructor for class org.genepattern.data.expr.ResExpressionData
- Constructs a new res expression data instance
- ResParser - class org.genepattern.io.expr.res.ResParser.
- Class for reading a res document using callbacks.
- ResParser() -
Constructor for class org.genepattern.io.expr.res.ResParser
-
- ResReader - class org.genepattern.io.expr.res.ResReader.
- Reads res files.
- ResReader() -
Constructor for class org.genepattern.io.expr.res.ResReader
-
- ResWriter - class org.genepattern.io.expr.res.ResWriter.
- Writes res files.
- ResWriter() -
Constructor for class org.genepattern.io.expr.res.ResWriter
-
- RunGenePatternTaskMain - class org.genepattern.util.RunGenePatternTaskMain.
- Create a network class loader to load Java bytecode from the remote
Omnigene/GenePattern server's tasklib directory (for a named task) and then
instantiate the public static void main(String args[]) method of that class
- RunGenePatternTaskMain(String, String, String, String, boolean) -
Constructor for class org.genepattern.util.RunGenePatternTaskMain
-
- RunGenePatternTaskMain(String, String, String, String) -
Constructor for class org.genepattern.util.RunGenePatternTaskMain
-
- rank() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Returns the effective numerical rank, obtained from Singular Value
Decomposition.
- read(String) -
Method in class org.genepattern.io.FeatureListReader
- Gets the list of features contained in the given file
- read(String, IExpressionDataCreator) -
Method in interface org.genepattern.io.expr.IExpressionDataReader
-
- read(IExpressionDataParser, String, IExpressionDataCreator) -
Static method in class org.genepattern.io.expr.ReaderUtil
-
- read(String) -
Method in class org.genepattern.io.expr.cls.ClsReader
-
- read(InputStream) -
Method in class org.genepattern.io.expr.cls.ClsReader
-
- read(String, IExpressionDataCreator) -
Method in class org.genepattern.io.expr.gct.GctReader
-
- read(String, IExpressionDataCreator) -
Method in class org.genepattern.io.expr.odf.OdfDatasetReader
-
- read(String, IExpressionDataCreator) -
Method in class org.genepattern.io.expr.res.ResReader
-
- read(String, IExpressionDataCreator) -
Method in class org.genepattern.io.expr.stanford.CdtReader
-
- readCls(String) -
Static method in class org.genepattern.io.IOUtil
- Reads the cls document at the given pathname
- readExpressionData(String, IExpressionDataCreator) -
Static method in class org.genepattern.io.IOUtil
- Reads the expression data at the given pathname.
- readExpressionData(String) -
Static method in class org.genepattern.io.IOUtil
- Reads the expression data at the given pathname and returns a new
ExpressionData instance.
- readFeatureList(String) -
Static method in class org.genepattern.io.IOUtil
- Gets a list of features at the given file pathname string
- readOdf(String, IOdfHandler) -
Static method in class org.genepattern.io.IOUtil
- Parses the odf document at the given pathname using the specified handler
- recordClientJob(int, ParameterInfo[], int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- recordClientJob(int, ParameterInfo[]) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- recordClientJob(int, ParameterInfo[]) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- recordClientJob(int, ParameterInfo[], int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- release -
Variable in class org.genepattern.util.Version
- The release which is usually Alpha, Beta, FCS, or Final
- removeParameterInfo(String) -
Method in class org.genepattern.webservice.JobInfo
- Removes all parameters with the given name.
- removeTableModelListener(TableModelListener) -
Method in class org.genepattern.io.OdfObject
-
- replace(String, String, String) -
Static method in class org.genepattern.webservice.TaskInfoAttributes
-
- replaceAll(String, String, String) -
Static method in class org.genepattern.util.StringUtils
- returns a new String where all occurances of the first string are
replaced with the second string
- revision -
Variable in class org.genepattern.util.Version
- the revision number - change here indicates bug fixes no new features
- rightDelimiter -
Static variable in class org.genepattern.webservice.TaskExecutor
-
- rowDescription(int, String) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- rowDescription(int, String) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- rowName(int, String) -
Method in class org.genepattern.io.expr.ExpressionDataCreator
-
- rowName(int, String) -
Method in interface org.genepattern.io.expr.IExpressionDataHandler
-
- run(String, String[], String, String, String, String, boolean) -
Static method in class org.genepattern.util.RunGenePatternTaskMain
- convenience method to create a network classloader, load the requested
class from the specified classpath for a specific GenePattern task on a
particular Omnigene server, and then invoke that class' main method,
passing it the specified arguments
- run(String, String[], String, String, String, String) -
Static method in class org.genepattern.util.RunGenePatternTaskMain
-
- runAnalysis(String, Parameter[]) -
Method in class org.genepattern.client.GPServer
- Submits the given task with the given parameters and waits for the job to
complete.
- runVisualizer(String, Parameter[]) -
Method in class org.genepattern.client.GPServer
- Downloads the support files for the given task from the server and
executes the given task locally.
S
- SCHEME -
Static variable in class org.genepattern.util.LSID
-
- SERIALIZED_MODEL -
Static variable in interface org.genepattern.util.IGPConstants
-
- STATUS_MAP -
Static variable in class org.genepattern.webservice.JobStatus
- an unmodifiable map that maps a string representation of the status to the numberic representation
- STDERR -
Static variable in interface org.genepattern.util.IGPConstants
- filename of well-known file that may be output by a job, representing the
output to the stderr stream of the process
- STDOUT -
Static variable in interface org.genepattern.util.IGPConstants
- filename of well-known file that may be output by a job, representing the
output to the stdout stream of the process
- SUITE_MANIFEST_FILENAME -
Static variable in interface org.genepattern.util.IGPConstants
-
- SUITE_NAMESPACE -
Static variable in interface org.genepattern.util.IGPConstants
-
- StanfordTxtWriter - class org.genepattern.io.expr.stanford.StanfordTxtWriter.
- Writes Stanford txt files.
- StanfordTxtWriter() -
Constructor for class org.genepattern.io.expr.stanford.StanfordTxtWriter
-
- StringUtils - class org.genepattern.util.StringUtils.
- Static methods for String manipulation
- SuiteInfo - class org.genepattern.webservice.SuiteInfo.
-
- SuiteInfo() -
Constructor for class org.genepattern.webservice.SuiteInfo
- Creates new SuiteInfo
- SuiteInfo(String, String, String, String, String, ArrayList, int, ArrayList) -
Constructor for class org.genepattern.webservice.SuiteInfo
-
- SuiteInfo(HashMap) -
Constructor for class org.genepattern.webservice.SuiteInfo
-
- saveGenePatternProperties() -
Static method in class org.genepattern.util.GPpropertiesManager
- saves the GenePattern Properties
- serialize() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- set(int, int, double) -
Method in class org.genepattern.data.expr.ExpressionData
- Sets a single element.
- set(String, String, double) -
Method in class org.genepattern.data.expr.ExpressionData
- Sets a single element.
- set(int, int, double) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Sets a single element.
- set(String, String, double) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Sets a single element.
- set(int, int, int) -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Sets a single element.
- setANALYSISPARAMETERS(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setANALYSISPARAMETERS(String) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- setAccessId(int) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setAccessId(int) -
Method in class org.genepattern.webservice.TaskInfo
-
- setAsInputFile() -
Method in class org.genepattern.webservice.ParameterInfo
- Sets this as an input file parameter.
- setAsOutputFile() -
Method in class org.genepattern.webservice.ParameterInfo
- Sets this as an output file parameter.
- setAttributes(HashMap) -
Method in class org.genepattern.webservice.ParameterInfo
- Sets attributes for the ParameterInfo
- setAuthor(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setAuthor(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setAuthority(String) -
Method in class org.genepattern.util.LSID
-
- setColumnDescription(int, String) -
Method in class org.genepattern.data.expr.ExpressionData
-
- setColumnDescriptions(String[]) -
Method in class org.genepattern.data.expr.ExpressionData
- Sets the column descriptions
- setColumnName(int, String) -
Method in class org.genepattern.data.expr.ExpressionData
-
- setColumnName(int, String) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Sets the column name at the specified index
- setColumnTypes(String[]) -
Method in class org.genepattern.io.OdfWriter
-
- setContent(String) -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- setDESCRIPTION(String) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- setDESCRIPTION(String) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- setDataHandler(DataHandler) -
Method in class org.genepattern.webservice.FileWrapper
-
- setDateCompleted(Date) -
Method in class org.genepattern.webservice.JobInfo
-
- setDateCompleted(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setDateSubmitted(Date) -
Method in class org.genepattern.webservice.JobInfo
-
- setDateSubmitted(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setDescription(String) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- setDescription(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setDescription(String) -
Method in class org.genepattern.webservice.ParameterInfo
-
- setDescription(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setDescription(String) -
Method in class org.genepattern.webservice.TaskInfo
-
- setDocFiles(String[]) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setDocumentationFiles(String[]) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setEncodingScheme(String) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- setEncodingScheme(String) -
Method in interface org.genepattern.webservice.WebService
- Sets the encoding scheme of the web service.
- setEncodingSchemeVersion(float) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- setEncodingSchemeVersion(float) -
Method in interface org.genepattern.webservice.WebService
- Sets the encoding scheme version.
- setExternalDataFilenameURI(String) -
Method in class org.genepattern.io.expr.mage.MAGEMLWriter
-
- setFilename(String) -
Method in class org.genepattern.webservice.FileWrapper
-
- setHandler(IOdfHandler) -
Method in class org.genepattern.io.OdfParser
- Allow an application to register an event handler.
- setHandler(IExpressionDataHandler) -
Method in interface org.genepattern.io.expr.IExpressionDataParser
- Sets the handler that will receive events
- setHandler(IClsHandler) -
Method in class org.genepattern.io.expr.cls.ClsParser
-
- setHandler(IExpressionDataHandler) -
Method in class org.genepattern.io.expr.gct.GctParser
-
- setHandler(IExpressionDataHandler) -
Method in class org.genepattern.io.expr.res.ResParser
-
- setHandler(IExpressionDataHandler) -
Method in class org.genepattern.io.expr.stanford.CdtParser
-
- setID(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setID(int) -
Method in class org.genepattern.webservice.TaskInfo
-
- setId(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setId(String) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- setIdentifier(String) -
Method in class org.genepattern.util.LSID
-
- setInputFilename(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setJobInfo(JobInfo) -
Method in class org.genepattern.webservice.AnalysisJob
- Sets the JobInfo for this analysis job
- setJobNumber(int) -
Method in class org.genepattern.webservice.JobInfo
-
- setJobStatus(int, String) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- setJobStatus(int, String) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- setKey(String) -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- setLSID(String) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- setLSID(String) -
Method in class org.genepattern.webservice.AnalysisJob
- Sets the LSID of the task that produced this analysis job.
- setLSID(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setLabel(String) -
Method in class org.genepattern.webservice.ParameterInfo
- Sets the parameter displaying label
- setLastModified(long) -
Method in class org.genepattern.webservice.FileWrapper
-
- setLength(long) -
Method in class org.genepattern.webservice.FileWrapper
-
- setLsid(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setLsid(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setModuleLSIDs(String[]) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setModuleLsids(String[]) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setNAME(String) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- setName(String) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- setName(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setName(String) -
Method in class org.genepattern.webservice.ParameterInfo
-
- setName(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setName(String) -
Method in class org.genepattern.webservice.TaskInfo
-
- setName(String) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- setNamespace(String) -
Method in class org.genepattern.util.LSID
-
- setOwner(String) -
Method in class org.genepattern.webservice.SuiteInfo
-
- setParameterInfo(String) -
Method in class org.genepattern.webservice.TaskInfo
- get
ParameterInfo array
- setParameterInfoArray(ParameterInfo[]) -
Method in class org.genepattern.webservice.JobInfo
- set
ParameterInfo array
- setParameterInfoArray(ParameterInfo[]) -
Method in class org.genepattern.webservice.TaskInfo
- set
ParameterInfo array
- setParameters(ParameterInfo[]) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- setPrependExecutionLog(boolean) -
Method in class org.genepattern.io.expr.odf.OdfDatasetWriter
-
- setPrivacy(boolean) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setPrivacy(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setProperty(String, String) -
Static method in class org.genepattern.util.GPpropertiesManager
-
- setResultFilename(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setRowDescription(int, String) -
Method in class org.genepattern.data.expr.ExpressionData
-
- setRowDescriptions(String[]) -
Method in class org.genepattern.data.expr.ExpressionData
- Sets the row descriptions
- setRowName(int, String) -
Method in class org.genepattern.data.expr.ExpressionData
-
- setRowName(int, String) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Sets the row name at the specified index
- setRuntimePrompt(boolean[]) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- setServer(String) -
Method in class org.genepattern.webservice.AnalysisJob
- Sets the server on which this analysis job was run
- setStatus(String) -
Method in class org.genepattern.webservice.JobInfo
-
- setStatus(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setTaskID(int) -
Method in class org.genepattern.webservice.JobInfo
-
- setTaskId(String) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- setTaskInfo(TaskInfo) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- setTaskInfoAttributes(Map) -
Method in class org.genepattern.webservice.TaskInfo
-
- setTaskLSID(String) -
Method in class org.genepattern.webservice.JobInfo
-
- setTaskName(String) -
Method in class org.genepattern.webservice.AnalysisJob
- Sets the task name of the task that produced this analysis job.
- setTaskName(String) -
Method in class org.genepattern.webservice.JobInfo
-
- setTimeout(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- setUserID(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setUserId(String) -
Method in class org.genepattern.webservice.JobInfo
-
- setUserId(String) -
Method in class org.genepattern.webservice.TaskInfo
-
- setUserid(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setValue(String) -
Method in class org.genepattern.webservice.ParameterInfo
-
- setValue(String) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- setValueAt(Object, int, int) -
Method in class org.genepattern.io.OdfObject
-
- setVersion(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- setVersion(String) -
Method in class org.genepattern.util.LSID
-
- setVisualizer(boolean) -
Method in class org.genepattern.data.pipeline.JobSubmission
-
- size() -
Method in class org.genepattern.data.matrix.ClassVector
- Gets the number of assignments in this class vector
- slice(String[], String[]) -
Method in class org.genepattern.data.expr.ExpressionData
-
- slice(int[], int[]) -
Method in class org.genepattern.data.expr.ExpressionData
-
- slice(int[], int[]) -
Method in class org.genepattern.data.expr.ResExpressionData
- Constructs and returns a new res expression data instance that contains
the indicated cells.
- slice(int[], boolean) -
Method in class org.genepattern.data.matrix.ClassVector
- Constructs and returns a new class vector that contains the indicated
cells.
- slice(int[]) -
Method in class org.genepattern.data.matrix.ClassVector
- Constructs and returns a new class vector that contains the indicated
cells.
- slice(String[], String[]) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Constructs and returns a new matrix that contains the indicated cells.
- slice(int[], int[]) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Constructs and returns a new matrix that contains the indicated cells.
- slice(int[], int[]) -
Method in class org.genepattern.data.matrix.IntMatrix2D
- Constructs and returns a new matrix that contains the indicated cells.
- splitStrings(String, char) -
Static method in class org.genepattern.util.StringUtils
- creates an array of Strings by parsing the input String using the
delimiter
- splitStrings(String, String) -
Static method in class org.genepattern.util.StringUtils
- creates an array of Strings by parsing the input String using the
delimiter
- statusMessage(String) -
Method in class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- store(OutputStream, String) -
Method in class org.genepattern.util.KeySortedProperties
-
- submitJob(int, ParameterInfo[], HashMap, int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- submitJob(int, ParameterInfo[], HashMap) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- submitJob(int, ParameterInfo[], int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
- Submits a job to be processed.
- submitJob(int, ParameterInfo[]) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
- Submits a job to be processed.
- submitJob(int, ParameterInfo[]) -
Method in class org.genepattern.webservice.RequestHandler
- Deprecated.
- synchronizeTaskFiles() -
Method in class org.genepattern.webservice.LocalTaskExecutor
- Downloads the support files for the given task to libdir.
T
- TASK - class org.genepattern.webservice.jaxb.task.TASK.
-
- TASK() -
Constructor for class org.genepattern.webservice.jaxb.task.TASK
-
- TASKLOG -
Static variable in interface org.genepattern.util.IGPConstants
- filename of well-known file that may be output by a job, representing the
provenance data of the process
- TASK_ID -
Static variable in interface org.genepattern.util.IGPConstants
- task ID (task_master ID) of running job
- TASK_INFO_ATTRIBUTES -
Static variable in interface org.genepattern.util.IGPConstants
- names of all expected TaskInfoAttributes from manifest file (or other new
task submission)
- TASK_NAMESPACE -
Static variable in interface org.genepattern.util.IGPConstants
-
- TASK_TYPE -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes task type key
- TASK_TYPE_PIPELINE -
Static variable in interface org.genepattern.util.IGPConstants
- well known task type that gets special handling in menus and browsers
- TASK_TYPE_VISUALIZER -
Static variable in interface org.genepattern.util.IGPConstants
- well known task type that gets special handling in menus and browsers
- TOMCAT -
Static variable in interface org.genepattern.util.IGPConstants
-
- TYPE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- TaskExecException - exception org.genepattern.webservice.TaskExecException.
-
- TaskExecException(String) -
Constructor for class org.genepattern.webservice.TaskExecException
-
- TaskExecException(Throwable) -
Constructor for class org.genepattern.webservice.TaskExecException
-
- TaskExecutor - class org.genepattern.webservice.TaskExecutor.
-
- TaskExecutor(TaskInfo, Map, String) -
Constructor for class org.genepattern.webservice.TaskExecutor
-
- TaskInfo - class org.genepattern.webservice.TaskInfo.
-
- TaskInfo() -
Constructor for class org.genepattern.webservice.TaskInfo
- Creates new TaskInfo
- TaskInfo(int, String, String, String) -
Constructor for class org.genepattern.webservice.TaskInfo
-
- TaskInfo(int, String, String, String, TaskInfoAttributes) -
Constructor for class org.genepattern.webservice.TaskInfo
-
- TaskInfo(int, String, String, String, TaskInfoAttributes, String, int) -
Constructor for class org.genepattern.webservice.TaskInfo
-
- TaskInfoAttributes - class org.genepattern.webservice.TaskInfoAttributes.
-
- TaskInfoAttributes(Map) -
Constructor for class org.genepattern.webservice.TaskInfoAttributes
-
- TaskInfoAttributes() -
Constructor for class org.genepattern.webservice.TaskInfoAttributes
-
- TaskIntegratorProxy - class org.genepattern.webservice.TaskIntegratorProxy.
-
- TaskIntegratorProxy(String, String) -
Constructor for class org.genepattern.webservice.TaskIntegratorProxy
-
- TaskIntegratorProxy(String, String, boolean) -
Constructor for class org.genepattern.webservice.TaskIntegratorProxy
-
- TaskIntegratorSoapBindingStub - class org.genepattern.webservice.TaskIntegratorSoapBindingStub.
-
- TaskIntegratorSoapBindingStub() -
Constructor for class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- TaskIntegratorSoapBindingStub(URL, Service) -
Constructor for class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- TaskIntegratorSoapBindingStub(Service) -
Constructor for class org.genepattern.webservice.TaskIntegratorSoapBindingStub
-
- terminateJob(int) -
Method in class org.genepattern.webservice.AnalysisSoapBindingStub
-
- terminateJob(int) -
Method in class org.genepattern.webservice.AnalysisWebServiceProxy
-
- text -
Variable in class org.genepattern.util.Version
- the String representation of this Version
- times(DoubleMatrix2D) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Linear algebraic matrix multiplication, A * B
- times(double) -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Multiply a matrix by a scalar, C = s*A
- toAssignmentString() -
Method in class org.genepattern.data.matrix.ClassVector
-
- toPipelineModel(String) -
Static method in class org.genepattern.data.pipeline.PipelineModel
-
- toPipelineModel(String, boolean) -
Static method in class org.genepattern.data.pipeline.PipelineModel
-
- toPipelineModel(InputSource, boolean) -
Static method in class org.genepattern.data.pipeline.PipelineModel
-
- toString() -
Method in class org.genepattern.data.matrix.ClassVector
-
- toString() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- toString() -
Method in class org.genepattern.util.LSID
-
- toString() -
Method in class org.genepattern.util.Version
- returns a String represention of this Version
- toString() -
Method in class org.genepattern.webservice.AnalysisService
- Returns a string representation of this AnalysisService
instance
- toString() -
Method in class org.genepattern.webservice.JobInfo
- standard method
- toString() -
Method in class org.genepattern.webservice.Parameter
- Returns a string representation of this parameter.
- toString() -
Method in class org.genepattern.webservice.ParameterInfo
- returns a String representation of this
- toString() -
Method in class org.genepattern.webservice.TaskInfoAttributes
-
- toString() -
Method in class org.genepattern.webservice.WebServiceException
-
- toString() -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- toString() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- toString() -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- toString() -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- toString() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- toString() -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- toString() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- toStringNoVersion() -
Method in class org.genepattern.util.LSID
-
- toXML() -
Method in class org.genepattern.data.pipeline.PipelineModel
-
- trace() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Computes the sum of the diagonal elements of matrix A; Sum(A[i,i]).
- transpose() -
Method in class org.genepattern.data.matrix.DoubleMatrix2D
- Matrix transpose.
U
- UNREQUIRED_PARAMETER_NAMES -
Static variable in interface org.genepattern.util.IGPConstants
-
- URL_INPUT_MODE -
Static variable in class org.genepattern.webservice.ParameterInfo
-
- URN -
Static variable in class org.genepattern.util.LSID
-
- USERID -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes userID key
- USER_LOGGED_OFF -
Static variable in interface org.genepattern.util.IGPConstants
- request attribute, set when the user has logged off
- UTF8 -
Static variable in interface org.genepattern.util.IGPConstants
-
- UnavailableException - exception org.genepattern.webservice.UnavailableException.
- Defines an exception that a web service throws to indicate that it is
permanently or temporarily unavailable.
- UnavailableException(String) -
Constructor for class org.genepattern.webservice.UnavailableException
- Constructs a new web service exeption with the specified message
indicating that the web service is permanently unavailable.
- UnavailableException(String, Throwable) -
Constructor for class org.genepattern.webservice.UnavailableException
- Constructs a new web service exeption with the specified message
indicating that the web service is permanently unavailable along with the
root cause exception.
- UnavailableException(WebService, String) -
Constructor for class org.genepattern.webservice.UnavailableException
- Constructs a new unavialable exeption with the specified message.
- UnavailableException(WebService, String, Throwable) -
Constructor for class org.genepattern.webservice.UnavailableException
- Constructs a new unavialable exeption with the specified message.
- UnavailableException(WebService, String, int) -
Constructor for class org.genepattern.webservice.UnavailableException
- Constructs a new unavialable exeption for a web service with the
specified message and the time in seconds it's unavialable.
- UnavailableException(WebService, String, int, Throwable) -
Constructor for class org.genepattern.webservice.UnavailableException
- Constructs a new unavialable exeption for a web service with the
specified message and the time in seconds it's unavialable.
- Util - class org.genepattern.client.Util.
- A utility class used to read user input from the console.
- union(ClassVector) -
Method in class org.genepattern.data.matrix.ClassVector
- Constructs a new class vector that is the union of this class vector with
the given class vector
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.job.JOB
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.job.JOB
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.job.JOB
-
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- unmarshal(Unmarshaller) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- unmarshal(InputStream) -
Static method in class org.genepattern.webservice.jaxb.task.TASK
-
- unmarshal(XMLScanner) -
Static method in class org.genepattern.webservice.jaxb.task.TASK
-
- unmarshal(XMLScanner, Dispatcher) -
Static method in class org.genepattern.webservice.jaxb.task.TASK
-
V
- VERSION -
Static variable in interface org.genepattern.util.IGPConstants
- TaskInfoAttributes version key
- VERSION_DELIMITER -
Static variable in class org.genepattern.util.LSID
-
- Version - class org.genepattern.util.Version.
-
- Version(String, int, int, int, Calendar, long) -
Constructor for class org.genepattern.util.Version
- Creates a new instance of Version
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- validate(Validator) -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.job.ANALYSISJOBINFO
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.job.JOB
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.parameter.ANALYSISPARAMETERS
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.parameter.ATTRIBUTE
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.parameter.PARAMETER
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.task.ANALYSISTASKINFO
-
- validateThis() -
Method in class org.genepattern.webservice.jaxb.task.TASK
-
- value -
Variable in class org.genepattern.io.OdfObject.Entry
-
W
- WebService - interface org.genepattern.webservice.WebService.
- Defines methods that all Web Services must implement.
- WebServiceErrorMessageException - exception org.genepattern.webservice.WebServiceErrorMessageException.
-
- WebServiceErrorMessageException(Vector) -
Constructor for class org.genepattern.webservice.WebServiceErrorMessageException
-
- WebServiceException - exception org.genepattern.webservice.WebServiceException.
- Defines a general exception a web service can throw when it encounters
problems.
- WebServiceException() -
Constructor for class org.genepattern.webservice.WebServiceException
- Constructs a new web service exeption.
- WebServiceException(String) -
Constructor for class org.genepattern.webservice.WebServiceException
- Constructs a new web service exeption with the specified message.
- WebServiceException(String, Throwable) -
Constructor for class org.genepattern.webservice.WebServiceException
- Constructs a new web service exeption when the service needs to throw an
exeption and include a message about the "root cause" exception.
- WebServiceException(Throwable) -
Constructor for class org.genepattern.webservice.WebServiceException
- Constructs a new web service exeption when the service needs to throw an
exeption and include a message about the "root cause" exception.
- write(IExpressionData, String, String, boolean) -
Static method in class org.genepattern.io.IOUtil
- Writes expression data to a file in the given format.
- write(IExpressionData, OutputStream) -
Method in interface org.genepattern.io.expr.IExpressionDataWriter
- Writes an
IExpressionData instance to a stream.
- write(ClassVector, OutputStream) -
Method in class org.genepattern.io.expr.cls.ClsWriter
- Writes an
ClassVector instance to a file.
- write(IExpressionData, OutputStream) -
Method in class org.genepattern.io.expr.gct.GctWriter
-
- write(IExpressionData, OutputStream) -
Method in class org.genepattern.io.expr.mage.MAGEMLWriter
-
- write(IExpressionData, OutputStream) -
Method in class org.genepattern.io.expr.odf.OdfDatasetWriter
-
- write(IExpressionData, OutputStream) -
Method in class org.genepattern.io.expr.res.ResWriter
-
- write(IExpressionData, OutputStream) -
Method in class org.genepattern.io.expr.stanford.StanfordTxtWriter
-
- writeCls(ClassVector, String, boolean) -
Static method in class org.genepattern.io.IOUtil
- Writes the given class vector to a file
- writeFeatureList(String[], String) -
Static method in class org.genepattern.io.IOUtil
- Writes the given feature list to a file
X
- xmlDecode(String) -
Static method in class org.genepattern.data.pipeline.PipelineModel
-
- xmlEncode(String) -
Method in class org.genepattern.data.pipeline.PipelineModel
-
A B C D E F G H I J K L M N O P Q R S T U V W X
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