Overview  Package   Class  Tree  Deprecated  Index  Help 
 PREV CLASS   NEXT CLASS FRAMES    NO FRAMES    
SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

org.genepattern.data.pipeline
Class PipelineModel

java.lang.Object
  extended byorg.genepattern.data.pipeline.PipelineModel
All Implemented Interfaces:
java.io.Serializable
public class PipelineModel
extends java.lang.Object
implements java.io.Serializable

See Also:
Serialized Form

Field Summary
static java.lang.String DESC
           
static java.lang.String INHERIT_FILENAME
           
static java.lang.String INHERIT_TASKNAME
           
static java.lang.String PIPELINE_MODEL
           
static java.lang.String RUNTIME_PARAM
           
 
Constructor Summary
PipelineModel()
           
 
Method Summary
 void addInputParameter(java.lang.String name, ParameterInfo p)
          Adds a runtime prompt parameter
 void addTask(JobSubmission jobSubmission)
           
 void addTask(JobSubmission jobSubmission, int slot)
           
static PipelineModel deserialize(java.lang.String serializedModel)
           
 java.lang.String getAuthor()
           
 java.lang.String getDescription()
           
 java.util.TreeMap getInputParameters()
          Gets a map that maps the parameter name as a String to a ParameterInfo object
 java.lang.String getLsid()
           
 java.util.Map getLsidDependencies()
           
 java.lang.String getName()
           
 JobSubmission getTask(int index)
          Gets the JobSubmission at the given index
 java.util.Vector getTasks()
           
 java.lang.String getUserid()
           
 java.lang.String getUserID()
           
 java.lang.String getVersion()
           
 void init()
           
 boolean isPrivate()
           
 java.lang.String serialize()
           
 void setAuthor(java.lang.String author)
           
 void setDescription(java.lang.String description)
           
 void setLsid(java.lang.String lsid)
           
 void setName(java.lang.String name)
           
 void setPrivacy(boolean privacy)
           
 void setPrivacy(java.lang.String privacy)
           
 void setUserid(java.lang.String userID)
           
 void setUserID(java.lang.String userID)
           
 void setVersion(java.lang.String version)
           
static PipelineModel toPipelineModel(org.xml.sax.InputSource inputXMLSource, boolean verify)
           
static PipelineModel toPipelineModel(java.lang.String inputXML)
           
static PipelineModel toPipelineModel(java.lang.String inputXML, boolean verify)
           
 java.lang.String toString()
           
 java.lang.String toXML()
           
static java.lang.String xmlDecode(java.lang.String what)
           
 java.lang.String xmlEncode(java.lang.String what)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

INHERIT_TASKNAME

public static final java.lang.String INHERIT_TASKNAME
See Also:
Constant Field Values

INHERIT_FILENAME

public static final java.lang.String INHERIT_FILENAME
See Also:
Constant Field Values

RUNTIME_PARAM

public static final java.lang.String RUNTIME_PARAM
See Also:
Constant Field Values

DESC

public static final java.lang.String DESC
See Also:
Constant Field Values

PIPELINE_MODEL

public static final java.lang.String PIPELINE_MODEL
See Also:
Constant Field Values
Constructor Detail

PipelineModel

public PipelineModel()
Method Detail

init

public void init()

getTask

public JobSubmission getTask(int index)
Gets the JobSubmission at the given index

Parameters:
index - The index of the task to get
Returns:
The JobSubmission at the given index
See Also:
getTasks

getTasks

public java.util.Vector getTasks()

getInputParameters

public java.util.TreeMap getInputParameters()
Gets a map that maps the parameter name as a String to a ParameterInfo object

Returns:
a map of runtime prompt parameters
See Also:
addInputParameter

addInputParameter

public void addInputParameter(java.lang.String name,
                              ParameterInfo p)
Adds a runtime prompt parameter

Parameters:
name - The parameter name. The name should be the task name + task number + . + parameter name. The name of the ParameterInfo object should NOT include the task name + task number prefix. It should have the parameter info attribute runTimePrompt set to 1. Additionally, the ParameterInfo should have the description and value fields set to the empty string.
p - The parameter

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

isPrivate

public boolean isPrivate()

setPrivacy

public void setPrivacy(boolean privacy)

setPrivacy

public void setPrivacy(java.lang.String privacy)

getDescription

public java.lang.String getDescription()

setDescription

public void setDescription(java.lang.String description)

getAuthor

public java.lang.String getAuthor()

setAuthor

public void setAuthor(java.lang.String author)

getUserID

public java.lang.String getUserID()

getUserid

public java.lang.String getUserid()

getVersion

public java.lang.String getVersion()

setUserID

public void setUserID(java.lang.String userID)

setUserid

public void setUserid(java.lang.String userID)

setVersion

public void setVersion(java.lang.String version)

getLsid

public java.lang.String getLsid()

setLsid

public void setLsid(java.lang.String lsid)

addTask

public void addTask(JobSubmission jobSubmission)

addTask

public void addTask(JobSubmission jobSubmission,
                    int slot)

serialize

public java.lang.String serialize()
                           throws java.io.IOException
Throws:
java.io.IOException

deserialize

public static PipelineModel deserialize(java.lang.String serializedModel)
                                 throws java.io.IOException,
                                        java.lang.ClassNotFoundException
Throws:
java.io.IOException
java.lang.ClassNotFoundException

xmlEncode

public java.lang.String xmlEncode(java.lang.String what)

xmlDecode

public static java.lang.String xmlDecode(java.lang.String what)

toXML

public java.lang.String toXML()

toPipelineModel

public static PipelineModel toPipelineModel(java.lang.String inputXML)
                                     throws java.io.IOException,
                                            org.xml.sax.SAXException,
                                            javax.xml.parsers.ParserConfigurationException,
                                            java.lang.IllegalArgumentException,
                                            java.lang.IllegalAccessException,
                                            java.lang.reflect.InvocationTargetException,
                                            java.lang.NoSuchMethodException,
                                            java.lang.SecurityException,
                                            OmnigeneException,
                                            java.lang.Exception
Throws:
java.io.IOException
org.xml.sax.SAXException
javax.xml.parsers.ParserConfigurationException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.reflect.InvocationTargetException
java.lang.NoSuchMethodException
java.lang.SecurityException
OmnigeneException
java.lang.Exception

toPipelineModel

public static PipelineModel toPipelineModel(java.lang.String inputXML,
                                            boolean verify)
                                     throws java.io.IOException,
                                            org.xml.sax.SAXException,
                                            javax.xml.parsers.ParserConfigurationException,
                                            java.lang.IllegalArgumentException,
                                            java.lang.IllegalAccessException,
                                            java.lang.reflect.InvocationTargetException,
                                            java.lang.NoSuchMethodException,
                                            java.lang.SecurityException,
                                            OmnigeneException,
                                            java.lang.Exception
Throws:
java.io.IOException
org.xml.sax.SAXException
javax.xml.parsers.ParserConfigurationException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.reflect.InvocationTargetException
java.lang.NoSuchMethodException
java.lang.SecurityException
OmnigeneException
java.lang.Exception

toPipelineModel

public static PipelineModel toPipelineModel(org.xml.sax.InputSource inputXMLSource,
                                            boolean verify)
                                     throws java.io.IOException,
                                            org.xml.sax.SAXException,
                                            javax.xml.parsers.ParserConfigurationException,
                                            java.lang.IllegalArgumentException,
                                            java.lang.IllegalAccessException,
                                            java.lang.reflect.InvocationTargetException,
                                            java.lang.NoSuchMethodException,
                                            java.lang.SecurityException,
                                            OmnigeneException,
                                            java.lang.Exception
Throws:
java.io.IOException
org.xml.sax.SAXException
javax.xml.parsers.ParserConfigurationException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.reflect.InvocationTargetException
java.lang.NoSuchMethodException
java.lang.SecurityException
OmnigeneException
java.lang.Exception

getLsidDependencies

public java.util.Map getLsidDependencies()

toString

public java.lang.String toString()
Overview  Package   Class  Tree  Deprecated  Index  Help 
 PREV CLASS   NEXT CLASS FRAMES    NO FRAMES    
SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD
Hosted by docs.bugaco.com