apollo.main
Class DataLoader

java.lang.Object
  apollo.main.DataLoader

public class DataLoader
extends java.lang.Object

This class handles loading of data into Apollo. used by Apollo and LoadUtil Keeps instance of CompositeDataHolder that it creates, used to get sequence from (should probably have cdh passed in for getSeq) should probably make singleton maybe this belongs in apollo.dataadapter?

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

DataLoader()

Method Summary

void	addToCurationSet() Layer data onto curationset (if multi species active species cur set)
CompositeDataHolder	getCompositeDataHolder(CommandLine commandLine)
CompositeDataHolder	getCompositeDataHolder(java.util.Properties props, org.bdgp.util.ProgressListener listener) Load data using props.
CompositeDataHolder	getCompositeDataHolder(java.lang.String[] args, org.bdgp.util.ProgressListener listener) String[0] in the args tells which data adapter to use: -g GFF, -x GAME, -b backup (serial), -gb GenBank/EMBL followed by the filename e.g., apollo -x data/example.xml quitOnCancel is false
ApolloDataAdapterI	getDataAdapter()
void	getSequence(CompositeDataHolder compositeDataHolder) This should have the simgle species cdh or cur set passed in
boolean	putCurationSet(ApolloDataAdapterI datasource, CurationSet curation_set)
boolean	saveCompositeDataHolder(ApolloDataAdapterI datasource, CompositeDataHolder cdh)
void	saveFileDialog(ApolloDataI apolloData)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

DataLoader

public DataLoader()

Method Detail

getCompositeDataHolder

public CompositeDataHolder getCompositeDataHolder(java.util.Properties props,
                                                  org.bdgp.util.ProgressListener listener)
                                           throws ApolloAdapterException

Load data using props. gets dataadapter from configs adapter registry using props adapter property, sets data adapters state information and region with props and calls getData

Throws:

ApolloAdapterException

getCompositeDataHolder

public CompositeDataHolder getCompositeDataHolder(java.lang.String[] args,
                                                  org.bdgp.util.ProgressListener listener)
                                           throws ApolloAdapterException

String[0] in the args tells which data adapter to use: -g GFF, -x GAME, -b backup (serial), -gb GenBank/EMBL followed by the filename e.g., apollo -x data/example.xml quitOnCancel is false

Throws:

ApolloAdapterException

getCompositeDataHolder

public CompositeDataHolder getCompositeDataHolder(CommandLine commandLine)
                                           throws ApolloAdapterException

Throws:

ApolloAdapterException

putCurationSet

public boolean putCurationSet(ApolloDataAdapterI datasource,
                              CurationSet curation_set)

saveCompositeDataHolder

public boolean saveCompositeDataHolder(ApolloDataAdapterI datasource,
                                       CompositeDataHolder cdh)

getSequence

public void getSequence(CompositeDataHolder compositeDataHolder)
                 throws ApolloAdapterException

This should have the simgle species cdh or cur set passed in

Throws:

ApolloAdapterException

getDataAdapter

public ApolloDataAdapterI getDataAdapter()

addToCurationSet

public void addToCurationSet()
                      throws ApolloAdapterException

Layer data onto curationset (if multi species active species cur set)

Throws:

ApolloAdapterException

saveFileDialog

public void saveFileDialog(ApolloDataI apolloData)