com.pacbio.secondary.vis.io.importer

Class ImportDataHelper

java.lang.Object

com.pacbio.secondary.vis.io.importer.ImportDataHelper

public class ImportDataHelper
extends java.lang.Object

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected VioletApp	app

Constructor Summary

Constructors

Constructor and Description
ImportDataHelper(VioletApp app) constructor

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addImportedFileInfo(java.io.File file, DataFileInfo.eFileType type)
protected void	doFullUIUpdate()
boolean	doLoadDataInBackgroundFromInputStream(java.io.InputStream input_stream, TrackDataInfo track_info)
boolean	doLoadDataInteractivelyFromFile(java.io.File file)
protected VioletFrame	getMainFrame()
protected boolean	importCommonFileTypesFromReader(DataFileInfo.eFileType file_type, java.io.Reader reader, java.lang.String file_name) reads file types common to interactive and bkg loading
protected boolean	importEpiProReadsFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importGFF3FileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importHTMLDocument(java.io.File file)
protected boolean	importModificationsGFFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importMultiSampleVCFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importNCBIGeneDB(java.io.Reader reader, java.lang.String file_name)
protected boolean	importSummaryGFFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importUCSCGTFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importVariantsGFFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importVCFFileFromReader(java.io.Reader reader, java.lang.String file_name)
protected boolean	importVioletHDFReadsFile(java.io.File file)
protected boolean	safeAddModelToSlots(VariableResolutionDataModel model)

Methods inherited from class java.lang.Object

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

Field Detail

app

protected VioletApp app

Constructor Detail

ImportDataHelper

public ImportDataHelper(VioletApp app)

constructor

Parameters:

app -

Method Detail

doLoadDataInBackgroundFromInputStream

public boolean doLoadDataInBackgroundFromInputStream(java.io.InputStream input_stream,
                                            TrackDataInfo track_info)

doLoadDataInteractivelyFromFile

public boolean doLoadDataInteractivelyFromFile(java.io.File file)

importCommonFileTypesFromReader

protected boolean importCommonFileTypesFromReader(DataFileInfo.eFileType file_type,
                                      java.io.Reader reader,
                                      java.lang.String file_name)
                                           throws FileFormatException,
                                                  java.io.IOException

reads file types common to interactive and bkg loading

Parameters:

file_type -

reader -

file_name -

Returns:

Throws:

FileFormatException

java.io.IOException

importUCSCGTFFileFromReader

protected boolean importUCSCGTFFileFromReader(java.io.Reader reader,
                                  java.lang.String file_name)
                                       throws FileFormatException,
                                              java.io.IOException

Throws:

FileFormatException

java.io.IOException

importGFF3FileFromReader

protected boolean importGFF3FileFromReader(java.io.Reader reader,
                               java.lang.String file_name)
                                    throws FileFormatException,
                                           java.io.IOException

Throws:

FileFormatException

java.io.IOException

importVCFFileFromReader

protected boolean importVCFFileFromReader(java.io.Reader reader,
                              java.lang.String file_name)
                                   throws FileFormatException,
                                          java.io.IOException

Throws:

FileFormatException

java.io.IOException

importSummaryGFFFileFromReader

protected boolean importSummaryGFFFileFromReader(java.io.Reader reader,
                                     java.lang.String file_name)
                                          throws FileFormatException,
                                                 java.io.IOException

Throws:

FileFormatException

java.io.IOException

importVariantsGFFFileFromReader

protected boolean importVariantsGFFFileFromReader(java.io.Reader reader,
                                      java.lang.String file_name)
                                           throws FileFormatException,
                                                  java.io.IOException

Throws:

FileFormatException

java.io.IOException

importMultiSampleVCFFileFromReader

protected boolean importMultiSampleVCFFileFromReader(java.io.Reader reader,
                                         java.lang.String file_name)
                                              throws FileFormatException,
                                                     java.io.IOException

Throws:

FileFormatException

java.io.IOException

importModificationsGFFFileFromReader

protected boolean importModificationsGFFFileFromReader(java.io.Reader reader,
                                           java.lang.String file_name)
                                                throws FileFormatException,
                                                       java.io.IOException

Throws:

FileFormatException

java.io.IOException

importNCBIGeneDB

protected boolean importNCBIGeneDB(java.io.Reader reader,
                       java.lang.String file_name)

importHTMLDocument

protected boolean importHTMLDocument(java.io.File file)

importVioletHDFReadsFile

protected boolean importVioletHDFReadsFile(java.io.File file)
                                    throws FileFormatException,
                                           java.io.IOException

Throws:

FileFormatException

java.io.IOException

importEpiProReadsFileFromReader

protected boolean importEpiProReadsFileFromReader(java.io.Reader reader,
                                      java.lang.String file_name)
                                           throws FileFormatException,
                                                  java.io.IOException

Throws:

FileFormatException

java.io.IOException

safeAddModelToSlots

protected boolean safeAddModelToSlots(VariableResolutionDataModel model)

addImportedFileInfo

protected void addImportedFileInfo(java.io.File file,
                       DataFileInfo.eFileType type)

doFullUIUpdate

protected void doFullUIUpdate()

getMainFrame

protected VioletFrame getMainFrame()