com.pacbio.secondary.vis.data.session

Class DataStorage

java.lang.Object

com.pacbio.secondary.vis.data.session.DataStorageBase

com.pacbio.secondary.vis.data.session.DataStorage

public class DataStorage
extends DataStorageBase

Author:

mmilletti

Field Summary

Fields inherited from class com.pacbio.secondary.vis.data.session.DataStorageBase

app, basemods_enabled, cdna_enabled, data_loaded, denovo_summary, epipro_reads_data, epipro_reads_palette, gene_db, ideogram_db, job_title, motifs_db, multisample_enabled, reference_info, slots_datasets, tracks_info

Constructor Summary

Constructors

Constructor and Description
DataStorage(VioletApp app)

Method Summary

Methods

Modifier and Type	Method and Description
void	addDataSetFromModelToSlots(VariableResolutionDataModel model)
boolean	createFilesListFromDataInfo(ProgressDialog progress)
int	createFilesListFromJobMetaDataInfo(ProgressDialog progress, CommandLineOptions cmd_line_options)
boolean	getAsyncIPDConsensusFromServer(GenomicViewDetailsData view, int contig_index, long start, long end)
boolean	getConsensusSequenceFromServer(GenomicViewDetailsData view, int contig_index, long start, long end)
int	getNumTracks()
boolean	getReferenceSequenceFromServer(GenomicViewDetailsData view, int contig_index, long start, long end)
boolean	getRemoteDataOnFirstTime()
void	getResultsForDetailsView(int contig, long start, long end, boolean updateData)
boolean	getSyncIPDConsensusFromServer(GenomicViewDetailsData view, int contig_index, long start, long end)
boolean	getTrackFromServer(TrackDataInfo info, int contig)
boolean	loadReferenceInfo(ProgressDialog progress, CommandLineOptions options)
boolean	parseTemplateInfo(ProgressDialog progress)
boolean	parseTracksInfo(java.lang.String tracks)
void	postRequestToUpdateApplicationFrame()
void	postRequestToUpdateDetailsView()
void	postRequestToUpdateGenomicTableDetails()
boolean	readMotifSummaryFile() reads from motif_summary.csv file
protected void	safeUpdateApplicationFrame()
protected void	safeUpdateDetailsView()
protected void	safeUpdateGenomicTablePanel(boolean bDetails)
protected boolean	serverCreateIdeogramAndGenesDB(ProgressDialog progress, VisServiceWrapper service)
protected boolean	serverLoadReferenceInfo(ProgressDialog progress, java.lang.String reference_file)

Methods inherited from class com.pacbio.secondary.vis.data.session.DataStorageBase

getDataTitle, getDeNovoSummary, getEpiProReadsDataModel, getEpiProReadsPalette, getGeneDB, getIdeogramDB, getMotifsDB, getNumContigs, getReadsDataPath, getReferenceInfo, getSlotsDatasets, getTracksInfoList, hasModificationsFile, hasMotifsFile, isCDNADataAvailable, isDataLoaded, isEpiProReadsDataAvailable, isIPDConsensusDataAvailable, isMultisampleDataAvailable, isReadsFile, isReferenceSequenceFileInfo, localCreateIdeogramAndGenesDB, localLoadReferenceInfo, readSpecialFiles, setEpiProReadsDataModel, setEpiProReadsPalette, setIsCDNADataAvailable, setIsIPDConsensusDataAvailable, setMultisampleDataAvailable, setSlotsDatasets, updateTracksListAfterRemovingSlot

Methods inherited from class java.lang.Object

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

Constructor Detail

DataStorage

public DataStorage(VioletApp app)

Method Detail

getRemoteDataOnFirstTime

public boolean getRemoteDataOnFirstTime()

getTrackFromServer

public boolean getTrackFromServer(TrackDataInfo info,
                         int contig)

addDataSetFromModelToSlots

public void addDataSetFromModelToSlots(VariableResolutionDataModel model)

getNumTracks

public int getNumTracks()

postRequestToUpdateApplicationFrame

public void postRequestToUpdateApplicationFrame()

safeUpdateApplicationFrame

protected void safeUpdateApplicationFrame()

postRequestToUpdateDetailsView

public void postRequestToUpdateDetailsView()

safeUpdateDetailsView

protected void safeUpdateDetailsView()

postRequestToUpdateGenomicTableDetails

public void postRequestToUpdateGenomicTableDetails()

safeUpdateGenomicTablePanel

protected void safeUpdateGenomicTablePanel(boolean bDetails)

getReferenceSequenceFromServer

public boolean getReferenceSequenceFromServer(GenomicViewDetailsData view,
                                     int contig_index,
                                     long start,
                                     long end)

getConsensusSequenceFromServer

public boolean getConsensusSequenceFromServer(GenomicViewDetailsData view,
                                     int contig_index,
                                     long start,
                                     long end)

getAsyncIPDConsensusFromServer

public boolean getAsyncIPDConsensusFromServer(GenomicViewDetailsData view,
                                     int contig_index,
                                     long start,
                                     long end)

getSyncIPDConsensusFromServer

public boolean getSyncIPDConsensusFromServer(GenomicViewDetailsData view,
                                    int contig_index,
                                    long start,
                                    long end)

getResultsForDetailsView

public void getResultsForDetailsView(int contig,
                            long start,
                            long end,
                            boolean updateData)

loadReferenceInfo

public boolean loadReferenceInfo(ProgressDialog progress,
                        CommandLineOptions options)

serverLoadReferenceInfo

protected boolean serverLoadReferenceInfo(ProgressDialog progress,
                              java.lang.String reference_file)

serverCreateIdeogramAndGenesDB

protected boolean serverCreateIdeogramAndGenesDB(ProgressDialog progress,
                                     VisServiceWrapper service)

parseTemplateInfo

public boolean parseTemplateInfo(ProgressDialog progress)

parseTracksInfo

public boolean parseTracksInfo(java.lang.String tracks)

createFilesListFromDataInfo

public boolean createFilesListFromDataInfo(ProgressDialog progress)

createFilesListFromJobMetaDataInfo

public int createFilesListFromJobMetaDataInfo(ProgressDialog progress,
                                     CommandLineOptions cmd_line_options)

readMotifSummaryFile

public boolean readMotifSummaryFile()

reads from motif_summary.csv file

Returns: