com.pacbio.secondary.vis.data.session

Class DataStorageBase

java.lang.Object

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

Direct Known Subclasses:

DataStorage

public class DataStorageBase
extends java.lang.Object

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected VioletApp	app
protected boolean	basemods_enabled
protected boolean	cdna_enabled
protected boolean	data_loaded
protected DeNovoSummaryStorage	denovo_summary
protected EpiProReadsReader	epipro_reads_data
protected EpiProPalette	epipro_reads_palette
protected GeneDB	gene_db
protected IdeogramDB	ideogram_db
protected java.lang.String	job_title
protected MotifsDB	motifs_db
protected boolean	multisample_enabled
protected ReferenceInfo	reference_info
protected java.util.Vector<VariableResolutionDataSet>	slots_datasets
protected TracksDataInfoList	tracks_info

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	DataStorageBase(VioletApp app)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getDataTitle()
DeNovoSummaryStorage	getDeNovoSummary()
EpiProReadsReader	getEpiProReadsDataModel()
EpiProPalette	getEpiProReadsPalette()
GeneDB	getGeneDB()
IdeogramDB	getIdeogramDB()
MotifsDB	getMotifsDB()
int	getNumContigs()
java.lang.String	getReadsDataPath()
ReferenceInfo	getReferenceInfo()
java.util.Vector<VariableResolutionDataSet>	getSlotsDatasets()
TracksDataInfoList	getTracksInfoList()
boolean	hasModificationsFile() returns true if file list has base mods file use to default base mods specific user options
boolean	hasMotifsFile() returns true if file list has motifs file use to classify or not base mods
boolean	isCDNADataAvailable() returns true if there is trace of gmap todo: should read from cmp.h5
boolean	isDataLoaded()
boolean	isEpiProReadsDataAvailable() returns true if we have an unmapped reads file around
boolean	isIPDConsensusDataAvailable() returns true if we have a modifications.gff file around todo: should read from cmp.h5
boolean	isMultisampleDataAvailable() returns true if we have a multisample .vcf file around
protected static boolean	isReadsFile(java.lang.String filename)
boolean	isReferenceSequenceFileInfo()
protected boolean	localCreateIdeogramAndGenesDB() Deprecated.
boolean	localLoadReferenceInfo(java.lang.String reference_file)
boolean	readSpecialFiles()
void	setEpiProReadsDataModel(EpiProReadsReader model)
void	setEpiProReadsPalette(EpiProPalette palette)
void	setIsCDNADataAvailable()
void	setIsIPDConsensusDataAvailable()
void	setMultisampleDataAvailable()
void	setSlotsDatasets(java.util.Vector<VariableResolutionDataSet> slots)
void	updateTracksListAfterRemovingSlot(java.lang.String trackinfo_to_remove) Called after user removes a track, updates trackslist and tracks indexes in remaining slots

Methods inherited from class java.lang.Object

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

Field Detail

data_loaded

protected transient boolean data_loaded

basemods_enabled

protected transient boolean basemods_enabled

cdna_enabled

protected transient boolean cdna_enabled

multisample_enabled

protected transient boolean multisample_enabled

epipro_reads_data

protected transient EpiProReadsReader epipro_reads_data

epipro_reads_palette

protected transient EpiProPalette epipro_reads_palette

reference_info

protected ReferenceInfo reference_info

tracks_info

protected TracksDataInfoList tracks_info

denovo_summary

protected DeNovoSummaryStorage denovo_summary

slots_datasets

protected java.util.Vector<VariableResolutionDataSet> slots_datasets

job_title

protected java.lang.String job_title

app

protected VioletApp app

ideogram_db

protected IdeogramDB ideogram_db

gene_db

protected GeneDB gene_db

motifs_db

protected MotifsDB motifs_db

Constructor Detail

DataStorageBase

protected DataStorageBase(VioletApp app)

Parameters:

app -

Method Detail

getSlotsDatasets

public java.util.Vector<VariableResolutionDataSet> getSlotsDatasets()

getGeneDB

public GeneDB getGeneDB()

getMotifsDB

public MotifsDB getMotifsDB()

getIdeogramDB

public IdeogramDB getIdeogramDB()

getNumContigs

public int getNumContigs()

isDataLoaded

public boolean isDataLoaded()

getReferenceInfo

public ReferenceInfo getReferenceInfo()

getDeNovoSummary

public DeNovoSummaryStorage getDeNovoSummary()

getTracksInfoList

public TracksDataInfoList getTracksInfoList()

hasMotifsFile

public boolean hasMotifsFile()

returns true if file list has motifs file use to classify or not base mods

hasModificationsFile

public boolean hasModificationsFile()

returns true if file list has base mods file use to default base mods specific user options

isIPDConsensusDataAvailable

public boolean isIPDConsensusDataAvailable()

returns true if we have a modifications.gff file around todo: should read from cmp.h5

Returns:

setIsIPDConsensusDataAvailable

public void setIsIPDConsensusDataAvailable()

isCDNADataAvailable

public boolean isCDNADataAvailable()

returns true if there is trace of gmap todo: should read from cmp.h5

Returns:

setIsCDNADataAvailable

public void setIsCDNADataAvailable()

isMultisampleDataAvailable

public boolean isMultisampleDataAvailable()

returns true if we have a multisample .vcf file around

Returns:

setMultisampleDataAvailable

public void setMultisampleDataAvailable()

isEpiProReadsDataAvailable

public boolean isEpiProReadsDataAvailable()

returns true if we have an unmapped reads file around

Returns:

getEpiProReadsDataModel

public EpiProReadsReader getEpiProReadsDataModel()

setEpiProReadsDataModel

public void setEpiProReadsDataModel(EpiProReadsReader model)

getEpiProReadsPalette

public EpiProPalette getEpiProReadsPalette()

setEpiProReadsPalette

public void setEpiProReadsPalette(EpiProPalette palette)

isReferenceSequenceFileInfo

public boolean isReferenceSequenceFileInfo()

setSlotsDatasets

public void setSlotsDatasets(java.util.Vector<VariableResolutionDataSet> slots)

getDataTitle

public java.lang.String getDataTitle()

Returns:

title for the data if available

getReadsDataPath

public java.lang.String getReadsDataPath()

isReadsFile

protected static boolean isReadsFile(java.lang.String filename)

readSpecialFiles

public boolean readSpecialFiles()

Returns:

updateTracksListAfterRemovingSlot

public void updateTracksListAfterRemovingSlot(java.lang.String trackinfo_to_remove)

Called after user removes a track, updates trackslist and tracks indexes in remaining slots

Parameters:

trackinfo_to_remove - path of file from removed slot

localLoadReferenceInfo

public boolean localLoadReferenceInfo(java.lang.String reference_file)

localCreateIdeogramAndGenesDB

@Deprecated
protected boolean localCreateIdeogramAndGenesDB()

Deprecated.

not used

Returns: