com.pacbio.secondary.vis.io.export

Class ExportDataUtils

java.lang.Object

com.pacbio.secondary.vis.io.export.ExportDataUtils

public class ExportDataUtils
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected VioletApp	main_app

Constructor Summary

Constructors

Constructor and Description
ExportDataUtils(VioletApp app)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	exportCMPH5DataToGFF(DetailsStorage data, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
void	exportDataAsGFF()
protected void	exportGenericMarker(Marker marker, java.io.FileWriter writer, java.lang.String contig_name, int track_index)
protected void	exportGenericMarkerTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	exportModification(Marker marker, java.io.FileWriter writer, java.lang.String contig_name, int track_index)
protected void	exportModificationsTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	exportRead(Marker marker, java.io.FileWriter writer, java.lang.String contig_name, int track_index)
protected void	exportTableAsGFF(VioletApp app, java.lang.String path) exports table view as gff
protected void	exportVariant(Marker marker, java.io.FileWriter writer, java.lang.String contig_name, int track_index)
protected void	exportVariantsTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index) coverage=4;length=1;reference=T
protected void	exportViewAsGFF(VioletApp app, java.lang.String path, boolean isDetails) exports region or details view as gff
protected java.lang.String	getDefaultDataFilename(int mode)

Methods inherited from class java.lang.Object

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

Field Detail

main_app

protected VioletApp main_app

Constructor Detail

ExportDataUtils

public ExportDataUtils(VioletApp app)

Parameters:

app -

Method Detail

exportDataAsGFF

public void exportDataAsGFF()

exportViewAsGFF

protected void exportViewAsGFF(VioletApp app,
                   java.lang.String path,
                   boolean isDetails)

exports region or details view as gff

Parameters:

app -

path -

isDetails -

exportTableAsGFF

protected void exportTableAsGFF(VioletApp app,
                    java.lang.String path)

exports table view as gff

Parameters:

app -

path -

isDetails -

exportModificationsTrack

protected void exportModificationsTrack(MarkerCollection markers,
                            java.io.FileWriter writer,
                            java.lang.String contig_name,
                            Interval curr_interval,
                            int track_index)

Parameters:

markers -

writer -

Throws:

java.io.IOException

exportModification

protected void exportModification(Marker marker,
                      java.io.FileWriter writer,
                      java.lang.String contig_name,
                      int track_index)

exportRead

protected void exportRead(Marker marker,
              java.io.FileWriter writer,
              java.lang.String contig_name,
              int track_index)

exportGenericMarkerTrack

protected void exportGenericMarkerTrack(MarkerCollection markers,
                            java.io.FileWriter writer,
                            java.lang.String contig_name,
                            Interval curr_interval,
                            int track_index)

Parameters:

markers -

writer -

Throws:

java.io.IOException

exportGenericMarker

protected void exportGenericMarker(Marker marker,
                       java.io.FileWriter writer,
                       java.lang.String contig_name,
                       int track_index)

exportVariantsTrack

protected void exportVariantsTrack(MarkerCollection markers,
                       java.io.FileWriter writer,
                       java.lang.String contig_name,
                       Interval curr_interval,
                       int track_index)

coverage=4;length=1;reference=T

Parameters:

markers -

writer -

Throws:

java.io.IOException

exportVariant

protected void exportVariant(Marker marker,
                 java.io.FileWriter writer,
                 java.lang.String contig_name,
                 int track_index)

exportCMPH5DataToGFF

protected void exportCMPH5DataToGFF(DetailsStorage data,
                        java.io.FileWriter writer,
                        java.lang.String contig_name,
                        Interval curr_interval,
                        int track_index)
                             throws java.io.IOException

Throws:

java.io.IOException

getDefaultDataFilename

protected java.lang.String getDefaultDataFilename(int mode)