com.pacbio.secondary.vis.io.export

Class ExportRegionAsGFF

java.lang.Object

com.pacbio.secondary.vis.io.export.ExportRegionAsGFF

public class ExportRegionAsGFF
extends java.lang.Object

Author:

Marco Milletti

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	size_disk_buffer

Constructor Summary

Constructors

Constructor and Description
ExportRegionAsGFF()

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)
protected void	exportDetailsAsGFF(VioletApp app, java.lang.String path)
void	exportDetailsViewDataAsGFF(VioletApp app)
protected void	exportGenericMarkerTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, 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
java.lang.String	getDefaultDataFilename(VioletApp app)

Methods inherited from class java.lang.Object

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

Field Detail

size_disk_buffer

protected static final int size_disk_buffer

See Also:

Constant Field Values

Constructor Detail

ExportRegionAsGFF

public ExportRegionAsGFF()

Method Detail

getDefaultDataFilename

public java.lang.String getDefaultDataFilename(VioletApp app)

exportDetailsViewDataAsGFF

public void exportDetailsViewDataAsGFF(VioletApp app)

exportDetailsAsGFF

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

exportGenericMarkerTrack

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

Parameters:

markers -

writer -

Throws:

java.io.IOException

exportVariantsTrack

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

coverage=4;length=1;reference=T

Parameters:

markers -

writer -

Throws:

java.io.IOException

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