com.pacbio.secondary.vis.svc.server.hdf

Class GenomicDataStructures

java.lang.Object

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

Direct Known Subclasses:

GenomicDataAssembler

public class GenomicDataStructures
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	GenomicDataStructures.WsReadStructure Inner helper class for sorting structured reads

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	BASE_DELETION
protected static int	BASE_LEFT_INSERTION
protected static int	BASE_MATCH
protected static int	BASE_POS_INSERTION
protected static int	BASE_RIGHT_INSERTION
protected static int	BASE_SVN

Constructor Summary

Constructors

Constructor and Description
GenomicDataStructures()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String	buildStats(int client_contig_index, long start, int length)
protected void	createFromRawRead(WsRead aligned_read, RawRead read_data, float metrics_factor, int mode) must report right or left insertion...
protected void	createFromRawReadWithInsertions(WsRead aligned_read, RawRead read_data, float metrics_factor, int mode, long start_from) report insertion at position...
protected void	reverse(byte[] array) Reverses the order of the given array.
protected void	reverse(float[] array) Reverses the order of the given array.
protected void	reverse(short[] array) Reverses the order of the given array.
protected void	reverseRawRead(RawRead read_data) handles reverse strand data
protected void	setQVValue(WsRead aligned_read, RawRead read_data, int raw_base_index, int annotated_base_index, float metrics_factor)
protected void	updateMetricsFromRawRead(WsRead aligned_read, RawRead read_data, float metrics_factor) must report right or left insertion...

Methods inherited from class java.lang.Object

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

Field Detail

BASE_MATCH

protected static final int BASE_MATCH

See Also:

Constant Field Values

BASE_DELETION

protected static final int BASE_DELETION

See Also:

Constant Field Values

BASE_SVN

protected static final int BASE_SVN

See Also:

Constant Field Values

BASE_RIGHT_INSERTION

protected static final int BASE_RIGHT_INSERTION

See Also:

Constant Field Values

BASE_LEFT_INSERTION

protected static final int BASE_LEFT_INSERTION

See Also:

Constant Field Values

BASE_POS_INSERTION

protected static final int BASE_POS_INSERTION

See Also:

Constant Field Values

Constructor Detail

GenomicDataStructures

public GenomicDataStructures()

Method Detail

updateMetricsFromRawRead

protected void updateMetricsFromRawRead(WsRead aligned_read,
                            RawRead read_data,
                            float metrics_factor)

must report right or left insertion...

Parameters:

read_data -

createFromRawRead

protected void createFromRawRead(WsRead aligned_read,
                     RawRead read_data,
                     float metrics_factor,
                     int mode)

must report right or left insertion...

Parameters:

read_data -

createFromRawReadWithInsertions

protected void createFromRawReadWithInsertions(WsRead aligned_read,
                                   RawRead read_data,
                                   float metrics_factor,
                                   int mode,
                                   long start_from)

report insertion at position...

Parameters:

read_data -

setQVValue

protected void setQVValue(WsRead aligned_read,
              RawRead read_data,
              int raw_base_index,
              int annotated_base_index,
              float metrics_factor)

Parameters:

aligned_read -

read_data -

raw_base_index -

annotated_base_index -

metrics_factor -

reverseRawRead

protected void reverseRawRead(RawRead read_data)

handles reverse strand data

Parameters:

read_data -

reverse

protected void reverse(byte[] array)

Reverses the order of the given array.

Parameters:

array - the array to reverse

reverse

protected void reverse(short[] array)

Reverses the order of the given array.

Parameters:

array - the array to reverse

reverse

protected void reverse(float[] array)

Reverses the order of the given array.

Parameters:

array - the array to reverse

buildStats

protected java.lang.String buildStats(int client_contig_index,
                          long start,
                          int length)

Parameters:

client_contig_index -

start -

length -