com.pacbio.secondary.vis.common.utils

Class GenomicUtils

java.lang.Object

com.pacbio.secondary.vis.common.utils.GenomicUtils

public class GenomicUtils
extends java.lang.Object

Author:

Marco Milletti

Field Summary

Fields

Modifier and Type	Field and Description
static int	ANNOTATED_READS_MAX_VALUE
static int	ANNOTATED_READS_WITH_BASES
static int	ANNOTATED_READS_WITH_NO_METRICS
static int	ANNOTATED_READS_WITH_PW
static int	ANNOTATED_READS_WITH_QV
static int	ANNOTATED_READS_WITH_RAW_IPD
static java.lang.String[]	BASEMODS_OPTIONS
static int	BITMASK_RESULTS_MAX_COVERAGE
static int	BITMASK_RESULTS_METRICS
static int	BITMASK_RESULTS_MISC
static int	BITMASK_RESULTS_READS
static int	BITMASK_RESULTS_STRUCTURES
static int	EPIPRO_FOLDED
static java.lang.String[]	EPIPRO_OPTIONS
static int	EPIPRO_SPLIT
static int	EPIPRO_UNFOLDED_MAPPED
static int	EPIPRO_UNFOLDED_SUBREAD
static int	MAX_CDNA_MAP_QV_VALID_RANGE
static int	MAX_PACBIO_MAP_QV_VALID_RANGE
static int	MIN_MAP_QV_VALID_RANGE
static int	READS_FOR_BASE_MODS
static int	READS_SEPARATE_STRANDS
static int	READS_UPDATE_DATA_REQUEST
static int	READS_WITH_INSERTIONS
static int	READS_WITHOUT_STRUCTURES
static int	RESULTS_OPTION_LINES_GRAPH
static int	RESULTS_OPTION_NODES_GRAPH
static int	RESULTS_OPTION_STRUCTURES
static int	RESULTS_OPTION_STRUCTURES_ONLY
static float	SCALE_FACTOR_READS_WITH_BASES
static float	SCALE_FACTOR_READS_WITH_PW
static float	SCALE_FACTOR_READS_WITH_QV
static float	SCALE_FACTOR_READS_WITH_RAW_IPD

Constructor Summary

Constructors

Constructor and Description
GenomicUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static int	getDefaultBaseModsMode()
static int	getDefaultResequencingMode()
static char[]	getDNAReverseComplementSequence(char[] in)
static int	getEpiProModeFromUIIndex(int index)
static int	getEpiProUIIndex(int mode)
static int	getKineticModeFromUIIndex(int index)
static java.lang.String	getKineticsScalingLabel(int mode)
static int	getMaxCoverageFromMode(int mode)
static float	getMetricsFactor(int mode)
static java.lang.String	getMetricsLabel(int mode, boolean bShort)
static int	getModeFromOptions(VioletApp app, boolean updateData) Creates mode value for results web services from runtime options
static java.awt.Color	getPastelReferenceColor(char c)
static java.awt.Color	getStrongReferenceColor(char c)
static int	getUIKineticIndex(int mode)
static boolean	isBaseMods(int mode)
static boolean	isBases(int mode)
static boolean	isEpiProFolded(int mode)
static boolean	isEpiProSplit(int mode)
static boolean	isEpiProUnFoldedMapped(int mode)
static boolean	isEpiProUnFoldedSubread(int mode)
static boolean	isNoMetrics(int mode)
static boolean	isNoStructures(int mode)
protected static boolean	isPW(int mode)
static boolean	isQV(int mode)
protected static boolean	isRawIPD(int mode)
static boolean	isRawKinetics(int mode)
static boolean	isResultsLinesGraph(int mode)
static boolean	isResultsNodesGraph(int mode)
static boolean	isResultsStructures(int mode)
static boolean	isResultsStructuresOnly(int mode)
static boolean	isSeparateStrands(int mode)
static boolean	isUpdateDataRequest(int mode)
static boolean	isViewInsertions(int mode) returns true when mode is raw data with insertions
static char	reverseComplement(char c)
static java.lang.String	reverseComplementSequence(java.lang.String s) Strings are immutable, use stringbuffer

Methods inherited from class java.lang.Object

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

Field Detail

BITMASK_RESULTS_METRICS

public static final int BITMASK_RESULTS_METRICS

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Constant Field Values

BITMASK_RESULTS_STRUCTURES

public static final int BITMASK_RESULTS_STRUCTURES

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Constant Field Values

BITMASK_RESULTS_READS

public static final int BITMASK_RESULTS_READS

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Constant Field Values

BITMASK_RESULTS_MAX_COVERAGE

public static final int BITMASK_RESULTS_MAX_COVERAGE

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Constant Field Values

BITMASK_RESULTS_MISC

public static final int BITMASK_RESULTS_MISC

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Constant Field Values

ANNOTATED_READS_WITH_NO_METRICS

public static final int ANNOTATED_READS_WITH_NO_METRICS

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Constant Field Values

ANNOTATED_READS_WITH_BASES

public static final int ANNOTATED_READS_WITH_BASES

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Constant Field Values

ANNOTATED_READS_WITH_QV

public static final int ANNOTATED_READS_WITH_QV

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Constant Field Values

ANNOTATED_READS_WITH_RAW_IPD

public static final int ANNOTATED_READS_WITH_RAW_IPD

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Constant Field Values

ANNOTATED_READS_WITH_PW

public static final int ANNOTATED_READS_WITH_PW

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Constant Field Values

RESULTS_OPTION_STRUCTURES

public static final int RESULTS_OPTION_STRUCTURES

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Constant Field Values

RESULTS_OPTION_STRUCTURES_ONLY

public static final int RESULTS_OPTION_STRUCTURES_ONLY

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Constant Field Values

RESULTS_OPTION_LINES_GRAPH

public static final int RESULTS_OPTION_LINES_GRAPH

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Constant Field Values

RESULTS_OPTION_NODES_GRAPH

public static final int RESULTS_OPTION_NODES_GRAPH

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Constant Field Values

READS_FOR_BASE_MODS

public static final int READS_FOR_BASE_MODS

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Constant Field Values

READS_WITHOUT_STRUCTURES

public static final int READS_WITHOUT_STRUCTURES

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Constant Field Values

READS_SEPARATE_STRANDS

public static final int READS_SEPARATE_STRANDS

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Constant Field Values

READS_UPDATE_DATA_REQUEST

public static final int READS_UPDATE_DATA_REQUEST

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Constant Field Values

EPIPRO_FOLDED

public static final int EPIPRO_FOLDED

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Constant Field Values

EPIPRO_UNFOLDED_MAPPED

public static final int EPIPRO_UNFOLDED_MAPPED

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Constant Field Values

EPIPRO_UNFOLDED_SUBREAD

public static final int EPIPRO_UNFOLDED_SUBREAD

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Constant Field Values

EPIPRO_SPLIT

public static final int EPIPRO_SPLIT

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Constant Field Values

READS_WITH_INSERTIONS

public static final int READS_WITH_INSERTIONS

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Constant Field Values

SCALE_FACTOR_READS_WITH_BASES

public static final float SCALE_FACTOR_READS_WITH_BASES

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Constant Field Values

SCALE_FACTOR_READS_WITH_QV

public static final float SCALE_FACTOR_READS_WITH_QV

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Constant Field Values

SCALE_FACTOR_READS_WITH_RAW_IPD

public static final float SCALE_FACTOR_READS_WITH_RAW_IPD

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Constant Field Values

SCALE_FACTOR_READS_WITH_PW

public static final float SCALE_FACTOR_READS_WITH_PW

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Constant Field Values

ANNOTATED_READS_MAX_VALUE

public static final int ANNOTATED_READS_MAX_VALUE

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Constant Field Values

MIN_MAP_QV_VALID_RANGE

public static final int MIN_MAP_QV_VALID_RANGE

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Constant Field Values

MAX_PACBIO_MAP_QV_VALID_RANGE

public static final int MAX_PACBIO_MAP_QV_VALID_RANGE

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Constant Field Values

MAX_CDNA_MAP_QV_VALID_RANGE

public static final int MAX_CDNA_MAP_QV_VALID_RANGE

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Constant Field Values

BASEMODS_OPTIONS

public static final java.lang.String[] BASEMODS_OPTIONS

EPIPRO_OPTIONS

public static final java.lang.String[] EPIPRO_OPTIONS

Constructor Detail

GenomicUtils

public GenomicUtils()

Method Detail

isRawKinetics

public static boolean isRawKinetics(int mode)

Parameters:

mode -

Returns:

isViewInsertions

public static boolean isViewInsertions(int mode)

returns true when mode is raw data with insertions

isNoMetrics

public static boolean isNoMetrics(int mode)

isBases

public static boolean isBases(int mode)

isQV

public static boolean isQV(int mode)

isRawIPD

protected static boolean isRawIPD(int mode)

isPW

protected static boolean isPW(int mode)

isEpiProFolded

public static boolean isEpiProFolded(int mode)

isEpiProUnFoldedMapped

public static boolean isEpiProUnFoldedMapped(int mode)

isEpiProUnFoldedSubread

public static boolean isEpiProUnFoldedSubread(int mode)

isEpiProSplit

public static boolean isEpiProSplit(int mode)

getMaxCoverageFromMode

public static int getMaxCoverageFromMode(int mode)

isBaseMods

public static boolean isBaseMods(int mode)

isNoStructures

public static boolean isNoStructures(int mode)

isSeparateStrands

public static boolean isSeparateStrands(int mode)

isUpdateDataRequest

public static boolean isUpdateDataRequest(int mode)

isResultsStructures

public static boolean isResultsStructures(int mode)

isResultsStructuresOnly

public static boolean isResultsStructuresOnly(int mode)

isResultsLinesGraph

public static boolean isResultsLinesGraph(int mode)

isResultsNodesGraph

public static boolean isResultsNodesGraph(int mode)

getDefaultBaseModsMode

public static int getDefaultBaseModsMode()

getDefaultResequencingMode

public static int getDefaultResequencingMode()

getModeFromOptions

public static int getModeFromOptions(VioletApp app,
                     boolean updateData)

Creates mode value for results web services from runtime options

Parameters:

app -

Returns:

getMetricsFactor

public static float getMetricsFactor(int mode)

Parameters:

mode -

Returns:

getMetricsLabel

public static java.lang.String getMetricsLabel(int mode,
                               boolean bShort)

Parameters:

mode -

Returns:

getKineticsScalingLabel

public static java.lang.String getKineticsScalingLabel(int mode)

Parameters:

mode -

Returns:

getPastelReferenceColor

public static java.awt.Color getPastelReferenceColor(char c)

Parameters:

c -

Returns:

getStrongReferenceColor

public static java.awt.Color getStrongReferenceColor(char c)

Parameters:

c -

Returns:

getDNAReverseComplementSequence

public static char[] getDNAReverseComplementSequence(char[] in)

reverseComplement

public static char reverseComplement(char c)

Parameters:

c -

Returns:

reverseComplementSequence

public static java.lang.String reverseComplementSequence(java.lang.String s)

Strings are immutable, use stringbuffer

Parameters:

s -

Returns:

getUIKineticIndex

public static int getUIKineticIndex(int mode)

getKineticModeFromUIIndex

public static int getKineticModeFromUIIndex(int index)

getEpiProUIIndex

public static int getEpiProUIIndex(int mode)

getEpiProModeFromUIIndex

public static int getEpiProModeFromUIIndex(int index)