com.pacbio.secondary.vis.io.gff.modifications

Class GFFModificationsReader

java.lang.Object

com.pacbio.secondary.vis.data.base.BaseDataModel

com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader

All Implemented Interfaces:

IVariableResolutionDataModelServer, IChangeNotifier, java.lang.Iterable<VariableValuesDataRecord>

public class GFFModificationsReader
extends GFFDataModel

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

BaseDataModel.eDataType

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	BASEMOD_BASE_ID_MASK
protected static int	BASEMOD_MOTIF_ID_MASK
static int	BASEMOD_NUM_SUMMARY_METRICS
static int	BASEMOD_TYPE_4MC
static int	BASEMOD_TYPE_5MC
static int	BASEMOD_TYPE_6MA
protected static int	BASEMOD_TYPE_MASK
static int	BASEMOD_TYPE_MODIFIED
static int	BASEMOD_TYPE_MOTIF
static int	BASEMOD_TYPE_UNKNOWN
protected static java.lang.String[]	BASEMOD_TYPES_LABELS
protected static java.lang.String[]	BASEMOD_TYPES_TAGS
protected java.util.TreeMap<java.lang.String,java.lang.Integer>	basemods_map
protected boolean	has_motifs_file
protected static java.lang.String	MODS_VALUE_CONTEXT_TAG
protected static java.lang.String	MODS_VALUE_COVERAGE_TAG
protected static java.lang.String	MODS_VALUE_FRAC_MOD_TAG
protected static java.lang.String	MODS_VALUE_ID_TAG
protected static java.lang.String	MODS_VALUE_IDENT_QV_TAG
protected static java.lang.String	MODS_VALUE_IPD_RATIO_TAG
protected static java.lang.String	MODS_VALUE_MOTIF_TAG
protected java.util.TreeMap<java.lang.String,java.lang.Integer>	motifs_map
protected int	NUM_RESULTS

Fields inherited from class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

data, fileName, min_max_values, valid

Fields inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

changeNotifier, data_type, mc

Constructor Summary

Constructors

Constructor and Description
GFFModificationsReader(boolean has_motifs_file)

Method Summary

Methods

Modifier and Type	Method and Description
static int	baseModID(float type)
static int	filterType(float type)
static java.lang.String	getBaseModFileTags(int type)
static java.lang.String	getBaseModLabel(int type) returns a base mod string from type
protected int	getBaseModType(java.lang.String type) returns a base mod type from string
protected float	getDataPointForInterval(VariableValuesDataRecord record, java.lang.String col, int mods_filter_threshold)
void	loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
static int	motifID(float type)
int	readElements(VioletApp app, java.io.Reader reader) Loads base mods or motifs info

Methods inherited from class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

clear, get, getDataInfo, getFileHeader, getFilePath, getMinMaxValues, getResults, invalidate, isValid, size, toCollection, validate

Methods inherited from class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

copyAsMarkerCollectionArray, detach, getNumItems, getResult, iterator

Methods inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

addChangeListener, fireChangeEvent, getDataType, getDataTypeAsString, getMarkersForContig, getNumContigs, hasData, isMarkerType, isModificationsType, isReadsType, isSummaryType, isVariantsType, removeChangeListener, setTypeAndNumContigs

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.pacbio.secondary.vis.gui.evt.IChangeNotifier

addChangeListener, removeChangeListener

Field Detail

motifs_map

protected java.util.TreeMap<java.lang.String,java.lang.Integer> motifs_map

basemods_map

protected java.util.TreeMap<java.lang.String,java.lang.Integer> basemods_map

has_motifs_file

protected boolean has_motifs_file

NUM_RESULTS

protected final int NUM_RESULTS

See Also:

Constant Field Values

MODS_VALUE_IDENT_QV_TAG

protected static final java.lang.String MODS_VALUE_IDENT_QV_TAG

See Also:

Constant Field Values

MODS_VALUE_ID_TAG

protected static final java.lang.String MODS_VALUE_ID_TAG

See Also:

Constant Field Values

MODS_VALUE_IPD_RATIO_TAG

protected static final java.lang.String MODS_VALUE_IPD_RATIO_TAG

See Also:

Constant Field Values

MODS_VALUE_CONTEXT_TAG

protected static final java.lang.String MODS_VALUE_CONTEXT_TAG

See Also:

Constant Field Values

MODS_VALUE_COVERAGE_TAG

protected static final java.lang.String MODS_VALUE_COVERAGE_TAG

See Also:

Constant Field Values

MODS_VALUE_MOTIF_TAG

protected static final java.lang.String MODS_VALUE_MOTIF_TAG

See Also:

Constant Field Values

MODS_VALUE_FRAC_MOD_TAG

protected static final java.lang.String MODS_VALUE_FRAC_MOD_TAG

See Also:

Constant Field Values

BASEMOD_TYPE_MODIFIED

public static final int BASEMOD_TYPE_MODIFIED

See Also:

Constant Field Values

BASEMOD_TYPE_6MA

public static final int BASEMOD_TYPE_6MA

See Also:

Constant Field Values

BASEMOD_TYPE_4MC

public static final int BASEMOD_TYPE_4MC

See Also:

Constant Field Values

BASEMOD_TYPE_5MC

public static final int BASEMOD_TYPE_5MC

See Also:

Constant Field Values

BASEMOD_TYPE_MOTIF

public static final int BASEMOD_TYPE_MOTIF

See Also:

Constant Field Values

BASEMOD_TYPE_UNKNOWN

public static final int BASEMOD_TYPE_UNKNOWN

See Also:

Constant Field Values

BASEMOD_NUM_SUMMARY_METRICS

public static final int BASEMOD_NUM_SUMMARY_METRICS

See Also:

Constant Field Values

BASEMOD_TYPE_MASK

protected static final int BASEMOD_TYPE_MASK

See Also:

Constant Field Values

BASEMOD_MOTIF_ID_MASK

protected static final int BASEMOD_MOTIF_ID_MASK

See Also:

Constant Field Values

BASEMOD_BASE_ID_MASK

protected static final int BASEMOD_BASE_ID_MASK

See Also:

Constant Field Values

BASEMOD_TYPES_TAGS

protected static final java.lang.String[] BASEMOD_TYPES_TAGS

BASEMOD_TYPES_LABELS

protected static final java.lang.String[] BASEMOD_TYPES_LABELS

Constructor Detail

GFFModificationsReader

public GFFModificationsReader(boolean has_motifs_file)

Method Detail

loadFromReader

public void loadFromReader(java.io.Reader reader,
                  java.lang.String file_name,
                  VioletApp app)
                    throws java.io.IOException,
                           FileFormatException

Throws:

java.io.IOException

FileFormatException

readElements

public int readElements(VioletApp app,
               java.io.Reader reader)
                 throws java.io.IOException,
                        FileFormatException

Loads base mods or motifs info

Specified by:

readElements in class GFFDataModel

Parameters:

app -

reader -

Returns:

number of contigs in data file

Throws:

java.io.IOException

FileFormatException

getDataPointForInterval

protected float getDataPointForInterval(VariableValuesDataRecord record,
                            java.lang.String col,
                            int mods_filter_threshold)

getBaseModType

protected int getBaseModType(java.lang.String type)

returns a base mod type from string

Parameters:

type -

Returns:

getBaseModLabel

public static java.lang.String getBaseModLabel(int type)

returns a base mod string from type

Parameters:

type -

Returns:

getBaseModFileTags

public static java.lang.String getBaseModFileTags(int type)

motifID

public static int motifID(float type)

baseModID

public static int baseModID(float type)

filterType

public static int filterType(float type)