com.pacbio.secondary.vis.io.gff.summary

Class GFFSummaryReader

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.summary.GFFSummaryReader

All Implemented Interfaces:

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

public class GFFSummaryReader
extends GFFDataModel

Author:

Marco Milletti

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 boolean	isV131
protected boolean	isV133

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
GFFSummaryReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	getDataPointForInterval(VariableValuesDataRecord record, java.lang.String col)
protected boolean	isV13()
void	loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
protected void	readContigFeature(DeNovoSummaryStorage storage, java.lang.String[] ar, java.util.TreeMap<java.lang.Integer,java.lang.Integer> map) parses a denovo contig record
int	readElements(VioletApp app, java.io.Reader reader) Loads summary information
protected void	readRegionFeature(java.lang.String[] ar, java.util.Vector<java.lang.String> contig_names, java.util.Vector<java.lang.String> contig_ids, java.util.Vector<java.lang.String> contig_full_names, java.util.TreeMap<java.lang.Integer,java.lang.Integer> map) Parses a standard region record
protected void	saveMaxValuesForRecord(VariableValuesDataRecord record, int contig)
protected void	updateConsensusQVLimits()

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

isV131

protected boolean isV131

isV133

protected boolean isV133

Constructor Detail

GFFSummaryReader

public GFFSummaryReader()

Method Detail

isV13

protected boolean isV13()

Returns:

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

updateConsensusQVLimits

protected void updateConsensusQVLimits()

readElements

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

Loads summary information

Specified by:

readElements in class GFFDataModel

Parameters:

app -

reader -

Returns:

number of contigs in data file

Throws:

java.io.IOException

FileFormatException

readContigFeature

protected void readContigFeature(DeNovoSummaryStorage storage,
                     java.lang.String[] ar,
                     java.util.TreeMap<java.lang.Integer,java.lang.Integer> map)

parses a denovo contig record

Parameters:

storage -

ar -

contig_names -

map -

readRegionFeature

protected void readRegionFeature(java.lang.String[] ar,
                     java.util.Vector<java.lang.String> contig_names,
                     java.util.Vector<java.lang.String> contig_ids,
                     java.util.Vector<java.lang.String> contig_full_names,
                     java.util.TreeMap<java.lang.Integer,java.lang.Integer> map)

Parses a standard region record

Parameters:

ar -

contig_names -

map -

getDataPointForInterval

protected void getDataPointForInterval(VariableValuesDataRecord record,
                           java.lang.String col)

saveMaxValuesForRecord

protected void saveMaxValuesForRecord(VariableValuesDataRecord record,
                          int contig)

Parameters:

record -

contig -