com.pacbio.secondary.vis.io.ucsc.gtf.reader

Class UCSCGTFReader

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.ucsc.gtf.reader.UCSCGTFReader

All Implemented Interfaces:

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

public class UCSCGTFReader
extends GFFDataModel

Author:

mmilletti

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	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
UCSCGTFReader()

Method Summary

Methods

Modifier and Type	Method and Description
void	loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	readElements(VioletApp app, java.io.Reader reader) Loads a marker collection from a stream.

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

NUM_RESULTS

protected static final int NUM_RESULTS

See Also:

Constant Field Values

Constructor Detail

UCSCGTFReader

public UCSCGTFReader()

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 a marker collection from a stream. Specialized version for generic tables downloaded from UCSC browser as GTF

Specified by:

readElements in class GFFDataModel

Parameters:

reader -

Returns:

number of contigs in data file

Throws:

java.io.IOException

FileFormatException