SMRT ® View 2.3.0
API Specification

SMRT ® View 2.3.0
API Specification

GUI 
Package Description
com.pacbio.secondary.vis.gui.app
Main application classes, support local, remote, webstart based deployment
com.pacbio.secondary.vis.gui.control
Specialized gui controls
com.pacbio.secondary.vis.gui.control.treetable
TreeTable control
com.pacbio.secondary.vis.gui.desktop
Support for dockable windows based desktop
com.pacbio.secondary.vis.gui.dialogs
Application dialogs
com.pacbio.secondary.vis.gui.draw.print
Print support
com.pacbio.secondary.vis.gui.draw.track
Track Abstraction
com.pacbio.secondary.vis.gui.draw.utils
Drawing utilities
com.pacbio.secondary.vis.gui.draw.views
Genomic views
com.pacbio.secondary.vis.gui.evt
Specialized event handlers
com.pacbio.secondary.vis.gui.frame
Client application main frame
com.pacbio.secondary.vis.gui.panels
Specialized dockable genomic panels
com.pacbio.secondary.vis.gui.panels.base
Generic dockable genomic panels
com.pacbio.secondary.vis.gui.table
Genomic data tables
com.pacbio.secondary.vis.gui.table.renderer
Specialized table renderers for genomic information
Data Models 
Package Description
com.pacbio.secondary.vis.data.base
Base genomic data model
com.pacbio.secondary.vis.data.chromosomeband
Chromosomal band abstraction
com.pacbio.secondary.vis.data.contig
Single, contiguous reference (contig)
com.pacbio.secondary.vis.data.db
Ideogram and genes collections support
com.pacbio.secondary.vis.data.filesystem
Abstraction layer for local and remote filesystem access
com.pacbio.secondary.vis.data.gene
Gene abstraction
com.pacbio.secondary.vis.data.graph
Graphic structures
com.pacbio.secondary.vis.data.interval
Support for genomic interval
com.pacbio.secondary.vis.data.locus
Support for genomic locus
com.pacbio.secondary.vis.data.marker
Marker data model
com.pacbio.secondary.vis.data.queue
Client/Server data requests utilities
com.pacbio.secondary.vis.data.read
Genomic read data model
com.pacbio.secondary.vis.data.session
Client side user session data models
com.pacbio.secondary.vis.data.session.options
Client side user options
com.pacbio.secondary.vis.data.session.timer
Timer and timer task for restoring user session
com.pacbio.secondary.vis.data.session.tracks
Tracks data model
com.pacbio.secondary.vis.data.table.model
Genomic tables data models
com.pacbio.secondary.vis.data.variableresolution.model
Variable resolution data models
com.pacbio.secondary.vis.data.variableresolution.model.gff
GFF3 variable resolution data model
com.pacbio.secondary.vis.data.variableresolution.record
Variable resolution record data model
com.pacbio.secondary.vis.data.xmlinfo
XML metadata files data models
Web Services 
Package Description
com.pacbio.secondary.vis.svc.hdf.client
HDFService client support
com.pacbio.secondary.vis.svc.hdf.client.auto
HDFService stubs
com.pacbio.secondary.vis.svc.server
SMRTView web services
com.pacbio.secondary.vis.svc.server.data
Server side data models
com.pacbio.secondary.vis.svc.server.data.parser
Server side data and metadata parsers
com.pacbio.secondary.vis.svc.server.hdf
HDFService utils
com.pacbio.secondary.vis.svc.server.jnlp
JNLPService utilities
com.pacbio.secondary.vis.svc.server.test
Local tests for smrt view web services
com.pacbio.secondary.vis.svc.server.threads
Parallel processing support
com.pacbio.secondary.vis.svc.server.utils
Utilities for web services
com.pacbio.secondary.vis.svc.vis.client
VisService client support
com.pacbio.secondary.vis.svc.vis.client.auto
VisService stubs
I/O 
Package Description
com.pacbio.secondary.vis.io.epipro
Parser for epipro/unmapped reads data
com.pacbio.secondary.vis.io.export
GFF3 export support
com.pacbio.secondary.vis.io.fasta
FASTA reader support
com.pacbio.secondary.vis.io.gff
GFF3 reader support
com.pacbio.secondary.vis.io.gff.modifications
GFF3 Base Modifications Info support
com.pacbio.secondary.vis.io.gff.summary
GFF3 Summary Info support
com.pacbio.secondary.vis.io.gff.variants
GFF3 variants support
com.pacbio.secondary.vis.io.hdf.constants
Constants definitions for hdf and cmp.h5 libraries
com.pacbio.secondary.vis.io.hdf.data
Data models for cmp.h5 file based data representation
com.pacbio.secondary.vis.io.hdf.exception
Exception specialization for hdf library
com.pacbio.secondary.vis.io.hdf.file.bash5
Support for reading/writing of bas.h5 and bax.h5 files
com.pacbio.secondary.vis.io.hdf.file.cmph5
Support for reading/writing of cmp.h5 files
com.pacbio.secondary.vis.io.hdf.file.hdf5
Support for reading/writing of HDF5 files
com.pacbio.secondary.vis.io.hdf.hyperslabinfo
Hdf5 hyperslab data model
com.pacbio.secondary.vis.io.hdf.referenceinfo
Cmp.h5 reference groups data model
com.pacbio.secondary.vis.io.hdf.streaming
Support for callback-based, asynchronous data streaming
com.pacbio.secondary.vis.io.hdf.test
Hdf library test suite
com.pacbio.secondary.vis.io.importer
Local and remote data files import support
com.pacbio.secondary.vis.io.indexer.fasta
FASTA indexer
com.pacbio.secondary.vis.io.indexer.gff
GFF indexer
com.pacbio.secondary.vis.io.indexer.gff.metadata
GFF3 metadata info
com.pacbio.secondary.vis.io.indexer.indexinfo
Generic ASCII files indexer
com.pacbio.secondary.vis.io.indexer.text
Text files indexer
com.pacbio.secondary.vis.io.motifs
Parser for Motifs files
com.pacbio.secondary.vis.io.ucsc.gtf.reader
Parser for UCSC generated gtf (gene transfer format) files
com.pacbio.secondary.vis.io.update
Support for interactive data updates after user preferences changes
com.pacbio.secondary.vis.io.vcf
Parser for VCF (variants) files
Common 
Package Description
com.pacbio.secondary.vis.common.collection
Specialized collection classes
com.pacbio.secondary.vis.common.utils
Client/Server common utilities
com.pacbio.secondary.vis.common.utils.constants
Client/Server common constants
com.pacbio.secondary.vis.common.utils.exception
Specialized exception handlers
com.pacbio.secondary.vis.common.utils.filefilter
Filters used for file open/save dialogs
External Components 
Package Description
pub.vlsolutions.swing.docking
Dockable windows framework
pub.vlsolutions.swing.docking.animation
Dockable windows framework
pub.vlsolutions.swing.docking.event
Dockable windows framework
pub.vlsolutions.swing.docking.ui
Dockable windows framework
pub.vlsolutions.swing.docking.ws
Dockable windows framework
pub.vlsolutions.swing.tabbedpane
Dockable windows framework
pub.vlsolutions.swing.toolbars
Dockable windows framework
Other Packages 
Package Description
com.pacbio.secondary.vis.smrtcloud
SMRT Cloud deployment support
com.pacbio.secondary.vis.update
Smrtview updating utilities
SMRT ® View 2.3.0
API Specification

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