| Package | Description |
|---|---|
| info.bioinfweb.jphyloio.factory |
Contains interfaces and general implementations for creating JPhyloIO readers and writers related to
JPhyloIOReaderWriterFactory. |
| info.bioinfweb.jphyloio.formatinfo |
Contains
JPhyloIOFormatInfo and related classes that describe a format supported by JPhyloIO. |
| info.bioinfweb.jphyloio.formats.fasta |
Contains classes for reading from and writing to streams/files in FASTA format.
|
| info.bioinfweb.jphyloio.formats.mega |
Contains classes for reading from and writing to streams/files in MEGA format.
|
| info.bioinfweb.jphyloio.formats.newick |
Contains classes for reading from and writing to streams/files in Newick tree format.
|
| info.bioinfweb.jphyloio.formats.nexml |
Contains classes for reading from and writing to streams/files in NeXML format.
|
| info.bioinfweb.jphyloio.formats.nexus |
Contains classes for reading from and writing to streams/files in Nexus format.
|
| info.bioinfweb.jphyloio.formats.pde |
Contains classes for reading from streams/files in PDE format.
|
| info.bioinfweb.jphyloio.formats.phylip |
Contains classes for reading from and writing to streams/files in Phylip format.
|
| info.bioinfweb.jphyloio.formats.phyloxml |
Contains classes for reading from and writing to streams/files in PhyloXML format.
|
| info.bioinfweb.jphyloio.formats.xml |
Contains classes implementing shared functionality for reading from and writing to streams/files in XML formats.
|
| info.bioinfweb.jphyloio.formats.xtg |
Contains classes for reading from and writing to streams/files in XTG format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractSingleReaderWriterFactory |
class |
AbstractStartStringSingleFactory
Abstract single format factory that implements the
checkFormat() methods by testing of the read content
start with a certain string, determined by AbstractStartStringSingleFactory.getExpectedStart(). |
| Modifier and Type | Method and Description |
|---|---|
SingleReaderWriterFactory |
JPhyloIOReaderWriterFactory.addFactory(SingleReaderWriterFactory factory)
Allows to add additional or replace existing single format factories to be used by this instance.
|
| Modifier and Type | Method and Description |
|---|---|
SingleReaderWriterFactory |
JPhyloIOReaderWriterFactory.addFactory(SingleReaderWriterFactory factory)
Allows to add additional or replace existing single format factories to be used by this instance.
|
| Constructor and Description |
|---|
JPhyloIOContentExtensionFileFilter(SingleReaderWriterFactory factory,
ReadWriteParameterMap defaultParamaters,
java.lang.String description,
boolean addExtensionListToDescription,
ContentExtensionFileFilter.TestStrategy testStrategy,
boolean acceptFilesWithExceptions,
java.lang.String... extensions) |
| Constructor and Description |
|---|
DefaultFormatInfo(SingleReaderWriterFactory factory,
java.lang.String formatID,
java.lang.String formatName,
java.util.Set<EventContentType> supportedReaderContentTypes,
java.util.Set<EventContentType> supportedWriterContentTypes,
java.util.Map<EventContentType,MetadataModeling> supportedReaderMetadataModeling,
java.util.Map<EventContentType,MetadataModeling> supportedWriterMetadataModeling,
java.util.Set<java.lang.String> supportedReaderParameters,
java.util.Set<java.lang.String> supportedWriterParameters,
ReadWriteParameterMap filterParameters,
java.lang.String filterDescription,
java.lang.String... filterExtensions)
Creates a new instance of this class.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FASTAFactory
Reader and writer factory for the FASTA format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MEGAFactory
Reader and writer factory for the MEGA format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NewickFactory
Reader and writer factory for the Newick format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NeXMLFactory
Reader and writer factory for the NeXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
NexusFactory
Reader and writer factory for the Nexus format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PDEFactory
Reader and writer factory for the PDE format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractPhylipFactory
Implements shared functionality for Phylip factories.
|
class |
PhylipFactory
Reader and writer factory for the (non-sequential) Phylip format.
|
class |
SequentialPhylipFactory
Reader and writer factory for the sequential Phylip format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PhyloXMLFactory
Reader and writer factory for the PhyloXML format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractXMLFactory
Implements shared functionality for reader and writer factories of XML formats.
|
| Modifier and Type | Class and Description |
|---|---|
class |
XTGFactory
Reader and writer factory for the XTG format.
|