NexusPhylogeniesParser

java.lang.Object
- org.forester.io.parsers.nexus.NexusPhylogeniesParser

All Implemented Interfaces:: IteratingPhylogenyParser, PhylogenyParser

public final class NexusPhylogeniesParser
extends java.lang.Object
implements IteratingPhylogenyParser, PhylogenyParser

Constructor Summary

Constructors
Constructor Description

NexusPhylogeniesParser()

Constructors
Constructor	Description
`NexusPhylogeniesParser()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`getName()`
`boolean`	`hasNext()`
`Phylogeny`	`next()`
`Phylogeny[]`	`parse()`
`void`	`reset()`
`void`	`setIgnoreQuotes(boolean ignore_quotes_in_nh_data)`
`void`	`setReplaceUnderscores(boolean replace_underscores)`
`void`	`setSource(java.lang.Object nexus_source)`
`void`	`setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- NexusPhylogeniesParser
```
public NexusPhylogeniesParser()
```

Method Detail

getName
```
public java.lang.String getName()
```
Specified by:

getName in interface PhylogenyParser

hasNext
```
public final boolean hasNext()
```
Specified by:

hasNext in interface IteratingPhylogenyParser

public final Phylogeny next()
                     throws NHXFormatException,
                            java.io.IOException

Specified by:: next in interface IteratingPhylogenyParser
Throws:: NHXFormatException; java.io.IOException

parse

public final Phylogeny[] parse()
                        throws java.io.IOException

Specified by:: parse in interface PhylogenyParser
Throws:: java.io.IOException

reset

public final void reset()
                 throws java.io.FileNotFoundException,
                        java.io.IOException

Specified by:: reset in interface IteratingPhylogenyParser
Throws:: java.io.FileNotFoundException; java.io.IOException

setIgnoreQuotes

public final void setIgnoreQuotes(boolean ignore_quotes_in_nh_data)

setReplaceUnderscores

public final void setReplaceUnderscores(boolean replace_underscores)

setSource

public final void setSource(java.lang.Object nexus_source)
                     throws PhylogenyParserException,
                            java.io.IOException

Specified by:: setSource in interface IteratingPhylogenyParser
Specified by:: setSource in interface PhylogenyParser
Throws:: PhylogenyParserException; java.io.IOException

setTaxonomyExtraction

public final void setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

Class NexusPhylogeniesParser

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

NexusPhylogeniesParser

Method Detail

getName

hasNext

next

parse

reset

setIgnoreQuotes

setReplaceUnderscores

setSource

setTaxonomyExtraction