Package org.biojavax.bio.phylo.io.nexus
Class DistancesBlockBuilder
java.lang.Object
org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
- All Implemented Interfaces:
DistancesBlockListener
,NexusBlockBuilder
,NexusBlockListener
public class DistancesBlockBuilder
extends NexusBlockBuilder.Abstract
implements DistancesBlockListener
Builds Nexus distances blocks.
- Since:
- 1.6
- Author:
- Richard Holland, Tobias Thierer, Jim Balhoff
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder
NexusBlockBuilder.Abstract
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addComment
(NexusComment comment) Tell the builder to add the given comment at the current location.void
addMatrixEntry
(String taxa) void
addTaxLabel
(String taxLabel) Add a TAXLABEL.void
appendMatrixData
(String taxa, Object data) void
endBlock()
Notifies the parser that a block is ending.void
Closing a line (semi-colon encountered).void
setDiagonal
(boolean diagonal) void
setDimensionsNChar
(int dimensionsNChar) Set the NCHAR value.void
setDimensionsNTax
(int dimensionsNTax) Set the NTAX value.void
setInterleaved
(boolean interleaved) void
setLabels
(boolean labels) void
setMissing
(String missing) void
setTriangle
(String triangle) protected NexusBlock
Tell the builder to start a new block object.Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
beginComment, commentText, endComment, getBlockName, getNexusBlock, startBlock
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
beginComment, commentText, endComment, startBlock
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Constructor Details
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DistancesBlockBuilder
public DistancesBlockBuilder()
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Method Details
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addComment
Description copied from class:NexusBlockBuilder.Abstract
Tell the builder to add the given comment at the current location.- Specified by:
addComment
in classNexusBlockBuilder.Abstract
- Parameters:
comment
- the comment to add.
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startBlockObject
Description copied from class:NexusBlockBuilder.Abstract
Tell the builder to start a new block object.- Specified by:
startBlockObject
in classNexusBlockBuilder.Abstract
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endBlock
Description copied from interface:NexusBlockListener
Notifies the parser that a block is ending.- Specified by:
endBlock
in interfaceNexusBlockListener
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endTokenGroup
Description copied from interface:NexusBlockListener
Closing a line (semi-colon encountered). This indicates that anything received after it is on the next logical line of the block.- Specified by:
endTokenGroup
in interfaceNexusBlockListener
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addMatrixEntry
- Specified by:
addMatrixEntry
in interfaceDistancesBlockListener
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addTaxLabel
Description copied from interface:DistancesBlockListener
Add a TAXLABEL. If it already exists, or is a number that refers to an index position that already exists, an exception is thrown.- Specified by:
addTaxLabel
in interfaceDistancesBlockListener
- Parameters:
taxLabel
- the label to add.- Throws:
ParseException
- if the label cannot be added.
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appendMatrixData
- Specified by:
appendMatrixData
in interfaceDistancesBlockListener
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setDimensionsNChar
Description copied from interface:DistancesBlockListener
Set the NCHAR value.- Specified by:
setDimensionsNChar
in interfaceDistancesBlockListener
- Parameters:
dimensionsNChar
- the NCHAR value.
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setDimensionsNTax
Description copied from interface:DistancesBlockListener
Set the NTAX value.- Specified by:
setDimensionsNTax
in interfaceDistancesBlockListener
- Parameters:
dimensionsNTax
- the NTAX value.
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setInterleaved
- Specified by:
setInterleaved
in interfaceDistancesBlockListener
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setLabels
- Specified by:
setLabels
in interfaceDistancesBlockListener
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setMissing
- Specified by:
setMissing
in interfaceDistancesBlockListener
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setDiagonal
- Specified by:
setDiagonal
in interfaceDistancesBlockListener
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setTriangle
- Specified by:
setTriangle
in interfaceDistancesBlockListener
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