Package org.biojavax.bio.phylo.io.nexus
Interface CharactersBlockListener
- All Superinterfaces:
NexusBlockListener
- All Known Subinterfaces:
DataBlockListener
- All Known Implementing Classes:
CharactersBlockBuilder,DataBlockBuilder
Listens to events that represent Nexus characters blocks.
- Since:
- 1.6
- Author:
- Richard Holland, Tobias Thierer, Jim Balhoff
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Method Summary
Modifier and TypeMethodDescriptionvoidaddCharLabel(String charLabel) voidaddCharState(String charState) voidaddCharStateKeyword(String charState, String keyword) voidvoidvoidaddMatrixEntry(String taxa) voidvoidaddStateLabel(String state, String label) voidvoidaddTaxLabel(String taxLabel) Add a TAXLABEL.voidappendMatrixData(String taxa, Object data) voidsetCharStateLabel(String charState, String label) voidsetDataType(String dataType) voidsetDimensionsNChar(int dimensionsNChar) Set the NCHAR value.voidsetDimensionsNTax(int dimensionsNTax) Set the NTAX value.voidsetEliminateEnd(int eliminateEnd) voidsetEliminateStart(int eliminateStart) voidvoidsetInterleaved(boolean interleaved) voidsetLabels(boolean labels) voidsetMatchChar(String matchChar) voidsetMissing(String missing) voidsetRespectCase(boolean respectCase) voidsetStatesFormat(String statesFormat) voidsetTokens(boolean tokens) voidsetTransposed(boolean transposed) Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
beginComment, commentText, endBlock, endComment, endTokenGroup, startBlock
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Method Details
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setDimensionsNTax
Set the NTAX value.- Parameters:
dimensionsNTax- the NTAX value.
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setDimensionsNChar
Set the NCHAR value.- Parameters:
dimensionsNChar- the NCHAR value.
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setDataType
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setRespectCase
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setMissing
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setGap
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addSymbol
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addEquate
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setMatchChar
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setLabels
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setTransposed
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setInterleaved
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addItem
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setStatesFormat
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setTokens
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setEliminateStart
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setEliminateEnd
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addTaxLabel
Add a TAXLABEL. If it already exists, or is a number that refers to an index position that already exists, an exception is thrown.- Parameters:
taxLabel- the label to add.- Throws:
ParseException- if the label cannot be added.
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addCharState
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setCharStateLabel
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addCharStateKeyword
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addCharLabel
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addState
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addStateLabel
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addMatrixEntry
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appendMatrixData
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