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java.lang.Objectorg.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
org.biojavax.bio.phylo.io.nexus.CharactersBlock
public class CharactersBlock
Represents Nexus characters blocks.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlock |
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NexusBlock.Abstract |
Field Summary | |
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static java.lang.String |
CHARACTERS_BLOCK
A constant representing the name of Characters blocks. |
Constructor Summary | |
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CharactersBlock()
Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name. |
protected |
CharactersBlock(java.lang.String replacementLabel)
For the DATA block subclass. |
Method Summary | |
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void |
addCharLabel(java.lang.String charLabel)
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void |
addCharState(java.lang.String charState)
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void |
addCharStateKeyword(java.lang.String charState,
java.lang.String keyword)
|
void |
addComment(NexusComment comment)
Adds a comment. |
void |
addEquate(java.lang.String symbol,
java.util.List symbols)
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void |
addItem(java.lang.String item)
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void |
addMatrixEntry(java.lang.String taxa)
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void |
addState(java.lang.String state)
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void |
addStateLabel(java.lang.String state,
java.lang.String label)
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void |
addSymbol(java.lang.String symbol)
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void |
addTaxLabel(java.lang.String taxLabel)
Add a TAXLABEL. |
void |
appendMatrixData(java.lang.String taxa,
java.lang.Object data)
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boolean |
containsCharLabel(java.lang.String charLabel)
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boolean |
containsTaxLabel(java.lang.String taxLabel)
Checks to see if we contain the given TAXLABEL. |
java.util.Set |
getAllCharStates()
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java.util.List |
getCharLabels()
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java.lang.String |
getCharStateLabel(java.lang.String charState)
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java.util.List |
getCharStateLabelKeywords(java.lang.String charState)
|
java.util.List |
getComments()
Returns all comments. |
java.lang.String |
getDataType()
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int |
getDimensionsNChar()
Get the NCHAR value. |
int |
getDimensionsNTax()
Get the NTAX value. |
int |
getEliminateEnd()
|
int |
getEliminateStart()
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java.util.Map |
getEquates()
|
java.lang.String |
getGap()
|
java.util.List |
getItems()
|
java.lang.String |
getMatchChar()
|
java.util.List |
getMatrixData(java.lang.String taxa)
|
java.lang.String |
getMissing()
|
java.util.List |
getStateLabels(java.lang.String state)
|
java.lang.String |
getStatesFormat()
|
java.util.List |
getSymbols()
|
java.util.List |
getTaxLabels()
Get the TAXLABEL values added so far. |
boolean |
isInterleaved()
|
boolean |
isLabels()
|
boolean |
isRespectCase()
|
boolean |
isTokens()
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boolean |
isTransposed()
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void |
removeAllItems()
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void |
removeAllSymbols()
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void |
removeCharLabel(java.lang.String charLabel)
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void |
removeCharState(java.lang.String charState)
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void |
removeComment(NexusComment comment)
Removes a comment. |
void |
removeEquate(java.lang.String symbol)
|
void |
removeItem(java.lang.String item)
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void |
removeState(java.lang.String state)
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void |
removeSymbol(java.lang.String symbol)
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void |
removeTaxLabel(java.lang.String taxLabel)
Removes the given TAXLABEL. |
void |
setCharStateLabel(java.lang.String charState,
java.lang.String label)
|
void |
setDataType(java.lang.String dataType)
|
void |
setDimensionsNChar(int dimensionsNChar)
Set the NCHAR value. |
void |
setDimensionsNTax(int dimensionsNTax)
Set the NTAX value. |
void |
setEliminateEnd(int eliminateEnd)
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void |
setEliminateStart(int eliminateStart)
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void |
setGap(java.lang.String gap)
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void |
setInterleaved(boolean interleaved)
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void |
setLabels(boolean labels)
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void |
setMatchChar(java.lang.String matchChar)
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void |
setMissing(java.lang.String missing)
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void |
setRespectCase(boolean respectCase)
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void |
setStatesFormat(java.lang.String statesFormat)
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void |
setTokens(boolean tokens)
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void |
setTransposed(boolean transposed)
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protected void |
writeBlockContents(java.io.Writer writer)
Implement this to write out block contents, not including the BEGIN and END tags. |
Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract |
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getBlockName, writeObject, writeToken |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String CHARACTERS_BLOCK
Constructor Detail |
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public CharactersBlock()
protected CharactersBlock(java.lang.String replacementLabel)
replacementLabel
- the different label to use.Method Detail |
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public void setDimensionsNTax(int dimensionsNTax)
dimensionsNTax
- the NTAX value.public int getDimensionsNTax()
public void setDimensionsNChar(int dimensionsNChar)
dimensionsNChar
- the NCHAR value.public int getDimensionsNChar()
public void setDataType(java.lang.String dataType)
public java.lang.String getDataType()
public void setRespectCase(boolean respectCase)
public boolean isRespectCase()
public void setMissing(java.lang.String missing)
public java.lang.String getMissing()
public void setGap(java.lang.String gap)
public java.lang.String getGap()
public void addSymbol(java.lang.String symbol)
public void removeSymbol(java.lang.String symbol)
public void removeAllSymbols()
public java.util.List getSymbols()
public void addEquate(java.lang.String symbol, java.util.List symbols)
public void removeEquate(java.lang.String symbol)
public java.util.Map getEquates()
public void setMatchChar(java.lang.String matchChar)
public java.lang.String getMatchChar()
public void setLabels(boolean labels)
public boolean isLabels()
public void setTransposed(boolean transposed)
public boolean isTransposed()
public void setInterleaved(boolean interleaved)
public boolean isInterleaved()
public void addItem(java.lang.String item)
public void removeItem(java.lang.String item)
public void removeAllItems()
public java.util.List getItems()
public void setStatesFormat(java.lang.String statesFormat)
public java.lang.String getStatesFormat()
public void setTokens(boolean tokens)
public boolean isTokens()
public void setEliminateStart(int eliminateStart)
public int getEliminateStart()
public void setEliminateEnd(int eliminateEnd)
public int getEliminateEnd()
public void addTaxLabel(java.lang.String taxLabel) throws ParseException
taxLabel
- the label to add.
ParseException
- if the label cannot be added.public void removeTaxLabel(java.lang.String taxLabel)
taxLabel
- the label to remove.public boolean containsTaxLabel(java.lang.String taxLabel)
taxLabel
- the label to check for.
public java.util.List getTaxLabels()
public void addCharState(java.lang.String charState)
public void setCharStateLabel(java.lang.String charState, java.lang.String label)
public void addCharStateKeyword(java.lang.String charState, java.lang.String keyword)
public java.lang.String getCharStateLabel(java.lang.String charState)
public java.util.List getCharStateLabelKeywords(java.lang.String charState)
public void removeCharState(java.lang.String charState)
public java.util.Set getAllCharStates()
public void addCharLabel(java.lang.String charLabel)
public void removeCharLabel(java.lang.String charLabel)
public boolean containsCharLabel(java.lang.String charLabel)
public java.util.List getCharLabels()
public void addState(java.lang.String state)
public void addStateLabel(java.lang.String state, java.lang.String label)
public java.util.List getStateLabels(java.lang.String state)
public void removeState(java.lang.String state)
public void addMatrixEntry(java.lang.String taxa)
public void appendMatrixData(java.lang.String taxa, java.lang.Object data)
public java.util.List getMatrixData(java.lang.String taxa)
public void addComment(NexusComment comment)
comment
- the comment to add.public void removeComment(NexusComment comment)
comment
- the comment to remove.public java.util.List getComments()
protected void writeBlockContents(java.io.Writer writer) throws java.io.IOException
NexusBlock.Abstract
writeBlockContents
in class NexusBlock.Abstract
writer
- the writer to write to.
java.io.IOException
- if writing failed.
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