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java.lang.Objectorg.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
org.biojavax.bio.phylo.io.nexus.TaxaBlock
public class TaxaBlock
Represents Nexus taxa 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 String |
TAXA_BLOCK
A constant representing the name of Taxa blocks. |
Constructor Summary | |
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TaxaBlock()
Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name. |
Method Summary | |
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void |
addComment(NexusComment comment)
Adds a comment. |
void |
addTaxLabel(String taxLabel)
Add a TAXLABEL. |
boolean |
containsTaxLabel(String taxLabel)
Checks to see if we contain the given TAXLABEL. |
List |
getComments()
Returns all comments. |
int |
getDimensionsNTax()
Get the NTAX value. |
List |
getTaxLabels()
Get the TAXLABEL values added so far. |
void |
removeComment(NexusComment comment)
Removes a comment. |
void |
removeTaxLabel(String taxLabel)
Removes the given TAXLABEL. |
void |
setDimensionsNTax(int dimensionsNTax)
Set the NTAX value. |
protected void |
writeBlockContents(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 String TAXA_BLOCK
Constructor Detail |
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public TaxaBlock()
Method Detail |
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public void setDimensionsNTax(int dimensionsNTax)
dimensionsNTax
- the NTAX value.public int getDimensionsNTax()
public void addTaxLabel(String taxLabel) throws ParseException
taxLabel
- the label to add.
ParseException
- if the label cannot be added.public void removeTaxLabel(String taxLabel)
taxLabel
- the label to remove.public boolean containsTaxLabel(String taxLabel)
taxLabel
- the label to check for.
public List getTaxLabels()
public void addComment(NexusComment comment)
comment
- the comment to add.public void removeComment(NexusComment comment)
comment
- the comment to remove.public List getComments()
protected void writeBlockContents(Writer writer) throws IOException
NexusBlock.Abstract
writeBlockContents
in class NexusBlock.Abstract
writer
- the writer to write to.
IOException
- if writing failed.
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