public class TreesBlock extends NexusBlock.Abstract
Modifier and Type | Class and Description |
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static class |
TreesBlock.NewickTreeString
A simple representation of a Newick tree as a single string.
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NexusBlock.Abstract
Modifier and Type | Field and Description |
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static String |
TREES_BLOCK
A constant representing the name of Trees blocks.
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Constructor and Description |
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TreesBlock()
Delegates to NexusBlock.Abstract constructor using TreesBlock.TREES_BLOCK
as the name.
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Modifier and Type | Method and Description |
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void |
addComment(NexusComment comment)
Adds a comment.
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void |
addTranslation(String label,
String taxa)
Add a translation.
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void |
addTree(String label,
TreesBlock.NewickTreeString tree)
Adds a tree.
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void |
addTree(String label,
org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> treegraph)
Add a tree, converting unweighted graph (JGraphT) to NewickString
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void |
addTree(String label,
org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph)
Add a tree, converting weighted graph (JGraphT) to NewickString
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boolean |
containsTranslation(String label)
Checks to see if we contain the given translation.
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boolean |
containsTree(String label)
Checks to see if we contain the given tree.
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List |
getComments()
Returns all comments.
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Map |
getTranslations()
Get the translations added so far.
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Object |
getTree(String label)
Returns a tree for given label
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org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> |
getTreeAsJGraphT(String label)
Get given (NewieckString) tree by label, converts it to unweighted graph (JGraphT).
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org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> |
getTreeAsWeightedJGraphT(String label)
Get given (NewieckString) tree by label, converts it to weighted graph (JGraphT).
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Map |
getTrees()
Returns all trees.
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void |
removeComment(NexusComment comment)
Removes a comment.
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void |
removeTranslation(String label)
Removes the given translation.
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void |
removeTree(String label)
Removes a tree.
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protected void |
writeBlockContents(Writer writer)
Implement this to write out block contents, not including the BEGIN
and END tags.
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getBlockName, writeObject, writeToken
public static final String TREES_BLOCK
public TreesBlock()
public void addTranslation(String label, String taxa)
label
- the label to add.taxa
- the taxa name this label will represent.public void removeTranslation(String label)
label
- the label to remove.public boolean containsTranslation(String label)
label
- the label to check for.public Map getTranslations()
public void addTree(String label, TreesBlock.NewickTreeString tree)
label
- the label to give the tree.tree
- the tree to add.public void removeTree(String label)
label
- the label to remove.public boolean containsTree(String label)
label
- the label to check for.public Map getTrees()
public Object getTree(String label)
label
- the label to select.public void addTree(String label, org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> treegraph)
label
- the label to addtreegraph
- the treegraph to convert.public void addTree(String label, org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph)
label
- the label to addtreegraph
- the treegraph to convert.public org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> getTreeAsJGraphT(String label)
label
- label for tree selectionpublic org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> getTreeAsWeightedJGraphT(String label)
label
- label for tree selectionpublic 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.