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java.lang.Objectuk.ac.vamsas.objects.utils.trees.NewickFile
DOCUMENT ME!
Constructor Summary | |
NewickFile(java.io.File inFile)
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NewickFile(SequenceNode newtree)
Creates a new NewickFile object. |
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NewickFile(SequenceNode newtree,
boolean bootstrap)
Creates a new NewickFile object. |
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NewickFile(SequenceNode newtree,
boolean bootstrap,
boolean distances)
Creates a new NewickFile object. |
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NewickFile(SequenceNode newtree,
boolean bootstrap,
boolean distances,
boolean rootdistance)
Creates a new NewickFile object. |
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NewickFile(java.lang.String inStr)
Creates a new NewickFile object |
Method Summary | |
void |
_print(java.lang.StringBuffer tf,
SequenceNode c)
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java.util.Vector |
attachTreeMap(Treenode[] tn)
re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode. |
java.util.Vector |
findLeaves(SequenceNode node,
java.util.Vector leaves)
Search for leaf nodes. |
SequenceNode |
getTree()
DOCUMENT ME! |
boolean |
HasBootstrap()
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boolean |
HasDistances()
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boolean |
HasRootDistance()
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static void |
main(java.lang.String[] args)
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Treenode[] |
makeTreeNodes()
make tree node vector from a newick tree structure with associated vamsas objects |
Treenode[] |
makeTreeNodes(boolean ignoreplaceholders)
make treenode vector for a parsed tree with/out leaf node associations |
Treenode[] |
matchTreeNodeNames(java.lang.String[] names,
Vobject[] boundObjects)
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java.lang.String |
nextLine()
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void |
parse()
call this to convert the newick string into a binary node linked tree Note: this is automatically called by the constructors, so you normally wouldn't need to use this. |
java.lang.String |
print()
Generate a newick format tree according to internal flags for bootstraps, distances and root distances. |
java.lang.String |
print(boolean withbootstraps)
Generate a newick format tree according to internal flags for distances and root distances and user specificied writing of bootstraps. |
java.lang.String |
print(boolean withbootstraps,
boolean withdists)
Generate newick format tree according to internal flags for writing root node distances. |
java.lang.String |
print(boolean withbootstraps,
boolean withdists,
boolean printRootInfo)
Generate newick format tree according to user specified flags |
void |
print(java.lang.StringBuffer tf,
SequenceNode root)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public NewickFile(java.lang.String inStr) throws java.io.IOException
inStr
- Newick style tree string
java.io.IOException
- if string is not a valid newick filepublic NewickFile(java.io.File inFile) throws java.io.IOException
public NewickFile(SequenceNode newtree)
newtree
- DOCUMENT ME!public NewickFile(SequenceNode newtree, boolean bootstrap)
newtree
- DOCUMENT ME!bootstrap
- DOCUMENT ME!public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
newtree
- DOCUMENT ME!bootstrap
- DOCUMENT ME!distances
- DOCUMENT ME!public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances, boolean rootdistance)
newtree
- DOCUMENT ME!bootstrap
- DOCUMENT ME!distances
- DOCUMENT ME!rootdistance
- DOCUMENT ME!Method Detail |
public boolean HasBootstrap()
public boolean HasDistances()
public boolean HasRootDistance()
public java.lang.String nextLine() throws java.io.IOException
java.io.IOException
public void parse() throws java.io.IOException
java.io.IOException
- if the newick string cannot be parsed.public SequenceNode getTree()
public Treenode[] matchTreeNodeNames(java.lang.String[] names, Vobject[] boundObjects)
public java.lang.String print()
public java.lang.String print(boolean withbootstraps)
withbootstraps
- controls if bootstrap values are explicitly written.
public java.lang.String print(boolean withbootstraps, boolean withdists)
withbootstraps
- explicitly write bootstrap valueswithdists
- explicitly write distances
public java.lang.String print(boolean withbootstraps, boolean withdists, boolean printRootInfo)
withbootstraps
- explicitly write bootstrap valueswithdists
- explicitly write distancesprintRootInfo
- explicitly write root distance
public void print(java.lang.StringBuffer tf, SequenceNode root)
public void _print(java.lang.StringBuffer tf, SequenceNode c)
public static void main(java.lang.String[] args)
public java.util.Vector findLeaves(SequenceNode node, java.util.Vector leaves)
node
- root node to search fromleaves
- Vector of leaves to add leaf node objects too.
public Treenode[] makeTreeNodes()
public Treenode[] makeTreeNodes(boolean ignoreplaceholders)
ignoreplaceholders
- if true means only associated nodes are returned
public java.util.Vector attachTreeMap(Treenode[] tn)
tn
-
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