public final class RIO
extends java.lang.Object
Constructor and Description |
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RIO()
Default constructor.
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Modifier and Type | Method and Description |
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int |
getBootstraps()
Returns the numbers of trees analyzed.
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double |
getDistance(java.lang.String name)
Returns the distance to a sequences/taxa after a distance list file has
been read in with readDistanceList(File).
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double |
getDistance(java.lang.String name1,
java.lang.String name2) |
int |
getExtNodesOfAnalyzedGeneTrees()
Returns the numbers of number of ext nodes in gene trees analyzed (after
stripping).
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java.util.HashMap<java.lang.String,java.lang.Integer> |
getInferredOrthologs(java.lang.String seq_name)
Returns a HashMap containing the inferred orthologs of the external gene
tree node with the sequence name seq_name.
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java.util.HashMap<java.lang.String,java.lang.Integer> |
getInferredSuperOrthologs(java.lang.String seq_name)
Returns a HashMap containing the inferred "super orthologs" of the
external gene tree node with the sequence name seq_name.
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java.util.HashMap<java.lang.String,java.lang.Integer> |
getInferredUltraParalogs(java.lang.String seq_name)
Returns a HashMap containing the inferred "ultra paralogs" of the
external gene tree node with the sequence name seq_name.
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static java.lang.String |
getOrder(int sort)
Returns the order in which ortholog (o), "super ortholog" (s) and
distance (d) are returned and sorted (priority of sort always goes from
left to right), given sort.
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static java.lang.StringBuffer |
getOrderHelp() |
long |
getTime()
Returns the time (in ms) needed to run "inferOrthologs".
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void |
inferOrthologs(java.io.File gene_trees_file,
Phylogeny species_tree,
java.lang.String query)
Infers the orthologs (as well the "super orthologs", the "subtree
neighbors", and the "ultra paralogs") for each external node of the gene
Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR,
for example).
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java.util.ArrayList<java.lang.String> |
inferredOrthologsToArrayList(java.lang.String seq_name,
double threshold_orthologs)
Returns an ArrayList containg the names of orthologs of the PhylogenyNode
with seq name seq_name.
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java.lang.StringBuffer |
inferredOrthologsToString(java.lang.String query_name,
int sort,
double threshold_orthologs,
double threshold_subtreeneighborings)
Returns a String containg the names of orthologs of the PhylogenyNode
with seq name query_name.
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void |
inferredOrthologTableToFile(java.io.File outfile)
Writes the orthologs for each external node of the gene trees to outfile
in the form of a table.
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void |
inferredSuperOrthologTableToFile(java.io.File outfile)
Writes the "super orthologs" for each external nodes of the gene trees to
outfile in the form of a table.
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java.lang.String |
inferredUltraParalogsToString(java.lang.String query_name,
boolean return_dists,
double threshold_ultra_paralogs)
Returns a String containg the names of orthologs of the PhylogenyNode
with seq name query_name.
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void |
readDistanceMatrix(java.io.File matrix_file) |
public final int getBootstraps()
public final double getDistance(java.lang.String name)
name
- a sequence namepublic final double getDistance(java.lang.String name1, java.lang.String name2)
public final int getExtNodesOfAnalyzedGeneTrees()
public final java.util.HashMap<java.lang.String,java.lang.Integer> getInferredOrthologs(java.lang.String seq_name)
seq_name
- sequence name of a external node of the gene treespublic final java.util.HashMap<java.lang.String,java.lang.Integer> getInferredSuperOrthologs(java.lang.String seq_name)
seq_name
- sequence name of a external node of the gene treespublic final java.util.HashMap<java.lang.String,java.lang.Integer> getInferredUltraParalogs(java.lang.String seq_name)
seq_name
- sequence name of a external node of the gene treespublic long getTime()
public void inferOrthologs(java.io.File gene_trees_file, Phylogeny species_tree, java.lang.String query) throws java.io.IOException, SDIException
To obtain the results use the methods listed below.
gene_trees_file
- a File containing gene Trees in NH format, which is the result
of performing a bootstrap analysis in PHYLIPspecies_tree
- a species Phylogeny, which has species names in its species
fieldsquery
- the sequence name of the squence whose orthologs are to be
inferredSDIException
java.io.IOException
public java.util.ArrayList<java.lang.String> inferredOrthologsToArrayList(java.lang.String seq_name, double threshold_orthologs)
seq_name
- sequence name of a external node of the gene treesthreshold_orthologs
- the minimal number of observations for a a sequence to be
reported as orthologous as percentage (0.0-100.0%)public java.lang.StringBuffer inferredOrthologsToString(java.lang.String query_name, int sort, double threshold_orthologs, double threshold_subtreeneighborings)
The sort priority of this is determined by sort in the following manner:
Returns "-" if no putative orthologs have been found (given threshold_orthologs).
Orthologs are to be inferred by method "inferOrthologs".
(Last modified: 05/08/01)
query_name
- sequence name of a external node of the gene treessort
- order and sort prioritythreshold_orthologs
- the minimal number of observations for a a sequence to be
reported as orthologous, in percents (0.0-100.0%)threshold_subtreeneighborings
- the minimal number of observations for a a sequence to be
reported as orthologous, in percents (0.0-100.0%)inferOrthologs(File,Phylogeny,String)
,
#inferOrthologs(Phylogeny[],Phylogeny)
,
#inferOrthologs(File,Phylogeny)
,
getOrder(int)
public void inferredOrthologTableToFile(java.io.File outfile) throws java.io.IOException
outfile
- the File to write tojava.io.IOException
public void inferredSuperOrthologTableToFile(java.io.File outfile) throws java.io.IOException
outfile
- the File to write tojava.io.IOException
public java.lang.String inferredUltraParalogsToString(java.lang.String query_name, boolean return_dists, double threshold_ultra_paralogs)
Orthologs are to be inferred by method "inferOrthologs".
query_name
- sequence name of a external node of the gene treesreturn_dists
- threshold_ultra_paralogs
- between 1 and 100public final void readDistanceMatrix(java.io.File matrix_file) throws java.io.IOException
java.io.IOException
public static final java.lang.String getOrder(int sort)
sort
- determines order and sort priorityinferredOrthologsToString(String,int,double,double)
public static final java.lang.StringBuffer getOrderHelp()