|
FORESTER 1.6 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--forester.tools.RIO
Field Summary | |
static java.lang.String |
DISTANCE_MATRIX_FILE_SUFFIX
|
static java.lang.String |
MULTIPLE_TREES_FILE_SUFFIX
|
static java.lang.String |
ORTHOLOG_OUTFILE_TABLE_SUFFIX
|
static java.lang.String |
OUTFILE_LIST_SUFFIX
|
static java.lang.String |
S_ORTHOLOG_OUTFILE_TABLE_SUFFIX
|
Constructor Summary | |
RIO()
Default constructor. |
Method Summary | |
double |
getDistance(java.lang.String name1,
java.lang.String name2)
Returns the distance between two sequences/taxa after a distance matrix file has been read in with readDistanceMatrix(File). |
java.util.HashMap |
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. |
java.util.HashMap |
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. |
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. |
long |
getTime()
Returns the time (in ms) needed to run "inferOrthologs". |
void |
inferOrthologs(java.io.File gene_trees_file,
Tree species_tree)
Infers the orthologs (and "super orthologs") for each external node of the gene Trees in multiple tree File gene_trees_file (=output of PHYLIP). |
void |
inferOrthologs(Tree[] gene_trees,
Tree species_tree)
Infers the orthologs (and "super orthologs") for each external node in Tree array gene_trees. |
java.util.ArrayList |
inferredOrthologsToArrayList(java.lang.String seq_name,
double threshhold_orthologs,
double threshhold_super_orthologs)
Returns an ArrayList containg the names of orthologs of the Node with seq name seq_name. |
void |
inferredOrthologsToFile(java.io.File outfile,
int sort,
double threshhold_orthologs,
double threshhold_super_orthologs)
Writes the orthologs as well as the "super orthologs" for each external nodes of the gene trees to outfile. |
java.lang.String |
inferredOrthologsToString(java.lang.String seq_name,
int sort,
double threshhold_orthologs,
double threshhold_super_orthologs)
Returns a String containg the names of orthologs of the Node with seq name seq_name. |
void |
inferredOrthologTableToFile(java.io.File outfile)
Writes the orthologs for each external nodes of the gene trees to outfile in the form of a table. |
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. |
static void |
main(java.lang.String[] args)
Main method for this class. |
void |
readDistanceMatrix(java.io.File matrix_file)
Reads in the distance matrix file matrix_file. |
Methods inherited from class java.lang.Object |
|
Field Detail |
public static final java.lang.String MULTIPLE_TREES_FILE_SUFFIX
public static final java.lang.String DISTANCE_MATRIX_FILE_SUFFIX
public static final java.lang.String OUTFILE_LIST_SUFFIX
public static final java.lang.String ORTHOLOG_OUTFILE_TABLE_SUFFIX
public static final java.lang.String S_ORTHOLOG_OUTFILE_TABLE_SUFFIX
Constructor Detail |
public RIO()
Method Detail |
public void inferOrthologs(Tree[] gene_trees, Tree species_tree)
gene_trees
- a Tree[] which is the result of performing
a bootstrap analysis, nodes of trees must have
species names and sequence names in the
appropriate fieldsspecies_tree
- a species Tree, which has species names in
its species fieldsgetInferredOrthologs(String)
,
getInferredSuperOrthologs(String)
,
inferredOrthologsToString(String,int,double,double)
,
inferredOrthologsToFile(File,int,double,double)
,
inferredOrthologTableToFile(File)
,
inferredSuperOrthologTableToFile(File)
public void inferOrthologs(java.io.File gene_trees_file, Tree species_tree) throws java.lang.Exception
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 Tree, which has species names in
its species fieldsgetInferredOrthologs(String)
,
getInferredSuperOrthologs(String)
,
inferredOrthologsToString(String,int,double,double)
,
inferredOrthologsToFile(File,int,double,double)
,
inferredOrthologTableToFile(File)
,
inferredSuperOrthologTableToFile(File)
public java.lang.String inferredOrthologsToString(java.lang.String seq_name, int sort, double threshhold_orthologs, double threshhold_super_orthologs) throws java.lang.Exception
seq_name
- sequence name of a external node of the gene treessort
- order and sort prioritythreshhold_orthologs
- the minimal number of observations for a
a sequence to be reported as orthologousthreshhold_super_orthologs
- the minimal number of observations for a
a sequence to be reported as super
orthologous -- the relation between
"threshhold_orthologs" and
"threshhold_super_orthologs" is ANDinferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
,
getOrder(int)
public java.util.ArrayList inferredOrthologsToArrayList(java.lang.String seq_name, double threshhold_orthologs, double threshhold_super_orthologs) throws java.lang.Exception
seq_name
- sequence name of a external node of the gene treesthreshhold_orthologs
- the minimal number of observations for a
a sequence to be reported as orthologousthreshhold_super_orthologs
- the minimal number of observations for a
a sequence to be reported as
super orthologous -- the relation between
"threshhold_orthologs" and
"threshhold_super_orthologs" is ANDinferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
,
getOrder(int)
public void inferredOrthologsToFile(java.io.File outfile, int sort, double threshhold_orthologs, double threshhold_super_orthologs) throws java.lang.Exception
sort
- order and sort prioritythreshhold_orthologs
- the minimal number of observations for a
a sequence to be reported as orthologousthreshhold_super_orthologs
- the minimal number of observations for a
a sequence to be reported as super
orthologous -- the relation between
"threshhold_orthologs" and
"threshhold_super_orthologs" is ANDOrthologs are to be inferred by method "inferOrthologs".
Overwrites without asking!
(Last modified: 12/07/00)
,
inferredOrthologsToString(String,int,double,double)
,
inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
,
getOrder(int)
public void inferredOrthologTableToFile(java.io.File outfile) throws java.lang.Exception
outfile
- the File to write toinferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public void inferredSuperOrthologTableToFile(java.io.File outfile) throws java.lang.Exception
outfile
- the File to write toinferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public java.util.HashMap getInferredOrthologs(java.lang.String seq_name) throws java.lang.Exception
seq_name
- sequence name of a external node of the gene treesinferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public java.util.HashMap getInferredSuperOrthologs(java.lang.String seq_name) throws java.lang.Exception
seq_name
- sequence name of a external node of the gene treesinferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public java.lang.String getOrder(int sort)
sort
- determines order and sort priority(Last modified: 11/29/00)
,
inferredOrthologsToString(String,int,double,double)
,
inferredOrthologsToFile(File,int,double,double)
public long getTime()
inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public void readDistanceMatrix(java.io.File matrix_file) throws java.lang.Exception
matrix_file
- a File containing a distance matrixgetDistance(String,String)
public double getDistance(java.lang.String name1, java.lang.String name2) throws java.lang.Exception
name1
- a sequence name
name2 a sequence namereadDistanceMatrix(File)
public static void main(java.lang.String[] args)
args[
- 0 ] multiple gene trees file nameargs[
- 1 ] species tree file nameargs[
- 2 ] output file nameargs[
- 3 ] order and priority of sortingargs[
- 4 ] threshhold for orthologargs[
- 5 ] threshhold for super ortholog
[@param args[ 6 ] distance matrix file name ](Last modified: 11/20/00)
|
FORESTER 1.6 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |