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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--forester.tools.RIO
Constructor Summary | |
RIO()
Default constructor. |
Method Summary | |
int |
getBootstraps()
Returns the numbers of trees analyzed. |
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). |
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). |
int |
getExtNodesOfAnalyzedGeneTrees()
Returns the numbers of number of ext nodes in gene trees analyzed (after stripping). |
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 NEIGHBOR, for example). |
void |
inferOrthologs(java.io.File gene_trees_file,
Tree species_tree,
java.lang.String query)
Infers the orthologs (and "super orthologs") for each external node of the gene Trees in multiple tree File gene_trees_file (=output of PHYLIP NEIGHBOR, for example). |
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 threshold_orthologs,
double threshold_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 threshold_orthologs,
double threshold_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 query_name,
int sort,
double threshold_orthologs,
double threshold_super_orthologs)
Returns a String containg the names of orthologs of the Node with seq name query_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. |
void |
readDistanceList(java.io.File dist_list)
Reads in the distance list file dist_list. |
void |
readDistanceMatrix(java.io.File matrix_file)
Reads in the distance matrix file matrix_file. |
static int |
roundToInt(double d)
Rounds a double to a int. |
Methods inherited from class java.lang.Object |
|
Constructor Detail |
public RIO()
Method Detail |
public void inferOrthologs(java.io.File gene_trees_file, Tree species_tree, java.lang.String query) throws java.lang.Exception
To obtain the results use the methods listed below.
(Last modified: 06/12/01)
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 fieldsquery
- the sequence name of the squence whose orthologs
are to be inferredgetInferredOrthologs(String)
,
getInferredSuperOrthologs(String)
,
inferredOrthologsToString(String,int,double,double)
,
inferredOrthologsToFile(File,int,double,double)
,
inferredOrthologTableToFile(File)
,
inferredSuperOrthologTableToFile(File)
public void inferOrthologs(Tree[] gene_trees, Tree species_tree)
To obtain the results use the methods listed below.
(Last modified: 12/07/00)
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
To obtain the results use the methods listed below.
(Last modified: 12/07/00)
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 fieldsinferOrthologs(File,Tree,String)
,
getInferredOrthologs(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 query_name, int sort, double threshold_orthologs, double threshold_super_orthologs) throws java.lang.Exception
Returns null if orthologs have not been calculated (successfully); or if distance list or matrix have not been read in (successfully) -- in case sort > 2.
Returns "-" if no putative orthologs have been found.
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 prioritybootstraps
- threshold_orthologs
- the minimal number of observations for a
a sequence to be reported as orthologous,
in percents (0.0-100.0%)threshold_super_orthologs
- the minimal number of observations for a
a sequence to be reported as super
orthologous, in percents (0.0-100.0%)
-- the relation between
"threshold_orthologs" and
"threshold_super_orthologs" is ANDinferOrthologs(File,Tree,String)
,
inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
,
getOrder(int)
public java.util.ArrayList inferredOrthologsToArrayList(java.lang.String seq_name, double threshold_orthologs, double threshold_super_orthologs) throws java.lang.Exception
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%)threshold_super_orthologs
- the minimal number of observations for a
a sequence to be reported as
super orthologous -- the relation between
"threshold_orthologs" and
"threshold_super_orthologs" is AND
as percentage (0.0-100.0%)inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
,
getOrder(int)
public void inferredOrthologsToFile(java.io.File outfile, int sort, double threshold_orthologs, double threshold_super_orthologs) throws java.lang.Exception
sort
- order and sort prioritythreshold_orthologs
- the minimal number of observations for a
a sequence to be reported as orthologousthreshold_super_orthologs
- the minimal number of observations for a
a sequence to be reported as super
orthologous -- the relation between
"threshold_orthologs" and
"threshold_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()
(Last modified: 11/14/00)
inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public int getBootstraps()
(Last modified: 02/20/00)
inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public int getExtNodesOfAnalyzedGeneTrees()
(Last modified: 05/02/00)
inferOrthologs(Tree[],Tree)
,
inferOrthologs(File,Tree)
public void readDistanceMatrix(java.io.File matrix_file) throws java.lang.Exception
[number of sequences, is ignored, and is not necessary] name x x x name x x x name x x x
Number of white spaces does not matter. Such files are produces by PHYLIP PROTDIST. Files produced by TREE-PUZZLE need to be modified to remove the newlines "inside" the rows.
(Last modified: 11/28/00)
matrix_file
- a File containing a distance matrixgetDistance(String,String)
public void readDistanceList(java.io.File dist_list) throws java.lang.Exception
name x name x name xNumber of white spaces does not matter. Such files are produces by modified TREE-PUZZLE.
(Last modified: 05/30/01)
dist_list
- a File containing a distance matrixgetDistance(String)
public double getDistance(java.lang.String name1, java.lang.String name2) throws java.lang.Exception
(Last modified: 11/28/00)
name1
- a sequence name
name2 a sequence namereadDistanceMatrix(File)
public double getDistance(java.lang.String name) throws java.lang.Exception
(Last modified: 05/30/01)
name
- a sequence namereadDistanceList(File)
public static int roundToInt(double d)
(Last modified: 03/15/01)
d
- a double to be rounded to a int
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FORESTER 1.8 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |