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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 | getInferredSubtreeNeighbors(java.lang.String seq_name)Returns a HashMap containing the inferred "subtree neighbors" 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.util.HashMap | 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. | 
|  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 (as well the "super orthologs", the "x orthologs", and the "ultra paralogs") for each external node in Tree array gene_trees. | 
|  void | inferOrthologs(java.io.File gene_trees_file,
               Tree 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). | 
|  void | inferOrthologs(Tree[] gene_trees,
               Tree species_tree)Infers the orthologs (as well the "super orthologs", the "x orthologs", and the "ultra paralogs") for each external node in Tree array gene_trees. | 
|  java.util.ArrayList | inferredOrthologsToArrayList(java.lang.String seq_name,
                             double threshold_orthologs)Returns an ArrayList containg the names of orthologs of the Node with seq name seq_name. | 
|  java.lang.String | inferredOrthologsToString(java.lang.String query_name,
                          int sort,
                          double threshold_orthologs,
                          double threshold_subtreeneighborings)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 node 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. | 
|  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 Node with seq name query_name. | 
|  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. | 
|  void | reset()Brings this into the same state as immediately after construction. | 
| 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 reset()
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: 10/19/01)
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), 
inferredOrthologTableToFile(File), 
inferredSuperOrthologTableToFile(File)
public void inferOrthologs(Tree[] gene_trees,
                           Tree species_tree)
                    throws java.lang.Exception
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), 
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: 10/19/01)
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 fieldsinferOrthologs(File,Tree,String), 
getInferredOrthologs(String), 
getInferredSuperOrthologs(String), 
inferredOrthologsToString(String,int,double,double), 
inferredOrthologTableToFile(File), 
inferredSuperOrthologTableToFile(File)
public java.lang.String inferredOrthologsToString(java.lang.String query_name,
                                                  int sort,
                                                  double threshold_orthologs,
                                                  double threshold_subtreeneighborings)
                                           throws java.lang.Exception
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,Tree,String), 
inferOrthologs(Tree[],Tree), 
inferOrthologs(File,Tree), 
getOrder(int)
public java.lang.String inferredUltraParalogsToString(java.lang.String query_name,
                                                      boolean return_dists,
                                                      double threshold_ultra_paralogs)
                                               throws java.lang.Exception
Orthologs are to be inferred by method "inferOrthologs".
(Last modified: 10/16/01)
query_name - sequence name of a external node of the gene treesreturn_dists -  threshold_ultra_paralogs - between 1 and 100inferOrthologs(File,Tree,String), 
inferOrthologs(Tree[],Tree), 
inferOrthologs(File,Tree), 
getOrder(int)
public java.util.ArrayList inferredOrthologsToArrayList(java.lang.String seq_name,
                                                        double threshold_orthologs)
                                                 throws java.lang.Exception
(Last modified: 10/07/01)
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%)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.util.HashMap getInferredSubtreeNeighbors(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 getInferredUltraParalogs(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: 10/07/01)
inferredOrthologsToString(String,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| 
 | FORESTER 1.92 | |||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
| SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | |||||||