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java.lang.Objectorg.forester.sdi.RIO
public final class RIO
Constructor Summary | |
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RIO()
Default constructor. |
Method Summary | |
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int |
getBootstraps()
Returns the numbers of trees analyzed. |
double |
getDistance(String name)
Returns the distance to a sequences/taxa after a distance list file has been read in with readDistanceList(File). |
double |
getDistance(String name1,
String name2)
|
int |
getExtNodesOfAnalyzedGeneTrees()
Returns the numbers of number of ext nodes in gene trees analyzed (after stripping). |
HashMap<String,Integer> |
getInferredOrthologs(String seq_name)
Returns a HashMap containing the inferred orthologs of the external gene tree node with the sequence name seq_name. |
HashMap<String,Integer> |
getInferredSuperOrthologs(String seq_name)
Returns a HashMap containing the inferred "super orthologs" of the external gene tree node with the sequence name seq_name. |
HashMap<String,Integer> |
getInferredUltraParalogs(String seq_name)
Returns a HashMap containing the inferred "ultra paralogs" of the external gene tree node with the sequence name seq_name. |
static 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. |
static StringBuffer |
getOrderHelp()
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long |
getTime()
Returns the time (in ms) needed to run "inferOrthologs". |
void |
inferOrthologs(File gene_trees_file,
Phylogeny species_tree,
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). |
ArrayList<String> |
inferredOrthologsToArrayList(String seq_name,
double threshold_orthologs)
Returns an ArrayList containg the names of orthologs of the PhylogenyNode with seq name seq_name. |
StringBuffer |
inferredOrthologsToString(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. |
void |
inferredOrthologTableToFile(File outfile)
Writes the orthologs for each external node of the gene trees to outfile in the form of a table. |
void |
inferredSuperOrthologTableToFile(File outfile)
Writes the "super orthologs" for each external nodes of the gene trees to outfile in the form of a table. |
String |
inferredUltraParalogsToString(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. |
void |
readDistanceMatrix(File matrix_file)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public RIO()
Method Detail |
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public final int getBootstraps()
public final double getDistance(String name)
name
- a sequence namepublic final double getDistance(String name1, String name2)
public final int getExtNodesOfAnalyzedGeneTrees()
public final HashMap<String,Integer> getInferredOrthologs(String seq_name)
seq_name
- sequence name of a external node of the gene trees
public final HashMap<String,Integer> getInferredSuperOrthologs(String seq_name)
seq_name
- sequence name of a external node of the gene trees
public final HashMap<String,Integer> getInferredUltraParalogs(String seq_name)
seq_name
- sequence name of a external node of the gene trees
public long getTime()
public void inferOrthologs(File gene_trees_file, Phylogeny species_tree, String query) throws IOException
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
inferred
IOException
public ArrayList<String> inferredOrthologsToArrayList(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 StringBuffer inferredOrthologsToString(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(File outfile) throws IOException
outfile
- the File to write to
IOException
public void inferredSuperOrthologTableToFile(File outfile) throws IOException
outfile
- the File to write to
IOException
public String inferredUltraParalogsToString(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 100
public final void readDistanceMatrix(File matrix_file) throws IOException
IOException
public static final String getOrder(int sort)
sort
- determines order and sort priority
inferredOrthologsToString(String,int,double,double)
public static final StringBuffer getOrderHelp()
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