public class GroupAggreg extends CommonCLI
java -cp procalign.jar fr.inrialpes.exmo.align.util.GroupAggreg [options]where the options are:
-l,--list <FILE> List of FILEs to be included in the results (required) -m,--aggmethod <METHOD> Method to use for aggregating (min|max|avg|pool) -P,--params <FILE> Read parameters from FILE -T,--cutmethod <METHOD> Method to use for triming (hard|perc|prop|best|span) -t,--threshold <DOUBLE> Trim the alignment with regard to threshold -w,--workDir <DIR> The DIRectory containing the data to evaluateThe input is taken in the current directory in a set of subdirectories (one per test which will be rendered by a line) each directory contains a number of alignment files (one per algorithms which will be renderer as a column). If output is requested (
-o
flags), then output will be written to
output
if present, stdout by default.
$Id: GroupAggreg.java 2173 2017-08-02 11:47:17Z euzenat $
Modifier and Type | Field and Description |
---|---|
(package private) java.lang.String |
aggMethod |
(package private) java.lang.String |
cutMethod |
(package private) java.lang.String |
dirName |
(package private) java.lang.String[] |
listAlgo |
(package private) static org.slf4j.Logger |
logger |
(package private) int |
size |
(package private) java.lang.String |
srcDir |
(package private) double |
threshold |
options, outputfilename, parameters
Constructor and Description |
---|
GroupAggreg() |
Modifier and Type | Method and Description |
---|---|
void |
iterateAlignments(java.io.File dir) |
void |
iterateDirectories()
Each directory contains various alignments between the same ontologies
|
BasicAlignment |
loadAlignment(java.lang.String alignName) |
static void |
main(java.lang.String[] args) |
void |
print(Alignment al,
java.lang.String outputfilename)
Print the aggregated alignment, it is not void...
|
void |
run(java.lang.String[] args) |
void |
usage() |
createListOption, createOption, createOptionalOption, createRequiredOption, exit, parseCommandLine, parseSpecificCommandLine, usage, usage, usage
static final org.slf4j.Logger logger
java.lang.String[] listAlgo
int size
java.lang.String srcDir
java.lang.String dirName
double threshold
java.lang.String cutMethod
java.lang.String aggMethod
public static void main(java.lang.String[] args)
public void run(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception
public void iterateDirectories()
public void iterateAlignments(java.io.File dir)
public BasicAlignment loadAlignment(java.lang.String alignName)
public void print(Alignment al, java.lang.String outputfilename)
al:
- the alignment to be printedoutputfilename:
- the name of the file in which to print it(C) INRIA & friends, 2003-2020