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## Uses of Package
calhoun.util

Packages that use calhoun.util
calhoun.analysis.crf | the interface, main `Conrad` class, and solver for the Conrad engine.
calhoun.analysis.crf.io | handles input and output of gene calling formats
calhoun.analysis.crf.solver | training and inference algorithms used in the CRF engine
calhoun.analysis.crf.test |
calhoun.analysis.crf.test.slow |
calhoun.seq |
calhoun.seq.test |
calhoun.util |

Classes in calhoun.util used by calhoun.analysis.crf
DenseBooleanMatrix2D

Classes in calhoun.util used by calhoun.analysis.crf.io
RangeMap A rangeMap contains a set of intervals and maps each interval to a set of objects that exist in that interval.

Classes in calhoun.util used by calhoun.analysis.crf.solver
DenseIntMatrix2D

Classes in calhoun.util used by calhoun.analysis.crf.test
AbstractTestCase Basic test case with file matching (XML and regular) added as well as improved logging for errors.

Classes in calhoun.util used by calhoun.analysis.crf.test.slow
AbstractTestCase Basic test case with file matching (XML and regular) added as well as improved logging for errors.

Classes in calhoun.util used by calhoun.seq
ErrorException Exception type for general errors.

Classes in calhoun.util used by calhoun.seq.test
AbstractTestCase Basic test case with file matching (XML and regular) added as well as improved logging for errors.

Classes in calhoun.util used by calhoun.util
ConfigException Exception type for system configuration exceptions.

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