* meanStateProb * * returns the geometric mean of the exon state posterior probabilities */

Returns the working directory when the first TEST() or TEST_F() was executed.

! @brief public parser interface @param[in] strict whether to expect the last token to be EOF @param[in,out] result parsed JSON val

* get the global malus for exonpart, etc depending on the length * precompute values the first time they are needed (for each type separately) */

* precompute tables for computing a local exonpart/UTRpart/CDSpart malus later */

* Read the next sequence from input file stream and store the sequence, * its name and length in the arguments. Memory for sequence and name are allo

Gets the number of disabled tests that will be reported in the XML report.

reset token_buffer; current character is beginning of token

returns the final similarity score

Determine the branch lengths for which matrices P should be stored, at most m. * For trees with few species, say <10, this could be all branch length

! @brief returns x - y @pre x.e == y.e and x.f >= y.f */

Returns the number of the test properties.

Gets the number of all test suites.

* NcModel::viterbiForwardAndSampling */

Matches a string that contains regular expression 'regex'. The matcher takes ownership of 'regex'.

Describes this matcher to an ostream.

Formats a countable noun. Depending on its quantity, either the singular form or the plural form is used. e.g. FormatCountableNoun(1, "formula", "fo

Utilty function to Open File for Writing

Sets the test part result reporter for the current thread.

! @brief public accept interface @param[in] strict whether to expect the last token to be EOF @return whether the input is a proper JSON

add new hint into the list of ASS hints

add new hint into the list of DSS hints

add a Row to the similarity matrix

iterator methods

! @brief returns a const iterator to one past the last element Returns a const iterator to one past the last element. @image html range-

If TOOL_PATH is provided as command line option, check whether the required binary is executable in that directory; return tool binary with

* Gene::completeCDS * checks whether it has a single or initial and terminal CDS and the first and last coding exons are not truncated */

creates and writes the wigfile*/

Returns the most specific TestResult currently running.

escape "~" to "~0" and "/" to "~1"

convert from alignment to chromosomal position (inverse function of getAliPos())

void print(vector<int> &counts, bool verbose, bool countsOnly);

generates an identification key

0x7F bit mask for retrieving bits 1-7

* Gene::getPercentSupported * in [0,1] */

access substates

the following methods can be used also when the map is NULL

! @brief inserts element Inserts element @a val before iterator @a pos. @param[in] pos iterator before which the content will be inserte