* append slash to the end of a directory name */

* expand the ~ to the $Home directory */

Function that tries to locate a tool with which

simple left-to-right search starting from given fragment 'from' efficient, when many 'chrPos' are searched in left-to-right order

* SequenceFeatureCollection::getAllActiveFeatures * */

* getExonListOvlpingRange * seqRelFrame is the position of a first (5' -> 3') nucleotide of a codon modulo 3, -1 if frame does not matter */

* SequenceFeatureCollection::getFeatureListAt * returns a pointer to the list of all features of type 'type' which end at 'endPosition' and are on st

Retrieve the length of the query sequence of the alignment, i.e the length of the SEQ Field */

* this clones the row */

* NAMGene::getTrainViterbiPath * * Does the whole job of finding the most likely path for training. * No splitting into chunks. No alternatives. N

* insert one hint into database * start and end are 0-based and inclusive */

returns true if alignment mapped to reverse strand */

! @brief return whether value is a floating-point number This function returns true if and only if the JSON value is a floating-point num

! @brief return whether value is an integer number This function returns true if and only if the JSON value is a signed or unsigned integ

* get the local malus for CDSpart and UTRpart depending on the length * CDSpart stands for (CDSpartF or exonpartF), UTRpart stands for (UTRpartF or e

Function that normalizes a float consisting of mantisse and exponent to a mantisse that has one digit in front of comma. Assumption is

* set flag to 1 for all positions covered by at last one feature */

parses the linked list of Data structs */

Returns the random seed used at the start of the current test run.

Initialization method

! @brief set the iterator past the last value @pre The iterator is initialized; i.e. `m_object != nullptr`. */

checking whether two alignments (or two alignment pairs) are similar Purpose: Due to separate handling of spliced and unspliced alignments it can happ

Gets the number of skipped tests.

* split a string into tokens based on a given delimiter */

position in the profile for a base coordinate specified by offset; returns (b,i) where b is the last block and i is the distance of lastValue() to the

Gets the number of all test suites that contain at least one test that should run.

! @brief unget current character (read it again on next get) We implement unget by setting variable next_unget to true. The input is not

* HintGroup::updateFeatureConformance * Updates conformance of the Features of this group to the other group. * For each Feature f of 'this', numSup

Adds a test to this test suite. Will delete the test upon destruction of the TestSuite object.

Returns true iff this number is at most kMaxUlps ULP's away from rhs. In particular, this function: - returns false if either number is (or both are