* Resets local data after partitioning is done. */

Creats the Alphabet structure for standard protein alphabet. * @return pointer to the alphabet structure. */

Frees the Alpha structure and underlying structures. * @param palpha the object to be freed [in] */

Calculates number of links in a chain of BlastSeqLoc's. * @param var Chain of BlastSeqLoc structures [in] * @return Number of links in the chain. *

Makes a copy of the BlastSeqLoc and also a copy of the * SSRange element. Does not copy BlastSeqLoc that is pointed * to by "next". * @param sour

Calculates sequence composition array values. * @param win the object to be analyzed [in] */

Decrements the value in the int32_t array for every element that matches class. * There is also another criteria that the next element must have a vl

Calculates entropy of a sequence window * @param win object to be analyzed [in] */

Finds the last element below hicut, looks from i to limit. * @param i first element to check [in] * @param limit last element to check [in] * @para

This function calculates the natural log of the value P sub 0 from * equation 3 of Wootton and Federhen (Methods Enzymol. 1996;266:554-71). * @para

Checks if sequence contains a dash. * @param win SSequence structure for a piece of a sequence [in] * @return true if dash is found in the sequence,

* Return true if either the query or the matching sequences * passes the test in s_HighPairFrequencies. */

Increments the value in the int32_t array for every element that matches class. * @param sv the array to be examined and incremented [in|out] * @par

Calculates natural log of "Farben" which is the number of compositions * in any complexity state. See equation 1 of Wootton and Federhen * (Comput.

calculate "K2" entropy per equation 3 of Wootton and Federhen * (Comput. Chem. 17, 149 (1993). * @param sv state vector [in] * @param window_length

------------------------------------------------------------(mergesegs)---*/ merge together overlapping segments, * hilenmin also does something, bu

Initializes SSequence structure */

Frees the SSeg structure * @param seg the object to be freed [in] */

High-level function to perform calculations to find * low-complexity segments. Thi function calls itself * recursively * * @param seq sequence

Converts the internal representation used by seg to that used by BLAST * * @param segs internal representation [in] * @param offset fixed value to

Calculates entropy for a given sequence and window * * @param seq Sequence to examine [in] * @param window amount of sequence to examine at once [

* A function used to choose a mode for composition-based statistics. * Decide whether a relative-entropy score adjustment should be used * based on

Trims view of sequence so as to minimize the probability returned by s_GetProb * @param seq the part of sequence to be examined [in] * @param leften

* Reset the number of threads. * No thread must currently be waiting at this barrier. */