///////////////// shortcut methods

* @brief Removes the specific entry from the index, and its conjugate. * @warning Don't use it on unclustered index, because hashmaps require set

* @brief Returns the copy of all points in a simple flat histogram. */

Function: esl_histogram_Destroy() * Synopsis: Frees a <ESL_HISTOGRAM>. * * Purpose: Frees an <ESL_HISTOGRAM> object <h>. */

Function: esl_msafile_GetLine() * Synopsis: Read next line of input alignment file. * * Purpose: Read next line of input <afp>, into its intern

Function: esl_strtok_adv() * Synopsis: More advanced interface to <esl_strtok()> * * Purpose: Same as <esl_strtok()>, except the caller may also

Insertion routines.

/ * * @brief generates man sections from command line parameters * with sections "synopsis" and "options" * *******************************

must be thread safe as it is called from stats_merge

Function: p7_Pipeline() * Synopsis: HMMER3's accelerated seq/profile comparison pipeline. * * Purpose: Run H3's accelerated pipeline to compare

Function: p7_oprofile_Convert() * Synopsis: Converts standard profile to an optimized one. * Incept: SRE, Mon Nov 26 07:38:57 2007 [Janelia] *

Getter for the position of this node in its parent.

Type tag

Formats a source file path and a line number as they would appear in an error message from the compiler used to compile this code.

Creates a polymorphic matcher that matches an empty container or C-style string. The container must support both size() and empty(), which all STL-lik

Result type

Data type of the foreign expression

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Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */

Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */

Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */

Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */

Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */

compare - Compare two strings; the result is -1, 0, or 1 if this string is lexicographically less than, equal to, or greater than the \p RHS.

Returns the number of live test objects that uses this fixture.

Gets the elapsed time, in milliseconds.

Compile time row arguments

Function: esl_sse_rightshiftz_float() * Synopsis: Shift float vector elements to the right, shifting zero on. * * Purpose: Same as <esl_sse_rig

find_first_of - Find the first character in the string that is in \arg Chars, or npos if not found. Note: O(size() + Chars.size())

@brief returns if a command line argument can be matched by a * combination of (partial) matches through any number of children */

Compile time submatrix arguments

make_digital_consensus_line() * * Exactly the same as make_text_consensus_line(), except for * digital mode <msa>. */

Function: p7_oprofile_Convert() * Synopsis: Converts standard profile to an optimized one. * Incept: SRE, Mon Nov 26 07:38:57 2007 [Janelia] *

Bitwise right rotate. Normally this will compile to a single instruction, especially if the shift is a manifest constant.

Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */

Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */

Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */

Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */