@brief position of the match within the subject string */

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. */

Function: p7_hmm_Destroy() * Synopsis: Free a <P7_HMM>. * * Purpose: Frees both the shell and body of an <hmm>. * Works even if the

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

Function: esl_randomness_Destroy() * Synopsis: Free an RNG. * * Purpose: Frees an <ESL_RANDOMNESS> object. */

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

* @todo : must be KMP or hashing instead of this */

Function: esl_sq_Destroy() * Synopsis: Frees an <ESL_SQ>. * Incept: SRE, Thu Dec 23 12:28:07 2004 [Zaragoza] * * Purpose: Free a Create()'d

Function: esl_opt_GetArg() * Synopsis: Retrieve numbered command line argument. * * Purpose: Returns a pointer to command line argument number

Compile time row arguments

Function: p7_bg_Destroy() * * Purpose: Frees a <P7_BG> object. * * Returns: (void) * * Xref: SRE:STL11/125. */

Function: p7_bg_Create() * Synopsis: Create a <P7_BG> null model object. * * Purpose: Allocate a <P7_BG> object for digital alphabet <abc>, *

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

Right operand access !\brief Returns the right-hand side dense vector operand. // // \return The right-hand side dense vector operand. */

Left operand access !\brief Returns the left-hand side sparse vector operand. // // \return The left-hand side sparse vector operand. */

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

! \cond BLAZE_INTERNAL */ !\brief Returns the index of the column containing the first element of the band. // // \return The first column index. */

! \cond BLAZE_INTERNAL */ !\brief Returns the index of the row of the underlying dense matrix. // // \return The index of the row. */

Function: esl_opt_IsOn() * Synopsis: Returns <TRUE> if option is set to a non-<NULL> value. * * Purpose: Returns <TRUE> if option is on (set to

Vector base type of the expression

Returns the explanation accumulated so far.

Type of the value element

Type of the random number

Compile time row arguments

startswith - Check if this string starts with the given \p Prefix.

Type tag

Creates a polymorphic matcher that matches a 2-tuple where the first field != the second field.

Remaining row indices

! \cond BLAZE_INTERNAL */ !\brief Returns the number of columns of the submatrix. // // \return The number of columns of the submatrix. */

! \cond BLAZE_INTERNAL */ !\brief Returns the number of rows of the submatrix. // // \return The number of rows of the submatrix. */

Storage order of the right-hand side matrix

/////////////////// Edge information

Function: p7_profile_Destroy() * Synopsis: Frees a profile. * * Purpose: Frees a profile <gm>. * * Returns: (void). * * Xref: STL11/

* String representation of this Seq * * @return ACGT-string of length size_ * @see nucl() */

Type tag

Storage order of the right-hand side matrix

Compile time submatrix arguments

Function: p7_ProfileConfig() * Synopsis: Configure a search profile. * * Purpose: Given a model <hmm> with core probabilities, the null1 *

Storage order of the right-hand side matrix

Function: p7_CreateDefaultApp() * Synopsis: Initialize a small/simple/standard HMMER application * Incept: SRE, Thu Oct 28 15:03:21 2010 [Janel

Function: esl_stopwatch_Start() * * Purpose: Start a stopwatch. This sets the base * for elapsed, cpu, and system time difference *

Type tag

Function: esl_stopwatch_Stop() * * Purpose: Stop a stopwatch. Record and store elapsed, * cpu, and system time difference relative to

Function: p7_bg_SetLength() * Synopsis: Set the null model length distribution. * * Purpose: Sets the geometric null model length *

Function: esl_msafile_Close() * Synopsis: Close an open <ESL_MSAFILE>. */

Function: p7_gmx_Create() * Synopsis: Allocate a new <P7_GMX>. * * Purpose: Allocate a reusable, resizeable <P7_GMX> for models up to *

Function: p7_gmx_Destroy() * Synopsis: Frees a DP matrix. * * Purpose: Frees a <P7_GMX>. * * Returns: (void) */

Type of the dense matrix

Matrix base type of the expression

Append function !\brief Appending an element to the sparse vector. // // \param index The index of the new element. The index has to be in the r

Function: esl_msafile_Open() * Synopsis: Open a multiple sequence alignment file for input. * * Purpose: Open a multiple sequence alignment fil