PSIMsa Struct Reference

Search Toolkit Book for PSIMsa

#include <blast_psi.h>

Collaboration diagram for PSIMsa:

[legend]List of all members.

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Detailed Description

Multiple sequence alignment (msa) data structure containing the raw data needed by the PSSM engine to create a PSSM.

By convention, the first row of the data field contains the query sequence

Definition at line 75 of file blast_psi.h.

Public Attributes
PSIMsaDimensions *	dimensions
	dimensions of the msa
PSIMsaCell **	data
	actual data, dimensions are (dimensions->num_seqs+1) by (dimensions->query_length)

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Member Data Documentation

PSIMsaCell** PSIMsa::data

actual data, dimensions are (dimensions->num_seqs+1) by (dimensions->query_length) Definition at line 77 of file blast_psi.h. Referenced by BOOST_AUTO_TEST_CASE(), CalculateInformationContent(), CdPssmInput::countResiduesInRow(), CPssmInputFlankingGaps::CPssmInputFlankingGaps(), CPssmInputGapsInQuery::CPssmInputGapsInQuery(), FillInAlignmentData(), PssmMaker::getPssmColumnResidues(), CdPssmInput::moveUpLongestRow(), CdPssmInput::Process(), PSIMsaFree(), PSIMsaNew(), CdPssmInput::read(), CPssmInputTestData::SetupSelfHit(), SU_PSSMInput::SU_PSSMInput(), CdPssmInput::unalignLeadingTrailingGaps(), CPsiBlastInputData::x_CopyQueryToMsa(), CPsiBlastInputClustalW::x_CopyQueryToMsa(), and CPsiBlastInputData::x_ProcessDenseg().

PSIMsaDimensions* PSIMsa::dimensions

dimensions of the msa Definition at line 76 of file blast_psi.h. Referenced by BOOST_AUTO_TEST_CASE(), CalculateInformationContent(), CPSIMsa::DebugDump(), FillInAlignmentData(), PssmMaker::getPssmColumnResidues(), PSIMsaFree(), PSIMsaNew(), and SU_PSSMInput::SU_PSSMInput().

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The documentation for this struct was generated from the following file:

• include/algo/blast/core/blast_psi.h

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