Search Toolkit Book for BlockModelPair
#include <algo/structure/cd_utils/cuBlock.hpp>
Collaboration diagram for BlockModelPair:
Public Member Functions | |
| BlockModelPair () | |
| BlockModelPair (const CRef< CSeq_align > seqAlign) | |
| BlockModelPair (const BlockModelPair &rhs) | |
| ~BlockModelPair () | |
| BlockModelPair & | operator= (const BlockModelPair &rhs) |
| BlockModel & | getMaster () |
| const BlockModel & | getMaster () const |
| BlockModel & | getSlave () |
| const BlockModel & | getSlave () const |
| void | degap () |
| CRef< CSeq_align > | toSeqAlign () const |
| int | mapToMaster (int slavePos) const |
| int | mapToSlave (int masterPos) const |
| bool | isValid () const |
| int | remaster (const BlockModelPair &guide) |
| bool | mask (const vector< Block > &maskBlocks, bool maskBasedOnMaster) |
| void | reverse () |
| void | reset () |
Private Member Functions | |
| void | extendMidway (int blockNum) |
Private Attributes | |
| BlockModel * | m_master |
| BlockModel * | m_slave |
Detailed Description
Definition at line 145 of file cuBlock.hpp.
Constructor & Destructor Documentation
◆ BlockModelPair() [1/3]
| BlockModelPair::BlockModelPair | ( | ) |
Definition at line 871 of file cuBlock.cpp.
◆ BlockModelPair() [2/3]
| BlockModelPair::BlockModelPair | ( | const CRef< CSeq_align > | seqAlign | ) |
Definition at line 878 of file cuBlock.cpp.
◆ BlockModelPair() [3/3]
| BlockModelPair::BlockModelPair | ( | const BlockModelPair & | rhs | ) |
Definition at line 885 of file cuBlock.cpp.
◆ ~BlockModelPair()
| BlockModelPair::~BlockModelPair | ( | ) |
Definition at line 911 of file cuBlock.cpp.
Member Function Documentation
◆ degap()
| void BlockModelPair::degap | ( | ) |
Definition at line 945 of file cuBlock.cpp.
References assert, BlockModel::blockMatch(), extendMidway(), BlockModel::getBlocks(), i, m_master, and m_slave.
Referenced by ConsensusMaker::degapAlignment(), and ConsensusMaker::remasterWithConsensus().
◆ extendMidway()
|
private |
Definition at line 955 of file cuBlock.cpp.
References Block::extendSelf(), BlockModel::getBlock(), BlockModel::getBlocks(), BlockModel::getGapToCTerminal(), BlockModel::getGapToNTerminal(), m_master, and m_slave.
Referenced by degap().
◆ getMaster() [1/2]
| BlockModel & BlockModelPair::getMaster | ( | ) |
Definition at line 925 of file cuBlock.cpp.
References m_master.
Referenced by ConsensusMaker::addRows(), ResidueProfiles::adjustConsensusAndGuide(), ConsensusMaker::makeConsensus(), ResidueProfiles::makeConsensus(), mask(), remaster(), remasterAlignannot(), and ConsensusMaker::remasterWithConsensus().
◆ getMaster() [2/2]
| const BlockModel & BlockModelPair::getMaster | ( | ) | const |
Definition at line 930 of file cuBlock.cpp.
References m_master.
◆ getSlave() [1/2]
| BlockModel & BlockModelPair::getSlave | ( | ) |
Definition at line 935 of file cuBlock.cpp.
References m_slave.
Referenced by ConsensusMaker::addRows(), ResidueProfiles::adjustConsensusAndGuide(), ConsensusMaker::makeConsensus(), ResidueProfiles::makeConsensus(), mask(), remaster(), remasterAlignannot(), and ConsensusMaker::remasterWithConsensus().
◆ getSlave() [2/2]
| const BlockModel & BlockModelPair::getSlave | ( | ) | const |
Definition at line 940 of file cuBlock.cpp.
References m_slave.
◆ isValid()
| bool BlockModelPair::isValid | ( | ) | const |
Definition at line 1005 of file cuBlock.cpp.
References BlockModel::blockMatch(), m_master, and m_slave.
Referenced by ResidueProfiles::adjustConsensusAndGuide(), ResidueProfiles::makeConsensus(), and mask().
◆ mapToMaster()
Definition at line 989 of file cuBlock.cpp.
References BlockModel::getBlock(), BlockModel::getBlockNumber(), Block::getStart(), m_master, and m_slave.
Referenced by mask(), and remasterAlignannot().
◆ mapToSlave()
Definition at line 997 of file cuBlock.cpp.
References BlockModel::getBlock(), BlockModel::getBlockNumber(), Block::getStart(), m_master, and m_slave.
Referenced by mask().
◆ mask()
Definition at line 1031 of file cuBlock.cpp.
References b, BlockModel::getBlocks(), getMaster(), getSlave(), i, isValid(), m_master, m_slave, mapToMaster(), mapToSlave(), and BlockModel::mask().
◆ operator=()
| BlockModelPair & BlockModelPair::operator= | ( | const BlockModelPair & | rhs | ) |
Definition at line 895 of file cuBlock.cpp.
◆ remaster()
| int BlockModelPair::remaster | ( | const BlockModelPair & | guide | ) |
Definition at line 1013 of file cuBlock.cpp.
References assert, getMaster(), BlockModel::getSeqId(), getSlave(), BlockModel::getTotalBlockLength(), BlockModel::intersect(), m_master, m_slave, and SeqIdsMatch().
Referenced by ConsensusMaker::remasterWithConsensus().
◆ reset()
| void BlockModelPair::reset | ( | ) |
Definition at line 917 of file cuBlock.cpp.
◆ reverse()
| void BlockModelPair::reverse | ( | ) |
Definition at line 1062 of file cuBlock.cpp.
References m_master, and m_slave.
Referenced by ReMasterCdWithoutUnifiedBlocks().
◆ toSeqAlign()
| CRef< CSeq_align > BlockModelPair::toSeqAlign | ( | ) | const |
Definition at line 983 of file cuBlock.cpp.
References m_master, m_slave, and BlockModel::toSeqAlign().
Referenced by ConsensusMaker::degapAlignment(), ConsensusMaker::getGuideSeqAlign(), ReMasterCdWithoutUnifiedBlocks(), and ConsensusMaker::remasterWithConsensus().
Member Data Documentation
◆ m_master
|
private |
Definition at line 184 of file cuBlock.hpp.
Referenced by BlockModelPair(), degap(), extendMidway(), getMaster(), isValid(), mapToMaster(), mapToSlave(), mask(), operator=(), remaster(), reset(), reverse(), toSeqAlign(), and ~BlockModelPair().
◆ m_slave
|
private |
Definition at line 185 of file cuBlock.hpp.
Referenced by BlockModelPair(), degap(), extendMidway(), getSlave(), isValid(), mapToMaster(), mapToSlave(), mask(), operator=(), remaster(), reset(), reverse(), toSeqAlign(), and ~BlockModelPair().
The documentation for this class was generated from the following files:
- include/algo/structure/cd_utils/cuBlock.hpp
- src/algo/structure/cd_utils/cuBlock.cpp
