libAMOS: Class Members - Functions

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a | b | c | d | e | f | g | h | i | k | l | m | o | r | s | t | u | w | ~

- a -

a_id() : AMOS::AlignmentException_t
addPartition() : AMOS::Bank_t
AlignmentException_t() : AMOS::AlignmentException_t
AllocException_t() : AMOS::AllocException_t
append() : AMOS::Bank_t
appendBID() : AMOS::Bank_t
ArgumentException_t() : AMOS::ArgumentException_t
assignEID() : AMOS::Bank_t
assignIID() : AMOS::Bank_t

- b -

b_id() : AMOS::AlignmentException_t
Bank_t() : AMOS::Bank_t
BankFlags_t() : AMOS::BankFlags_t
BankPartition_t() : AMOS::Bank_t::BankPartition_t
BankSet_t() : AMOS::BankSet_t
BankStream_t() : AMOS::BankStream_t
BankStreamSet_t() : AMOS::BankStreamSet_t
begin() : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Message_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Range_t
buildContigFeature() : AMOS::Index_t
buildContigScaffold() : AMOS::Index_t
buildReadContig() : AMOS::Index_t
buildReadLibrary() : AMOS::Index_t
buildReadMate() : AMOS::Index_t
buildScaffoldFeature() : AMOS::Index_t

- c -

clean() : AMOS::Bank_t
clear() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Message_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::BankFlags_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::IEdge_t, AMOS::Tile_t, AMOS::Range_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::BankStream_t, AMOS::Bank_t, AMOS::IBankable_t
clearAll() : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t
close() : AMOS::BankStream_t, AMOS::Bank_t
closeAll() : AMOS::BankStreamSet_t, AMOS::BankSet_t
compress() : AMOS::Sequence_t, AMOS::Kmer_t
concat() : AMOS::IDMap_t, AMOS::Bank_t
const_iterator() : AMOS::BankStreamSet_t::const_iterator, AMOS::BankSet_t::const_iterator, AMOS::UniversalSet_t::const_iterator, AMOS::IDMap_t::const_iterator, AMOS::Message_t, AMOS::Index_t
Contig_t() : AMOS::Contig_t
ContigEdge_t() : AMOS::ContigEdge_t
ContigLink_t() : AMOS::ContigLink_t
count() : AMOS::Index_t
countFields() : AMOS::Message_t
countSubMessages() : AMOS::Message_t
create() : AMOS::BankStream_t, AMOS::Bank_t

- d -

destroy() : AMOS::BankStream_t, AMOS::Bank_t
Distribution_t() : AMOS::Distribution_t

- e -

Edge_t() : AMOS::Edge_t
empty() : AMOS::Message_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::BankStream_t, AMOS::Bank_t
end() : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Message_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Range_t
eof() : AMOS::BankStream_t
Exception_t() : AMOS::Exception_t
exists() : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Message_t, AMOS::IDMap_t, AMOS::BankStream_t, AMOS::Bank_t
existsEID() : AMOS::BankStream_t, AMOS::Bank_t
existsIID() : AMOS::BankStream_t, AMOS::Bank_t

- f -

Feature_t() : AMOS::Feature_t
fetch() : AMOS::Bank_t
fetchBID() : AMOS::Bank_t
file() : AMOS::Exception_t
flip() : AMOS::Overlap_t, AMOS::Link_t
Fragment_t() : AMOS::Fragment_t

- g -

gap2ungap() : AMOS::Contig_t
getAdjacency() : AMOS::Overlap_t, AMOS::Link_t
getAhang() : AMOS::Overlap_t
getBase() : AMOS::Sequence_t, AMOS::Kmer_t
getBasePositions() : AMOS::Read_t
getBegin() : AMOS::Range_t
getBhang() : AMOS::Overlap_t
getBuckets() : AMOS::IDMap_t
getClearRange() : AMOS::Read_t
getComment() : AMOS::Universal_t
getContigEdges() : AMOS::Scaffold_t
getContigLinks() : AMOS::ContigEdge_t
getContigs() : AMOS::ContigLink_t
getContigTiling() : AMOS::Scaffold_t
getCount() : AMOS::Kmer_t
getDistribution() : AMOS::Library_t
getEID() : AMOS::IBankable_t
getEnd() : AMOS::Range_t
getField() : AMOS::Message_t
getFragment() : AMOS::Read_t
getFragmentPosition() : AMOS::Read_t
getGappedLength() : AMOS::Tile_t
getHi() : AMOS::Range_t
getIDMap() : AMOS::BankStream_t, AMOS::Bank_t
getIDMapSize() : AMOS::BankStream_t, AMOS::Bank_t
getIID() : AMOS::IBankable_t
getIndexSize() : AMOS::Bank_t
getLastPartition() : AMOS::Bank_t
getLength() : AMOS::Sequence_t, AMOS::Kmer_t, AMOS::Range_t
getLibrary() : AMOS::Fragment_t
getLinks() : AMOS::IEdge_t
getLo() : AMOS::Range_t
getMatePair() : AMOS::Fragment_t
getMaxIID() : AMOS::BankStream_t, AMOS::Bank_t
getMembers() : AMOS::Group_t
getMemberType() : AMOS::Group_t
getMessageCode() : AMOS::Message_t
getNCode() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::IMessagable_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::IEdge_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
getNodes() : AMOS::Link_t
getNodeType() : AMOS::ScaffoldLink_t, AMOS::Link_t, AMOS::ContigLink_t
getPartition() : AMOS::Bank_t
getQualityClearRange() : AMOS::Read_t
getQualString() : AMOS::Sequence_t
getRange() : AMOS::Feature_t
getReads() : AMOS::Overlap_t, AMOS::Kmer_t
getReadTiling() : AMOS::Contig_t
getScaffoldLinks() : AMOS::ScaffoldEdge_t
getScaffolds() : AMOS::ScaffoldLink_t
getScore() : AMOS::Overlap_t
getSD() : AMOS::Link_t
getSeqString() : AMOS::Sequence_t, AMOS::Kmer_t
getSize() : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Link_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::BankStream_t, AMOS::Bank_t
getSource() : AMOS::Link_t, AMOS::Fragment_t, AMOS::Feature_t
getSpan() : AMOS::Scaffold_t, AMOS::Layout_t, AMOS::Contig_t
getStatus() : AMOS::Universal_t, AMOS::BankStream_t, AMOS::Bank_t
getSubMessages() : AMOS::Message_t
getTiling() : AMOS::Layout_t
getType() : AMOS::Read_t, AMOS::Link_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::BankStream_t, AMOS::Bank_t
getUngappedLength() : AMOS::Contig_t
getUngappedQualString() : AMOS::Contig_t
getUngappedSeqString() : AMOS::Contig_t
getVectorClearRange() : AMOS::Read_t
Group_t() : AMOS::Group_t

- h -

HashTriple_t() : AMOS::IDMap_t::HashTriple_t

- i -

IBankable_t() : AMOS::IBankable_t
IDMap_t() : AMOS::IDMap_t
IEdge_t() : AMOS::IEdge_t
ignore() : AMOS::BankStream_t
IMessagable_t() : AMOS::IMessagable_t
Index_t() : AMOS::Index_t
init() : AMOS::BankStream_t, AMOS::Bank_t
inrange() : AMOS::BankStream_t
insert() : AMOS::Index_t, AMOS::IDMap_t
IOException_t() : AMOS::IOException_t
isCompressed() : AMOS::Sequence_t
isFlagA() : AMOS::IBankable_t
isFlagB() : AMOS::IBankable_t
isFlagC() : AMOS::Overlap_t
isModified() : AMOS::IBankable_t
isMulti() : AMOS::Index_t
isOpen() : AMOS::BankStream_t, AMOS::Bank_t
isRemoved() : AMOS::IBankable_t
isReverse() : AMOS::Range_t
iterator() : AMOS::BankStreamSet_t::iterator, AMOS::BankSet_t::iterator, AMOS::UniversalSet_t::iterator, AMOS::Index_t

- k -

Kmer_t() : AMOS::Kmer_t

- l -

Layout_t() : AMOS::Layout_t
Library_t() : AMOS::Library_t
line() : AMOS::Exception_t
Link_t() : AMOS::Link_t
localizeBID() : AMOS::Bank_t
lockIFO() : AMOS::Bank_t
lookup() : AMOS::Index_t
lookupAll() : AMOS::Index_t
lookupBID() : AMOS::IDMap_t, AMOS::BankStream_t, AMOS::Bank_t
lookupEID() : AMOS::IDMap_t, AMOS::BankStream_t, AMOS::Bank_t
lookupIID() : AMOS::IDMap_t, AMOS::BankStream_t, AMOS::Bank_t

- m -

Message_t() : AMOS::Message_t

- o -

open() : AMOS::BankStream_t, AMOS::Bank_t
openPartition() : AMOS::Bank_t
operator *() : AMOS::BankStreamSet_t::const_iterator, AMOS::BankStreamSet_t::iterator, AMOS::BankSet_t::const_iterator, AMOS::BankSet_t::iterator, AMOS::UniversalSet_t::const_iterator, AMOS::UniversalSet_t::iterator, AMOS::IDMap_t::const_iterator
operator bool() : AMOS::BankStream_t
operator const HashTriple_t *() : AMOS::IDMap_t::const_iterator
operator!() : AMOS::BankStream_t
operator!=() : AMOS::BankStreamSet_t::const_iterator, AMOS::BankStreamSet_t::iterator, AMOS::BankSet_t::const_iterator, AMOS::BankSet_t::iterator, AMOS::UniversalSet_t::const_iterator, AMOS::UniversalSet_t::iterator
operator++() : AMOS::BankStreamSet_t::const_iterator, AMOS::BankStreamSet_t::iterator, AMOS::BankSet_t::const_iterator, AMOS::BankSet_t::iterator, AMOS::UniversalSet_t::const_iterator, AMOS::UniversalSet_t::iterator, AMOS::Kmer_t, AMOS::IDMap_t::const_iterator
operator->() : AMOS::BankStreamSet_t::const_iterator, AMOS::BankStreamSet_t::iterator, AMOS::BankSet_t::const_iterator, AMOS::BankSet_t::iterator, AMOS::UniversalSet_t::const_iterator, AMOS::UniversalSet_t::iterator, AMOS::IDMap_t::const_iterator
operator<<() : AMOS::BankStream_t
operator=() : AMOS::Sequence_t, AMOS::Kmer_t, AMOS::IDMap_t, AMOS::IDMap_t::HashTriple_t, AMOS::Bank_t
operator==() : AMOS::BankStreamSet_t::const_iterator, AMOS::BankStreamSet_t::iterator, AMOS::BankSet_t::const_iterator, AMOS::BankSet_t::iterator, AMOS::UniversalSet_t::const_iterator, AMOS::UniversalSet_t::iterator
operator>>() : AMOS::BankStream_t
operator[]() : AMOS::BankStreamSet_t, AMOS::BankSet_t, AMOS::UniversalSet_t, AMOS::Message_t
Overlap_t() : AMOS::Overlap_t

- r -

Range_t() : AMOS::Range_t
read() : AMOS::Message_t, AMOS::IDMap_t
Read_t() : AMOS::Read_t
readMessage() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::IMessagable_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::IEdge_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t
readRecord() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::Index_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::IEdge_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
readUMD() : AMOS::Contig_t
remove() : AMOS::Index_t, AMOS::IDMap_t, AMOS::Bank_t
removeBID() : AMOS::Bank_t
removeField() : AMOS::Message_t
replace() : AMOS::Bank_t
replaceBID() : AMOS::Bank_t
resize() : AMOS::IDMap_t

- s -

Scaffold_t() : AMOS::Scaffold_t
ScaffoldEdge_t() : AMOS::ScaffoldEdge_t
ScaffoldLink_t() : AMOS::ScaffoldLink_t
seekg() : AMOS::BankStream_t
Sequence_t() : AMOS::Sequence_t
setAdjacency() : AMOS::Overlap_t, AMOS::Link_t
setAhang() : AMOS::Overlap_t
setBase() : AMOS::Sequence_t, AMOS::Kmer_t
setBasePositions() : AMOS::Read_t
setBegin() : AMOS::Range_t
setBhang() : AMOS::Overlap_t
setClearRange() : AMOS::Read_t
setComment() : AMOS::Universal_t
setContigEdges() : AMOS::Scaffold_t
setContigLinks() : AMOS::ContigEdge_t
setContigs() : AMOS::ContigLink_t
setContigTiling() : AMOS::Scaffold_t
setCount() : AMOS::Kmer_t
setDistribution() : AMOS::Library_t
setEID() : AMOS::IBankable_t
setEnd() : AMOS::Range_t
setField() : AMOS::Message_t
setFlagA() : AMOS::IBankable_t
setFlagB() : AMOS::IBankable_t
setFlagC() : AMOS::Overlap_t
setFragment() : AMOS::Read_t
setFragmentPosition() : AMOS::Read_t
setIID() : AMOS::IBankable_t
setLibrary() : AMOS::Fragment_t
setLinks() : AMOS::IEdge_t
setMembers() : AMOS::Group_t
setMemberType() : AMOS::Group_t
setMessageCode() : AMOS::Message_t
setMode() : AMOS::Bank_t
setNodes() : AMOS::Link_t
setNodeType() : AMOS::Link_t
setQualityClearRange() : AMOS::Read_t
setRange() : AMOS::Feature_t, AMOS::Range_t
setReads() : AMOS::Overlap_t, AMOS::Kmer_t, AMOS::Fragment_t
setReadTiling() : AMOS::Contig_t
setScaffoldLinks() : AMOS::ScaffoldEdge_t
setScaffolds() : AMOS::ScaffoldLink_t
setScore() : AMOS::Overlap_t
setSD() : AMOS::Link_t
setSeqString() : AMOS::Kmer_t
setSequence() : AMOS::Sequence_t
setSize() : AMOS::Link_t, AMOS::Fragment_t
setSource() : AMOS::Link_t, AMOS::Fragment_t, AMOS::Feature_t
setStatus() : AMOS::Universal_t, AMOS::BankStream_t, AMOS::Bank_t
setSubMessages() : AMOS::Message_t
setTiling() : AMOS::Layout_t
setType() : AMOS::Read_t, AMOS::Link_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Fragment_t, AMOS::Feature_t
setVectorClearRange() : AMOS::Read_t
skip() : AMOS::Message_t
swap() : AMOS::Range_t
syncIFO() : AMOS::Bank_t

- t -

tellg() : AMOS::BankStream_t
tellp() : AMOS::BankStream_t
Tile_t() : AMOS::Tile_t
touchFile() : AMOS::Bank_t

- u -

uncompress() : AMOS::Sequence_t, AMOS::Kmer_t
ungap2gap() : AMOS::Contig_t
Universal_t() : AMOS::Universal_t
UniversalSet_t() : AMOS::UniversalSet_t
unlockIFO() : AMOS::Bank_t

- w -

what() : AMOS::Exception_t
write() : AMOS::Message_t, AMOS::IDMap_t
writeMessage() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::IMessagable_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::Index_t, AMOS::IDMap_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::IEdge_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t
writeRecord() : AMOS::Universal_t, AMOS::Sequence_t, AMOS::ScaffoldLink_t, AMOS::ScaffoldEdge_t, AMOS::Scaffold_t, AMOS::Read_t, AMOS::Overlap_t, AMOS::Link_t, AMOS::Library_t, AMOS::Layout_t, AMOS::Kmer_t, AMOS::Index_t, AMOS::Group_t, AMOS::Fragment_t, AMOS::Feature_t, AMOS::Edge_t, AMOS::IEdge_t, AMOS::Tile_t, AMOS::Distribution_t, AMOS::ContigLink_t, AMOS::ContigEdge_t, AMOS::Contig_t, AMOS::IBankable_t
writeUMD() : AMOS::Contig_t

- ~ -

~Bank_t() : AMOS::Bank_t
~BankFlags_t() : AMOS::BankFlags_t
~BankPartition_t() : AMOS::Bank_t::BankPartition_t
~BankSet_t() : AMOS::BankSet_t
~BankStream_t() : AMOS::BankStream_t
~BankStreamSet_t() : AMOS::BankStreamSet_t
~Contig_t() : AMOS::Contig_t
~ContigEdge_t() : AMOS::ContigEdge_t
~ContigLink_t() : AMOS::ContigLink_t
~Distribution_t() : AMOS::Distribution_t
~Edge_t() : AMOS::Edge_t
~Exception_t() : AMOS::Exception_t
~Feature_t() : AMOS::Feature_t
~Fragment_t() : AMOS::Fragment_t
~Group_t() : AMOS::Group_t
~HashTriple_t() : AMOS::IDMap_t::HashTriple_t
~IBankable_t() : AMOS::IBankable_t
~IDMap_t() : AMOS::IDMap_t
~IEdge_t() : AMOS::IEdge_t
~IMessagable_t() : AMOS::IMessagable_t
~Index_t() : AMOS::Index_t
~Kmer_t() : AMOS::Kmer_t
~Layout_t() : AMOS::Layout_t
~Library_t() : AMOS::Library_t
~Link_t() : AMOS::Link_t
~Message_t() : AMOS::Message_t
~Overlap_t() : AMOS::Overlap_t
~Range_t() : AMOS::Range_t
~Read_t() : AMOS::Read_t
~Scaffold_t() : AMOS::Scaffold_t
~ScaffoldEdge_t() : AMOS::ScaffoldEdge_t
~ScaffoldLink_t() : AMOS::ScaffoldLink_t
~Sequence_t() : AMOS::Sequence_t
~Tile_t() : AMOS::Tile_t
~Universal_t() : AMOS::Universal_t
~UniversalSet_t() : AMOS::UniversalSet_t

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