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Next: Scripts for Updating Code Up: Naming Conventions Previous: Library Functions

Name Conversion List

From To
-----
AAAP AAAToInt
ACS AC
AP AToInt
AaCount GetAaCount
AaFrequency GetAaFrequency
AddGF AddGrid
AlignGaps AdjustGaps
AlignedIntrons GetIntrons
AlignedPeptide GetPeptides
AllMatches GetAllMatches
AminoP AminoToInt
ApprTextSearch ApproxSearchString
BBBC NucToCode
BBBP NucToInt
BP NToInt
BBBP NuctoInt
BackDynProgr BackDynProg
BaseP NucleicToInt
BestPamMatch GetPam
BestPamShake LocalAlignBestPam
BestStringMatch SearchString
BisectTree DrawBisectTree
CBBB CodeToNuc
CleanMSA RemoveGaps
CT_Species AddSpecies
CloseGF CloseGrid
ColorMap GetColorMap
ColorTree CreateColoredTree
Complement GetComplement
CompressGF CompressGrid
ConvertSP SpToDarwin
ConvertToDF DbToDarwin
CreateDB CreateAcGrid
CreateGF CreateGrid
DF DB
DMDMS CreateDayMatrices
DnaFile database
DNAPepDayhoffM ApproxDnaDayMatrix
Dayhoff CreateOrigDayMatrix
DayhoffM CreateDayMatrix
DelFixed FixedDel
DelIncr IncDel
DigestSeqs DigestSeq
Distribution DrawDistribution
DnaFile database
DotPlot DarwDotplot
DynProgr DynProg
ERROR error
EndOverlayPlot StopOverlayPlot
Entries Entry
Entropy FindEntropy
EntryInfo GetEntryInfo
EntryNumber GetEntryNumber
EqradTree DrawEqualRadialTree
ExponFit ExpFit
ExpFit2 BoundedExpFit
ExtCallFrame CreateCProgram
FlushGF FlushGrid
FragSearch SearchFrag
GetBetween GetLcaSubtree
GetIndex FindTreeFitIndex
GetLabels GetTreeLabels
GetMatchSequence GetAlignSequences
GetTreeLength TotalTreeDistance
GetPath GetPathDistance
GridFile grid
Histogram DrawHistogram
IDS ID
IPCconnect ConnectTcp
IPCdisconnect DisconnectTcp
IPCread ReadTcp
IPCreceive ReceiveTcp
IPCsend SendTcp
IPCreceiveDATA ReceiveDataTcp
IPCsendDATA SendDataTcp
IndexSP CreateSpGrid
LabelTree ChangeLeafLabels
LarsonTree DarwUnrootedTree
LeafNames GetLeafLabels
LinRegr LinearRegression
LinearIntron CreateLinearIntron
LinearIntron0 CreateLinearZeroIntron
LinearIntron1 CreateLinearProbIntron
LoadFile ReadDb
LongestRep FindLongestRep
MAlignment MultiAlign
MachineUsage GetMachineUsage
MapGF MapGrid
MassDyn DynProgMass
MassDynAll DynProgMassDb
MassProfile SearchMassDb
Maximize MaximizeFunc
MinSqTree MinSquareTree
Minimize MinimizeFunc
Minimize2D Minimize2DFunc
Minimizex DisconMinimize
MolWeight GetMolWeight
MostFrequent GetMostFrequentGrams
MoveGap MoveGap
MultAlign CreateMultiAlign
NewArray CreateArray
NewString CreateString
NextGF GetNextGrid
NPAlignMatch AlignNucPepMatch
NPAllMatches GetAllNucPepMatches
NPBackDynProgr NucPepBackDynProg
NPBestPamMatch FindNucPepPam
NPBestPamShake BestLocalAlignNucPep
NPDynProgr NucPepDynProg
NPMatch NucPepMatch
NPMultiAllMatches ParallelAllNucPepMatches
NPOneAllMatch AlignNucPepAll
NPRefine GlobalNucPepAlign
NPRefineShake LocalAlignNucPep
NPRegions NucPepRegions
NPSprintMatch DynProgNucPepString
Offsets Offset
OneAllMatch AlignOneAll
OpenGF OpenGrid
OrderedSearch SearchOrderedArray
PA IntToA
PAAA IntToAAA
PAmino IntToAmino
PB IntToN
PBBB IntToNNN
PBase IntToNucleic
PItoPam PerIdentToPam
PamtoPI PamToPerIdent
ParExec ParExecute
ParExec2 ParExecuteSmall
ParTest ParExecuteTest
PatEntries PatEntry
PepPepSearch SearchPepAll
PhyloTree CreatePhyloTree
PickTree FindLabeledSubtree
PlotPam DrawSimPam
PlotOptions Plot
PosInfo GetPosition
PositionDF GetOffset
PrintSeqsInTree PrintTreeSeq
ProbDynProgr ProbDynProg
ProfileEnter EnterProfile
ProfileExit ExitProfile
QueryAll AllQueryGrid
QueryGF QueryGrid
RETURN return
RandTree CreateRandMultAlign
RandomPermut CreateRandPermutation
RandomSeq CreateRandSeq
RandomTrees CreateRandTrees
Refine GlobalAlign
RefineLog LogDelLocalRefine
RefineShake LocalAlign
SameTree IdenticalTrees
Scale DayMatrixScale
SearchDF SearchDb
SearchPepDF SearchSeqTagDb
SearchText CaseSearchString
SelfMatch GetSelfAlign
Sequences Sequence
ShortestPath ConShortestPath
ShortestPath2 ShortestPath
Smooth SmoothData
SplatTree DrawSplatTree
SprintMatch DynProgStrings
Ssystem TimedCallSystem
StackedBar DrawStackedBar
Stats Stat
string name
Strings String
SummarizeTree CollapseNodes
TSP ComputeTSP
TSP3 ComputeCubicTSP
TSP4 ComputeQuadraticTSP
TreeOrder FindCircularOrder
TrulyRandom SetRandSeed
UUUP GenCodeToInt
UnCompressGF UncompressGrid
UnLabelTree UnlabelLeaves
UnionStats UnionStat
View ViewPlot
Violations FindSpeciesViolations
WriteMSA WriteMsa
anitparallel GetAntiparallel
appendto AppendFile
clearw ClearStat
currentOfs CurrentOff
dpuTime DpuTime
eigenvalues Eigenvalues
externcall CallExternal
findkey FindKey
function uneval
gausselim GaussElim
gcm GenCode
kGramRegion GramRegion
kGramRegionScore GetGramRegionScore
kGramSite GramSite
kGramSiteScore GetGramSiteScore
load ReadLibrary
numeric real
plot DrawPlot
srand SetRand
rand Rand
read ReadProgram
readBRK ReadBrk
readDSSP ReadDssp
readfile ReadRawFile
readpipelines OpenPipe
readstat ReadLine
readstatAt ReadOffsetLine
searchtext SearchString
specfunc specuneval
srand SetSeed
string name
system CallSystem
text string
update UpdateStat
writeto WriteFile
Predict PredictSecStruct
NDF NucDB
Simil Sim
string symbols
Text string
PDF PepDB
MaxSimil MaxSim
MinSimil MinSim
GetPam FindBestPam
Entries_print Entry_print
Entries_Offsets Entry_Offset
Entries_Strings Entry_String
Entries_Sequences Entry_Sequence
Entries_Match Entry_Match
Entries_select Entry_select
Offsets_Entries Offset_Entry
Offsets_PatEntries Offset_PatEntry
Offsets_print Offset_print
Offsets_Sequences Offset_Sequence
Offsets_Strings Offset_String
Offsets_Match Offset_Match
PatEntries_Entries PatEntry_Entry
PatEntries_Offsets PatEntry_Offset
PatEntries_Strings PatEntry_String
PatEntries_print PatEntry_print
PatEntries_Sequences PatEntry_Sequence
PatEntries_Match PatEntry_Match
Sequences_Entries Sequence_Entry
Sequences_Offsets Sequence_Offset
Sequences_PatEntries Sequence_PatEntry
Sequences_print Sequence_print
Sequences_Strings Sequence_String
Sequences_Match Sequence_Match
Match_Offsets Match_Offset
Match_Entries Match_Entry
Match_Strings Match_String
Entries_IDS Entry_ID
Match_IDS Match_ID
Sequences_IDS Sequence_ID
Offsets_IDS Offset_ID
PatEntries_IDS PatEntry_ID
IDS_Offsets ID_Offset
IDS_Entries ID_Entry
IDS_Match ID_Match
IDS_Sequences ID_Sequence
Entries_ACS Entry_AC
IDS_Entries ID_Entry
IDS_Match ID_Match
IDS_Sequences ID_Sequence
IDS_Strings ID_String
Match_ACS Match_AC
Entries_ACS Entry_AC
Offsets_ACS Offset_AC
Sequences_ACS Sequence_AC
PatEntries_ACS PatEntry_AC
ACS_Offsets AC_Offset
ACS_Entries AC_Entry
ACS_Match AC_Match
ACS_Sequences AC_Sequence
ACS_Strings AC_String
IDS_ACS ID_AC
ACS_IDS AC_ID
Text string


next up previous contents
Next: Scripts for Updating Code Up: Naming Conventions Previous: Library Functions
Gaston Gonnet
1998-09-15