~ubuntu-branches/ubuntu/oneiric/libbpp-seq/oneiric

« back to all changes in this revision

Viewing changes to src/Bpp/Seq/Alphabet/AlphabetTools.cpp

Committer: Bazaar Package Importer
Author(s): Julien Dutheil
Date: 2011-06-09 11:00:00 UTC
Revision ID: james.westby@ubuntu.com-20110609110000-hnfrd9it0np58l54

Tags: upstream-2.0.2

Import upstream version 2.0.2

files added:

AUTHORS.txt

CMakeLists.txt

COPYING.txt

ChangeLog

Doxyfile

INSTALL.txt

Seq.spec

debian

debian/changelog

debian/compat

debian/control

debian/copyright

debian/docs

debian/libbpp-seq-dev.install

debian/libbpp-seq9.install

debian/rules

debian/source

debian/source/format

src/Bpp

src/Bpp/Seq

src/Bpp/Seq.all

src/Bpp/Seq/Alphabet

src/Bpp/Seq/Alphabet.all

src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp

src/Bpp/Seq/Alphabet/AbstractAlphabet.h

src/Bpp/Seq/Alphabet/Alphabet.h

src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp

src/Bpp/Seq/Alphabet/AlphabetExceptions.h

src/Bpp/Seq/Alphabet/AlphabetState.h

src/Bpp/Seq/Alphabet/AlphabetTools.cpp

src/Bpp/Seq/Alphabet/AlphabetTools.h

src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp

src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h

src/Bpp/Seq/Alphabet/CodonAlphabet.cpp

src/Bpp/Seq/Alphabet/CodonAlphabet.h

src/Bpp/Seq/Alphabet/DNA.cpp

src/Bpp/Seq/Alphabet/DNA.h

src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp

src/Bpp/Seq/Alphabet/DefaultAlphabet.h

src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp

src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h

src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp

src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h

src/Bpp/Seq/Alphabet/LetterAlphabet.h

src/Bpp/Seq/Alphabet/NucleicAlphabet.h

src/Bpp/Seq/Alphabet/NucleicAlphabetState.h

src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp

src/Bpp/Seq/Alphabet/ProteicAlphabet.h

src/Bpp/Seq/Alphabet/ProteicAlphabetState.h

src/Bpp/Seq/Alphabet/RNA.cpp

src/Bpp/Seq/Alphabet/RNA.h

src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp

src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h

src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp

src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h

src/Bpp/Seq/Alphabet/WordAlphabet.cpp

src/Bpp/Seq/Alphabet/WordAlphabet.h

src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp

src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h

src/Bpp/Seq/App

src/Bpp/Seq/App.all

src/Bpp/Seq/App/SequenceApplicationTools.cpp

src/Bpp/Seq/App/SequenceApplicationTools.h

src/Bpp/Seq/CodonSiteTools.cpp

src/Bpp/Seq/CodonSiteTools.h

src/Bpp/Seq/Container

src/Bpp/Seq/Container.all

src/Bpp/Seq/Container/AbstractSequenceContainer.cpp

src/Bpp/Seq/Container/AbstractSequenceContainer.h

src/Bpp/Seq/Container/AlignedSequenceContainer.cpp

src/Bpp/Seq/Container/AlignedSequenceContainer.h

src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp

src/Bpp/Seq/Container/CompressedVectorSiteContainer.h

src/Bpp/Seq/Container/MapSequenceContainer.cpp

src/Bpp/Seq/Container/MapSequenceContainer.h

src/Bpp/Seq/Container/OrderedSequenceContainer.h

src/Bpp/Seq/Container/SequenceContainer.h

src/Bpp/Seq/Container/SequenceContainerExceptions.h

src/Bpp/Seq/Container/SequenceContainerTools.cpp

src/Bpp/Seq/Container/SequenceContainerTools.h

src/Bpp/Seq/Container/SiteContainer.h

src/Bpp/Seq/Container/SiteContainerExceptions.cpp

src/Bpp/Seq/Container/SiteContainerExceptions.h

src/Bpp/Seq/Container/SiteContainerTools.cpp

src/Bpp/Seq/Container/SiteContainerTools.h

src/Bpp/Seq/Container/SiteIterator.cpp

src/Bpp/Seq/Container/SiteIterator.h

src/Bpp/Seq/Container/VectorSequenceContainer.cpp

src/Bpp/Seq/Container/VectorSequenceContainer.h

src/Bpp/Seq/Container/VectorSiteContainer.cpp

src/Bpp/Seq/Container/VectorSiteContainer.h

src/Bpp/Seq/DNAToRNA.cpp

src/Bpp/Seq/DNAToRNA.h

src/Bpp/Seq/DistanceMatrix.cpp

src/Bpp/Seq/DistanceMatrix.h

src/Bpp/Seq/GeneticCode

src/Bpp/Seq/GeneticCode.all

src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp

src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h

src/Bpp/Seq/GeneticCode/GeneticCode.cpp

src/Bpp/Seq/GeneticCode/GeneticCode.h

src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp

src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h

src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp

src/Bpp/Seq/GeneticCode/StandardGeneticCode.h

src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp

src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h

src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp

src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h

src/Bpp/Seq/Io

src/Bpp/Seq/Io.all

src/Bpp/Seq/Io/AbstractISequence.h

src/Bpp/Seq/Io/AbstractISequence2.h

src/Bpp/Seq/Io/AbstractOSequence.h

src/Bpp/Seq/Io/Clustal.cpp

src/Bpp/Seq/Io/Clustal.h

src/Bpp/Seq/Io/Dcse.cpp

src/Bpp/Seq/Io/Dcse.h

src/Bpp/Seq/Io/Fasta.cpp

src/Bpp/Seq/Io/Fasta.h

src/Bpp/Seq/Io/GenBank.cpp

src/Bpp/Seq/Io/GenBank.h

src/Bpp/Seq/Io/ISequence.h

src/Bpp/Seq/Io/ISequenceStream.h

src/Bpp/Seq/Io/IoSequence.h

src/Bpp/Seq/Io/IoSequenceFactory.cpp

src/Bpp/Seq/Io/IoSequenceFactory.h

src/Bpp/Seq/Io/IoSequenceStream.h

src/Bpp/Seq/Io/MafAlignmentParser.cpp

src/Bpp/Seq/Io/MafAlignmentParser.h

src/Bpp/Seq/Io/MafIterator.cpp

src/Bpp/Seq/Io/MafIterator.h

src/Bpp/Seq/Io/Mase.cpp

src/Bpp/Seq/Io/Mase.h

src/Bpp/Seq/Io/MaseTools.cpp

src/Bpp/Seq/Io/MaseTools.h

src/Bpp/Seq/Io/NexusIoSequence.cpp

src/Bpp/Seq/Io/NexusIoSequence.h

src/Bpp/Seq/Io/NexusTools.cpp

src/Bpp/Seq/Io/NexusTools.h

src/Bpp/Seq/Io/OSequence.h

src/Bpp/Seq/Io/OSequenceStream.h

src/Bpp/Seq/Io/PhredPhd.cpp

src/Bpp/Seq/Io/PhredPhd.h

src/Bpp/Seq/Io/PhredPoly.cpp

src/Bpp/Seq/Io/PhredPoly.h

src/Bpp/Seq/Io/Phylip.cpp

src/Bpp/Seq/Io/Phylip.h

src/Bpp/Seq/Io/SequenceFileIndex.h

src/Bpp/Seq/Io/Stockholm.cpp

src/Bpp/Seq/Io/Stockholm.h

src/Bpp/Seq/NucleicAcidsReplication.cpp

src/Bpp/Seq/NucleicAcidsReplication.h

src/Bpp/Seq/Sequence.cpp

src/Bpp/Seq/Sequence.h

src/Bpp/Seq/SequenceExceptions.cpp

src/Bpp/Seq/SequenceExceptions.h

src/Bpp/Seq/SequencePositionIterators.cpp

src/Bpp/Seq/SequencePositionIterators.h

src/Bpp/Seq/SequenceTools.cpp

src/Bpp/Seq/SequenceTools.h

src/Bpp/Seq/SequenceWithAnnotation.cpp

src/Bpp/Seq/SequenceWithAnnotation.h

src/Bpp/Seq/SequenceWithAnnotationTools.cpp

src/Bpp/Seq/SequenceWithAnnotationTools.h

src/Bpp/Seq/SequenceWithQuality.cpp

src/Bpp/Seq/SequenceWithQuality.h

src/Bpp/Seq/SequenceWithQualityTools.cpp

src/Bpp/Seq/SequenceWithQualityTools.h

src/Bpp/Seq/Site.cpp

src/Bpp/Seq/Site.h

src/Bpp/Seq/SiteExceptions.cpp

src/Bpp/Seq/SiteExceptions.h

src/Bpp/Seq/SiteTools.cpp

src/Bpp/Seq/SiteTools.h

src/Bpp/Seq/StateProperties

src/Bpp/Seq/StateProperties.all

src/Bpp/Seq/StateProperties/AAChargeIndex.h

src/Bpp/Seq/StateProperties/AAChenGuHuangHydrophobicityIndex.h

src/Bpp/Seq/StateProperties/AAChouFasmanAHelixIndex.h

src/Bpp/Seq/StateProperties/AAChouFasmanBSheetIndex.h

src/Bpp/Seq/StateProperties/AAChouFasmanTurnIndex.h

src/Bpp/Seq/StateProperties/AAIndex1Entry.cpp

src/Bpp/Seq/StateProperties/AAIndex1Entry.h

src/Bpp/Seq/StateProperties/AAIndex2Entry.cpp

src/Bpp/Seq/StateProperties/AAIndex2Entry.h

src/Bpp/Seq/StateProperties/AAMassIndex.h

src/Bpp/Seq/StateProperties/AASEA1030Index.h

src/Bpp/Seq/StateProperties/AASEAInf10Index.h

src/Bpp/Seq/StateProperties/AASEASup30Index.h

src/Bpp/Seq/StateProperties/AASurfaceIndex.h

src/Bpp/Seq/StateProperties/AAVolumeIndex.h

src/Bpp/Seq/StateProperties/AlphabetIndex1.h

src/Bpp/Seq/StateProperties/AlphabetIndex2.h

src/Bpp/Seq/StateProperties/BLOSUM50.cpp

src/Bpp/Seq/StateProperties/BLOSUM50.h

src/Bpp/Seq/StateProperties/ChenGuHuangAAHydrophobicityIndex.h

src/Bpp/Seq/StateProperties/DefaultNucleotideScore.cpp

src/Bpp/Seq/StateProperties/DefaultNucleotideScore.h

src/Bpp/Seq/StateProperties/GranthamAAChemicalDistance.cpp

src/Bpp/Seq/StateProperties/GranthamAAChemicalDistance.h

src/Bpp/Seq/StateProperties/GranthamAAPolarityIndex.h

src/Bpp/Seq/StateProperties/GranthamAAVolumeIndex.h

src/Bpp/Seq/StateProperties/KleinAANetChargeIndex.h

src/Bpp/Seq/StateProperties/MiyataAAChemicalDistance.cpp

src/Bpp/Seq/StateProperties/MiyataAAChemicalDistance.h

src/Bpp/Seq/StateProperties/SimpleIndexDistance.h

src/Bpp/Seq/StateProperties/SimpleScore.cpp

src/Bpp/Seq/StateProperties/SimpleScore.h

src/Bpp/Seq/StateProperties/__BLOSUM50MatrixCode

src/Bpp/Seq/StateProperties/__GranthamMatrixCode

src/Bpp/Seq/StateProperties/__MiyataMatrixCode

src/Bpp/Seq/StringSequenceTools.cpp

src/Bpp/Seq/StringSequenceTools.h

src/Bpp/Seq/SymbolList.cpp

src/Bpp/Seq/SymbolList.h

src/Bpp/Seq/SymbolListTools.cpp

src/Bpp/Seq/SymbolListTools.h

src/Bpp/Seq/Transliterator.cpp

src/Bpp/Seq/Transliterator.h

src/CMakeLists.txt

test

test/CMakeLists.txt

test/example.aln

test/example.fasta

test/example.mase

test/example.ph

test/example.ph3

test/test_alphabets.cpp

test/test_bowker.cpp

test/test_containers.cpp

test/test_io.cpp

Show diffs side-by-side

added added

removed removed

src/Bpp/Seq/Alphabet/AlphabetTools.cpp

// File: AlphabetTools.cpp

// Created by: Julien Dutheil

// Created on: Fri Oct 10 17:27:39 2003

#include "AlphabetTools.h"

#include <Bpp/Text/TextTools.h>

using namespace bpp;

// From the STL:

#include <ctype.h>

#include <iostream>

using namespace std;

/**********************************************************************************************/

const DNA AlphabetTools::DNA_ALPHABET;

const RNA AlphabetTools::RNA_ALPHABET;

const ProteicAlphabet AlphabetTools::PROTEIN_ALPHABET;

const DefaultAlphabet AlphabetTools::DEFAULT_ALPHABET;

/**********************************************************************************************/

int AlphabetTools::getType(char state)

{

if(state == '-') return -1;

state = toupper(state);

bool d = DNA_ALPHABET.isCharInAlphabet(TextTools::toString(state));

bool r = RNA_ALPHABET.isCharInAlphabet(TextTools::toString(state));

bool p = PROTEIN_ALPHABET.isCharInAlphabet(TextTools::toString(state));

if(!d && !r && !p) return 0; //Unknown character

else if(d && !r && !p) return 1; //DNA specific

else if(!d && r && !p) return 2; //RNA specific

else if(!d && !r && p) return 3; //Protein specific

else if(d && r && !p) return 4; //Nucleotide specific

else if(d && !r && p) return 5; //DNA or Protein specific

else if(!d && r && p) return 6; //RNA or Protein specific

else return 7; //Non-specific character

}

/**********************************************************************************************/

bool AlphabetTools::checkAlphabetCodingSize(const Alphabet & alphabet) throw (AlphabetException)

{

if(alphabet.getNumberOfChars() == 0) return true; //Will this really happen?

unsigned int size = alphabet.intToChar(0).size();

for(unsigned int i = 1; i < alphabet.getNumberOfTypes(); i++)

{

if(alphabet.intToChar(i).size() != size) return false;

}

return true;

}

/**********************************************************************************************/

bool AlphabetTools::checkAlphabetCodingSize(const Alphabet * alphabet) throw (AlphabetException)

{

return checkAlphabetCodingSize(* alphabet);

}

/**********************************************************************************************/

int AlphabetTools::getAlphabetCodingSize(const Alphabet & alphabet) throw (AlphabetException)

{

if(!checkAlphabetCodingSize(alphabet)) throw AlphabetException("Bad alphabet in function Alphabet::getAlphabetCodingSize().");

return alphabet.intToChar(0).size();

}

/**********************************************************************************************/

int AlphabetTools::getAlphabetCodingSize(const Alphabet * alphabet) throw (AlphabetException)

{

return getAlphabetCodingSize(* alphabet);

}

/**********************************************************************************************/

Older »