The clustal sequence file format.
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#include <Bpp/Seq/Io/Clustal.h>
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| Clustal (bool checkSequenceNames=true, unsigned int nbExtraSpacesBeforeSeq=5, unsigned int charsByLine=100) throw (Exception) |
| Build a new Clustal object. More...
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virtual | ~Clustal () |
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bool | checkNames () const |
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void | checkNames (bool yn) |
| Tell whether the sequence names should be checked when reading from files. More...
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const std::string | getDataType () const |
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void | appendAlignmentFromStream (std::istream &input, SiteContainer &sc) const throw (Exception) |
| Append sequences to a container from a stream. More...
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As a SiteContainer is a subclass of SequenceContainer, we hereby implement the ISequence interface by downcasting the interface.
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virtual SequenceContainer * | readSequences (std::istream &input, const Alphabet *alpha) const throw (Exception) |
| Create a new container from a stream. More...
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virtual SequenceContainer * | readSequences (const std::string &path, const Alphabet *alpha) const throw (Exception) |
| Create a new container from a file. More...
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void | writeAlignment (std::ostream &output, const SiteContainer &sc) const throw (Exception) |
| Write a container to a stream. More...
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void | writeAlignment (const std::string &path, const SiteContainer &sc, bool overwrite=true) const throw (Exception) |
| Write a container to a file. More...
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const std::string | getFormatName () const |
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const std::string | getFormatDescription () const |
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virtual void | readAlignment (std::istream &input, SiteContainer &sc) const throw (Exception) |
| Add sequences to a container from a stream. More...
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virtual void | readAlignment (const std::string &path, SiteContainer &sc) const throw (Exception) |
| Add sequences to a container from a file. More...
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virtual AlignedSequenceContainer * | readAlignment (const std::string &path, const Alphabet *alpha) const throw (Exception) |
| Create a new container from a file. More...
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virtual AlignedSequenceContainer * | readAlignment (std::istream &input, const Alphabet *alpha) const throw (Exception) |
| Create a new container from a stream. More...
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The clustal sequence file format.
An AlignedSequenceContainer object is used instead of a VectorSequenceContainer.
Definition at line 57 of file Clustal.h.
◆ Clustal()
bpp::Clustal::Clustal |
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bool |
checkSequenceNames = true , |
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unsigned int |
nbExtraSpacesBeforeSeq = 5 , |
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unsigned int |
charsByLine = 100 |
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) |
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throw | ( | Exception |
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inline |
Build a new Clustal object.
- Parameters
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checkSequenceNames | Tell if the names in the file should be checked for unicity (slower, in o(n*n) where n is the number of sequences). |
nbExtraSpacesBeforeSeq | Specify the number of extra space characters separating the sequence name form content. The default is 5 (hence 6 spaces in total) for backward compatibility, using 0 will not allow for any space in the sequence names. |
charsByLine | Number of character per line when writing file. |
Definition at line 75 of file Clustal.h.
◆ ~Clustal()
virtual bpp::Clustal::~Clustal |
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inlinevirtual |
◆ appendAlignmentFromFile()
virtual void bpp::AbstractIAlignment::appendAlignmentFromFile |
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const std::string & |
path, |
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SiteContainer & |
sc |
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throw | ( | Exception |
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inlineprotectedvirtualinherited |
◆ appendAlignmentFromStream()
void Clustal::appendAlignmentFromStream |
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std::istream & |
input, |
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SiteContainer & |
sc |
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throw | ( | Exception |
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virtual |
Append sequences to a container from a stream.
This is the unique method to implement!
- Parameters
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input | The input stream to read. |
sc | The sequence container to update. |
- Exceptions
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Exception | If the file is not in the specified format. |
Implements bpp::AbstractIAlignment.
Definition at line 52 of file Clustal.cpp.
◆ checkNames() [1/2]
bool bpp::Clustal::checkNames |
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const |
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inline |
- Returns
- true if the names are to be checked when reading sequences from files.
Definition at line 134 of file Clustal.h.
References checkNames_.
◆ checkNames() [2/2]
void bpp::Clustal::checkNames |
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bool |
yn | ) |
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inline |
Tell whether the sequence names should be checked when reading from files.
- Parameters
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yn | whether the sequence names should be checked when reading from files. |
Definition at line 141 of file Clustal.h.
References checkNames_.
◆ getDataType()
const std::string bpp::IOSequence::getDataType |
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const |
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inlineinherited |
◆ getFormatDescription()
const std::string bpp::Clustal::getFormatDescription |
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const |
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inline |
◆ getFormatName()
const std::string bpp::Clustal::getFormatName |
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const |
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◆ readAlignment() [1/4]
virtual void bpp::AbstractIAlignment::readAlignment |
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std::istream & |
input, |
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SiteContainer & |
sc |
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throw | ( | Exception |
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inlinevirtualinherited |
◆ readAlignment() [2/4]
virtual void bpp::AbstractIAlignment::readAlignment |
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const std::string & |
path, |
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SiteContainer & |
sc |
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throw | ( | Exception |
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inlinevirtualinherited |
◆ readAlignment() [3/4]
◆ readAlignment() [4/4]
◆ readAlignmentFromFile()
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inlineprotectedvirtualinherited |
◆ readAlignmentFromStream()
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inlineprotectedvirtualinherited |
◆ readSequences() [1/2]
virtual SequenceContainer* bpp::Clustal::readSequences |
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std::istream & |
input, |
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const Alphabet * |
alpha |
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throw | ( | Exception |
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inlinevirtual |
◆ readSequences() [2/2]
virtual SequenceContainer* bpp::Clustal::readSequences |
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const std::string & |
path, |
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const Alphabet * |
alpha |
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throw | ( | Exception |
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inlinevirtual |
◆ writeAlignment() [1/2]
void Clustal::writeAlignment |
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std::ostream & |
output, |
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const SiteContainer & |
sc |
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throw | ( | Exception |
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◆ writeAlignment() [2/2]
void bpp::Clustal::writeAlignment |
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const std::string & |
path, |
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const SiteContainer & |
sc, |
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bool |
overwrite = true |
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throw | ( | Exception |
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inlinevirtual |
Write a container to a file.
- Parameters
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path | The path to the file to write. |
sc | The container to write. |
overwrite | If true the sequences are written at the beginning of the file instead of being appended. Any previous content will be lost. |
- Exceptions
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Exception | If the file is not in the specified format. |
Reimplemented from bpp::AbstractOAlignment.
Definition at line 114 of file Clustal.h.
References bpp::AbstractOAlignment::writeAlignment().
◆ charsByLine_
unsigned int bpp::Clustal::charsByLine_ |
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private |
◆ checkNames_
bool bpp::Clustal::checkNames_ |
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private |
◆ nbSpacesBeforeSeq_
unsigned int bpp::Clustal::nbSpacesBeforeSeq_ |
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private |
The documentation for this class was generated from the following files: