bpp-seq
2.2.0
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Create a AlphabetIndex2 object from an AAIndex2 entry. More...
#include <Bpp/Seq/AlphabetIndex/AAIndex2Entry.h>
Public Member Functions | |
AAIndex2Entry (std::istream &input, bool sym=true) throw (IOException) | |
Create a new AAIndex2Entry from an input stream. More... | |
AAIndex2Entry (const AAIndex2Entry &index) | |
AAIndex2Entry & | operator= (const AAIndex2Entry &index) |
virtual | ~AAIndex2Entry () |
const Alphabet * | getAlphabet () const |
Get the alphabet associated to this index. More... | |
AAIndex2Entry * | clone () const |
double | getIndex (int state1, int state2) const throw (BadIntException) |
Get the index associated to a pair of states. More... | |
double | getIndex (const std::string &state1, const std::string &state2) const throw (BadCharException) |
Get the index associated to a pair of states. More... | |
LinearMatrix< double > * | getIndexMatrix () const |
bool | isSymmetric () const |
Private Attributes | |
LinearMatrix< double > | property_ |
const ProteicAlphabet * | alpha_ |
bool | sym_ |
Create a AlphabetIndex2 object from an AAIndex2 entry.
Definition at line 52 of file AAIndex2Entry.h.
AAIndex2Entry::AAIndex2Entry | ( | std::istream & | input, |
bool | sym = true |
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throw | ( | IOException | |
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Create a new AAIndex2Entry from an input stream.
input | The input stream to use. |
sym | Tell if the matrix is symmetric. This option as an effect only if the matrix is specified as a triangle in the entry. If sym==true, the oher triangle will be built by symmetry. If sym==false, the other triangle will be set to (-) the given triangle. If the input matrix is square, it will be considered non-symetric. |
IOException | if the stream content does not follow the AAIndex2 database entry format. |
Definition at line 50 of file AAIndex2Entry.cpp.
Referenced by clone().
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inline |
Definition at line 74 of file AAIndex2Entry.h.
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inlinevirtual |
Definition at line 88 of file AAIndex2Entry.h.
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inlinevirtual |
Implements bpp::AlphabetIndex2.
Definition at line 93 of file AAIndex2Entry.h.
References AAIndex2Entry().
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inlinevirtual |
Get the alphabet associated to this index.
Implements bpp::AlphabetIndex2.
Definition at line 91 of file AAIndex2Entry.h.
References alpha_.
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inlinevirtual |
Get the index associated to a pair of states.
state1 | First state to consider, as a int value. |
state2 | Second state to consider, as a int value. |
Implements bpp::AlphabetIndex2.
Definition at line 95 of file AAIndex2Entry.h.
References alpha_, bpp::AbstractAlphabet::getStateIndex(), and property_.
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inlinevirtual |
Get the index associated to a pair of states.
state1 | First state to consider, as a string value. |
state2 | Second state to consider, as a string value. |
Implements bpp::AlphabetIndex2.
Definition at line 102 of file AAIndex2Entry.h.
References alpha_, bpp::AbstractAlphabet::getStateIndex(), and property_.
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inlinevirtual |
Implements bpp::AlphabetIndex2.
Definition at line 109 of file AAIndex2Entry.h.
References property_.
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inlinevirtual |
Implements bpp::AlphabetIndex2.
Definition at line 111 of file AAIndex2Entry.h.
References sym_.
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inline |
Definition at line 80 of file AAIndex2Entry.h.
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private |
Definition at line 57 of file AAIndex2Entry.h.
Referenced by getAlphabet(), getIndex(), and operator=().
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private |
Definition at line 56 of file AAIndex2Entry.h.
Referenced by getIndex(), getIndexMatrix(), and operator=().
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private |
Definition at line 58 of file AAIndex2Entry.h.
Referenced by isSymmetric(), and operator=().