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| Alignment () |
| Default constructor.
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| Alignment (const Alignment &orig) |
| Copy constructor.
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virtual | ~Alignment () |
| Destructor.
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virtual void | addAlignment (const Alignment &other) |
| Combine two multiple sequence alignments of same target.
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virtual void | addAlignment (const AlignmentBase &other) |
| Combine two multiple sequence alignments of same target. More...
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virtual double | calculateIdentity () |
| Calculate overall identity. More...
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virtual double | calculatePairwiseIdentity (const string &seq1, const string &seq2) |
| Calculate pairwise identity between seq1 and seq2. More...
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virtual void | clearAlignment () |
| Clear alignment data.
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virtual void | clearTemplate () |
| Clear template.
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virtual void | copy (const Alignment &orig) |
| Copy orig object to this object ("deep copy").
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virtual void | copy (const AlignmentBase &orig) |
| Copy orig object to this object ("deep copy"). More...
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virtual void | cutTemplate (unsigned int index) |
| Remove all templates below index. More...
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string | deleteChar (const string &s, unsigned int n) |
| Delete n-th character. More...
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void | deletePos (unsigned int p) |
| Delete character (or '-') from target and all templates at position p. More...
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virtual void | doMatchPlusHeader (ostream &os, string headerTarget, int startTarget, int endTarget, string headerTemplate, int startTemplate, int endTemplate, string alignType, string gapOpen, string gapExtension, double pWeigth, double sWeigth, double tWeigth, string seqTarget, string seqTemplat) const |
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double | getEvalue (unsigned int index=0) const |
| Return E-value of template index.
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unsigned int | getLength () |
| Return length of alignment.
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virtual vector< vector< int > > | getMatchSubset () |
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double | getScore (unsigned int index=0) const |
| Return score of template index.
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unsigned int | getSequenceLength (const string &seq) |
| Return length of seq. More...
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virtual string | getTarget () const |
| Return target sequence.
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virtual int | getTargetAminoAcidOffset () const |
| Return target aa offset (only needed for alignment, default = 0).
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virtual string | getTargetName () const |
| Return target name.
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virtual char | getTargetPos (unsigned int p) const |
| Return target position p.
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virtual string | getTemplate (unsigned int index=0) const |
| Return template index sequence.
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virtual int | getTemplateAminoAcidOffset (unsigned int index=0) const |
| Return template index aa offset (counting from zero).
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virtual string | getTemplateName (unsigned int index=0) const |
| Return template index name.
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virtual char | getTemplatePos (unsigned int p, unsigned int index=0) const |
| Return template index position p.
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vector< string > | getTokens (const string &text) |
| Return vector of words of a line of text. More...
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int | getTrueMapFromPdb (istream &is, string startingChain, int structEntryMapCe) |
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void | insertCharacter (unsigned int p, char c) |
| Insert character c in target and all templates at position p. More...
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void | insertDash (unsigned int p) |
| Insert character '-' in target and all templates at position p. More...
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virtual bool | isConserved (unsigned int p, unsigned int index=9999) const |
| Check for conservation. If index is 9999 check on all templates. More...
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virtual bool | isDeletion (unsigned int p) const |
| Check for deletion at position p. More...
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virtual bool | isGap (unsigned int p, unsigned int index=0) const |
| Check for gap at position p. More...
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virtual bool | isInsertion (unsigned int p, unsigned int index=0) const |
| Check for insertion at position p. More...
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void | loadBlastMode6 (istream &input) |
| Read BLAST output produced with blast option -m 6 this stands for a convenient form of multiple sequence alignment.
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void | loadBlastMode6FullSeq (istream &input, string masterTarget) |
| Read BLAST output produced with blast option -m 4 this stands for a convenient form of multiple sequence alignment (safe version).
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void | loadCE (istream &input) |
| Read output of CE program.
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void | loadCEBody (istream &input) |
| Read output of CE program. More...
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void | loadFasta (istream &input) |
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vector< vector< int > > | loadMap (istream &is) |
| Read map file and build a matrix 2*N .
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void | loadMSAF (istream &input) |
| Read MSAF.
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void | loadPsiBlastMode4 (istream &input) |
| Read BLAST output produced with blast option -m 4 this stands for a convenient form of multiple sequence alignment.
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vector< int > | mapStructureCE2Sequence (vector< vector< int > > mapIn, istream &pdbstream, string startingChain, vector< int > shiftedSeqresEntries) |
| Return the first aminoacids on the sequence that match the first on CE.
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virtual double | matchPositionVector (vector< int > CeTarget, vector< int > CeTemplate, vector< int > seqTarget, vector< int > seqTemplate) |
| Companion class to the previous. More...
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virtual AlignmentBase * | newCopy () |
| Construct a new "deep copy" of this object. More...
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Alignment & | operator= (const Alignment &orig) |
| Assignment operator.
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void | purgeTargetInsertions () |
| Delete all gaps from target and all templates.
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virtual void | RemoveLowerAll (double ID) |
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virtual void | RemoveLowerSimple (double ID) |
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virtual void | RemoveUpperAll (double ID) |
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virtual void | RemoveUpperSimple (double ID) |
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virtual void | saveClustal (ostream &output) const |
| Save as CLUSTAL like output. More...
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virtual void | saveFasta (ostream &output) const |
| Save as FASTA like output. More...
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void | saveMSAF (ostream &output) const |
| Save as MSAF (Mannheim Sequence Alignment Format) like output. More...
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void | setEvalue (long double val, unsigned int index=0) |
| Set E-value of template index.
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void | setScore (double val, unsigned int index=0) |
| Set score of template index.
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virtual void | setTarget (string t, string tName="target") |
| Set target to t.
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virtual void | setTargetAminoAcidOffset (int orig) |
| Set target aa offset (only needed for alignment, default = 0).
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virtual void | setTargetPos (unsigned int p, char res) |
| Set target residue to res.
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virtual void | setTemplate (string t, string tName="template", double tScore=0.0, double tEvalue=-1.0) |
| Set template to t.
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virtual void | setTemplate (string t, string tName="template") |
| Set template to t. More...
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virtual void | setTemplateAminoAcidOffset (unsigned int index, int val) |
| Set template index aa offset (counting from zero).
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virtual void | setTemplatePos (unsigned int p, char res, unsigned int index=0) |
| Set template index residue to res.
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virtual vector< int > | shiftMatchSubset (vector< int > inputVector, int newStartPos) |
| Return a new vector with positions shifted, depending on new position. More...
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unsigned int | size () const |
| Return size of alignment.
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virtual void | swapTemplate (unsigned int index1, unsigned int index2) |
| Swap templates index1 and index2. More...
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Implement a simple alignment type.