+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-/**
- * The Alignment class is used to store the alignment that is being constructed.
- * It also contains other information such as gap penalty masks etc.
- * An object of this type will be passed by reference to the FileReader. This FileReader
- * and the FileParsers will then set it up properly from the information given in the file.
- * I have decided to put everything into vectors, string etc. No more array*'s, gets rid
- * of the memory allocation problem.
- *
- * CHANGE:
- * Mark Jan 16th 2007. I have changed the pasteSequencesIntoPosition function to allow
- * explicit pastes into profile2.
- * Mark 25-1-2007. I have changed the class so that each of the sequences have a unique
- * identifier. Several functions were changed to allow this.
- *
- * 16-02-07,Nigel Brown(EMBL): Added friend NameIterator to allow a caller to
- * process the name vector.
- *
- * 23-03-07,Nigel Brown(EMBL): added testUniqueNames() predicate, which
- * compares new sequence names with those in the alignment vector BEFORE
- * appending them.
- */
-
- // NOTE NOTE NOTE Very important! The list of sequences begins from 1 to numSeqs.
- // This is because of the fact that the code was written in Fortran where arrays begin at
- // 1. It has become difficult to change this. Ramu has tried before and had problems
- // so we decided to leave it this way.
-
-#ifndef ALIGNMENT_H
-#define ALIGNMENT_H
-
-#include <vector>
-#include <string>
-#include <iomanip>
-#include <exception>
-#include <stdexcept>
-#include "Sequence.h"
-#include "../substitutionMatrix/globalmatrix.h"
-#include "../general/userparams.h"
-#include "../general/VectorOutOfRange.h"
-#include "../general/SequenceNotFoundException.h"
-
-
-// FIXME because this object is used for aligned and unaligned
-// sequences it would be nice to have a isAligned flag here (AW)
-
-using namespace std;
-
-namespace clustalw
-{
-
-typedef std::vector<vector <int> > SeqArray;
-
-class Alignment
-{
- public:
- /* Functions */
- Alignment();
- void addSequences(vector<Sequence>* seqVector);
- void addSequences(SeqArray* seqVector);
- void appendSequences(vector<Sequence>* seqVector);
- vector<Sequence> cutSelectedSequencesFromAlignment(vector<int>* selected);
- void pasteSequencesIntoPosition(vector<Sequence>* seqVector, int pos,
- bool explicitPasteToProfile2 = false);
-
- void resizeSeqArray(int size){seqArray.resize(size); numSeqs = size - 1;
- outputIndex.resize(size - 1); names.resize(size);
- titles.resize(size);};
- bool addOutputIndex(vector<int>* outputIndexToAdd);
- bool appendOutputIndex(vector<int>* outputIndexToAppend);
- void addSecStructMask1(vector<char>* secStructMaskToAdd);
- void addSecStructMask2(vector<char>* secStructMaskToAdd);
- void addSeqWeight(vector<int>* _seqWeight);
- void addGapPenaltyMask1(vector<char>* gapPenaltyMaskToAdd);
- void addGapPenaltyMask2(vector<char>* gapPenaltyMaskToAdd);
- vector<char>* getSecStructMask1();
- vector<char>* getSecStructMask2();
- const vector<int>* getOutputIndex();
- vector<char>* getGapPenaltyMask1();
- vector<char>* getGapPenaltyMask2();
- void addSecStructName1(string nameToAdd);
- void addSecStructName2(string nameToAdd);
- int alignScore(void);
- int countGaps(int s1, int s2, int l);
- void resetAlign();
- void fixGaps();
- float countid(int s1, int s2);
-
- const vector<int>* getSequence(int index){return &seqArray[index];}; // For Pairwise!
- const vector<int>* getSequence(int index) const {return &seqArray[index];};
- const vector<int>* getSequenceFromUniqueId(unsigned long id); // For iteration
- const SeqArray* getSeqArray() const {return &seqArray;}; // For multiple align!
- SeqArray* getSeqArrayForRealloc(){return &seqArray;};
- void updateSequence(int index, const vector<int>* seq);
-
- bool checkAllNamesDifferent(string *offendingSeq);
- bool testUniqueNames(vector<Sequence>* seqVector, string *offendingSeq);
- void clearAlignment();
- void clearSecStruct1();
- void clearSecStruct2();
- void printSequencesAddedInfo();
-
- string getSecStructName1();
- string getSecStructName2();
- int getNumSeqs() const {return numSeqs;};
- int getMaxNames();
- int getMaxAlnLength(){return maxAlignmentLength;};
- void setMaxAlnLength(int len){maxAlignmentLength = len;};
- int getLengthLongestSequence();
- int getLengthLongestSequence(int firstSeq, int lastSeq);
- int getSeqLength(int index) const {return seqArray[index].size() - 1;};
- int getSecStructMask1Element(int index);
- int getSecStructMask2Element(int index);
- int getGapPenaltyMask1Element(int index);
- int getGapPenaltyMask2Element(int index);
- int getOutputIndex(int index);
- int getSeqWeight(int index) const;
- const vector<int>* getSeqWeights() const{return &seqWeight;}
- string getName(int index);
- string getTitle(int index);
- vector<int>* QTcalcHistColumnHeights(int firstSeq, int nSeqs,
- Array2D<int>* exceptionalRes);
- // NOTE July 13, for Qt
-
- // NOTE the following functions are to be used when we are doing a profile
- // alignment. It resets the gaps from fixed.
- void resetProfile1();
- void resetProfile2();
- void resetAllSeqWeights();
-
- int searchForString(bool* found, int seq, int beginRes, string search);
- void removeGapsFromSelectedSeqs(vector<int>* selected);
- void removeGapOnlyColsFromSelectedSeqs(vector<int>* selected);
- void removeAllGapOnlyColumns(int fSeq, int lSeq, int profileNum);
- void setDefaultOutputIndex();
- bool removeAllOutsideRange(int beginPos, int endPos);
- bool updateRealignedRange(SeqArray realignedSeqs, int beginPos, int endPos);
- bool reloadAlignment();
-
- int getProfile1NumSeqs(){return profile1NumSeqs;};
- void setProfile1NumSeqs(int value){profile1NumSeqs = value;}
- bool isGap(int seq, int col) const;
- void calculateMaxLengths();
-
- /**
- * The following functions are for the iteration output order.
- */
- unsigned long getUniqueId(int seq);
-
- void debugPrintArray(){debugPrintSeqArray(&seqArray);}
- void debugPrintSeqArray(SeqArray* arrayToPrint);
- void debugPrintProfile1();
- void debugPrintProfile2();
- void debugPrintOutAlignInfo();
- void debugPrintAllNames();
- void debugPrintSequences();
-
- /* Attributes */
-
- /* Friends */
- class NameIterator;
- friend class NameIterator;
-
- class NameIterator
- {
- private:
- Alignment *alignment;
- vector<string>::iterator i;
- public:
- void begin(Alignment *alignment);
- const string next();
- bool end();
- };
- private:
- /* Functions */
-
- void addSequencesToVector(vector<Sequence>* seqVector);
- int getSequenceLength(int index);
- void sortScores(vector<float>* scores, int f, int l);
- void swap(vector<float>* scores, int s1, int s2);
- bool keepPortionOfSeqArray(int beginRangeIndex, int endRangeIndex);
-
- void clearSeqArray();
- /* Attributes */
- int maxNames;
- int maxAlignmentLength;
- int lengthLongestSequence;
- int numSeqs;
- vector<int> outputIndex;
- vector<unsigned long> sequenceIds; // Mark change: To help with output order
- vector<int> seqWeight;
- SeqArray seqArray;
- vector<string> names;
- vector<string> titles;
- vector<char> gapPenaltyMask1;
- vector<char> gapPenaltyMask2;
- vector<char> secStructMask1;
- vector<char> secStructMask2;
- string secStructName1;
- string secStructName2;
- vector<int> histogramColumnHeights; // NOTE July 13, for Qt
- int profile1NumSeqs;
- int gapPos1, gapPos2;
-};
-}
-#endif
-
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