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/**
* 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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