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introduce msacontainer object, overhaul main alignment routine
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10 files changed

+676
-460
lines changed

10 files changed

+676
-460
lines changed

‎src/commons/CMakeLists.txt

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@@ -5,4 +5,6 @@ set(commons_source_files
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commons/StructureSmithWaterman.h
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commons/newick.cpp
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commons/newick.h
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commons/MSA.cpp
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commons/MSA.h
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PARENT_SCOPE)

‎src/commons/MSA.cpp

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#include "MSA.h"
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SubMSA::SubMSA() {}
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SubMSA::SubMSA(size_t a) : id(a), members({ a }) {}
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SubMSA::SubMSA(size_t a, size_t b) : members({ a, b }) {}
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void SubMSA::pushMember(size_t other) {
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members.insert(members.end(), other);
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}
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void SubMSA::update(const SubMSA &other) {
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members.clear();
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members.assign(other.members.begin(), other.members.end());
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profile_aa = other.profile_aa;
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profile_ss = other.profile_ss;
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mask = other.mask;
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}
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void SubMSA::concat(const SubMSA &other) {
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members.insert(members.end(), other.members.begin(), other.members.end());
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}
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void SubMSA::concat(const std::vector<size_t> &other) {
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members.insert(members.end(), other.begin(), other.end());
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}
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MSAContainer::MSAContainer() {}
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MSAContainer::MSAContainer(size_t n) : dbKeys(n), dbIdToSubMSAVec(n, n), cigars_aa(n), cigars_ss(n) {}
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std::vector<SubMSA>::iterator MSAContainer::begin() {
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return data.begin();
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}
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std::vector<SubMSA>::iterator MSAContainer::end() {
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return data.end();
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}
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std::vector<SubMSA>::const_iterator MSAContainer::begin() const {
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return data.begin();
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}
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std::vector<SubMSA>::const_iterator MSAContainer::end() const {
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return data.end();
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}
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SubMSA& MSAContainer::operator[](size_t index) {
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return data[index];
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}
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SubMSA& MSAContainer::operator[](const std::vector<SubMSA>::iterator& it) {
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return *it;
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}
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SubMSA& MSAContainer::back() {
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return data.back();
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}
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size_t MSAContainer::size() const {
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return data.size();
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}
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void MSAContainer::add(size_t index) {
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data.emplace_back(index);
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dbIdToSubMSAVec[index] = data.size() - 1;
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}
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void MSAContainer::add(const SubMSA &msa) {
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data.push_back(msa);
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for (size_t i = 0; i < msa.members.size(); i++) {
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dbIdToSubMSAVec[msa.members[i]] = data.size() - 1;
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}
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}
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void MSAContainer::remove(std::vector<size_t> &toRemove) {
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std::sort(toRemove.begin(), toRemove.end(), std::greater<int>());
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for (size_t index : toRemove) {
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data.erase(data.begin() + index);
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}
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for (size_t i = 0; i < data.size(); i++) {
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const SubMSA &msa = data[i];
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for (size_t member : msa.members) {
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dbIdToSubMSAVec[member] = i;
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}
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}
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}
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void MSAContainer::addStructure(size_t id, unsigned int key, size_t length, const char* aa, const char* ss) {
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for (size_t j = 0; j < length; j++) {
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cigars_aa[id].emplace_back(aa[j]);
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cigars_ss[id].emplace_back(ss[j]);
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}
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dbKeys[id] = key;
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}
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// Merge SubMSA of db id b into SubMSA of db id a
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// Returns index of updated SubMSA of db id a
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size_t MSAContainer::mergeInto(size_t a, size_t b) {
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size_t aIdx = dbIdToSubMSAVec[a];
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size_t bIdx = dbIdToSubMSAVec[b];
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if (bIdx == cigars_aa.size()) {
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// b isn't a profile
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data[aIdx].pushMember(b);
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dbIdToSubMSAVec[b] = aIdx;
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} else {
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data[aIdx].concat(data[bIdx]);
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for (size_t i = 0; i < data[bIdx].members.size(); i++) {
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size_t member = data[bIdx].members[i];
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dbIdToSubMSAVec[member] = aIdx;
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}
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}
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return aIdx;
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}
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// Update the container with newly created SubMSAs, remove stale ones
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// 1: new submsa --> add to msa
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// 2: one profile, one structure -> add to profile
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// 3: both profile -> merge into query
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// cases 2 and 3 always identical since profile always made query
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void MSAContainer::update(const std::vector<SubMSA> &newMSAs, std::vector<size_t> &toRemove) {
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for (const SubMSA &sub : newMSAs) {
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add(sub);
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}
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if (toRemove.size() > 0) {
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remove(toRemove);
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}
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}
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bool MSAContainer::isProfile(size_t index) {
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return (dbIdToSubMSAVec[index] != cigars_aa.size());
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}

‎src/commons/MSA.h

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#ifndef MSA_H
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#define MSA_H
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#include <vector>
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#include <string>
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#include <map>
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#include <numeric>
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#include <cstdint>
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#include <algorithm>
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// Bit field version
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// First bit = match or gap
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// Remaining bits = ASCII character or (gap) count
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union Instruction {
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struct BitFields {
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std::uint8_t state : 1; // 0 = match, 1 = gap
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std::uint8_t count : 7; // count < 127
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} bits;
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unsigned char data;
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Instruction() {
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data = 0;
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}
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Instruction(int state, int count) {
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data = 0;
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bits.state = static_cast<std::uint8_t>(state);
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bits.count = static_cast<std::uint8_t>(count);
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}
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Instruction(char c) {
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data = 0;
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bits.state = static_cast<std::uint8_t>(0);
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bits.count = static_cast<std::uint8_t>(c);
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}
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Instruction(int count) {
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data = 0;
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bits.state = static_cast<std::uint8_t>(1);
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bits.count = static_cast<std::uint8_t>(count);
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}
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char getCharacter() const {
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return (bits.state == 0) ? static_cast<char>(bits.count) : '-';
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}
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bool isSeq() const {
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return (bits.state == 0);
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}
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bool isFull() const {
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return (bits.count == 127);
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}
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};
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struct SubMSA {
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size_t id; // Database ID of 'merged' representative
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std::vector<size_t> members; // Database IDs of member structures
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std::string profile_aa; // Amino acid profile
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std::string profile_ss; // 3Di profile
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std::string mask; // Profile mask string
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SubMSA();
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SubMSA(size_t a);
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SubMSA(size_t a, size_t b);
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void pushMember(size_t other);
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void update(const SubMSA &other);
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void concat(const SubMSA &other);
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void concat(const std::vector<size_t> &other);
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};
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class MSAContainer {
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private:
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std::vector<SubMSA> data;
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public:
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std::vector<size_t> dbKeys;
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std::vector<size_t> dbIdToSubMSAVec;
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std::vector<std::vector<Instruction> > cigars_aa;
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std::vector<std::vector<Instruction> > cigars_ss;
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MSAContainer();
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MSAContainer(size_t n);
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std::vector<SubMSA>::iterator begin();
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std::vector<SubMSA>::iterator end();
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std::vector<SubMSA>::const_iterator begin() const;
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std::vector<SubMSA>::const_iterator end() const;
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SubMSA& operator[](size_t index);
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SubMSA& operator[](const std::vector<SubMSA>::iterator& it);
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SubMSA& back();
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size_t size() const;
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void add(size_t index);
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void add(const SubMSA &msa);
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void remove(std::vector<size_t> &toRemove);
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void addStructure(size_t id, unsigned int key, size_t length, const char* aa, const char* ss);
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size_t mergeInto(size_t a, size_t b);
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void update(const std::vector<SubMSA> &newMSAs, std::vector<size_t> &toRemove);
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bool isProfile(size_t index);
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};
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#endif

‎src/commons/StructureSmithWaterman.cpp

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@@ -877,6 +877,7 @@ Matcher::result_t StructureSmithWaterman::simpleGotoh(
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// Adjust CIGAR string to start/end on M
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// q/dbStart and q/dbEnd are already correct, no need to adjust here
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// q/dbStart set to last M j/i, q/dbEnd last M .ref/.read
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size_t alnLength = cigar.length();
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trimCIGAR(cigar, qEnd, dbEnd);
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delete[] workspace;
@@ -889,7 +890,7 @@ Matcher::result_t StructureSmithWaterman::simpleGotoh(
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0, // align.tCov,
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0, // seqId
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0, // align.evalue,
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0, // alnLength
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alnLength, // alnLength
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qStart,
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qEnd,
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query_end,

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