mirror of
https://github.com/zeek/zeek.git
synced 2025-10-04 23:58:20 +00:00
Move BroSubstring to zeek::detail, rename to Substring
This commit is contained in:
Tim Wojtulewicz
Tim Wojtulewicz
parent
c7dc7fc955
commit
55d699af59
3 changed files with 74 additions and 58 deletions
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@ -11,14 +11,16 @@
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#include "Reporter.h"
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#include "Val.h"
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BroSubstring::BroSubstring(const BroSubstring& bst)
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namespace zeek::detail {
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Substring::Substring(const Substring& bst)
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: zeek::String((const zeek::String&) bst), _num(), _new(bst._new)
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{
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for ( BSSAlignVecCIt it = bst._aligns.begin(); it != bst._aligns.end(); ++it )
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_aligns.push_back(*it);
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}
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const BroSubstring& BroSubstring::operator=(const BroSubstring& bst)
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const Substring& Substring::operator=(const Substring& bst)
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{
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zeek::String::operator=(bst);
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@ -32,12 +34,12 @@ const BroSubstring& BroSubstring::operator=(const BroSubstring& bst)
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return *this;
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}
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void BroSubstring::AddAlignment(const zeek::String* str, int index)
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void Substring::AddAlignment(const zeek::String* str, int index)
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{
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_aligns.push_back(BSSAlign(str, index));
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}
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bool BroSubstring::DoesCover(const BroSubstring* bst) const
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bool Substring::DoesCover(const Substring* bst) const
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{
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if ( _aligns.size() != bst->_aligns.size() )
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return false;
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@ -56,7 +58,7 @@ bool BroSubstring::DoesCover(const BroSubstring* bst) const
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return true;
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}
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zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
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zeek::VectorVal* Substring::VecToPolicy(Vec* vec)
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{
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static auto sw_substring_type = zeek::id::find_type<zeek::RecordType>("sw_substring");
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static auto sw_align_type = zeek::id::find_type<zeek::RecordType>("sw_align");
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@ -69,7 +71,7 @@ zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
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{
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for ( size_t i = 0; i < vec->size(); ++i )
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{
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BroSubstring* bst = (*vec)[i];
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Substring* bst = (*vec)[i];
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auto st_val = zeek::make_intrusive<zeek::RecordVal>(sw_substring_type);
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st_val->Assign(0, zeek::make_intrusive<zeek::StringVal>(new zeek::String(*bst)));
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@ -96,7 +98,7 @@ zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
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return result.release();
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}
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BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
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Substring::Vec* Substring::VecFromPolicy(zeek::VectorVal* vec)
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{
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Vec* result = new Vec();
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@ -108,7 +110,7 @@ BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
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continue;
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const zeek::String* str = v->AsRecordVal()->GetField(0)->AsString();
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BroSubstring* substr = new BroSubstring(*str);
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auto* substr = new Substring(*str);
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const zeek::VectorVal* aligns = v->AsRecordVal()->GetField(1)->AsVectorVal();
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for ( unsigned int j = 1; j <= aligns->Size(); ++j )
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@ -128,11 +130,11 @@ BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
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return result;
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}
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char* BroSubstring::VecToString(Vec* vec)
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char* Substring::VecToString(Vec* vec)
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{
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std::string result("[");
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for ( BroSubstring::VecIt it = vec->begin(); it != vec->end(); ++it )
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for ( Substring::VecIt it = vec->begin(); it != vec->end(); ++it )
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{
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result += (*it)->CheckString();
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result += ",";
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@ -142,14 +144,14 @@ char* BroSubstring::VecToString(Vec* vec)
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return strdup(result.c_str());
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}
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zeek::String::IdxVec* BroSubstring::GetOffsetsVec(const Vec* vec, unsigned int index)
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zeek::String::IdxVec* Substring::GetOffsetsVec(const Vec* vec, unsigned int index)
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{
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zeek::String::IdxVec* result = new zeek::String::IdxVec();
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for ( VecCIt it = vec->begin(); it != vec->end(); ++it )
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{
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int start, end;
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const BroSubstring* bst = (*it);
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const Substring* bst = (*it);
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if ( bst->_aligns.size() <= index )
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continue;
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@ -166,13 +168,13 @@ zeek::String::IdxVec* BroSubstring::GetOffsetsVec(const Vec* vec, unsigned int i
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}
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bool BroSubstringCmp::operator()(const BroSubstring* bst1,
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const BroSubstring* bst2) const
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bool SubstringCmp::operator()(const Substring* bst1,
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const Substring* bst2) const
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{
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if ( _index >= bst1->GetNumAlignments() ||
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_index >= bst2->GetNumAlignments() )
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{
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reporter->Warning("BroSubstringCmp::operator(): invalid index for input strings.\n");
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reporter->Warning("SubstringCmp::operator(): invalid index for input strings.\n");
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return false;
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}
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@ -260,7 +262,7 @@ private:
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// @node: starting node.
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// @params: SW parameters.
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//
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static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
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static void sw_collect_single(Substring::Vec* result, SWNodeMatrix& matrix,
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SWNode* node, SWParams& params)
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{
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std::string substring("");
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@ -287,7 +289,7 @@ static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
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if ( substring.size() >= params._min_toklen )
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{
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reverse(substring.begin(), substring.end());
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BroSubstring* bst = new BroSubstring(substring);
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auto* bst = new Substring(substring);
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bst->AddAlignment(matrix.GetRowsString(), row-1);
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bst->AddAlignment(matrix.GetColsString(), col-1);
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result->push_back(bst);
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@ -305,7 +307,7 @@ static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
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if ( substring.size() > 0 )
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{
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reverse(substring.begin(), substring.end());
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BroSubstring* bst = new BroSubstring(substring);
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auto* bst = new Substring(substring);
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bst->AddAlignment(matrix.GetRowsString(), row-1);
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bst->AddAlignment(matrix.GetColsString(), col-1);
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result->push_back(bst);
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@ -324,10 +326,10 @@ static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
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// common subsequences while tracking which nodes were visited earlier and which
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// substrings are redundant (i.e., fully covered by a larger common substring).
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//
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static void sw_collect_multiple(BroSubstring::Vec* result,
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static void sw_collect_multiple(Substring::Vec* result,
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SWNodeMatrix& matrix, SWParams& params)
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{
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std::vector<BroSubstring::Vec*> als;
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std::vector<Substring::Vec*> als;
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for ( int i = matrix.GetHeight() - 1; i > 0; --i )
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{
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@ -338,21 +340,21 @@ static void sw_collect_multiple(BroSubstring::Vec* result,
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if ( ! (node->swn_byte_assigned && ! node->swn_visited) )
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continue;
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BroSubstring::Vec* new_al = new BroSubstring::Vec();
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auto* new_al = new Substring::Vec();
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sw_collect_single(new_al, matrix, node, params);
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for ( std::vector<BroSubstring::Vec*>::iterator it = als.begin();
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for ( std::vector<Substring::Vec*>::iterator it = als.begin();
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it != als.end(); ++it )
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{
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BroSubstring::Vec* old_al = *it;
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Substring::Vec* old_al = *it;
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if ( old_al == nullptr )
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continue;
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for ( BroSubstring::VecIt it2 = old_al->begin();
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for ( Substring::VecIt it2 = old_al->begin();
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it2 != old_al->end(); ++it2 )
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{
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for ( BroSubstring::VecIt it3 = new_al->begin();
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for ( Substring::VecIt it3 = new_al->begin();
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it3 != new_al->end(); ++it3 )
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{
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if ( (*it2)->DoesCover(*it3) )
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@ -380,15 +382,15 @@ end_loop:
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}
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}
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for ( std::vector<BroSubstring::Vec*>::iterator it = als.begin();
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for ( std::vector<Substring::Vec*>::iterator it = als.begin();
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it != als.end(); ++it )
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{
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BroSubstring::Vec* al = *it;
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Substring::Vec* al = *it;
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if ( al == nullptr )
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continue;
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for ( BroSubstring::VecIt it2 = al->begin();
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for ( Substring::VecIt it2 = al->begin();
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it2 != al->end(); ++it2 )
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result->push_back(*it2);
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@ -398,10 +400,10 @@ end_loop:
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// The main Smith-Waterman algorithm.
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//
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BroSubstring::Vec* smith_waterman(const zeek::String* s1, const zeek::String* s2,
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Substring::Vec* smith_waterman(const zeek::String* s1, const zeek::String* s2,
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SWParams& params)
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{
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BroSubstring::Vec* result = new BroSubstring::Vec();
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auto* result = new Substring::Vec();
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if ( ! s1 || s1->Len() < int(params._min_toklen) ||
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! s2 || s2->Len() < int(params._min_toklen) )
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@ -558,9 +560,11 @@ BroSubstring::Vec* smith_waterman(const zeek::String* s1, const zeek::String* s2
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sw_collect_single(result, matrix, node_max, params);
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if ( len1 > len2 )
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sort(result->begin(), result->end(), BroSubstringCmp(0));
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sort(result->begin(), result->end(), SubstringCmp(0));
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else
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sort(result->begin(), result->end(), BroSubstringCmp(1));
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sort(result->begin(), result->end(), SubstringCmp(1));
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return result;
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}
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} // namespace zeek::detail
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@ -5,16 +5,18 @@
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#include "ZeekString.h"
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#include <map>
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// BroSubstrings are essentially BroStrings, augmented with indexing
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// information required for the Smith-Waterman algorithm. Each substring
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// can be marked as being a common substring of arbitrarily many strings,
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// for each of which we store where the substring starts.
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//
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//
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class BroSubstring : public zeek::String {
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namespace zeek::detail {
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/**
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* Substrings are essentially Strings, augmented with indexing information
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* required for the Smith-Waterman algorithm. Each substring can be
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* marked as being a common substring of arbitrarily many strings, for each
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* of which we store where the substring starts.
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*/
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class Substring : public zeek::String {
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public:
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typedef std::vector<BroSubstring*> Vec;
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typedef std::vector<Substring*> Vec;
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typedef Vec::iterator VecIt;
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typedef Vec::const_iterator VecCIt;
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@ -39,22 +41,22 @@ public:
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typedef BSSAlignVec::iterator BSSAlignVecIt;
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typedef BSSAlignVec::const_iterator BSSAlignVecCIt;
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explicit BroSubstring(const std::string& string)
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explicit Substring(const std::string& string)
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: zeek::String(string), _num(), _new(false) { }
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explicit BroSubstring(const zeek::String& string)
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explicit Substring(const zeek::String& string)
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: zeek::String(string), _num(), _new(false) { }
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BroSubstring(const BroSubstring& bst);
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Substring(const Substring& bst);
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const BroSubstring& operator=(const BroSubstring& bst);
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const Substring& operator=(const Substring& bst);
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// Returns true if this string completely covers the given one.
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// "Covering" means that the substring must be at least as long
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// as the one compared to, and completely covers the range occupied
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// by the given one.
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//
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bool DoesCover(const BroSubstring* bst) const;
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bool DoesCover(const Substring* bst) const;
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void AddAlignment(const zeek::String* string, int index);
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const BSSAlignVec& GetAlignments() const { return _aligns; }
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@ -78,7 +80,7 @@ private:
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typedef std::map<std::string, void*> DataMap;
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typedef DataMap::iterator DataMapIt;
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BroSubstring();
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Substring();
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// The alignments registered for this substring.
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BSSAlignVec _aligns;
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@ -90,13 +92,13 @@ private:
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bool _new;
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};
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// A comparison class that sorts BroSubstrings according to the string
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// A comparison class that sorts Substrings according to the string
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// offset value of the nth input string, where "nth" starts from 0.
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//
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class BroSubstringCmp {
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class SubstringCmp {
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public:
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explicit BroSubstringCmp(unsigned int index) { _index = index; }
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bool operator()(const BroSubstring* bst1, const BroSubstring* bst2) const;
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explicit SubstringCmp(unsigned int index) { _index = index; }
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bool operator()(const Substring* bst1, const Substring* bst2) const;
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private:
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unsigned int _index;
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@ -148,6 +150,16 @@ struct SWParams {
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// input strings where the string occurs. On error, or if no common
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// subsequence exists, an empty vector is returned.
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//
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extern BroSubstring::Vec* smith_waterman(const zeek::String* s1,
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const zeek::String* s2,
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SWParams& params);
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extern Substring::Vec* smith_waterman(const zeek::String* s1,
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const zeek::String* s2,
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SWParams& params);
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} // namespace zeek::detail
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using BroSubstring [[deprecated("Remove in v4.1. Use zeek::detail::Substring.")]] = zeek::detail::Substring;
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using BroSubstringCmp [[deprecated("Remove in v4.1 Use zeel::detail::SubstringCmp.")]] = zeek::detail::SubstringCmp;
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using SWParams [[deprecated("Remove in v4.1. Use zeek::detail::SWParams.")]] = zeek::detail::SWParams;
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constexpr auto SW_SINGLE [[deprecated("Remove in v4.1. Use zeek::detai::SW_SINGLE.")]] = zeek::detail::SW_SINGLE;
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constexpr auto SW_MULTIPLE [[deprecated("Remove in v4.1. Use zeek::detai::SW_MULTIPLE.")]] = zeek::detail::SW_MULTIPLE;
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constexpr auto smith_waterman [[deprecated("Remove in v4.1. Use zeek::detail::smith_waterman.")]] = zeek::detail::smith_waterman;
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@ -681,12 +681,12 @@ function string_to_ascii_hex%(s: string%): string
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## Returns: The result of the Smith-Waterman algorithm calculation.
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function str_smith_waterman%(s1: string, s2: string, params: sw_params%) : sw_substring_vec
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%{
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SWParams sw_params(params->AsRecordVal()->GetField(0)->AsCount(),
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SWVariant(params->AsRecordVal()->GetField(1)->AsCount()));
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zeek::detail::SWParams sw_params(
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params->AsRecordVal()->GetField(0)->AsCount(),
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zeek::detail::SWVariant(params->AsRecordVal()->GetField(1)->AsCount()));
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BroSubstring::Vec* subseq =
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smith_waterman(s1->AsString(), s2->AsString(), sw_params);
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auto result = zeek::VectorValPtr{zeek::AdoptRef{}, BroSubstring::VecToPolicy(subseq)};
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auto* subseq = zeek::detail::smith_waterman(s1->AsString(), s2->AsString(), sw_params);
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auto result = zeek::VectorValPtr{zeek::AdoptRef{}, zeek::detail::Substring::VecToPolicy(subseq)};
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delete_each(subseq);
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delete subseq;
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