Mirror/zeek
1
0
Fork 0
mirror of https://github.com/zeek/zeek.git synced 2025-10-04 15:48:19 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions 2

Move BroSubstring to zeek::detail, rename to Substring

Browse source
This commit is contained in:
Tim Wojtulewicz 2020-07-19 20:38:00 -07:00 • committed by Tim Wojtulewicz
parent c7dc7fc955
commit 55d699af59
3 changed files with 74 additions and 58 deletions
Download patch file Download diff file Expand all files Collapse all files

68
src/SmithWaterman.cc
View file

@ -11,14 +11,16 @@
#include "Reporter.h"
#include "Val.h"
BroSubstring::BroSubstring(const BroSubstring& bst)
namespace zeek::detail {
Substring::Substring(const Substring& bst)
: zeek::String((const zeek::String&) bst), _num(), _new(bst._new)
{
for ( BSSAlignVecCIt it = bst._aligns.begin(); it != bst._aligns.end(); ++it )
_aligns.push_back(*it);
}
const BroSubstring& BroSubstring::operator=(const BroSubstring& bst)
const Substring& Substring::operator=(const Substring& bst)
{
zeek::String::operator=(bst);
@ -32,12 +34,12 @@ const BroSubstring& BroSubstring::operator=(const BroSubstring& bst)
return *this;
}
void BroSubstring::AddAlignment(const zeek::String* str, int index)
void Substring::AddAlignment(const zeek::String* str, int index)
{
_aligns.push_back(BSSAlign(str, index));
}
bool BroSubstring::DoesCover(const BroSubstring* bst) const
bool Substring::DoesCover(const Substring* bst) const
{
if ( _aligns.size() != bst->_aligns.size() )
return false;
@ -56,7 +58,7 @@ bool BroSubstring::DoesCover(const BroSubstring* bst) const
return true;
}
zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
zeek::VectorVal* Substring::VecToPolicy(Vec* vec)
{
static auto sw_substring_type = zeek::id::find_type<zeek::RecordType>("sw_substring");
static auto sw_align_type = zeek::id::find_type<zeek::RecordType>("sw_align");
@ -69,7 +71,7 @@ zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
{
for ( size_t i = 0; i < vec->size(); ++i )
{
BroSubstring* bst = (*vec)[i];
Substring* bst = (*vec)[i];
auto st_val = zeek::make_intrusive<zeek::RecordVal>(sw_substring_type);
st_val->Assign(0, zeek::make_intrusive<zeek::StringVal>(new zeek::String(*bst)));
@ -96,7 +98,7 @@ zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
return result.release();
}
BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
Substring::Vec* Substring::VecFromPolicy(zeek::VectorVal* vec)
{
Vec* result = new Vec();
@ -108,7 +110,7 @@ BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
continue;
const zeek::String* str = v->AsRecordVal()->GetField(0)->AsString();
BroSubstring* substr = new BroSubstring(*str);
auto* substr = new Substring(*str);
const zeek::VectorVal* aligns = v->AsRecordVal()->GetField(1)->AsVectorVal();
for ( unsigned int j = 1; j <= aligns->Size(); ++j )
@ -128,11 +130,11 @@ BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
return result;
}
char* BroSubstring::VecToString(Vec* vec)
char* Substring::VecToString(Vec* vec)
{
std::string result("[");
for ( BroSubstring::VecIt it = vec->begin(); it != vec->end(); ++it )
for ( Substring::VecIt it = vec->begin(); it != vec->end(); ++it )
{
result += (*it)->CheckString();
result += ",";
@ -142,14 +144,14 @@ char* BroSubstring::VecToString(Vec* vec)
return strdup(result.c_str());
}
zeek::String::IdxVec* BroSubstring::GetOffsetsVec(const Vec* vec, unsigned int index)
zeek::String::IdxVec* Substring::GetOffsetsVec(const Vec* vec, unsigned int index)
{
zeek::String::IdxVec* result = new zeek::String::IdxVec();
for ( VecCIt it = vec->begin(); it != vec->end(); ++it )
{
int start, end;
const BroSubstring* bst = (*it);
const Substring* bst = (*it);
if ( bst->_aligns.size() <= index )
continue;
@ -166,13 +168,13 @@ zeek::String::IdxVec* BroSubstring::GetOffsetsVec(const Vec* vec, unsigned int i
}
bool BroSubstringCmp::operator()(const BroSubstring* bst1,
const BroSubstring* bst2) const
bool SubstringCmp::operator()(const Substring* bst1,
const Substring* bst2) const
{
if ( _index >= bst1->GetNumAlignments() ||
_index >= bst2->GetNumAlignments() )
{
reporter->Warning("BroSubstringCmp::operator(): invalid index for input strings.\n");
reporter->Warning("SubstringCmp::operator(): invalid index for input strings.\n");
return false;
}
@ -260,7 +262,7 @@ private:
// @node: starting node.
// @params: SW parameters.
//
static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
static void sw_collect_single(Substring::Vec* result, SWNodeMatrix& matrix,
SWNode* node, SWParams& params)
{
std::string substring("");
@ -287,7 +289,7 @@ static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
if ( substring.size() >= params._min_toklen )
{
reverse(substring.begin(), substring.end());
BroSubstring* bst = new BroSubstring(substring);
auto* bst = new Substring(substring);
bst->AddAlignment(matrix.GetRowsString(), row-1);
bst->AddAlignment(matrix.GetColsString(), col-1);
result->push_back(bst);
@ -305,7 +307,7 @@ static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
if ( substring.size() > 0 )
{
reverse(substring.begin(), substring.end());
BroSubstring* bst = new BroSubstring(substring);
auto* bst = new Substring(substring);
bst->AddAlignment(matrix.GetRowsString(), row-1);
bst->AddAlignment(matrix.GetColsString(), col-1);
result->push_back(bst);
@ -324,10 +326,10 @@ static void sw_collect_single(BroSubstring::Vec* result, SWNodeMatrix& matrix,
// common subsequences while tracking which nodes were visited earlier and which
// substrings are redundant (i.e., fully covered by a larger common substring).
//
static void sw_collect_multiple(BroSubstring::Vec* result,
static void sw_collect_multiple(Substring::Vec* result,
SWNodeMatrix& matrix, SWParams& params)
{
std::vector<BroSubstring::Vec*> als;
std::vector<Substring::Vec*> als;
for ( int i = matrix.GetHeight() - 1; i > 0; --i )
{
@ -338,21 +340,21 @@ static void sw_collect_multiple(BroSubstring::Vec* result,
if ( ! (node->swn_byte_assigned && ! node->swn_visited) )
continue;
BroSubstring::Vec* new_al = new BroSubstring::Vec();
auto* new_al = new Substring::Vec();
sw_collect_single(new_al, matrix, node, params);
for ( std::vector<BroSubstring::Vec*>::iterator it = als.begin();
for ( std::vector<Substring::Vec*>::iterator it = als.begin();
it != als.end(); ++it )
{
BroSubstring::Vec* old_al = *it;
Substring::Vec* old_al = *it;
if ( old_al == nullptr )
continue;
for ( BroSubstring::VecIt it2 = old_al->begin();
for ( Substring::VecIt it2 = old_al->begin();
it2 != old_al->end(); ++it2 )
{
for ( BroSubstring::VecIt it3 = new_al->begin();
for ( Substring::VecIt it3 = new_al->begin();
it3 != new_al->end(); ++it3 )
{
if ( (*it2)->DoesCover(*it3) )
@ -380,15 +382,15 @@ end_loop:
}
}
for ( std::vector<BroSubstring::Vec*>::iterator it = als.begin();
for ( std::vector<Substring::Vec*>::iterator it = als.begin();
it != als.end(); ++it )
{
BroSubstring::Vec* al = *it;
Substring::Vec* al = *it;
if ( al == nullptr )
continue;
for ( BroSubstring::VecIt it2 = al->begin();
for ( Substring::VecIt it2 = al->begin();
it2 != al->end(); ++it2 )
result->push_back(*it2);
@ -398,10 +400,10 @@ end_loop:
// The main Smith-Waterman algorithm.
//
BroSubstring::Vec* smith_waterman(const zeek::String* s1, const zeek::String* s2,
Substring::Vec* smith_waterman(const zeek::String* s1, const zeek::String* s2,
SWParams& params)
{
BroSubstring::Vec* result = new BroSubstring::Vec();
auto* result = new Substring::Vec();
if ( ! s1 || s1->Len() < int(params._min_toklen) ||
! s2 || s2->Len() < int(params._min_toklen) )
@ -558,9 +560,11 @@ BroSubstring::Vec* smith_waterman(const zeek::String* s1, const zeek::String* s2
sw_collect_single(result, matrix, node_max, params);
if ( len1 > len2 )
sort(result->begin(), result->end(), BroSubstringCmp(0));
sort(result->begin(), result->end(), SubstringCmp(0));
else
sort(result->begin(), result->end(), BroSubstringCmp(1));
sort(result->begin(), result->end(), SubstringCmp(1));
return result;
}
} // namespace zeek::detail