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Move BroString to zeek namespace

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This commit is contained in:
Tim Wojtulewicz 2020-06-24 10:54:29 -07:00
parent 464efbe66a
commit 58c6e10b62
54 changed files with 317 additions and 303 deletions
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34
src/SmithWaterman.cc
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@ -12,7 +12,7 @@
#include "Val.h"
BroSubstring::BroSubstring(const BroSubstring& bst)
: BroString((const BroString&) bst), _num(), _new(bst._new)
: zeek::BroString((const zeek::BroString&) bst), _num(), _new(bst._new)
{
for ( BSSAlignVecCIt it = bst._aligns.begin(); it != bst._aligns.end(); ++it )
_aligns.push_back(*it);
@ -20,7 +20,7 @@ BroSubstring::BroSubstring(const BroSubstring& bst)
const BroSubstring& BroSubstring::operator=(const BroSubstring& bst)
{
BroString::operator=(bst);
zeek::BroString::operator=(bst);
_aligns.clear();
@ -32,7 +32,7 @@ const BroSubstring& BroSubstring::operator=(const BroSubstring& bst)
return *this;
}
void BroSubstring::AddAlignment(const BroString* str, int index)
void BroSubstring::AddAlignment(const zeek::BroString* str, int index)
{
_aligns.push_back(BSSAlign(str, index));
}
@ -72,7 +72,7 @@ zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
BroSubstring* bst = (*vec)[i];
auto st_val = zeek::make_intrusive<zeek::RecordVal>(sw_substring_type);
st_val->Assign(0, zeek::make_intrusive<zeek::StringVal>(new BroString(*bst)));
st_val->Assign(0, zeek::make_intrusive<zeek::StringVal>(new zeek::BroString(*bst)));
auto aligns = zeek::make_intrusive<zeek::VectorVal>(sw_align_vec_type);
@ -81,7 +81,7 @@ zeek::VectorVal* BroSubstring::VecToPolicy(Vec* vec)
const BSSAlign& align = (bst->GetAlignments())[j];
auto align_val = zeek::make_intrusive<zeek::RecordVal>(sw_align_type);
align_val->Assign(0, zeek::make_intrusive<zeek::StringVal>(new BroString(*align.string)));
align_val->Assign(0, zeek::make_intrusive<zeek::StringVal>(new zeek::BroString(*align.string)));
align_val->Assign(1, val_mgr->Count(align.index));
aligns->Assign(j + 1, std::move(align_val));
@ -107,14 +107,14 @@ BroSubstring::Vec* BroSubstring::VecFromPolicy(zeek::VectorVal* vec)
if ( ! v )
continue;
const BroString* str = v->AsRecordVal()->GetField(0)->AsString();
const zeek::BroString* str = v->AsRecordVal()->GetField(0)->AsString();
BroSubstring* substr = new BroSubstring(*str);
const zeek::VectorVal* aligns = v->AsRecordVal()->GetField(1)->AsVectorVal();
for ( unsigned int j = 1; j <= aligns->Size(); ++j )
{
const zeek::RecordVal* align = aligns->AsVectorVal()->At(j)->AsRecordVal();
const BroString* str = align->GetField(0)->AsString();
const zeek::BroString* str = align->GetField(0)->AsString();
int index = align->GetField(1)->AsCount();
substr->AddAlignment(str, index);
}
@ -142,9 +142,9 @@ char* BroSubstring::VecToString(Vec* vec)
return strdup(result.c_str());
}
BroString::IdxVec* BroSubstring::GetOffsetsVec(const Vec* vec, unsigned int index)
zeek::BroString::IdxVec* BroSubstring::GetOffsetsVec(const Vec* vec, unsigned int index)
{
BroString::IdxVec* result = new BroString::IdxVec();
zeek::BroString::IdxVec* result = new zeek::BroString::IdxVec();
for ( VecCIt it = vec->begin(); it != vec->end(); ++it )
{
@ -209,7 +209,7 @@ struct SWNode {
//
class SWNodeMatrix {
public:
SWNodeMatrix(const BroString* s1, const BroString* s2)
SWNodeMatrix(const zeek::BroString* s1, const zeek::BroString* s2)
: _s1(s1), _s2(s2), _rows(s1->Len() + 1), _cols(s2->Len() + 1)
{
_nodes = new SWNode[_cols * _rows];
@ -229,8 +229,8 @@ public:
return &(_nodes[row * _cols + col]);
}
const BroString* GetRowsString() const { return _s1; }
const BroString* GetColsString() const { return _s2; }
const zeek::BroString* GetRowsString() const { return _s1; }
const zeek::BroString* GetColsString() const { return _s2; }
int GetHeight() const { return _rows; }
int GetWidth() const { return _cols; }
@ -247,8 +247,8 @@ public:
}
private:
const BroString* _s1;
const BroString* _s2;
const zeek::BroString* _s1;
const zeek::BroString* _s2;
int _rows, _cols;
SWNode* _nodes;
@ -398,7 +398,7 @@ end_loop:
// The main Smith-Waterman algorithm.
//
BroSubstring::Vec* smith_waterman(const BroString* s1, const BroString* s2,
BroSubstring::Vec* smith_waterman(const zeek::BroString* s1, const zeek::BroString* s2,
SWParams& params)
{
BroSubstring::Vec* result = new BroSubstring::Vec();
@ -415,8 +415,8 @@ BroSubstring::Vec* smith_waterman(const BroString* s1, const BroString* s2,
int row = 0, col = 0;
byte_vec string1 = s1->Bytes();
byte_vec string2 = s2->Bytes();
zeek::byte_vec string1 = s1->Bytes();
zeek::byte_vec string2 = s2->Bytes();
SWNodeMatrix matrix(s1, s2); // dynamic programming matrix.
SWNode* node_max = nullptr; // pointer to the best score's node