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Update const qualifications in kmc_api #161

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Update const qualifications in kmc_api #161

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8b5ef16
mark more of the API methods const, when possible
EQt Jan 27, 2021
b7116f1
the same for parameters
EQt Jan 27, 2021
ac780c0
<ext/algorithm> is a GNU extension that is not needed
EQt Jan 27, 2021
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42 changes: 21 additions & 21 deletions kmc_api/kmc_file.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,7 @@ bool CKMCFile::ReadParamsFrom_prefix_file_buf(uint64 &size)
// OUT: count - kmer's counter if kmer exists
// RET: true - if kmer exists
//------------------------------------------------------------------------------------------
bool CKMCFile::CheckKmer(CKmerAPI &kmer, float &count)
bool CKMCFile::CheckKmer(const CKmerAPI &kmer, float &count) const
{
uint32 int_counter;
if (CheckKmer(kmer, int_counter))
Expand All @@ -327,7 +327,7 @@ bool CKMCFile::CheckKmer(CKmerAPI &kmer, float &count)
// OUT: count - kmer's counter if kmer exists
// RET: true - if kmer exists
//------------------------------------------------------------------------------------------
bool CKMCFile::CheckKmer(CKmerAPI &kmer, uint32 &count)
bool CKMCFile::CheckKmer(const CKmerAPI &kmer, uint32 &count) const
{
if(is_opened != opened_for_RA)
return false;
Expand Down Expand Up @@ -371,7 +371,7 @@ bool CKMCFile::CheckKmer(CKmerAPI &kmer, uint32 &count)
// OUT: count - kmer's counter if kmer exists
// RET: true - if kmer exists
//------------------------------------------------------------------------------------------
bool CKMCFile::CheckKmer(CKmerAPI &kmer, uint64 &count)
bool CKMCFile::CheckKmer(const CKmerAPI &kmer, uint64 &count) const
{
if (is_opened != opened_for_RA)
return false;
Expand Down Expand Up @@ -410,7 +410,7 @@ bool CKMCFile::CheckKmer(CKmerAPI &kmer, uint64 &count)
// Check if end of file
// RET: true - all kmers are listed
//-----------------------------------------------------------------------------------------------
bool CKMCFile::Eof(void)
bool CKMCFile::Eof(void) const
{
return end_of_file;
}
Expand Down Expand Up @@ -707,7 +707,7 @@ bool CKMCFile::SetMinCount(uint32 x)
// Return a value of min_count. Kmers with counters below this theshold are ignored
// RET : a value of min_count
//----------------------------------------------------------------------------------------
uint32 CKMCFile::GetMinCount(void)
uint32 CKMCFile::GetMinCount(void) const
{
return min_count;
}
Expand All @@ -733,7 +733,7 @@ bool CKMCFile::SetMaxCount(uint32 x)
// Return a value of max_count. Kmers with counters above this theshold are ignored
// RET : a value of max_count
//----------------------------------------------------------------------------------------
uint64 CKMCFile::GetMaxCount(void)
uint64 CKMCFile::GetMaxCount(void) const
{
return max_count;
}
Expand All @@ -742,7 +742,7 @@ uint64 CKMCFile::GetMaxCount(void)
// Return true if KMC was run without -b switch
// RET : a value of both_strands
//----------------------------------------------------------------------------------------
bool CKMCFile::GetBothStrands(void)
bool CKMCFile::GetBothStrands(void) const
{
return both_strands;
}
Expand All @@ -762,7 +762,7 @@ void CKMCFile::ResetMinMaxCounts(void)
// Return the length of kmers
// RET : the length of kmers
//----------------------------------------------------------------------------------------
uint32 CKMCFile::KmerLength(void)
uint32 CKMCFile::KmerLength(void) const
{
return kmer_length;
}
Expand All @@ -772,7 +772,7 @@ uint32 CKMCFile::KmerLength(void)
// IN : kmer - kmer
// RET : true if kmer exists
//----------------------------------------------------------------------------------------
bool CKMCFile::IsKmer(CKmerAPI &kmer)
bool CKMCFile::IsKmer(const CKmerAPI &kmer) const
{
uint32 _count;
if(CheckKmer(kmer, _count))
Expand Down Expand Up @@ -852,7 +852,7 @@ uint64 CKMCFile::KmerCount(void)
// _total_kmers - the total number of kmers
// RET : true if kmer_database has been opened
//---------------------------------------------------------------------------------
bool CKMCFile::Info(uint32 &_kmer_length, uint32 &_mode, uint32 &_counter_size, uint32 &_lut_prefix_length, uint32 &_signature_len, uint32 &_min_count, uint64 &_max_count, uint64 &_total_kmers)
bool CKMCFile::Info(uint32 &_kmer_length, uint32 &_mode, uint32 &_counter_size, uint32 &_lut_prefix_length, uint32 &_signature_len, uint32 &_min_count, uint64 &_max_count, uint64 &_total_kmers) const
{
if(is_opened)
{
Expand All @@ -873,7 +873,7 @@ bool CKMCFile::Info(uint32 &_kmer_length, uint32 &_mode, uint32 &_counter_size,
}

// Get current parameters from kmer_database
bool CKMCFile::Info(CKMCFileInfo& info)
bool CKMCFile::Info(CKMCFileInfo& info) const
{
if (is_opened)
{
Expand Down Expand Up @@ -901,7 +901,7 @@ bool CKMCFile::Info(CKMCFileInfo& info)
// IN : read -
// RET : true if success, false if k > read length or some failure
//---------------------------------------------------------------------------------
bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<uint32>& counters)
bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<uint32>& counters) const
{
if (is_opened != opened_for_RA)
return false;
Expand Down Expand Up @@ -936,7 +936,7 @@ bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<uint32>&
// IN : read -
// RET : true if success
//---------------------------------------------------------------------------------
bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<float>& counters)
bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<float>& counters) const
{
if (is_opened != opened_for_RA)
return false;
Expand Down Expand Up @@ -964,7 +964,7 @@ bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<float>& c
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
uint32 CKMCFile::count_for_kmer_kmc1(CKmerAPI& kmer)
uint32 CKMCFile::count_for_kmer_kmc1(const CKmerAPI& kmer) const
{
//recognize a prefix:

Expand All @@ -989,7 +989,7 @@ uint32 CKMCFile::count_for_kmer_kmc1(CKmerAPI& kmer)
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
uint32 CKMCFile::count_for_kmer_kmc2(CKmerAPI& kmer, uint32 bin_start_pos)
uint32 CKMCFile::count_for_kmer_kmc2(const CKmerAPI& kmer, uint32 bin_start_pos) const
{
//recognize a prefix:
uint64 pattern_prefix_value = kmer.kmer_data[0];
Expand All @@ -1013,7 +1013,7 @@ uint32 CKMCFile::count_for_kmer_kmc2(CKmerAPI& kmer, uint32 bin_start_pos)
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
bool CKMCFile::GetCountersForRead_kmc1_both_strands(const std::string& read, std::vector<uint32>& counters)
bool CKMCFile::GetCountersForRead_kmc1_both_strands(const std::string& read, std::vector<uint32>& counters) const
{
uint32 read_len = static_cast<uint32>(read.length());
counters.resize(read.length() - kmer_length + 1);
Expand Down Expand Up @@ -1091,7 +1091,7 @@ bool CKMCFile::GetCountersForRead_kmc1_both_strands(const std::string& read, std
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
bool CKMCFile::GetCountersForRead_kmc1(const std::string& read, std::vector<uint32>& counters)
bool CKMCFile::GetCountersForRead_kmc1(const std::string& read, std::vector<uint32>& counters) const
{
uint32 read_len = static_cast<uint32>(read.length());
counters.resize(read.length() - kmer_length + 1);
Expand Down Expand Up @@ -1155,7 +1155,7 @@ bool CKMCFile::GetCountersForRead_kmc1(const std::string& read, std::vector<uint
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
void CKMCFile::GetSuperKmers(const std::string& transformed_read, super_kmers_t& super_kmers)
void CKMCFile::GetSuperKmers(const std::string& transformed_read, super_kmers_t& super_kmers) const
{
uint32 i = 0;
uint32 len = 0; //length of super k-mer
Expand Down Expand Up @@ -1244,7 +1244,7 @@ void CKMCFile::GetSuperKmers(const std::string& transformed_read, super_kmers_t&
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
bool CKMCFile::GetCountersForRead_kmc2_both_strands(const std::string& read, std::vector<uint32>& counters)
bool CKMCFile::GetCountersForRead_kmc2_both_strands(const std::string& read, std::vector<uint32>& counters) const
{
counters.resize(read.length() - kmer_length + 1);
std::string transformed_read = read;
Expand Down Expand Up @@ -1316,7 +1316,7 @@ bool CKMCFile::GetCountersForRead_kmc2_both_strands(const std::string& read, std
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
bool CKMCFile::GetCountersForRead_kmc2(const std::string& read, std::vector<uint32>& counters)
bool CKMCFile::GetCountersForRead_kmc2(const std::string& read, std::vector<uint32>& counters) const
{
counters.resize(read.length() - kmer_length + 1);
std::string transformed_read = read;
Expand Down Expand Up @@ -1380,7 +1380,7 @@ bool CKMCFile::GetCountersForRead_kmc2(const std::string& read, std::vector<uint
//---------------------------------------------------------------------------------
// Auxiliary function.
//---------------------------------------------------------------------------------
bool CKMCFile::BinarySearch(int64 index_start, int64 index_stop, const CKmerAPI& kmer, uint64& counter, uint32 pattern_offset)
bool CKMCFile::BinarySearch(int64 index_start, int64 index_stop, const CKmerAPI& kmer, uint64& counter, uint32 pattern_offset) const
{
if (index_start >= static_cast<int64>(total_kmers))
return false;
Expand Down
47 changes: 23 additions & 24 deletions kmc_api/kmc_file.h
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Original file line number Diff line number Diff line change
Expand Up @@ -70,34 +70,33 @@ class CKMCFile
uint64 original_max_count;

static uint64 part_size; // the size of a block readed to sufix_file_buf, in listing mode
bool BinarySearch(int64 index_start, int64 index_stop, const CKmerAPI& kmer, uint64& counter, uint32 pattern_offset);

bool BinarySearch(int64 index_start, int64 index_stop, const CKmerAPI& kmer, uint64& counter, uint32 pattern_offset) const;

// Open a file, recognize its size and check its marker. Auxiliary function.
bool OpenASingleFile(const std::string &file_name, FILE *&file_handler, uint64 &size, char marker[]);

// Recognize current parameters. Auxiliary function.
bool ReadParamsFrom_prefix_file_buf(uint64 &size);
bool ReadParamsFrom_prefix_file_buf(uint64 &size);

// Reload a contents of an array "sufix_file_buf" for listing mode. Auxiliary function.
void Reload_sufix_file_buf();

// Implementation of GetCountersForRead for kmc1 database format for both strands
bool GetCountersForRead_kmc1_both_strands(const std::string& read, std::vector<uint32>& counters);
bool GetCountersForRead_kmc1_both_strands(const std::string& read, std::vector<uint32>& counters) const;

// Implementation of GetCountersForRead for kmc1 database format without choosing canonical k-mer
bool GetCountersForRead_kmc1(const std::string& read, std::vector<uint32>& counters);
bool GetCountersForRead_kmc1(const std::string& read, std::vector<uint32>& counters) const;

using super_kmers_t = std::vector<std::tuple<uint32, uint32, uint32>>;//start_pos, len, bin_no
void GetSuperKmers(const std::string& transformed_read, super_kmers_t& super_kmers);
void GetSuperKmers(const std::string& transformed_read, super_kmers_t& super_kmers) const;

// Implementation of GetCountersForRead for kmc2 database format for both strands
bool GetCountersForRead_kmc2_both_strands(const std::string& read, std::vector<uint32>& counters);
bool GetCountersForRead_kmc2_both_strands(const std::string& read, std::vector<uint32>& counters) const;

// Implementation of GetCountersForRead for kmc2 database format
bool GetCountersForRead_kmc2(const std::string& read, std::vector<uint32>& counters);
bool GetCountersForRead_kmc2(const std::string& read, std::vector<uint32>& counters) const;
public:

CKMCFile();
~CKMCFile();

Expand All @@ -120,54 +119,54 @@ class CKMCFile
bool SetMinCount(uint32 x);

// Return a value of min_count. Kmers with counters below this theshold are ignored
uint32 GetMinCount(void);
uint32 GetMinCount(void) const;

// Set the maximal value for a counter. Kmers with counters above this theshold are ignored
bool SetMaxCount(uint32 x);

// Return a value of max_count. Kmers with counters above this theshold are ignored
uint64 GetMaxCount(void);
uint64 GetMaxCount(void) const;

//Return true if kmc was run without -b switch.
bool GetBothStrands(void);
bool GetBothStrands(void) const;

// Return the total number of kmers between min_count and max_count
uint64 KmerCount(void);

// Return the length of kmers
uint32 KmerLength(void);
uint32 KmerLength(void) const;

// Set initial values to enable listing kmers from the begining. Only in listing mode
bool RestartListing(void);

// Return true if all kmers are listed
bool Eof(void);
bool Eof(void) const;

// Return true if kmer exists. In this case return kmer's counter in count
bool CheckKmer(CKmerAPI &kmer, float &count);
bool CheckKmer(const CKmerAPI &kmer, float &count) const;

bool CheckKmer(CKmerAPI &kmer, uint32 &count);
bool CheckKmer(const CKmerAPI &kmer, uint32 &count) const;

bool CheckKmer(CKmerAPI &kmer, uint64 &count);
bool CheckKmer(const CKmerAPI &kmer, uint64 &count) const;

// Return true if kmer exists
bool IsKmer(CKmerAPI &kmer);
bool IsKmer(const CKmerAPI &kmer) const;

// Set original (readed from *.kmer_pre) values for min_count and max_count
void ResetMinMaxCounts(void);

// Get current parameters from kmer_database
bool Info(uint32 &_kmer_length, uint32 &_mode, uint32 &_counter_size, uint32 &_lut_prefix_length, uint32 &_signature_len, uint32 &_min_count, uint64 &_max_count, uint64 &_total_kmers);
bool Info(uint32 &_kmer_length, uint32 &_mode, uint32 &_counter_size, uint32 &_lut_prefix_length, uint32 &_signature_len, uint32 &_min_count, uint64 &_max_count, uint64 &_total_kmers) const;

// Get current parameters from kmer_database
bool Info(CKMCFileInfo& info);
bool Info(CKMCFileInfo& info) const;

// Get counters for all k-mers in read
bool GetCountersForRead(const std::string& read, std::vector<uint32>& counters);
bool GetCountersForRead(const std::string& read, std::vector<float>& counters);
bool GetCountersForRead(const std::string& read, std::vector<uint32>& counters) const;
bool GetCountersForRead(const std::string& read, std::vector<float>& counters) const;
private:
uint32 count_for_kmer_kmc1(CKmerAPI& kmer);
uint32 count_for_kmer_kmc2(CKmerAPI& kmer, uint32 bin_start_pos);
uint32 count_for_kmer_kmc1(const CKmerAPI& kmer) const;
uint32 count_for_kmer_kmc2(const CKmerAPI& kmer, uint32 bin_start_pos) const;
};

#endif
Expand Down
22 changes: 11 additions & 11 deletions kmc_api/kmer_api.h
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Original file line number Diff line number Diff line change
Expand Up @@ -46,12 +46,12 @@ class CKmerAPI
kmer_data[(pos + byte_alignment) >> 5] += (uint64)val << (62 - (((pos + byte_alignment) & 31) * 2));
}

inline uchar extract2bits(uint32 pos)
inline uchar extract2bits(uint32 pos) const
{
return (kmer_data[(pos + byte_alignment) >> 5] >> (62 - (((pos + byte_alignment) & 31) * 2))) & 3;
}
//----------------------------------------------------------------------------------
inline void SHL_insert2bits(uchar val)
inline void SHL_insert2bits(uchar val) const
{
kmer_data[0] <<= 2;
if (byte_alignment)
Expand All @@ -68,7 +68,7 @@ class CKmerAPI
}

//----------------------------------------------------------------------------------
inline void SHR_insert2bits(uchar val)
inline void SHR_insert2bits(uchar val) const
{
for (uint32 i = no_of_rows - 1; i > 0; --i)
{
Expand Down Expand Up @@ -98,7 +98,7 @@ class CKmerAPI

// ----------------------------------------------------------------------------------
template<typename RandomAccessIterator>
inline void to_string_impl(RandomAccessIterator iter)
inline void to_string_impl(RandomAccessIterator iter) const
{
uchar *byte_ptr;
uchar c;
Expand Down Expand Up @@ -391,7 +391,7 @@ class CKmerAPI
// IN : pos - a position of a symbol
// RET : symbol - a symbol placed on a position pos
//-----------------------------------------------------------------------
inline char get_asci_symbol(unsigned int pos)
inline char get_asci_symbol(unsigned int pos) const
{
if(pos >= kmer_length)
return 0;
Expand All @@ -411,7 +411,7 @@ class CKmerAPI
// IN : pos - a position of a symbol
// RET : symbol - a symbol placed on a position pos
//-----------------------------------------------------------------------
inline uchar get_num_symbol(unsigned int pos)
inline uchar get_num_symbol(unsigned int pos) const
{
if (pos >= kmer_length)
return 0;
Expand All @@ -430,7 +430,7 @@ class CKmerAPI
// Convert kmer into string (an alphabet ACGT)
// RET : string kmer
//-----------------------------------------------------------------------
inline std::string to_string()
inline std::string to_string() const
{
std::string string_kmer;
string_kmer.resize(kmer_length);
Expand All @@ -441,14 +441,14 @@ class CKmerAPI
// Convert kmer into string (an alphabet ACGT). The function assumes enough memory was allocated
// OUT : str - string kmer.
//-----------------------------------------------------------------------
inline void to_string(char *str)
inline void to_string(char *str) const
{
to_string_impl(str);
str[kmer_length] = '\0';
};


inline void to_long(std::vector<uint64>& kmer)
inline void to_long(std::vector<uint64>& kmer) const
{
kmer.resize(no_of_rows);
uint32 offset = 62 - ((kmer_length - 1 + byte_alignment) & 31) * 2;
Expand All @@ -472,7 +472,7 @@ class CKmerAPI
// Convert kmer into string (an alphabet ACGT)
// OUT : str - string kmer
//-----------------------------------------------------------------------
inline void to_string(std::string &str)
inline void to_string(std::string &str) const
{
str.resize(kmer_length);
to_string_impl(str.begin());
Expand Down Expand Up @@ -650,7 +650,7 @@ class CKmerAPI
// IN : sig_len - the length of a signature
// RET : signature value
//-----------------------------------------------------------------------
uint32 get_signature(uint32 sig_len)
uint32 get_signature(uint32 sig_len) const
{
uchar symb;
CMmer cur_mmr(sig_len);
Expand Down
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