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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2006 Louis Warschaw Prostate Cancer Center
// Cedars Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#define PWIZ_SOURCE
#include "IPIFASTADatabase.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>
#include <cstdlib>
namespace pwiz {
namespace proteome {
IPIFASTADatabase::const_iterator IPIFASTADatabase::begin()
{
return records().begin();
}
IPIFASTADatabase::const_iterator IPIFASTADatabase::end()
{
return records().end();
}
class IPIFASTADatabase::Impl
{
public:
Impl(const string& filename);
const vector<Record>& records() const {return records_;}
private:
vector<Record> records_;
void readRecords(istream& is);
};
IPIFASTADatabase::Impl::Impl(const string& filename)
{
ifstream is(filename.c_str());
if (!is) throw runtime_error(("[IPIFASTADatabase::Impl::Impl()] Unable to open file " + filename).c_str());
//cout << "Reading records from " << filename << "..." << flush;
readRecords(is);
//cout << "done.\n";
}
void IPIFASTADatabase::Impl::readRecords(istream& is)
{
Record* current = 0;
for (string buffer; getline(is, buffer); )
{
// std::cout<<"||||"<<buffer<<"$$$$"<<std::endl;
if (buffer.find(">IPI:IPI") == 0)
{
// start a new record, and set current pointer
records_.push_back(Record(atoi(buffer.c_str()+8)));
current = &records_.back();
current->fullSeqDescription = buffer;
// get protein ID (e.g. IPI number, or whatever precedes first pipe)
// TODO: Increase flexibility (e.g. what if no pipe, get all ids between pipes as different
// variables, etc ...
const char* pipe = "|";
if (buffer.find(pipe) != string::npos)
{
const size_t& pipeLocation = buffer.find(pipe);
char protein[30];
memset(protein, '\0', 30);
buffer.copy(protein, pipeLocation - 1, 1); // skip initial '>'
current->faID = protein;
}
else current->faID ="unknown";
}
else if(buffer.find(">") == 0){ //there is likely a better way to handle these cases.
// start a new record, and set current pointer
records_.push_back(Record(atoi(buffer.c_str())));
current = &records_.back();
current->fullSeqDescription = buffer;
// get protein ID (e.g. IPI number, or whatever precedes first space)
// TODO: Increase flexibility (e.g. what if no pipe, get all ids between pipes as different
// variables, etc ...
const char* space = " ";
if (buffer.find(space) != string::npos)
{
const size_t& spaceLocation = buffer.find(space);
char protein[50];
memset(protein, '\0', 50);
buffer.copy(protein, spaceLocation - 1, 1); // skip initial '>'
current->faID = protein;
}
else current->faID ="unknown";
}
else if (current)
{
// update current record with next line of the sequence
if(buffer.find("*") != string::npos){
const size_t& stringLocation = buffer.find("*");
buffer.erase(stringLocation);
}
current->sequence += buffer;
}
}
}
PWIZ_API_DECL IPIFASTADatabase::IPIFASTADatabase(const string& filename) : impl_(new Impl(filename)) {}
PWIZ_API_DECL IPIFASTADatabase::~IPIFASTADatabase(){} // auto-destruction of impl_
PWIZ_API_DECL const vector<IPIFASTADatabase::Record>& IPIFASTADatabase::records() const {return impl_->records();}
PWIZ_API_DECL ostream& operator<<(ostream& os, const IPIFASTADatabase::Record& record)
{
os << ">IPI:IPI" << setfill('0') << setw(8) << record.id << endl;
for (unsigned int i=0; i<record.sequence.size(); i++)
{
os << record.sequence[i];
if (i%60==59) os << endl;
}
return os;
}
} // namespace proteome
} // namespace pwiz
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