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//Copyright 2007 Asim Siddiqui
//
// 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.
//
//
//
#include <cstddef>
#include <cstdlib>
#include <cstring>
#include <SRF_util.hh>
#include <SRF_Container.hh>
#include <SRF_ReadSet.hh>
#define HEADERBLOCKTYPE "SSRF"
#define CONTAINERTYPE 'Z'
#define FORMATVERSION "1.3"
SRF_Container::SRF_Container( void )
{
formatVersion = FORMATVERSION;
headerBlockType = HEADERBLOCKTYPE;
containerType = CONTAINERTYPE;
sizeContainerHeader = 0;
}
SRF_Container::~SRF_Container( void )
{
// null
}
bool
SRF_Container::populate( std::fstream& file )
{
containerPositionInFile = file.tellg();
//read blockType, blockSize, version, containerType, baseCaller, baseCallerVersion
char tmp[4];
file.read(tmp, 4);
headerBlockType = std::string(tmp, 4);;
if ( headerBlockType.compare( HEADERBLOCKTYPE ) != 0 )
{
SRF_ReportError( "incorrect block type header" );
return FALSE;
}
sizeContainerHeader = 0;
file.read( reinterpret_cast<char *>(&sizeContainerHeader), 4 );
sizeContainerHeader = be_int4(sizeContainerHeader);
formatVersion = SRF_readString( file );
if ( formatVersion.compare( FORMATVERSION ) != 0 )
{
SRF_ReportError( "incorrect format version" );
return FALSE;
}
file.read ( &containerType, 1);
if ( containerType != CONTAINERTYPE )
{
SRF_ReportError( "unsupported container type" );
return FALSE;
}
baseCaller = SRF_readString( file );
baseCallerVersion = SRF_readString( file );
return TRUE;
}
bool
SRF_Container::setup( const std::string& baseCallerIn,
const std::string& baseCallerVersionIn )
{
baseCaller = baseCallerIn;
baseCallerVersion = baseCallerVersionIn;
return TRUE;
}
char
SRF_Container::getContainerType( void )
{
return containerType;
}
const std::string&
SRF_Container::getBaseCaller( void )
{
return baseCaller;
}
const std::string&
SRF_Container::getBaseCallerVersion( void )
{
return baseCallerVersion;
}
const std::string&
SRF_Container::getHeaderBlockType( void )
{
return headerBlockType;
}
const std::string&
SRF_Container::getFormatVersion( void )
{
return formatVersion;
}
bool
SRF_Container::filePtrToContainerStart( std::fstream& file )
{
file.seekg( containerPositionInFile );
return TRUE;
}
bool
SRF_Container::nextReadSet( std::fstream& file )
{
SRF_ReportError( "Not implemented" );
return FALSE;
}
bool
SRF_Container::previousReadSet( std::fstream& file )
{
SRF_ReportError( "Not implemented" );
return FALSE;
}
bool
SRF_Container::write( std::fstream& file )
{
sizeContainerHeader = 0;
//write blockType, blockSize, version, containerType, baseCaller, baseCallerVersion
sizeContainerHeader += headerBlockType.length();
sizeContainerHeader += 4;
char* formatVersionStr = ADOPT SRF_cStrToPascalStr( formatVersion.c_str() );
sizeContainerHeader += strlen( formatVersionStr );
sizeContainerHeader += 1;
char* baseCallerStr = ADOPT SRF_cStrToPascalStr( baseCaller.c_str() );
sizeContainerHeader += strlen( baseCallerStr );
char* baseCallerVersionStr = ADOPT SRF_cStrToPascalStr( baseCallerVersion.c_str() );
sizeContainerHeader += strlen( baseCallerVersionStr );
file << headerBlockType;
int32_t be_sizeContainerHeader = be_int4(sizeContainerHeader);
file.write(reinterpret_cast<const char*>(&be_sizeContainerHeader),4);
file << formatVersionStr;
file << containerType;
file << baseCallerStr;
file << baseCallerVersionStr;
delete [] formatVersionStr;
delete [] baseCallerStr;
delete [] baseCallerVersionStr;
}
void
SRF_Container::dump( void )
{
std::cout << "Container Block Type:" << headerBlockType <<std::endl;
std::cout << "Format Version:" << formatVersion <<std::endl;
std::cout << "Container Type:" << containerType <<std::endl;
std::cout << "Base Caller:" << baseCaller <<std::endl;
std::cout << "Base Caller Version:" << baseCallerVersion <<std::endl;
}
bool
SRF_Container::writeReadSet( std::fstream& file,
const std::string& ztrHeader,
const std::vector<ztr_t>& ztrBlobs,
const std::vector<std::string>& readIds,
const std::string& uniqueIdPrefix )
{
SRF_ReadSet newReadSet;
if ( !newReadSet.setup( uniqueIdPrefix, ztrHeader ) )
{
SRF_ReportError( "can't initialize readSet" );
return FALSE;
}
if ( !newReadSet.write( file, ztrBlobs, readIds ) )
{
SRF_ReportError( "can't write readSet" );
return FALSE;
}
return TRUE;
}
ADOPT SRF_ReadSet*
SRF_Container::firstReadSet( std::fstream& file )
{
file.seekg( ((off_t) containerPositionInFile + sizeContainerHeader) ); // TO DO fix to work with XML files
SRF_ReadSet* readSet = new SRF_ReadSet;
if ( !readSet->populate( file ) )
{
SRF_ReportError( "can't populate first read set" );
delete readSet;
return NULL;
}
return readSet;
}
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