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gnMultiSpec.cpp Go to the documentation of this file. // File: gnMultiSpec.cpp // Purpose: abstract Spec class // Description: Defines a basic interface for all specs // Changes: // Version: libGenome 0.1.0 // Author: Aaron Darling // Last Edited: April 15, 2001, 11:13:00pm // Modified by: // Copyright: (c) Aaron Darling // Licenses: Proprietary #include "gn/gnDefs.h" #include <string> #include <vector> #include "gn/gnMultiSpec.h" #include "gn/gnBaseSource.h" #include "gn/gnBaseFeature.h" #include "gn/gnDebug.h" #include "gn/gnException.h" void gnMultiSpec::Clear() { gnBaseSpec::Clear(); uint32 list_size = m_headerList.size(); for(uint32 i=0; i < list_size; i++) delete m_headerList[i]; m_headerList.clear(); } gnSeqI gnMultiSpec::GetLength() const { gnSeqI subLen = 0; //aggregate the lower levels. for(uint32 i=0; i < GetSpecListLength(); i++) subLen += GetSpec(i)->GetLength(); return subLen; } //Return the index of the subspec which contains the base in question uint32 gnMultiSpec::GetSpecIndexByBase( const gnSeqI baseI ) const{ gnSeqI cur_length = 0; for(uint32 i=0; i < GetSpecListLength(); i++){ cur_length += GetSpec(i)->GetLength(); if(baseI < cur_length) return i; } //if we made it here then the base was out of bounds Throw_gnEx(SeqIndexOutOfBounds()); } uint32 gnMultiSpec::GetSpecIndexByName( const string& name ) const{ for(uint32 i=0; i < GetSpecListLength(); i++){ if(name == GetSpec(i)->GetName()) return i; } Throw_gnEx(SpecIndexOutOfBounds()); } //returns the starting base pair index of the given subspec. gnSeqI gnMultiSpec::GetSpecStartBase( const uint32 specI ) const{ uint32 i; if(specI >= GetSpecListLength()) Throw_gnEx(SpecIndexOutOfBounds()); gnSeqI start_base = 0; for(i=0; i < specI; i++){ start_base += GetSpec(i)->GetLength(); } return start_base; } gnSeqI gnMultiSpec::GetSpecEndBase( const uint32 specI ) const{ uint32 i; if(specI >= GetSpecListLength()) Throw_gnEx(SpecIndexOutOfBounds()); gnSeqI end_base = 0; for(i=0; i <= specI; i++){ end_base += GetSpec(i)->GetLength(); } return end_base; } void gnMultiSpec::CropStart( gnSeqI cropLen ){ gnSeqI curbase = 0; for(uint32 specI = 0; specI < GetSpecListLength(); specI++){ curbase += GetSpec(specI)->GetLength(); if(curbase <= cropLen){ //delete the spec completely gnBaseSpec *tmp_spec = GetSpec(specI); RemoveSpec(specI); delete tmp_spec; specI--; }else{ //recurse and break gnSeqI sub_len = cropLen - (curbase - GetSpec(specI)->GetLength()); GetSpec(specI)->CropStart(sub_len); break; } } } void gnMultiSpec::CropEnd( gnSeqI cropLen ){ gnSeqI curbase = 0; gnSeqI cropbase = GetLength() - cropLen; //last base to keep boolean trash_the_rest = false; for(uint32 specI = 0; specI < GetSpecListLength(); specI++){ curbase += GetSpec(specI)->GetLength(); if(trash_the_rest){ //delete the spec entirely gnBaseSpec *tmp_spec = GetSpec(specI); RemoveSpec(specI); delete tmp_spec; specI--; continue; }else if(curbase > cropbase){ GetSpec(specI)->CropEnd(curbase - cropbase); trash_the_rest = true; }else if(curbase == cropbase) trash_the_rest = true; } } void gnMultiSpec::AddHeader( gnBaseHeader* head, const uint32 i) { uint32 index = i == UINT32_MAX ? m_headerList.size() : i; m_headerList.insert(m_headerList.begin() + index, head); } gnBaseHeader* gnMultiSpec::GetHeader( const string& name, uint32& i) const{ for(; i < m_headerList.size(); i++){ if( m_headerList[i]->GetHeaderName() == name) return m_headerList[i]; } Throw_gnEx(HeaderIndexOutOfBounds()); } void gnMultiSpec::RemoveHeader( uint32 i) { if(i <= m_headerList.size()){ m_headerList.erase(m_headerList.begin() + i); } Throw_gnEx(HeaderIndexOutOfBounds()); } boolean gnMultiSpec::SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const{ if(contigI == ALL_CONTIGS){ gnSeqI curpos = 0; uint32 readBytes = 0; uint32 remainingBytes = bufLen; uint32 curSpecI = 0; //seek to start spec. for(curSpecI=0; curSpecI < GetSpecListLength(); curSpecI++){ curpos += GetSpec(curSpecI)->GetLength(); if(curpos > start) break; } if(curpos <= start) Throw_gnEx(SeqIndexOutOfBounds()); //read until we're done; while((remainingBytes > 0) && (curSpecI < GetSpecListLength())) { gnSeqI readable = GetSpec(curSpecI)->GetLength(); //check for circular uint32 start_pos = readBytes == 0 ? start - (curpos - readable) : 0; uint32 to_read = readable - start_pos >= remainingBytes ? remainingBytes : readable - start_pos; boolean success = GetSpec(curSpecI)->SeqRead(start_pos, buf+readBytes, to_read, contigI); readBytes += to_read; remainingBytes -= to_read; if(!success) break; curSpecI++; } bufLen = readBytes; return true; }else{ //read from the specified contig. if(contigI < GetSpecListLength()) return GetSpec(contigI)->SeqRead(start, buf, bufLen, ALL_CONTIGS); else Throw_gnEx(SpecIndexOutOfBounds()); } return false; }