bool ProNovoConfig::getResidueElementalComposition(string & sAtomicCompositionTable)
{
sAtomicCompositionTable = "";
map<string, string> mapResidueTable;
if( ! getConfigMasterKeyValue("[Peptide_Identification]Residue", mapResidueTable) )
{
cerr << "Error: cannot retrieve Elemental composition of amino acid residues." << endl;
return false;
}
map<string, string>::iterator iter;
for (iter = mapResidueTable.begin(); iter != mapResidueTable.end(); ++iter)
{
sAtomicCompositionTable.append( iter->first );
sAtomicCompositionTable.append( ",\t" );
sAtomicCompositionTable.append( iter->second );
sAtomicCompositionTable.append( "\n" );
}
replaceDelimitor( sAtomicCompositionTable, ',', '\t' );
return true;
}
bool ProRataConfig::getResidueAtomicComposition(residueMap & mIsotopologue)
{
mIsotopologue.clear();
// Creat a TinyXML document for ProRataConfig.XML
TiXmlDocument txdConfigFile;
// Try loading the file.
if ( ! ( txdConfigFile.LoadFile( sFilename.c_str() ) ) )
{
cout << "ERROR! Loading Configuration file" << endl;
return false;
}
/*
* move the node pointer to RESIDUE_ATOMIC_COMPOSITION
* if failed, return an empty map
*/
TiXmlNode * txnTemp = NULL;
txnTemp = txdConfigFile.FirstChild( "CONFIG" );
if ( ! txnTemp )
return false;
txnTemp = txnTemp->FirstChild( "SIC_EXTRACTION" );
if ( ! txnTemp )
return false;
txnTemp = txnTemp->FirstChild( "RESIDUE_ATOMIC_COMPOSITION" );
if ( ! txnTemp )
return false;
// a node pointer to a ISOTOPOLOGUE element
TiXmlNode * txnTable = NULL;
// a element pointer for retrieving the attribute of the ISOTOPOLOGUE element
TiXmlElement * txeElement = NULL;
// a text pointer for retrieving the text inside ISOTOPOLOGUE element
TiXmlText * txsText = NULL;
/*
* the node type can any one of the following:
* enum NodeType
* {
* DOCUMENT,
* ELEMENT,
* COMMENT,
* UNKNOWN,
* TEXT,
* DECLARATION,
* TYPECOUNT
* };
*
*/
// loop thru all ISOTOPOLOGUE elements
for( txnTemp = txnTemp->FirstChild( "ISOTOPOLOGUE" ); txnTemp; txnTemp = txnTemp->NextSibling( "ISOTOPOLOGUE" ) )
{
// the string for holding the text inside
string sTable = "";
/*
* loop thru all the text nodes inside ISOTOPOLOGUE;
* the text nodes can be separated by the comment nodes or other
* cast the node to a text node, only if it is of type TEXT, which equals 4
* then concatenate all the text
*/
for( txnTable = txnTemp->FirstChild("R"); txnTable; txnTable = txnTable->NextSibling("R") )
{
txsText = txnTable->FirstChild()->ToText();
sTable.append( txsText->Value() );
sTable.append( "\n" );
/*
// get the type of the node
if( txnTable->Type() == 4 )
{
// cast the node to a TEXT node
txsText = txnTable->ToText();
// get the value of the TEXT node and append it to sTable
sTable.append( txnTable->Value() );
}
*/
}
replaceDelimitor( sTable, ',', '\t' );
// points txeElement to the ISOTOPOLOGUE element
txeElement = txnTemp->ToElement();
if( txeElement )
{
// get the "name" Attribute of the element
string sName = txeElement->Attribute( "name" );
// save the sName-sTable pair to the return value
mIsotopologue[ sName ] = sTable;
}
}
return true;
}
bool ProRataConfig::getAtomIsotopicComposition( char cAtom,
vector<double> & vdAtomicMass,
vector<double> & vdNaturalComposition,
vector<double> & vdEnrichedComposition)
{
// clear the input vectors
vdAtomicMass.clear();
vdNaturalComposition.clear();
vdEnrichedComposition.clear();
// Creat a TinyXML document for ProRataConfig.XML
TiXmlDocument txdConfigFile;
// Try loading the file.
if ( ! ( txdConfigFile.LoadFile( sFilename.c_str() ) ) )
{
cout << "ERROR! Loading Configuration file" << endl;
return false;
}
string sData;
istringstream issStream;
double dValue;
string sAtom = "X";
sAtom[0] = cAtom;
// creat the path to the MASS_DA element of the input sAtom
vector<string> vsTagList;
vsTagList.push_back( "CONFIG" );
vsTagList.push_back( "SIC_EXTRACTION" );
vsTagList.push_back( "ATOM_ISOTOPIC_COMPOSITION" );
vsTagList.push_back( sAtom );
vsTagList.push_back( "MASS_DA" );
// get the text inside and extract the value
sData = getValue( txdConfigFile, vsTagList );
replaceDelimitor( sData, ',', '\t' );
// clear end of file state
issStream.clear();
// re-set the string associated with issStream
issStream.str( sData );
while( !( issStream.eof() ) )
{
issStream >> dValue;
vdAtomicMass.push_back( dValue );
}
// move to the NATURAL element
vsTagList.pop_back();
vsTagList.push_back( "NATURAL" );
sData = getValue( txdConfigFile, vsTagList );
replaceDelimitor( sData, ',', '\t' );
issStream.clear();
issStream.str( sData );
while( !( issStream.eof() ) )
{
issStream >> dValue;
vdNaturalComposition.push_back( dValue );
}
// move to the ENRICHED element
vsTagList.pop_back();
vsTagList.push_back( "ENRICHED" );
sData = getValue( txdConfigFile, vsTagList );
replaceDelimitor( sData, ',', '\t' );
issStream.clear();
issStream.str( sData );
while( !( issStream.eof() ) )
{
issStream >> dValue;
vdEnrichedComposition.push_back( dValue );
}
return true;
}
bool ProNovoConfig::getAtomIsotopicComposition( char cAtom,
vector<double> & vdAtomicMass,
vector<double> & vdComposition)
{
// clear the input vectors
vdAtomicMass.clear();
vdComposition.clear();
string sData;
istringstream issStream;
double dValue;
string sAtom = "X";
sAtom[0] = cAtom;
map<string, string> mapElementMasses;
if( ! getConfigMasterKeyValue("[Peptide_Identification]Element_Masses", mapElementMasses) )
{
cerr << "Error: cannot retrieve Element Masses." << endl;
return false;
}
map<string, string> mapElementPercent;
if( ! getConfigMasterKeyValue("[Peptide_Identification]Element_Percent", mapElementPercent) )
{
cerr << "Error: cannot retrieve Element Percent." << endl;
return false;
}
map<string, string>::iterator iterMass = mapElementMasses.find(sAtom);
if( iterMass == mapElementMasses.end() )
{
cerr << "Error: cannot find element masses for element " << sAtom << endl;
return false;
}
sData = iterMass->second;
replaceDelimitor( sData, ',', '\t' );
// clear end of file state
issStream.clear();
// re-set the string associated with issStream
issStream.str( sData );
while( !( issStream.eof() ) )
{
issStream >> dValue;
vdAtomicMass.push_back( dValue );
}
map<string, string>::iterator iterPercent = mapElementPercent.find(sAtom);
if( iterPercent == mapElementPercent.end() )
{
cerr << "Error: cannot find element percent for element " << sAtom << endl;
return false;
}
sData = iterPercent->second;
replaceDelimitor( sData, ',', '\t' );
// clear end of file state
issStream.clear();
// re-set the string associated with issStream
issStream.str( sData );
while( !( issStream.eof() ) )
{
issStream >> dValue;
vdComposition.push_back( dValue );
}
return true;
}
