int main(int argc, char **argv)
{
welcome();
defineverbose();
filenames.clear();
ClustalWInitializers();
clustalw::ClustalWResources *resources = clustalw::ClustalWResources::Instance();
resources->setPathToExecutable(string(argv[0]));
setUserParameters();
InputFile start;// object reads from an input file and creates a new file
start.run();
string offendingSeq;
Clustal* clustalObj;
clustalObj = new clustalw::Clustal();
int u = clustalObj->sequenceInput(false, &offendingSeq);
string phylipName;
clustalObj->align(&phylipName);
AminoAcidFrequency Table;
Table.openFile("TEST-OutputFile.aln");
vector<ProteinSequence> p1;
p1 = start.getProteinData();
Table.generateAminoAcidTables(p1);
p1.clear();
p1 = Table.getFinalSeqs();
DistanceMatrix dm;
dm.createDistanceTableCodes(p1);
dm.createSimilarityMatrixCodes(p1);
dm.createDistanceTableColours(p1);
dm.createSimilarityMatrixColours(p1);
VerticalPosition vp;
vp.run(p1);
cout<< "\nPROCESS COMPLETED!\nThe following files were created:\n" << endl;
for ( size_t i = 0; i < filenames.size(); i++ )
{
cout << "\t" << i+1 << ". " << filenames[i] << endl;
}
return 0;
}
int main(int argc, char **argv)
{
welcome();
verbose = false;
//defineverbose();
CreateDirectory ("outFiles", NULL);
InputFile start;// object reads from an input file and creates a new file
start.run();
vector<ProteinSequence> p1;
ClustalWInitializers(); // this wont work without void ClustalWInitializers() above
clustalw::ClustalWResources *resources = clustalw::ClustalWResources::Instance();
resources->setPathToExecutable(string(argv[0]));
userParameters->toggleOutputFasta();
//userParameters->getOutputFasta();
setUserParameters(); // this wont work without void setUserParameters()
if ( checker == true )
{
string offendingSeq;
Clustal* clustalObj;
clustalObj = new clustalw::Clustal();
clustalObj->sequenceInput(false, &offendingSeq);
string phylipName;
clustalObj->align(&phylipName);
delete clustalObj;
alignment_file = "outFiles//Alignment.aln";
p1 = start.getProteinData();
}
else
{
// get p1 from the alignment file
p1 = start.getAlignmentData();
// do nothing
}
AminoAcidComposition Table;
if ( Table.openFile(alignment_file) == true ) // open the specified alignment file
{
}
Table.generateAminoAcidTables(p1); // from the alignment file
/* Calls the following:
vector<ProteinSequence> p2 = assembleSeq(p);
p3 = processSeq(p2);
createPropertyTable(p3);
createAminoAcidComposition(p3);
*/
p1.clear();
p1 = Table.getFinalSeqs();
/* cout << "size of p1 : " << p1.size() << endl;
for ( size_t i = 0; i < p1.size(); i++ )
{
string s = p1[i].getPDB();
cout << s << endl;
s = p1[i].getSeq();
cout << s << endl;
} */
DistanceAndSimilarity dm;
dm.createDistanceTableCodes(p1);
dm.createSimilarityMatrixCodes(p1);
dm.createDistanceTableColours(p1);
dm.createSimilarityMatrixColours(p1);
VerticalColumn vp;
vp.generateVerticalColumnComposition(p1);
cout<< "\nPROCESS COMPLETED! \nThe following files were created:\n" << endl;
for ( size_t i = 0; i < filenames.size(); i++ )
{
cout << "\t" << i+1 << ". " << filenames[i] << endl;
}
delete userParameters;
delete utilityObject;
delete subMatrix;
if(logObject)
{
delete logObject;
}
//system("pause");
return 0;
}
