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; }