/**************************************************************************************/
void FilterSeqsCommand::doTrump() {
- //trump = globaldata->getTrump();
-//
-// for(int i = 0; i < db->size(); i++) {
-// Sequence cur = db->get(i);
-// string curAligned = cur.getAligned();
-//
-// for(int j = 0; j < curAligned.length-1; j++) {
-// string curChar = curAligned.substr(j, j+1);
-//
-// if(curChar.compare(trump) == 0)
-// columnsToRemove[j] = true;
-// }
-// }
+ trump = globaldata->getTrump();
+ for(int i = 0; i < db->size(); i++) {
+ Sequence cur = db->get(i);
+ string curAligned = cur.getAligned();
+ for(int j = 0; j < curAligned.length(); j++) {
+ string curChar = curAligned.substr(j, 1);
+ if(curChar.compare(trump) == 0)
+ columnsToRemove[j] = true;
+ }
+ }
}
/**************************************************************************************/
void FilterSeqsCommand::doSoft() {
- //soft = atoi(globaldata->getSoft().c_str());
-// vector<vector<int> > columnSymbolSums;
-// vector<vector<string> > columnSymbols;
-// for(int i = 0; i < db->get(0).getLength(); i++) {
-// vector<string> symbols;
-// vector<int> sums;
-// columnSymbols[i] = symbols;
-// columnSymbolSums[i] = sums;
-// }
-//
-// for(int i = 0; i < db->size(); i++) {
-// Sequence cur = db->get(i);
-// string curAligned = cur.getAligned();
-//
-// for(int j = 0; j < curAligned.length-1; j++) {
-// string curChar = curAligned.substr(j, j+1);
-// vector<string> curColumnSymbols = columnSymbols[j];
-//
-// bool newSymbol = true;
-//
-// for(int k = 0; j < curColumnSymbols.size(); j++)
-// if(curChar.compare(curColumnSymbols[k]) == 0) {
-// newSymbol = false;
-// columnSymbolSums[j][k]++;
-// }
-//
-// if(newSymbol) {
-// columnSymbols.push_back(curChar);
-// columnSymbolSums[j].push_back(1);
-// }
-// }
-// }
-//
-// for(int i = 0; i < columnSymbolSums.size(); i++) {
-// int totalSum = 0;
-// int max = 0;
-// vector<int> curColumn = columnSymbolSums[i];
-//
-// for(int j = 0; j < curColumn.size(); j++) {
-// int curSum = curColumn[j];
-// if(curSum > max)
-// max = curSum;
-// totalSum += curSum;
-// }
-//
-// if((double)max/(double)totalSum * 100 < soft)
-// columnsToRemove[i] = true;
-// }
-}
-void FilterSeqsCommand::doFilter() {}
-/**************************************************************************************/
-int FilterSeqsCommand::execute() {
- try {
- globaldata = GlobalData::getInstance();
- filename = globaldata->inputFileName;
+ soft = atoi(globaldata->getSoft().c_str());
+ vector<vector<int> > columnSymbolSums;
+ vector<vector<string> > columnSymbols;
+ for(int i = 0; i < db->get(0).getLength(); i++) {
+ vector<string> symbols;
+ vector<int> sums;
+ columnSymbols.push_back(symbols);
+ columnSymbolSums.push_back(sums);
+ }
+
+ for(int i = 0; i < db->size(); i++) {
+ Sequence cur = db->get(i);
+ string curAligned = cur.getAligned();
- if(globaldata->getFastaFile().compare("") != 0) {
- readFasta = new ReadFasta(filename);
- readFasta->read();
- db = readFasta->getDB();
+ for(int j = 0; j < curAligned.length(); j++) {
+ string curChar = curAligned.substr(j, 1);
+ vector<string> curColumnSymbols = columnSymbols[j];
+ bool newSymbol = true;
+
+ for(int k = 0; k < curColumnSymbols.size(); k++)
+ if(curChar.compare(curColumnSymbols[k]) == 0) {
+ newSymbol = false;
+ columnSymbolSums[j][k]++;
+ }
+
+ if(newSymbol) {
+ columnSymbols[j].push_back(curChar);
+ columnSymbolSums[j].push_back(1);
+ }
}
+ }
+
+
+ for(int i = 0; i < columnSymbolSums.size(); i++) {
+ int totalSum = 0;
+ int max = 0;
+ vector<int> curColumnSymbols = columnSymbolSums[i];
- else if(globaldata->getNexusFile().compare("") != 0) {
- readNexus = new ReadNexus(filename);
- readNexus->read();
- db = readNexus->getDB();
+ for(int j = 0; j < curColumnSymbols.size(); j++) {
+ int curSum = curColumnSymbols[j];
+ //cout << columnSymbols[i][j] << ": " << curSum << "\n";
+ if(curSum > max)
+ max = curSum;
+ totalSum += curSum;
}
+ //cout << "\n";
- else if(globaldata->getClustalFile().compare("") != 0) {
- readClustal = new ReadClustal(filename);
- readClustal->read();
- db = readClustal->getDB();
- }
+ if((double)max/(double)totalSum * 100 < soft)
+ columnsToRemove[i] = true;
+ }
+}
- else if(globaldata->getPhylipFile().compare("") != 0) {
- readPhylip = new ReadPhylip(filename);
- readPhylip->read();
- db = readPhylip->getDB();
- }
+/**************************************************************************************/
+void FilterSeqsCommand::doFilter() {
+ filter = globaldata->getFilter();
+ ifstream filehandle;
+ openInputFile(filter, filehandle);
- for(int i = 0; i < db->get(0).getLength(); i++)
- columnsToRemove[i] = false;
-
- // Trump
- if(globaldata->getTrump().compare("") != 0) {
-
-
- }
-
- // Soft
- if(globaldata->getSoft().compare("") != 0) {}
+ char c;
+ int count = 0;
+ while(!filehandle.eof()) {
+ c = filehandle.get();
+ if(c == '0')
+ columnsToRemove[count] = true;
+ count++;
+ }
+}
+/**************************************************************************************/
+int FilterSeqsCommand::execute() {
+ try {
+ globaldata = GlobalData::getInstance();
+ db = globaldata->gSequenceDB;
+
+ for(int i = 0; i < db->get(0).getLength(); i++)
+ columnsToRemove.push_back(false);
+
+ if(globaldata->getTrump().compare("") != 0)
+ doTrump();
+ else if(globaldata->getSoft().compare("") != 0)
+ doSoft();
+ else if(globaldata->getFilter().compare("") != 0)
+ doFilter();
- // Filter
- //if(globaldata->getFilter().compare("") != 0) {
-//
-// filter = globaldata->getFilter();
-// ifstream filehandle;
-// openInputFile(filter, filehandle);
-//
-// char c;
-// int count = 0;
-// while(!filehandle.eof()) {
-// c = filehandle.get();
-// if(c == '0')
-// columnsToRemove[count] = true;
-// count++;
-// }
+ //for(int i = 0; i < columnsToRemove.size(); i++)
+// {
+// cout << "Remove Column " << i << " = ";
+// if(columnsToRemove[i])
+// cout << "true\n";
+// else
+// cout << "false\n";
// }
-
-
-
+ //Creating the new SequenceDB
+ SequenceDB newDB;
+ for(int i = 0; i < db->size(); i++) {
+ Sequence curSeq = db->get(i);
+ string curAligned = curSeq.getAligned();
+ string curName = curSeq.getName();
+ string newAligned = "";
+ for(int j = 0; j < curAligned.length(); j++)
+ if(!columnsToRemove[j])
+ newAligned += curAligned.substr(j, 1);
+ Sequence newSeq(curName, newAligned);
+ newDB.add(newSeq);
+ }
+
+ ofstream outfile;
+ outfile.open("filtertest.txt");
+ newDB.print(outfile);
+ outfile.close();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
ReadSeqsCommand::ReadSeqsCommand(){
try {
globaldata = GlobalData::getInstance();
-
+ filename = globaldata->inputFileName;
+ if(globaldata->getFastaFile().compare("") != 0) {
+ readFasta = new ReadFasta(filename);
+ readFasta->read();
+ globaldata->gSequenceDB = readFasta->getDB();
+ }
+ else if(globaldata->getNexusFile().compare("") != 0) {
+ readNexus = new ReadNexus(filename);
+ readNexus->read();
+ globaldata->gSequenceDB = readNexus->getDB();
+ }
+ else if(globaldata->getClustalFile().compare("") != 0) {
+ readClustal = new ReadClustal(filename);
+ readClustal->read();
+ globaldata->gSequenceDB = readClustal->getDB();
+ }
+ else if(globaldata->getPhylipFile().compare("") != 0) {
+ readPhylip = new ReadPhylip(filename);
+ readPhylip->read();
+ globaldata->gSequenceDB = readPhylip->getDB();
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadSeqsCommand class Function ReadSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the ReadSeqsCommand class function ReadSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
filebuf fb;
//fb.open ("fasta.txt",ios::out);
-// readFasta->read();
+ //readFasta->read();
// SequenceDB* db = readFasta->getDB();
//fb.open("nexus.txt",ios::out);
//for(int i = 0; i < db->size(); i++) {
-// cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getUnaligned() << "\n\n";
+// cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getAligned() << "\n\n";
// }
//ostream os(&fb);