/***********************************************************************/
FormatColumnMatrix::FormatColumnMatrix(string df) : filename(df){
- openInputFile(filename, fileHandle);
+ m->openInputFile(filename, fileHandle);
}
/***********************************************************************/
-void FormatColumnMatrix::read(NameAssignment* nameMap){
+int FormatColumnMatrix::read(NameAssignment* nameMap){
try {
string firstName, secondName;
ofstream out;
string tempOutFile = filename + ".temp";
- openOutputFile(tempOutFile, out);
+ m->openOutputFile(tempOutFile, out);
while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
+ if (m->control_pressed) { out.close(); m->mothurRemove(tempOutFile); fileHandle.close(); delete reading; return 0; }
+
fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
- if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
if (distance == -1) { distance = 1000000; }
-
- if(distance < cutoff && itA != itB){
-
+
+ if((distance < cutoff) && (itA != itB)){
if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
refRow = itA->second;
refCol = itB->second;
reading->update(itA->second * nseqs / 2);
}
- gobble(fileHandle);
+ m->gobble(fileHandle);
}
out.close();
fileHandle.close();
-
+
string squareFile;
if(lt == 0){ // oops, it was square
squareFile = filename;
}else{ squareFile = tempOutFile; }
//sort file by first column so the distances for each row are together
- string outfile = getRootName(squareFile) + "sorted.dist.temp";
+ string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
//use the unix sort
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n " + squareFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
system(command.c_str());
#endif
+ if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
//output to new file distance for each row and save positions in file where new row begins
ifstream in;
- openInputFile(outfile, in);
+ m->openInputFile(outfile, in);
distFile = outfile + ".rowFormatted";
- openOutputFile(distFile, out);
+ m->openOutputFile(distFile, out);
rowPos.resize(nseqs, -1);
int currentRow;
for(int k = 0; k < firstString.length(); k++) { in.putback(firstString[k]); }
while(!in.eof()) {
- in >> first >> second >> dist; gobble(in);
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+
+ in >> first >> second >> dist; m->gobble(in);
if (first != currentRow) {
//save position in file of each new row
rowMap.clear();
//save row you just read
- rowMap[second] = dist;
-
+ if (dist < cutoff) {
+ rowMap[second] = dist;
+ }
}else{
- rowMap[second] = dist;
+ if (dist < cutoff) {
+ rowMap[second] = dist;
+ }
}
}
in.close();
out.close();
+ if (m->control_pressed) { m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
- remove(tempOutFile.c_str());
- remove(outfile.c_str());
+ m->mothurRemove(tempOutFile);
+ m->mothurRemove(outfile);
reading->finish();
+
+ delete reading;
list->setLabel("0");
+
+ if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FormatColumnMatrix", "read");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int FormatColumnMatrix::read(CountTable* nameMap){
+ try {
+
+ string firstName, secondName;
+ float distance;
+ int nseqs = nameMap->size();
+
+ list = new ListVector(nameMap->getListVector());
+
+ Progress* reading = new Progress("Formatting matrix: ", nseqs * nseqs);
+
+ int lt = 1;
+ int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+ int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
+
+ //need to see if this is a square or a triangular matrix...
+
+ ofstream out;
+ string tempOutFile = filename + ".temp";
+ m->openOutputFile(tempOutFile, out);
+
+ while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
+
+ if (m->control_pressed) { out.close(); m->mothurRemove(tempOutFile); fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance
+
+ int itA = nameMap->get(firstName);
+ int itB = nameMap->get(secondName);
+
+ if (distance == -1) { distance = 1000000; }
+
+ if((distance < cutoff) && (itA != itB)){
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+
+ //making it square
+ out << itA << '\t' << itB << '\t' << distance << endl;
+ out << itB << '\t' << itA << '\t' << distance << endl;
+ }
+ else if(refRow == itA && refCol == itB){ lt = 0; } //you are square
+ else if(refRow == itB && refCol == itA){ lt = 0; } //you are square
+ else{ //making it square
+ out << itA << '\t' << itB << '\t' << distance << endl;
+ out << itB << '\t' << itA << '\t' << distance << endl;
+ }
+
+ reading->update(itA * nseqs / 2);
+ }
+ m->gobble(fileHandle);
+ }
+ out.close();
+ fileHandle.close();
+
+ string squareFile;
+ if(lt == 0){ // oops, it was square
+ squareFile = filename;
+ }else{ squareFile = tempOutFile; }
+
+ //sort file by first column so the distances for each row are together
+ string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
+
+ //use the unix sort
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + squareFile + " -o " + outfile;
+ system(command.c_str());
+#else //sort using windows sort
+ string command = "sort " + squareFile + " /O " + outfile;
+ system(command.c_str());
+#endif
+
+ if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+
+ //output to new file distance for each row and save positions in file where new row begins
+ ifstream in;
+ m->openInputFile(outfile, in);
+
+ distFile = outfile + ".rowFormatted";
+ m->openOutputFile(distFile, out);
+
+ rowPos.resize(nseqs, -1);
+ int currentRow;
+ int first, second;
+ float dist;
+ map<int, float> rowMap;
+ map<int, float>::iterator itRow;
+
+ //get first currentRow
+ in >> first;
+ currentRow = first;
+
+ string firstString = toString(first);
+ for(int k = 0; k < firstString.length(); k++) { in.putback(firstString[k]); }
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+
+ in >> first >> second >> dist; m->gobble(in);
+
+ if (first != currentRow) {
+ //save position in file of each new row
+ rowPos[currentRow] = out.tellp();
+
+ out << currentRow << '\t' << rowMap.size() << '\t';
+
+ for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+ out << itRow->first << '\t' << itRow->second << '\t';
+ }
+ out << endl;
+
+ currentRow = first;
+ rowMap.clear();
+
+ //save row you just read
+ if (dist < cutoff) {
+ rowMap[second] = dist;
+ }
+ }else{
+ if (dist < cutoff) {
+ rowMap[second] = dist;
+ }
+ }
+ }
+
+ //print last Row
+ //save position in file of each new row
+ rowPos[currentRow] = out.tellp();
+
+ out << currentRow << '\t' << rowMap.size() << '\t';
+
+ for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+ out << itRow->first << '\t' << itRow->second << '\t';
+ }
+ out << endl;
+
+
+ in.close();
+ out.close();
+
+ if (m->control_pressed) { m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+
+ m->mothurRemove(tempOutFile);
+ m->mothurRemove(outfile);
+
+ reading->finish();
+
+ delete reading;
+ list->setLabel("0");
+
+ if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
+
+ return 1;
+
}
catch(exception& e) {
- errorOut(e, "FormatColumnMatrix", "read");
+ m->errorOut(e, "FormatColumnMatrix", "read");
exit(1);
}
}
projects / mothur.git / blobdiff