/***********************************************************************/
FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
- openInputFile(filename, fileHandle);
+ m->openInputFile(filename, fileHandle);
}
/***********************************************************************/
//not using nameMap
string name;
ofstream out;
- fileHandle >> nseqs >> name;
-
- list = new ListVector(nseqs);
- list->set(0, name);
+ string numTest;
+ fileHandle >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+ if(nameMap == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{
+ list = new ListVector(nameMap->getListVector());
+ if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+ }
char d;
while((d=fileHandle.get()) != EOF){
fileHandle.close(); //reset file
//open and get through numSeqs, code below formats rest of file
- openInputFile(filename, fileHandle);
- fileHandle >> nseqs; gobble(fileHandle);
+ m->openInputFile(filename, fileHandle);
+ fileHandle >> nseqs; m->gobble(fileHandle);
distFile = filename + ".rowFormatted";
- openOutputFile(distFile, out);
+ m->openOutputFile(distFile, out);
break;
}
if(d == '\n'){
ofstream outTemp;
string tempFile = filename + ".temp";
- openOutputFile(tempFile, outTemp);
+ m->openOutputFile(tempFile, outTemp);
//convert to square column matrix
for(int i=1;i<nseqs;i++){
fileHandle >> name;
- list->set(i, name);
+ if(nameMap == NULL){ list->set(i, name); }
+ else { if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+ }
for(int j=0;j<i;j++){
- if (m->control_pressed) { outTemp.close(); remove(tempFile.c_str()); fileHandle.close(); delete reading; return 0; }
+ if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close(); delete reading; return 0; }
fileHandle >> distance;
//format from square column to rowFormatted
//sort file by first column so the distances for each row are together
- string outfile = getRootName(tempFile) + "sorted.dist.temp";
+ string outfile = m->getRootName(tempFile) + "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 " + tempFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
system(command.c_str());
#endif
- if (m->control_pressed) { remove(tempFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { m->mothurRemove(tempFile); 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()) {
- if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); remove(distFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); m->mothurRemove(distFile); m->mothurRemove(outfile); delete reading; return 0; }
- in >> first >> second >> dist; gobble(in);
+ in >> first >> second >> dist; m->gobble(in);
if (first != currentRow) {
//save position in file of each new row
in.close();
out.close();
- remove(tempFile.c_str());
- remove(outfile.c_str());
+ m->mothurRemove(tempFile);
+ m->mothurRemove(outfile);
- if (m->control_pressed) { remove(distFile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { m->mothurRemove(distFile); delete reading; return 0; }
}
else{ //square matrix convert directly to formatted row file
for(int i=0;i<nseqs;i++){
fileHandle >> name;
- list->set(i, name);
+ if(nameMap == NULL){ list->set(i, name); }
+ else { if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+ }
for(int j=0;j<nseqs;j++){
- if (m->control_pressed) { fileHandle.close(); out.close(); remove(distFile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { fileHandle.close(); out.close(); m->mothurRemove(distFile); delete reading; return 0; }
fileHandle >> distance;
reading->update(index);
}
- gobble(fileHandle);
+ m->gobble(fileHandle);
//save position in file of each new row
rowPos[i] = out.tellp();
fileHandle.close();
out.close();
- if (m->control_pressed) { remove(distFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
list->setLabel("0");
exit(1);
}
}
+/***********************************************************************/
+//not using nameMap
+int FormatPhylipMatrix::read(CountTable* nameMap){
+ try {
+
+ float distance;
+ int square, nseqs;
+ string name;
+ ofstream out;
+
+ string numTest;
+ fileHandle >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+ if(nameMap == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{
+ list = new ListVector(nameMap->getListVector());
+ nameMap->get(name);
+ }
+
+ char d;
+ while((d=fileHandle.get()) != EOF){
+
+ if(isalnum(d)){ //you are square
+ square = 1;
+ fileHandle.close(); //reset file
+
+ //open and get through numSeqs, code below formats rest of file
+ m->openInputFile(filename, fileHandle);
+ fileHandle >> nseqs; m->gobble(fileHandle);
+
+ distFile = filename + ".rowFormatted";
+ m->openOutputFile(distFile, out);
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ Progress* reading;
+ reading = new Progress("Formatting matrix: ", nseqs * nseqs);
+
+ //lower triangle, so must go to column then formatted row file
+ if(square == 0){
+ int index = 0;
+
+ ofstream outTemp;
+ string tempFile = filename + ".temp";
+ m->openOutputFile(tempFile, outTemp);
+
+ //convert to square column matrix
+ for(int i=1;i<nseqs;i++){
+
+ fileHandle >> name;
+
+ if(nameMap == NULL){ list->set(i, name); }
+ else { nameMap->get(name); }
+
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff){
+ outTemp << i << '\t' << j << '\t' << distance << endl;
+ outTemp << j << '\t' << i << '\t' << distance << endl;
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ outTemp.close();
+
+ //format from square column to rowFormatted
+ //sort file by first column so the distances for each row are together
+ string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
+
+ //use the unix sort
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + tempFile + " -o " + outfile;
+ system(command.c_str());
+#else //sort using windows sort
+ string command = "sort " + tempFile + " /O " + outfile;
+ system(command.c_str());
+#endif
+
+ if (m->control_pressed) { m->mothurRemove(tempFile); 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(tempFile); m->mothurRemove(distFile); 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
+ rowMap[second] = dist;
+
+ index++;
+ reading->update(index);
+ }else{
+ 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();
+
+ m->mothurRemove(tempFile);
+ m->mothurRemove(outfile);
+
+ if (m->control_pressed) { m->mothurRemove(distFile); delete reading; return 0; }
+
+ }
+ else{ //square matrix convert directly to formatted row file
+ int index = nseqs;
+ map<int, float> rowMap;
+ map<int, float>::iterator itRow;
+ rowPos.resize(nseqs, -1);
+
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> name;
+
+ if(nameMap == NULL){ list->set(i, name); }
+ else { nameMap->get(name); }
+
+ for(int j=0;j<nseqs;j++){
+ if (m->control_pressed) { fileHandle.close(); out.close(); m->mothurRemove(distFile); delete reading; return 0; }
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if((distance < cutoff) && (j != i)){
+ rowMap[j] = distance;
+ }
+ index++;
+ reading->update(index);
+ }
+
+ m->gobble(fileHandle);
+
+ //save position in file of each new row
+ rowPos[i] = out.tellp();
+
+ //output row to file
+ out << i << '\t' << rowMap.size() << '\t';
+ for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+ out << itRow->first << '\t' << itRow->second << '\t';
+ }
+ out << endl;
+
+ //clear map for new row's info
+ rowMap.clear();
+ }
+ }
+ reading->finish();
+ delete reading;
+ fileHandle.close();
+ out.close();
+
+ if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
+
+ list->setLabel("0");
+
+ return 1;
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FormatPhylipMatrix", "read");
+ exit(1);
+ }
+}
+
/***********************************************************************/
FormatPhylipMatrix::~FormatPhylipMatrix(){}
/***********************************************************************/
projects / mothur.git / blobdiff