/***********************************************************************/
-ReadCluster::ReadCluster(string distfile, float c){
+ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
+ m = MothurOut::getInstance();
distFile = distfile;
cutoff = c;
+ outputDir = o;
+ sortWanted = s;
+ list = NULL;
}
/***********************************************************************/
-void ReadCluster::read(NameAssignment* nameMap){
+int ReadCluster::read(NameAssignment*& nameMap){
try {
if (format == "phylip") { convertPhylip2Column(nameMap); }
else { list = new ListVector(nameMap->getListVector()); }
- createHClusterFile();
+ if (m->control_pressed) { return 0; }
+
+ if (sortWanted) { OutPutFile = m->sortFile(distFile, outputDir); }
+ else { OutPutFile = distFile; } //for use by clusters splitMatrix to convert a phylip matrix to column
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ReadCluster", "read");
+ m->errorOut(e, "ReadCluster", "read");
exit(1);
}
}
/***********************************************************************/
-
-void ReadCluster::createHClusterFile(){
- try {
- string outfile = getRootName(distFile) + "sorted.dist";
-
- //if you can, use the unix sort since its been optimized for years
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- string command = "sort -n -k +3 " + distFile + " -o " + outfile;
- system(command.c_str());
- #else //you are stuck with my best attempt...
- //windows sort does not have a way to specify a column, only a character in the line
- //since we cannot assume that the distance will always be at the the same character location on each line
- //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
-
- //read in file line by file and put distance first
- string tempDistFile = distFile + ".temp";
- ifstream input;
- ofstream output;
- openInputFile(distFile, input);
- openOutputFile(tempDistFile, output);
-
- string firstName, secondName;
- float dist;
- while (input) {
- input >> firstName >> secondName >> dist;
- output << dist << '\t' << firstName << '\t' << secondName << endl;
- gobble(input);
- }
- input.close();
- output.close();
+int ReadCluster::read(CountTable*& ct){
+ try {
+
+ if (format == "phylip") { convertPhylip2Column(ct); }
+ else { list = new ListVector(ct->getListVector()); }
-
- //sort using windows sort
- string tempOutfile = outfile + ".temp";
- string command = "sort " + tempDistFile + " /O " + tempOutfile;
- system(command.c_str());
-
- //read in sorted file and put distance at end again
- ifstream input2;
- openInputFile(tempOutfile, input2);
- openOutputFile(outfile, output);
-
- while (input2) {
- input2 >> dist >> firstName >> secondName;
- output << firstName << '\t' << secondName << '\t' << dist << endl;
- gobble(input2);
- }
- input2.close();
- output.close();
+ if (m->control_pressed) { return 0; }
- //remove temp files
- remove(tempDistFile.c_str());
- remove(tempOutfile.c_str());
- #endif
+ if (sortWanted) { OutPutFile = m->sortFile(distFile, outputDir); }
+ else { OutPutFile = distFile; } //for use by clusters splitMatrix to convert a phylip matrix to column
- OutPutFile = outfile;
+ return 0;
+
}
catch(exception& e) {
- errorOut(e, "ReadCluster", "createHClusterFile");
+ m->errorOut(e, "ReadCluster", "read");
exit(1);
}
}
-
-
/***********************************************************************/
-void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
+int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
try {
//convert phylip file to column file
map<int, string> rowToName;
ofstream out;
string tempFile = distFile + ".column.temp";
- openInputFile(distFile, in);
- openOutputFile(tempFile, out);
+ m->openInputFile(distFile, in); m->gobble(in);
+ m->openOutputFile(tempFile, out);
float distance;
int square, nseqs;
string name;
vector<string> matrixNames;
-
- in >> nseqs >> name;
+
+ string numTest;
+ in >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
rowToName[0] = name;
matrixNames.push_back(name);
}
else{
list = new ListVector(nameMap->getListVector());
- if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+ if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
}
char d;
list->set(i, name);
for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
in >> distance;
if (distance == -1) { distance = 1000000; }
}
else{
- if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+ 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) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
in >> distance;
if (distance == -1) { distance = 1000000; }
}
}
else{
-
for(int i=1;i<nseqs;i++){
in >> name;
rowToName[i] = name;
matrixNames.push_back(name);
-
+
if(nameMap == NULL){
list->set(i, name);
for(int j=0;j<nseqs;j++){
- in >> distance;
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+ in >> distance;
+
if (distance == -1) { distance = 1000000; }
if(distance < cutoff && j < i){
out << i << '\t' << j << '\t' << distance << endl;
}
}
-
}
else{
- if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+ 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) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
in >> distance;
if (distance == -1) { distance = 1000000; }
list->setLabel("0");
in.close();
out.close();
-
+
if(nameMap == NULL){
+ nameMap = new NameAssignment();
for(int i=0;i<matrixNames.size();i++){
nameMap->push_back(matrixNames[i]);
}
}
+
ifstream in2;
ofstream out2;
- string outputFile = getRootName(distFile) + "column.dist";
- openInputFile(tempFile, in2);
- openOutputFile(outputFile, out2);
+ string outputFile = m->getRootName(distFile) + "column.dist";
+ m->openInputFile(tempFile, in2);
+ m->openOutputFile(outputFile, out2);
int first, second;
float dist;
while (in2) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(tempFile); m->mothurRemove(outputFile); return 0; }
+
in2 >> first >> second >> dist;
out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
- gobble(in2);
+ m->gobble(in2);
}
in2.close();
out2.close();
- remove(tempFile.c_str());
+ m->mothurRemove(tempFile);
distFile = outputFile;
+
+ if (m->control_pressed) { m->mothurRemove(outputFile); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadCluster", "convertPhylip2Column");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int ReadCluster::convertPhylip2Column(CountTable*& ct){
+ try {
+ //convert phylip file to column file
+ map<int, string> rowToName;
+ map<int, string>::iterator it;
+
+ ifstream in;
+ ofstream out;
+ string tempFile = distFile + ".column.temp";
+
+ m->openInputFile(distFile, in); m->gobble(in);
+ m->openOutputFile(tempFile, out);
+
+ float distance;
+ int square, nseqs;
+ string name;
+ vector<string> matrixNames;
+
+ string numTest;
+ in >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+ rowToName[0] = name;
+ matrixNames.push_back(name);
+
+ if(ct == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{ list = new ListVector(ct->getListVector()); }
+
+ char d;
+ while((d=in.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ in.putback(d);
+ for(int i=0;i<nseqs;i++){
+ in >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ if(square == 0){
+
+ for(int i=1;i<nseqs;i++){
+ in >> name;
+ rowToName[i] = name;
+ matrixNames.push_back(name);
+
+ //there's A LOT of repeated code throughout this method...
+ if(ct == NULL){
+ list->set(i, name);
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+ }
+
+ }
+ else{
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+ }
+ }
+ }
+ }
+ else{
+ for(int i=1;i<nseqs;i++){
+ in >> name;
+ rowToName[i] = name;
+ matrixNames.push_back(name);
+
+ if(ct == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff && j < i){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+ }
+ }
+ else{
+ for(int j=0;j<nseqs;j++){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff && j < i){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+
+ }
+ }
+ }
+ }
+
+ list->setLabel("0");
+ in.close();
+ out.close();
+
+ if(ct == NULL){
+ ct = new CountTable();
+ for(int i=0;i<matrixNames.size();i++){
+ ct->push_back(matrixNames[i]);
+ }
+ }
+
+
+ ifstream in2;
+ ofstream out2;
+
+ string outputFile = m->getRootName(distFile) + "column.dist";
+ m->openInputFile(tempFile, in2);
+ m->openOutputFile(outputFile, out2);
+
+ int first, second;
+ float dist;
+
+ while (in2) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(tempFile); m->mothurRemove(outputFile); return 0; }
+
+ in2 >> first >> second >> dist;
+ out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
+ m->gobble(in2);
+ }
+ in2.close();
+ out2.close();
+
+ m->mothurRemove(tempFile);
+ distFile = outputFile;
+
+ if (m->control_pressed) { m->mothurRemove(outputFile); }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "ReadCluster", "convertPhylip2Column");
+ m->errorOut(e, "ReadCluster", "convertPhylip2Column");
exit(1);
}
}
projects / mothur.git / blobdiff