/***********************************************************************/
ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
-
- successOpen = openInputFile(distFile, fileHandle);
-
+
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim=false;
+
}
-
/***********************************************************************/
-void ReadPhylipMatrix::read(NameAssignment* nameMap){
- try {
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
- float distance;
- int square, nseqs;
- string name;
- vector<string> matrixNames;
-
- fileHandle >> nseqs >> name;
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim=s;
+}
- matrixNames.push_back(name);
- if(nameMap == NULL){
- list = new ListVector(nseqs);
- list->set(0, name);
- }
- else{
- list = new ListVector(nameMap->getListVector());
- if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
- }
-
- char d;
- while((d=fileHandle.get()) != EOF){
-
- if(isalnum(d)){
- square = 1;
- fileHandle.putback(d);
- for(int i=0;i<nseqs;i++){
- fileHandle >> distance;
- }
- break;
- }
- if(d == '\n'){
- square = 0;
- break;
- }
- }
-
- Progress* reading;
-
- if(square == 0){
+/***********************************************************************/
- reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
-
- int index = 0;
-
- for(int i=1;i<nseqs;i++){
- fileHandle >> name;
- matrixNames.push_back(name);
-
- //there's A LOT of repeated code throughout this method...
- if(nameMap == NULL){
- list->set(i, name);
-
- for(int j=0;j<i;j++){
- fileHandle >> distance;
-
- if (distance == -1) { distance = 1000000; }
+int ReadPhylipMatrix::read(NameAssignment* nameMap){
+ try {
+
+ float distance;
+ int square, nseqs;
+ string name;
+ vector<string> matrixNames;
- if(distance < cutoff){
- PCell value(i, j, distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
-
- }
- else{
- if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
-
- for(int j=0;j<i;j++){
- fileHandle >> distance;
-
- if (distance == -1) { distance = 1000000; }
-
- if(distance < cutoff){
- PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
- }
- }
- }
- else{
-
- reading = new Progress("Reading matrix: ", nseqs * nseqs);
+ string numTest;
+ fileHandle >> numTest >> name;
- int index = nseqs;
-
- for(int i=1;i<nseqs;i++){
- fileHandle >> name;
- matrixNames.push_back(name);
-
- if(nameMap == NULL){
- list->set(i, name);
- for(int j=0;j<nseqs;j++){
- fileHandle >> distance;
-
- if (distance == -1) { distance = 1000000; }
-
- if(distance < cutoff && j < i){
- PCell value(i, j, distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
-
- }
- else{
- if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
-
- for(int j=0;j<nseqs;j++){
- fileHandle >> distance;
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
- if (distance == -1) { distance = 1000000; }
-
- if(distance < cutoff && j < i){
- PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
- }
- }
- }
- reading->finish();
- delete reading;
+ matrixNames.push_back(name);
- list->setLabel("0");
- fileHandle.close();
+ 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){
+
+ if(isalnum(d)){
+ square = 1;
+ fileHandle.putback(d);
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ Progress* reading;
+ DMatrix->resize(nseqs);
+
+ if(square == 0){
- if(nameMap != NULL){
- for(int i=0;i<matrixNames.size();i++){
- nameMap->erase(matrixNames[i]);
- }
- if(nameMap->size() > 0){
- //should probably tell them what is missing if we missed something
- cout << "missed something" << '\t' << nameMap->size() << endl;
- }
- }
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+
+ int index = 0;
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+ //there's A LOT of repeated code throughout this method...
+ if(nameMap == NULL){
+ list->set(i, name);
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ 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++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ PDistCell value(nameMap->get(matrixNames[i]), distance);
+ DMatrix->addCell(nameMap->get(matrixNames[j]), value);
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+ else{
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadPhylipMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadPhylipMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int index = nseqs;
+
+ for(int i=1;i<nseqs;i++){
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+
+ if(nameMap == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ 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++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ PDistCell value(nameMap->get(matrixNames[i]), distance);
+ DMatrix->addCell(nameMap->get(matrixNames[j]), value);
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ delete reading;
+
+ list->setLabel("0");
+ fileHandle.close();
+
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadPhylipMatrix", "read");
+ exit(1);
+ }
+ }
/***********************************************************************/
-ReadPhylipMatrix::~ReadPhylipMatrix(){
- delete D;
- delete list;
+int ReadPhylipMatrix::read(CountTable* countTable){
+ try {
+
+ float distance;
+ int square, nseqs;
+ string name;
+ vector<string> matrixNames;
+
+ 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); }
+
+ matrixNames.push_back(name);
+
+ if(countTable == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{ list = new ListVector(countTable->getListVector()); }
+
+ if (m->control_pressed) { return 0; }
+
+ char d;
+ while((d=fileHandle.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ fileHandle.putback(d);
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ Progress* reading;
+ DMatrix->resize(nseqs);
+
+ if(square == 0){
+
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+
+ int index = 0;
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+ //there's A LOT of repeated code throughout this method...
+ if(countTable == NULL){
+ list->set(i, name);
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ for(int j=0;j<i;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ int iIndex = countTable->get(matrixNames[i]);
+ int jIndex = countTable->get(matrixNames[j]);
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+ if (iIndex < jIndex) {
+ PDistCell value(jIndex, distance);
+ DMatrix->addCell(iIndex, value);
+ }else {
+ PDistCell value(iIndex, distance);
+ DMatrix->addCell(jIndex, value);
+
+ }
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+ else{
+
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int index = nseqs;
+
+ for(int i=1;i<nseqs;i++){
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+
+ if(countTable == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ int iIndex = countTable->get(matrixNames[i]);
+ int jIndex = countTable->get(matrixNames[j]);
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+ if (iIndex < jIndex) {
+ PDistCell value(jIndex, distance);
+ DMatrix->addCell(iIndex, value);
+ }else {
+ PDistCell value(iIndex, distance);
+ DMatrix->addCell(jIndex, value);
+
+ }
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ delete reading;
+
+ list->setLabel("0");
+ fileHandle.close();
+
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadPhylipMatrix", "read");
+ exit(1);
+ }
}
+/***********************************************************************/
+ReadPhylipMatrix::~ReadPhylipMatrix(){}
+/***********************************************************************/
projects / mothur.git / blobdiff