ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
successOpen = m->openInputFile(distFile, fileHandle);
+ sim=false;
}
+/***********************************************************************/
+
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
+
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim=s;
+}
+
/***********************************************************************/
try {
float distance;
- int square, nseqs;
+ int square, nseqs;
string name;
vector<string> matrixNames;
-
- fileHandle >> nseqs >> 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); }
+
matrixNames.push_back(name);
if(nameMap == NULL){
}
Progress* reading;
-
+ DMatrix->resize(nseqs);
+
if(square == 0){
reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
fileHandle >> distance;
-
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff){
- PCell value(i, j, distance);
- D->addCell(value);
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
}
index++;
reading->update(index);
if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff){
- PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
- D->addCell(value);
+ 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; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff && j < i){
- PCell value(i, j, distance);
- D->addCell(value);
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
}
index++;
reading->update(index);
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff && j < i){
- PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
- D->addCell(value);
+ PDistCell value(nameMap->get(matrixNames[i]), distance);
+ DMatrix->addCell(nameMap->get(matrixNames[j]), value);
}
index++;
reading->update(index);
reading->finish();
delete reading;
-
+
list->setLabel("0");
fileHandle.close();
- /* 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
- m->mothurOut("missed something\t" + toString(nameMap->size())); m->mothurOutEndLine();
- }
- } */
-
+
return 1;
}
}
/***********************************************************************/
+ReadPhylipMatrix::~ReadPhylipMatrix(){}
+/***********************************************************************/
-ReadPhylipMatrix::~ReadPhylipMatrix(){
- // delete D;
- // delete list;
-}