@@ -60,8+60,13 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
int square, nseqs;
string name;
vector<string> matrixNames;
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);
rowToName[0] = name;
matrixNames.push_back(name);
@@ -104,7+109,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
for(int j=0;j<i;j++){
for(int j=0;j<i;j++){
- if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
in >> distance;
in >> distance;
@@ -121,7+126,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
for(int j=0;j<i;j++){
for(int j=0;j<i;j++){
- if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
in >> distance;
in >> distance;
@@ -143,7+148,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
if(nameMap == NULL){
list->set(i, name);
for(int j=0;j<nseqs;j++){
if(nameMap == NULL){
list->set(i, name);
for(int j=0;j<nseqs;j++){
- if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
in >> distance;
in >> distance;
@@ -158,7+163,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
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(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(); remove(tempFile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
in >> distance;
in >> distance;
@@ -196,7+201,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){