#include "sparsematrix.hpp"
/***********************************************************************/
-HCluster::HCluster(RAbundVector* rav, ListVector* lv, string m, string d, NameAssignment* n, float c) : rabund(rav), list(lv), method(m), distfile(d), nameMap(n), cutoff(c) {
+HCluster::HCluster(RAbundVector* rav, ListVector* lv, string ms, string d, NameAssignment* n, float c) : rabund(rav), list(lv), method(ms), distfile(d), nameMap(n), cutoff(c) {
try {
+ m = MothurOut::getInstance();
mapWanted = false;
exitedBreak = false;
numSeqs = list->getNumSeqs();
}
if (method != "average") {
- openInputFile(distfile, filehandle);
+ m->openInputFile(distfile, filehandle);
}else{
processFile();
}
}
catch(exception& e) {
- errorOut(e, "HCluster", "HCluster");
+ m->errorOut(e, "HCluster", "HCluster");
exit(1);
}
}
//cout << '\t' << rabund->get(clusterArray[smallRow].smallChild) << '\t' << rabund->get(clusterArray[smallCol].smallChild) << endl;
}
catch(exception& e) {
- errorOut(e, "HCluster", "clusterBins");
+ m->errorOut(e, "HCluster", "clusterBins");
exit(1);
}
}
catch(exception& e) {
- errorOut(e, "HCluster", "clusterNames");
+ m->errorOut(e, "HCluster", "clusterNames");
exit(1);
}
return node;
}
catch(exception& e) {
- errorOut(e, "HCluster", "getUpmostParent");
+ m->errorOut(e, "HCluster", "getUpmostParent");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "HCluster", "getUpmostParent");
+ m->errorOut(e, "HCluster", "getUpmostParent");
exit(1);
}
}
return linkValue;
}
catch(exception& e) {
- errorOut(e, "HCluster", "makeActive");
+ m->errorOut(e, "HCluster", "makeActive");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "HCluster", "updateArrayandLinkTable");
+ m->errorOut(e, "HCluster", "updateArrayandLinkTable");
exit(1);
}
}
//printInfo();
}
catch(exception& e) {
- errorOut(e, "HCluster", "update");
+ m->errorOut(e, "HCluster", "update");
exit(1);
}
}
/***********************************************************************/
-void HCluster::setMapWanted(bool m) {
+void HCluster::setMapWanted(bool ms) {
try {
- mapWanted = m;
+ mapWanted = ms;
//initialize map
for (int i = 0; i < list->getNumBins(); i++) {
}
catch(exception& e) {
- errorOut(e, "HCluster", "setMapWanted");
+ m->errorOut(e, "HCluster", "setMapWanted");
exit(1);
}
}
seq2Bin[names] = clusterArray[smallCol].smallChild;
}
catch(exception& e) {
- errorOut(e, "HCluster", "updateMap");
+ m->errorOut(e, "HCluster", "updateMap");
exit(1);
}
}
return sameSeqs;
}
catch(exception& e) {
- errorOut(e, "HCluster", "getSeqs");
+ m->errorOut(e, "HCluster", "getSeqs");
exit(1);
}
}
//get entry
while (!filehandle.eof()) {
- filehandle >> firstName >> secondName >> distance; gobble(filehandle);
+ filehandle >> firstName >> secondName >> distance; m->gobble(filehandle);
//save first one
if (prevDistance == -1) { prevDistance = distance; }
return sameSeqs;
}
catch(exception& e) {
- errorOut(e, "HCluster", "getSeqsFNNN");
+ m->errorOut(e, "HCluster", "getSeqsFNNN");
exit(1);
}
}
vector<seqDist> sameSeqs;
prevDistance = -1;
- openInputFile(distfile, filehandle, "no error");
+ m->openInputFile(distfile, filehandle, "no error");
//is the smallest value in mergedMin or the distfile?
float mergedMinDist = 10000;
if (mergedMin.size() > 0) { mergedMinDist = mergedMin[0].dist; }
if (!filehandle.eof()) {
- filehandle >> firstName >> secondName >> distance; gobble(filehandle);
+ filehandle >> firstName >> secondName >> distance; m->gobble(filehandle);
//save first one
if (prevDistance == -1) { prevDistance = distance; }
if (distance != -1) { //-1 means skip me
seqDist temp(firstName, secondName, distance);
sameSeqs.push_back(temp);
- }
+ }else{ distance = 10000; }
}
if (mergedMinDist < distance) { //get minimum distance from mergedMin
//get entry
while (!filehandle.eof()) {
- filehandle >> firstName >> secondName >> distance; gobble(filehandle);
+ filehandle >> firstName >> secondName >> distance; m->gobble(filehandle);
if (prevDistance == -1) { prevDistance = distance; }
return temp;
}
catch(exception& e) {
- errorOut(e, "HCluster", "getSeqsAN");
+ m->errorOut(e, "HCluster", "getSeqsAN");
exit(1);
}
}
/***********************************************************************/
-void HCluster::combineFile() {
+int HCluster::combineFile() {
try {
//int bufferSize = 64000; //512k - this should be a variable that the user can set to optimize code to their hardware
//char* inputBuffer;
string tempDistFile = distfile + ".temp";
ofstream out;
- openOutputFile(tempDistFile, out);
+ m->openOutputFile(tempDistFile, out);
//FILE* in;
//in = fopen(distfile.c_str(), "rb");
ifstream in;
- openInputFile(distfile, in);
+ m->openInputFile(distfile, in, "no error");
int first, second;
float dist;
//since file is sorted and mergedMin is sorted
//you can put the smallest distance from each through the code below and keep the file sorted
- in >> first >> second >> dist; gobble(in);
+ in >> first >> second >> dist; m->gobble(in);
+
+ if (m->control_pressed) { in.close(); out.close(); remove(tempDistFile.c_str()); return 0; }
//while there are still values in mergedMin that are smaller than the distance read from file
while (count < mergedMin.size()) {
mergedMin.clear();
//rename tempfile to distfile
- int renameOK = remove(distfile.c_str());
- int ok = rename(tempDistFile.c_str(), distfile.c_str());
+ remove(distfile.c_str());
+ rename(tempDistFile.c_str(), distfile.c_str());
//cout << "remove = "<< renameOK << " rename = " << ok << endl;
//merge clustered rows averaging the distances
//sort merged values
sort(mergedMin.begin(), mergedMin.end(), compareSequenceDistance);
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "HCluster", "combineFile");
+ m->errorOut(e, "HCluster", "combineFile");
exit(1);
}
}
if ((buffer[index] == 10) || (buffer[index] == 13)) { //newline in unix or windows
gotDist = true;
- //gobble space
+ //m->gobble space
while (index < size) {
if (isspace(buffer[index])) { index++; }
else { break; }
return next;
}
catch(exception& e) {
- errorOut(e, "HCluster", "getNextDist");
+ m->errorOut(e, "HCluster", "getNextDist");
exit(1);
}
}
/***********************************************************************/
-void HCluster::processFile() {
+int HCluster::processFile() {
try {
string firstName, secondName;
float distance;
ifstream in;
- openInputFile(distfile, in);
+ m->openInputFile(distfile, in, "no error");
ofstream out;
string outTemp = distfile + ".temp";
- openOutputFile(outTemp, out);
+ m->openOutputFile(outTemp, out);
//get entry
while (!in.eof()) {
+ if (m->control_pressed) { in.close(); out.close(); remove(outTemp.c_str()); return 0; }
- in >> firstName >> secondName >> distance; gobble(in);
+ in >> firstName >> secondName >> distance; m->gobble(in);
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
remove(distfile.c_str());
rename(outTemp.c_str(), distfile.c_str());
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "HCluster", "processFile");
+ m->errorOut(e, "HCluster", "processFile");
exit(1);
}
}