created mothurOut class to handle logfiles

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index ee6040bb8802b36a6728a8abcd7dee7c7e3f2001..7da10a271125fadf7e4833ea37e68ce24cfcd16f 100644 (file)
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -13,8 +13,9 @@
 #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();
@@ -32,7 +33,7 @@ HCluster::HCluster(RAbundVector* rav, ListVector* lv, string m, string d, NameAs
                }
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "HCluster");
+               m->errorOut(e, "HCluster", "HCluster");
                exit(1);
        }
 }
@@ -49,7 +50,7 @@ void HCluster::clusterBins(){
                //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);
        }
 
@@ -71,7 +72,7 @@ void HCluster::clusterNames(){
 
     }
        catch(exception& e) {
-               errorOut(e, "HCluster", "clusterNames");
+               m->errorOut(e, "HCluster", "clusterNames");
                exit(1);
        }
 
@@ -86,7 +87,7 @@ int HCluster::getUpmostParent(int node){
                return node;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "getUpmostParent");
+               m->errorOut(e, "HCluster", "getUpmostParent");
                exit(1);
        }
 }
@@ -116,7 +117,7 @@ void HCluster::printInfo(){
                
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "getUpmostParent");
+               m->errorOut(e, "HCluster", "getUpmostParent");
                exit(1);
        }
 }
@@ -184,7 +185,7 @@ int HCluster::makeActive() {
                return linkValue;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "makeActive");
+               m->errorOut(e, "HCluster", "makeActive");
                exit(1);
        }
 }
@@ -253,7 +254,7 @@ void HCluster::updateArrayandLinkTable() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "updateArrayandLinkTable");
+               m->errorOut(e, "HCluster", "updateArrayandLinkTable");
                exit(1);
        }
 }
@@ -299,14 +300,14 @@ bool HCluster::update(int row, int col, float distance){
                //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++) {
@@ -327,7 +328,7 @@ void HCluster::setMapWanted(bool m)  {
                
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "setMapWanted");
+               m->errorOut(e, "HCluster", "setMapWanted");
                exit(1);
        }
 }
@@ -348,7 +349,7 @@ try {
                seq2Bin[names] = clusterArray[smallCol].smallChild;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "updateMap");
+               m->errorOut(e, "HCluster", "updateMap");
                exit(1);
        }
 }
@@ -366,7 +367,7 @@ vector<seqDist> HCluster::getSeqs(){
                return sameSeqs;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "getSeqs");
+               m->errorOut(e, "HCluster", "getSeqs");
                exit(1);
        }
 }
@@ -424,7 +425,7 @@ vector<seqDist> HCluster::getSeqsFNNN(){
                return sameSeqs;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "getSeqsFNNN");
+               m->errorOut(e, "HCluster", "getSeqsFNNN");
                exit(1);
        }
 }
@@ -495,7 +496,7 @@ vector<seqDist> HCluster::getSeqsAN(){
                return temp;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "getSeqsAN");
+               m->errorOut(e, "HCluster", "getSeqsAN");
                exit(1);
        }
 }
@@ -649,7 +650,7 @@ void HCluster::combineFile() {
                sort(mergedMin.begin(), mergedMin.end(), compareSequenceDistance);      
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "combineFile");
+               m->errorOut(e, "HCluster", "combineFile");
                exit(1);
        }
 }
@@ -725,7 +726,7 @@ seqDist HCluster::getNextDist(char* buffer, int& index, int size){
                return next;
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "getNextDist");
+               m->errorOut(e, "HCluster", "getNextDist");
                exit(1);
        }
 }
@@ -767,7 +768,7 @@ void HCluster::processFile() {
                rename(outTemp.c_str(), distfile.c_str());
        }
        catch(exception& e) {
-               errorOut(e, "HCluster", "processFile");
+               m->errorOut(e, "HCluster", "processFile");
                exit(1);
        }
 }