moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 4303cfde13d3c4250c8f952c7a6eeb4bd9a2553d..49780314bca4d40be6a96a9593831b39317faaca 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -44,7 +44,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
        
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "SharedListVector");
+               m->errorOut(e, "SharedListVector", "SharedListVector");
                exit(1);
        }
 }
@@ -52,9 +52,9 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
 /***********************************************************************/
 void SharedListVector::set(int binNumber, string seqNames){
        try {
-               int nNames_old = getNumNames(data[binNumber]);
+               int nNames_old = m->getNumNames(data[binNumber]);
                data[binNumber] = seqNames;
-               int nNames_new = getNumNames(seqNames);
+               int nNames_new = m->getNumNames(seqNames);
        
                if(nNames_old == 0)                     {       numBins++;                              }
                if(nNames_new == 0)                     {       numBins--;                              }
@@ -63,7 +63,7 @@ void SharedListVector::set(int binNumber, string seqNames){
                numSeqs += (nNames_new - nNames_old);
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "set");
+               m->errorOut(e, "SharedListVector", "set");
                exit(1);
        }
 }
@@ -79,7 +79,7 @@ string SharedListVector::get(int index){
 void SharedListVector::push_back(string seqNames){
        try {
                data.push_back(seqNames);
-               int nNames = getNumNames(seqNames);
+               int nNames = m->getNumNames(seqNames);
        
                numBins++;
        
@@ -88,7 +88,7 @@ void SharedListVector::push_back(string seqNames){
                numSeqs += nNames;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "push_back");
+               m->errorOut(e, "SharedListVector", "push_back");
                exit(1);
        }
 }
@@ -128,7 +128,7 @@ void SharedListVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "print");
+               m->errorOut(e, "SharedListVector", "print");
                exit(1);
        }
 }
@@ -141,7 +141,7 @@ RAbundVector SharedListVector::getRAbundVector(){
                RAbundVector rav;
        
                for(int i=0;i<data.size();i++){
-                       int binSize = getNumNames(data[i]);
+                       int binSize = m->getNumNames(data[i]);
                        rav.push_back(binSize);
                }
        
@@ -159,7 +159,7 @@ RAbundVector SharedListVector::getRAbundVector(){
                return rav;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getRAbundVector");
+               m->errorOut(e, "SharedListVector", "getRAbundVector");
                exit(1);
        }
 }
@@ -171,7 +171,7 @@ SAbundVector SharedListVector::getSAbundVector(){
                SAbundVector sav(maxRank+1);
        
                for(int i=0;i<data.size();i++){
-                       int binSize = getNumNames(data[i]);     
+                       int binSize = m->getNumNames(data[i]);  
                        sav.set(binSize, sav.get(binSize) + 1); 
                }
                sav.set(0, 0);
@@ -180,7 +180,7 @@ SAbundVector SharedListVector::getSAbundVector(){
                return sav;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getSAbundVector");
+               m->errorOut(e, "SharedListVector", "getSAbundVector");
                exit(1);
        }
 }
@@ -194,20 +194,20 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
                order->setLabel(label);
        
                for(int i=0;i<numBins;i++){
-                       int binSize = getNumNames(get(i));      //find number of individual in given bin        
+                       int binSize = m->getNumNames(get(i));   //find number of individual in given bin        
                        names = get(i);
                        while (names.find_first_of(',') != -1) { 
                                name = names.substr(0,names.find_first_of(','));
                                names = names.substr(names.find_first_of(',')+1, names.length());
                                groupName = groupmap->getGroup(name);
                                
-                               if(groupName == "not found") {  mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                               if(groupName == "not found") {  m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                                
                                order->push_back(i, binSize, groupName);  //i represents what bin you are in
                        }
                        //get last name
                        groupName = groupmap->getGroup(names);
-                       if(groupName == "not found") {  mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                       if(groupName == "not found") {  m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                        order->push_back(i, binSize, groupName);
                }
 
@@ -217,7 +217,7 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
                return order;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getSharedOrderVector");
+               m->errorOut(e, "SharedListVector", "getSharedOrderVector");
                exit(1);
        }
 }
@@ -233,7 +233,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                                name = names.substr(0,names.find_first_of(','));
                                names = names.substr(names.find_first_of(',')+1, names.length());
                                group = groupmap->getGroup(name);
-                               if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                               if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                                if (group == groupName) { //this name is in the group you want the vector for.
                                        rav.set(i, rav.getAbundance(i) + 1, group);  //i represents what bin you are in
                                }
@@ -241,7 +241,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                        
                        //get last name
                        groupName = groupmap->getGroup(names);
-                       if(groupName == "not found") {  mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                       if(groupName == "not found") {  m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                        if (group == groupName) { //this name is in the group you want the vector for.
                                        rav.set(i, rav.getAbundance(i) + 1, group);  //i represents what bin you are in
                        }
@@ -254,7 +254,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getSharedRAbundVector");
+               m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
                exit(1);
        }
 }
@@ -275,7 +275,7 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                        finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
                        finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
                        finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
-                       if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
+                       if (m->inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) {  //if this group is in user groups
                                lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
                        }
                }
@@ -287,13 +287,13 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                                name = names.substr(0,names.find_first_of(','));
                                names = names.substr(names.find_first_of(',')+1, names.length());
                                group = groupmap->getGroup(name);
-                               if(group == "not found") {      mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                               if(group == "not found") {      m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                                finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
                        }
                        
                        //get last name
                        group = groupmap->getGroup(names);
-                       if(group == "not found") {      mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine();  exit(1); }
+                       if(group == "not found") {      m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                        finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
                        
                }
@@ -301,7 +301,7 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                return lookup;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getSharedRAbundVector");
+               m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
                exit(1);
        }
 }
@@ -318,7 +318,7 @@ SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {
                return sav;
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getSharedSAbundVector");
+               m->errorOut(e, "SharedListVector", "getSharedSAbundVector");
                exit(1);
        }
 }
@@ -331,7 +331,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                        OrderVector ov;
                
                        for(int i=0;i<data.size();i++){
-                               int binSize = getNumNames(data[i]);             
+                               int binSize = m->getNumNames(data[i]);          
                                for(int j=0;j<binSize;j++){
                                        ov.push_back(i);
                                }
@@ -359,7 +359,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                                        }
                                        else{
                                                if(orderMap->count(seqName) == 0){
-                                                       mothurOut(seqName + " not found, check *.names file\n");
+                                                       m->mothurOut(seqName + " not found, check *.names file\n");
                                                        exit(1);
                                                }
                                        
@@ -369,7 +369,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                                }
                        
                                if(orderMap->count(seqName) == 0){
-                                       mothurOut(seqName + " not found, check *.names file\n");
+                                       m->mothurOut(seqName + " not found, check *.names file\n");
                                        exit(1);
                                }
                                ov.set((*orderMap)[seqName], i);        
@@ -382,7 +382,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SharedListVector", "getOrderVector");
+               m->errorOut(e, "SharedListVector", "getOrderVector");
                exit(1);
        }
 }