fixed bug in cluster.split

[mothur.git] / sharedlistvector.cpp

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 3cb3e9e57c4da06f0589272cff4b3e97bd92eea4..cc3cd8df4205e2f37182a8a80037bc02bb37ca45 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -44,11 +44,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "SharedListVector");
                exit(1);
        }
 }
@@ -67,11 +63,7 @@ void SharedListVector::set(int binNumber, string seqNames){
                numSeqs += (nNames_new - nNames_old);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "set");
                exit(1);
        }
 }
@@ -96,11 +88,7 @@ void SharedListVector::push_back(string seqNames){
                numSeqs += nNames;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "push_back");
                exit(1);
        }
 }
@@ -140,11 +128,7 @@ void SharedListVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "print");
                exit(1);
        }
 }
@@ -175,11 +159,7 @@ RAbundVector SharedListVector::getRAbundVector(){
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getRAbundVector");
                exit(1);
        }
 }
@@ -200,11 +180,7 @@ SAbundVector SharedListVector::getSAbundVector(){
                return sav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getSAbundVector");
                exit(1);
        }
 }
@@ -224,10 +200,14 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
                                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") {  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") {  m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
                        order->push_back(i, binSize, groupName);
                }
 
@@ -237,14 +217,9 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){
                return order;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getSharedOrderVector");
                exit(1);
        }
-
 }
 /***********************************************************************/
 SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
@@ -258,6 +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") {      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
                                }
@@ -265,6 +241,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                        
                        //get last name
                        groupName = groupmap->getGroup(names);
+                       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
                        }
@@ -277,11 +254,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
                exit(1);
        }
 }
@@ -290,23 +263,23 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
        try {
                SharedUtil* util;
                util = new SharedUtil();
-               vector<SharedRAbundVector*> lookup;
-               map<string, SharedRAbundVector*> finder;
+               vector<SharedRAbundVector*> lookup;  //contains just the groups the user selected
+               map<string, SharedRAbundVector*> finder;  //contains all groups in groupmap
                string group, names, name;
-               
+       
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-               
                delete util;
 
-               for (int i = 0; i < globaldata->Groups.size(); i++) {
+               for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
                        SharedRAbundVector* temp = new SharedRAbundVector(data.size());
-                       finder[globaldata->Groups[i]] = temp;
-                       finder[globaldata->Groups[i]]->setLabel(label);
-                       finder[globaldata->Groups[i]]->setGroup(globaldata->Groups[i]);
-                       //*temp = getSharedRAbundVector(globaldata->Groups[i]);
-                       lookup.push_back(finder[globaldata->Groups[i]]);
+                       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
+                               lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+                       }
                }
-               
+       
                //fill vectors
                for(int i=0;i<numBins;i++){
                        names = get(i);  
@@ -314,11 +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") {      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") {      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
                        
                }
@@ -326,14 +301,9 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
                return lookup;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
                exit(1);
        }
-       
 }
 
 /***********************************************************************/
@@ -348,11 +318,7 @@ SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {
                return sav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getSharedSAbundVector");
                exit(1);
        }
 }
@@ -393,7 +359,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                                        }
                                        else{
                                                if(orderMap->count(seqName) == 0){
-                                                       cerr << seqName << " not found, check *.names file\n";
+                                                       m->mothurOut(seqName + " not found, check *.names file\n");
                                                        exit(1);
                                                }
                                        
@@ -403,7 +369,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                                }
                        
                                if(orderMap->count(seqName) == 0){
-                                       cerr << seqName << " not found, check *.names file\n";
+                                       m->mothurOut(seqName + " not found, check *.names file\n");
                                        exit(1);
                                }
                                ov.set((*orderMap)[seqName], i);        
@@ -416,11 +382,7 @@ OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedListVector", "getOrderVector");
                exit(1);
        }
 }