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

[mothur.git] / treemap.cpp

diff --git a/treemap.cpp b/treemap.cpp
index ad8a2af17ac2b8fe954c3bff402f6d1bb20381db..b2fc591c0adb24820d6f603bd8016154ad1c626c 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -13,7 +13,7 @@
 
  TreeMap::TreeMap(string filename) {
        groupFileName = filename;
-       openInputFile(filename, fileHandle);
+       m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
@@ -26,10 +26,10 @@ void TreeMap::readMap() {
                while(fileHandle){
                        fileHandle >> seqName;                  //read from first column
                        fileHandle >> seqGroup;                 //read from second column
-                       
+
                        namesOfSeqs.push_back(seqName);
                        setNamesOfGroups(seqGroup);
-                                               
+                                       
                        treemap[seqName].groupname = seqGroup;  //store data in map
                        
                        it2 = seqsPerGroup.find(seqGroup);
@@ -39,11 +39,30 @@ void TreeMap::readMap() {
                                seqsPerGroup[seqGroup]++;
                        }
 
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                fileHandle.close();
 }
 /************************************************************/
+void TreeMap::removeSeq(string seqName) {
+       
+       //erase name from namesOfSeqs
+       for (int i = 0; i < namesOfSeqs.size(); i++) {
+               if (namesOfSeqs[i] == seqName)  {
+                       namesOfSeqs.erase(namesOfSeqs.begin()+i);
+                       break;
+               }
+       }
+       
+       //decrement sequences in this group
+       string group = treemap[seqName].groupname;
+       seqsPerGroup[group]--;
+       
+       //remove seq from treemap
+       it = treemap.find(seqName);
+       treemap.erase(it);
+}
+/************************************************************/
 
 int TreeMap::getNumGroups() {
                        
@@ -116,11 +135,7 @@ bool TreeMap::isValidGroup(string groupname) {
                return false;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "isValidGroup");
                exit(1);
        }
 }
@@ -134,11 +149,7 @@ void TreeMap::print(ostream& output){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "print");
                exit(1);
        }
 }
@@ -162,11 +173,7 @@ void TreeMap::makeSim(GroupMap* groupmap) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "makeSim");
                exit(1);
        }
 }
@@ -192,11 +199,7 @@ void TreeMap::makeSim(ListVector* list) {
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the TreeMap class function makeSim. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "TreeMap", "makeSim");
                exit(1);
        }
 }