fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / treemap.cpp

diff --git a/treemap.cpp b/treemap.cpp
index 58379da96ee0be5110f36d8ab022be04aea6e4f2..fee309c5877138039c2ecdff8f54428a8060bc24 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -31,7 +31,14 @@ void TreeMap::readMap() {
                        setNamesOfGroups(seqGroup);
                                                
                        treemap[seqName].groupname = seqGroup;  //store data in map
-               
+                       
+                       it2 = seqsPerGroup.find(seqGroup);
+                       if (it2 == seqsPerGroup.end()) { //if it's a new group
+                               seqsPerGroup[seqGroup] = 1;
+                       }else {//it's a group we already have
+                               seqsPerGroup[seqGroup]++;
+                       }
+
                        gobble(fileHandle);
                }
                fileHandle.close();
@@ -65,7 +72,13 @@ string TreeMap::getGroup(string sequenceName) {
 }
 /************************************************************/
 void TreeMap::setIndex(string seq, int index) {
-       treemap[seq].vectorIndex = index;
+       it = treemap.find(seq);
+       if (it != treemap.end()) { //sequence name was in group file
+               treemap[seq].vectorIndex = index;       
+       }else {
+               treemap[seq].vectorIndex = index;
+               treemap[seq].groupname = "not found";
+       }
 }
 /************************************************************/
 int TreeMap::getIndex(string seq) {
@@ -93,7 +106,24 @@ void TreeMap::setNamesOfGroups(string seqGroup) {
                                namesOfGroups.push_back(seqGroup); //new group
                        }
 }
-
+/************************************************************/
+bool TreeMap::isValidGroup(string groupname) {
+       try {
+               for (int i = 0; i < namesOfGroups.size(); i++) {
+                       if (groupname == namesOfGroups[i]) { return true; }
+               }
+               
+               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";
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 void TreeMap::print(ostream& output){
@@ -113,4 +143,4 @@ void TreeMap::print(ostream& output){
        }
 }
 
-/************************************************************/
\ No newline at end of file
+/************************************************************/