fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / treemap.cpp

diff --git a/treemap.cpp b/treemap.cpp
index 1fc5c01b796a67bd948a70147fa4dead9320ea08..c228162aab1d511af3fc5318aaf3e5eb5b39610c 100644 (file)
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -19,6 +19,43 @@
 
 /************************************************************/
  TreeMap::~TreeMap(){}
+/************************************************************/
+int TreeMap::readMap(string gf) {
+    
+    groupFileName = gf;
+       m->openInputFile(gf, fileHandle);
+    
+    string seqName, seqGroup;
+    int error = 0;
+    
+    while(fileHandle){
+        fileHandle >> seqName;       m->gobble(fileHandle);    //read from first column
+        fileHandle >> seqGroup;                        //read from second column
+        
+        if (m->control_pressed) {  fileHandle.close();  return 1; }
+        
+        setNamesOfGroups(seqGroup);
+        
+        map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
+        if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+        else {
+            namesOfSeqs.push_back(seqName);
+            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]++;
+            }                          
+        }
+        
+        m->gobble(fileHandle);
+    }
+    fileHandle.close();
+    
+    return error;
+}
 
 /************************************************************/
 int TreeMap::readMap() {
@@ -26,7 +63,7 @@ int TreeMap::readMap() {
                int error = 0;
                
                while(fileHandle){
-                       fileHandle >> seqName;          //read from first column
+                       fileHandle >> seqName;           m->gobble(fileHandle); //read from first column
                        fileHandle >> seqGroup;                 //read from second column
                        
                        if (m->control_pressed) {  fileHandle.close();  return 1; }
@@ -229,6 +266,60 @@ void TreeMap::makeSim(ListVector* list) {
                exit(1);
        }
 }
+/************************************************************/
+int TreeMap::getCopy(TreeMap& copy){
+       try {
+         
+        namesOfGroups = copy.getNamesOfGroups();
+               numGroups = copy.getNumGroups();
+        namesOfSeqs = copy.namesOfSeqs;
+        seqsPerGroup = copy.seqsPerGroup;
+        treemap = copy.treemap;
+        
+        return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TreeMap", "getCopy");
+               exit(1);
+       }
+}
+/************************************************************/
+vector<string> TreeMap::getNamesSeqs(){
+       try {
+        
+               vector<string> names;
+               
+        for(it = treemap.begin(); it != treemap.end(); it++){
+            names.push_back(it->first);
+               }
+               
+               return names;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TreeMap", "getNamesSeqs");
+               exit(1);
+       }
+}
+/************************************************************/
+vector<string> TreeMap::getNamesSeqs(vector<string> picked){
+       try {
+               
+               vector<string> names;
+               
+               for(it = treemap.begin(); it != treemap.end(); it++){
+                       //if you are belong to one the the groups in the picked vector add you
+                       if (m->inUsersGroups(it->second.groupname, picked)) {
+                               names.push_back(it->first);
+                       }
+               }
+               
+               return names;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TreeMap", "getNamesSeqs");
+               exit(1);
+       }
+}
 
 /************************************************************/