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

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 0e0be0e8cf2799527e2664bb79b1cdded09e215c..92a43e965044c06c2fdcaca78d50779440b301ab 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,9 +44,65 @@ int GroupMap::readMap() {
                        m->gobble(fileHandle);
                }
                fileHandle.close();
+               m->setAllGroups(namesOfGroups);
                return error;
 }
 /************************************************************/
+int GroupMap::readDesignMap() {
+               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);
+                       
+                       it = groupmap.find(seqName);
+                       
+                       if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine();  }
+                       else {
+                               groupmap[seqName] = seqGroup;   //store data in map
+                               seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
+                       }
+                       m->gobble(fileHandle);
+               }
+               fileHandle.close();
+               m->setAllGroups(namesOfGroups);
+               return error;
+}
+/************************************************************/
+int GroupMap::readDesignMap(string filename) {
+    groupFileName = filename;
+       m->openInputFile(filename, fileHandle);
+       index = 0;
+    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);
+        
+        it = groupmap.find(seqName);
+        
+        if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine();  }
+        else {
+            groupmap[seqName] = seqGroup;      //store data in map
+            seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
+        }
+        m->gobble(fileHandle);
+    }
+    fileHandle.close();
+    m->setAllGroups(namesOfGroups);
+    return error;
+}
+/************************************************************/
 int GroupMap::getNumGroups() { return namesOfGroups.size();    }
 /************************************************************/
 
@@ -63,7 +119,15 @@ string GroupMap::getGroup(string sequenceName) {
 /************************************************************/
 
 void GroupMap::setGroup(string sequenceName, string groupN) {
-       groupmap[sequenceName] = groupN;
+       setNamesOfGroups(groupN);
+       
+       it = groupmap.find(sequenceName);
+       
+       if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+       else {
+               groupmap[sequenceName] = groupN;        //store data in map
+               seqsPerGroup[groupN]++;  //increment number of seqs in that group
+       }
 }
 
 /************************************************************/
@@ -135,4 +199,25 @@ vector<string> GroupMap::getNamesSeqs(){
        }
 }
 /************************************************************/
+vector<string> GroupMap::getNamesSeqs(vector<string> picked){
+       try {
+               
+               vector<string> names;
+               
+               for (it = groupmap.begin(); it != groupmap.end(); it++) {
+                       //if you are belong to one the the groups in the picked vector add you
+                       if (m->inUsersGroups(it->second, picked)) {
+                               names.push_back(it->first);
+                       }
+               }
+               
+               return names;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GroupMap", "getNamesSeqs");
+               exit(1);
+       }
+}
+
+/************************************************************/