added design and sets parameters to the rarefaction.shared command. finished work...

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index f6705e53db2048691b95050f3005bdccecf21347..92a43e965044c06c2fdcaca78d50779440b301ab 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,6 +44,7 @@ int GroupMap::readMap() {
                        m->gobble(fileHandle);
                }
                fileHandle.close();
+               m->setAllGroups(namesOfGroups);
                return error;
 }
 /************************************************************/
@@ -69,9 +70,38 @@ int GroupMap::readDesignMap() {
                        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();    }
 /************************************************************/
@@ -89,7 +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
+       }
 }
 
 /************************************************************/
@@ -161,4 +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);
+       }
+}
+
+/************************************************************/