added rename.seqs command.

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index fb2495c13fe8c09095221fbff3fb79c29c9d129a..9b8aa3f8abc87ef9ff93520a80b3da9169d406f4 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -20,7 +20,6 @@
 
 /************************************************************/
  GroupMap::~GroupMap(){}
-
 /************************************************************/
 int GroupMap::readMap() {
     try {
@@ -45,6 +44,7 @@ int GroupMap::readMap() {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -69,7 +69,7 @@ int GroupMap::readMap() {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -114,7 +114,7 @@ int GroupMap::readDesignMap() {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -139,7 +139,7 @@ int GroupMap::readDesignMap() {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -188,7 +188,7 @@ int GroupMap::readMap(string filename) {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -213,7 +213,7 @@ int GroupMap::readMap(string filename) {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -261,7 +261,7 @@ int GroupMap::readDesignMap(string filename) {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -286,7 +286,7 @@ int GroupMap::readDesignMap(string filename) {
                     setNamesOfGroups(seqGroup);
                     
                     if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
-                    
+                    m->checkName(seqName);
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -317,6 +317,10 @@ string GroupMap::getGroup(string sequenceName) {
        if (it != groupmap.end()) { //sequence name was in group file
                return it->second;      
        }else {
+        //look for it in names of groups to see if the user accidently used the wrong file
+        if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+            m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine(); 
+        }
                return "not found";
        }
 }
@@ -325,7 +329,7 @@ string GroupMap::getGroup(string sequenceName) {
 
 void GroupMap::setGroup(string sequenceName, string groupN) {
        setNamesOfGroups(groupN);
-       
+       m->checkName(sequenceName);
        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();  }
@@ -368,6 +372,22 @@ bool GroupMap::isValidGroup(string groupname) {
        }
 }
 /************************************************************/
+int GroupMap::getCopy(GroupMap* g) {
+       try {
+        vector<string> names = g->getNamesSeqs();
+        for (int i = 0; i < names.size(); i++) {
+            if (m->control_pressed) { break; }
+            string group = g->getGroup(names[i]);
+            setGroup(names[i], group);
+        }
+        return names.size();
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GroupMap", "getCopy");
+               exit(1);
+       }
+}
+/************************************************************/
 int GroupMap::getNumSeqs(string group) {
        try {
                
@@ -385,7 +405,66 @@ int GroupMap::getNumSeqs(string group) {
                exit(1);
        }
 }
-
+/************************************************************/
+int GroupMap::renameSeq(string oldName, string newName) {
+       try {
+               
+               map<string, string>::iterator itName;
+               
+               itName = groupmap.find(oldName);
+               
+               if (itName == groupmap.end()) {
+            m->mothurOut("[ERROR]: cannot find " + toString(oldName) + " in group file");
+            m->control_pressed = true;
+            return 0;
+        }else {
+            string group = itName->second;
+            groupmap.erase(itName);
+            groupmap[newName] = group;
+        }
+        
+        return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GroupMap", "renameSeq");
+               exit(1);
+       }
+}
+/************************************************************/
+int GroupMap::print(ofstream& out) {
+       try {
+               
+               for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+            out << itName->first << '\t' << itName->second << endl;
+        }
+             
+        return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GroupMap", "print");
+               exit(1);
+       }
+}
+/************************************************************/
+int GroupMap::print(ofstream& out, vector<string> userGroups) {
+       try {
+               
+               for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+            if (m->inUsersGroups(itName->second, userGroups)) {
+                out << itName->first << '\t' << itName->second << endl;
+            }
+        }
+        
+        return 0;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GroupMap", "print");
+               exit(1);
+       }
+}
 /************************************************************/
 vector<string> GroupMap::getNamesSeqs(){
        try {