finished dereplicate changes to chimera commands. added taxonomy file to subsample...

[mothur.git] / counttable.cpp

diff --git a/counttable.cpp b/counttable.cpp
index a79047d0af943e1c2bbef6d169aeefa884c1e164..c16bf9227a51580cac00de78a215b89e2a93e001 100644 (file)
--- a/counttable.cpp
+++ b/counttable.cpp
@@ -131,6 +131,9 @@ int CountTable::createTable(string namefile, string groupfile, bool createGroup)
             string firstCol, secondCol;
             in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
             
+            m->checkName(firstCol);
+            m->checkName(secondCol);
+            
             vector<string> names;
             m->splitAtChar(secondCol, names, ',');
             
@@ -280,7 +283,23 @@ int CountTable::printTable(string file) {
         for (int i = 0; i < groups.size(); i++) { out << groups[i] << '\t'; }
         out << endl;
         
-        for (map<string, int>::iterator itNames = indexNameMap.begin(); itNames != indexNameMap.end(); itNames++) {
+        map<int, string> reverse; //use this to preserve order
+        for (map<string, int>::iterator it = indexNameMap.begin(); it !=indexNameMap.end(); it++) { reverse[it->second] = it->first;  }
+        
+        for (int i = 0; i < totals.size(); i++) {
+            map<int, string>::iterator itR = reverse.find(i);
+            
+            if (itR != reverse.end()) { //will equal end if seqs were removed because remove just removes from indexNameMap
+                out << itR->second << '\t' << totals[i] << '\t';
+                if (hasGroups) {
+                    for (int j = 0; j < groups.size(); j++) {
+                        out << counts[i][j] << '\t';
+                    }
+                }
+                out << endl;
+            }
+        }
+        /*for (map<string, int>::iterator itNames = indexNameMap.begin(); itNames != indexNameMap.end(); itNames++) {
             out << itNames->first << '\t' << totals[itNames->second] << '\t';
             if (hasGroups) {
                 
@@ -289,7 +308,7 @@ int CountTable::printTable(string file) {
                 }
             }
             out << endl;
-        }
+        }*/
         out.close();
         return 0;
     }
@@ -361,7 +380,7 @@ int CountTable::getGroupCount(string groupName) {
         if (hasGroups) {
             map<string, int>::iterator it = indexGroupMap.find(groupName);
             if (it == indexGroupMap.end()) {
-                m->mothurOut("[ERROR]: " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+                m->mothurOut("[ERROR]: group " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
             }else { 
                 return totalGroups[it->second];
             }
@@ -381,11 +400,11 @@ int CountTable::getGroupCount(string seqName, string groupName) {
         if (hasGroups) {
             map<string, int>::iterator it = indexGroupMap.find(groupName);
             if (it == indexGroupMap.end()) {
-                m->mothurOut("[ERROR]: " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+                m->mothurOut("[ERROR]: group " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
             }else { 
                 map<string, int>::iterator it2 = indexNameMap.find(seqName);
                 if (it2 == indexNameMap.end()) {
-                    m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+                    m->mothurOut("[ERROR]: seq " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
                 }else { 
                     return counts[it2->second][it->second];
                 }
@@ -481,6 +500,10 @@ int CountTable::addGroup(string groupName) {
 int CountTable::removeGroup(string groupName) {
     try {        
         if (hasGroups) {
+            //save for later in case removing a group means we need to remove a seq.
+            map<int, string> reverse;
+            for (map<string, int>::iterator it = indexNameMap.begin(); it !=indexNameMap.end(); it++) { reverse[it->second] = it->first;  }
+            
             map<string, int>::iterator it = indexGroupMap.find(groupName);
             if (it == indexGroupMap.end()) {
                 m->mothurOut("[ERROR]: " + groupName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
@@ -491,13 +514,15 @@ int CountTable::removeGroup(string groupName) {
                 for (int i = 0; i < groups.size(); i++) {
                     if (groups[i] != groupName) { 
                         newGroups.push_back(groups[i]);
-                        indexGroupMap[groups[i]] = i;
+                        indexGroupMap[groups[i]] = newGroups.size()-1;
                     }
                 }
                 indexGroupMap.erase(groupName);
                 groups = newGroups;
                 totalGroups.erase(totalGroups.begin()+indexOfGroupToRemove);
-                 
+                
+                int thisIndex = 0;
+                map<string, int> newIndexNameMap;
                 for (int i = 0; i < counts.size(); i++) {
                     int num = counts[i][indexOfGroupToRemove];
                     counts[i].erase(counts[i].begin()+indexOfGroupToRemove);
@@ -509,7 +534,11 @@ int CountTable::removeGroup(string groupName) {
                         uniques--;
                         i--;
                     }
+                    newIndexNameMap[reverse[thisIndex]] = i;
+                    thisIndex++;
                 }
+                indexNameMap = newIndexNameMap;
+                
                 if (groups.size() == 0) { hasGroups = false; }
             }
         }else { m->mothurOut("[ERROR]: your count table does not contain group information, can not remove group " + groupName + ".\n"); m->control_pressed = true; }