added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 210dd9641a1736f8b0ea509f96b210dbbe3bd2e1..75d21c2250166d202f71ed21786dca16db40a38f 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -10,6 +10,7 @@
 #include "countseqscommand.h"
 #include "groupmap.h"
 #include "sharedutilities.h"
+#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> CountSeqsCommand::setParameters(){      
@@ -175,7 +176,7 @@ int CountSeqsCommand::execute(){
         int total = 0;
         if (!large) { total = processSmall(outputFileName); }
         else { total = processLarge(outputFileName);  }
-                               
+        
                if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
                
         //set rabund file as new current rabundfile
@@ -450,6 +451,26 @@ map<int, string> CountSeqsCommand::processNameFile(string name) {
                in.close();
         out.close();
                
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    //parse names into vector
+                    vector<string> theseNames;
+                    m->splitAtComma(secondCol, theseNames);
+                    for (int i = 0; i < theseNames.size(); i++) {  out << theseNames[i] << '\t' << count << endl;  }
+                    indexToNames[count] = firstCol;
+                    pairDone = false; 
+                    count++;
+                }
+            }
+
+        }
+        
         return indexToNames;
     }
        catch(exception& e) {
@@ -502,6 +523,26 @@ map<int, string> CountSeqsCommand::getGroupNames(string filename, set<string>& n
                }
                in.close();
         out.close();
+        
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    it = groupIndex.find(secondCol);
+                    if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
+                        groupIndex[secondCol] = count;
+                        count++;
+                    }
+                    out << firstCol << '\t' << groupIndex[secondCol] << endl; 
+                    namesOfGroups.insert(secondCol);
+                    pairDone = false; 
+                }
+            }
+        }
                
         for (it = groupIndex.begin(); it != groupIndex.end(); it++) {  indexToGroups[it->second] = it->first;  }