removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index ee449cc9fd30f7ec521a03311473a805739159d1..78c9f9e9e24d0138b158791d7d3bce2f39eca026 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -44,7 +44,7 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
        }
 }
 //***************************************************************************************************************
-ChimeraSlayer::ChimeraSlayer(string file, string temp, string name, string mode, int k, int ms, int mms, int win, float div, 
+ChimeraSlayer::ChimeraSlayer(string file, string temp, string name, string mode, string abunds, int k, int ms, int mms, int win, float div, 
                                                         int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera()  {      
        try {
                fastafile = file; templateSeqs = readSeqs(fastafile);
@@ -64,6 +64,7 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, string name, string mode,
                increment = inc;
                numWanted = numw;
                realign = r; 
+               includeAbunds = abunds;
                
                //read name file and create nameMapRank
                readNameFile(name);
@@ -283,10 +284,26 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q) {
                //create list of names we want to put into the template
                set<string> namesToAdd;
                for (itRank = nameMapRank.begin(); itRank != nameMapRank.end(); itRank++) {
-                       if ((itRank->second).size() > thisRank) {
-                               //you are more abundant than me
-                               for (int i = 0; i < (itRank->second).size(); i++) {
-                                       namesToAdd.insert((itRank->second)[i]);
+                       if (itRank->first != thisName) {
+                               if (includeAbunds == "greaterequal") {
+                                       if ((itRank->second).size() >= thisRank) {
+                                               //you are more abundant than me or equal to my abundance
+                                               for (int i = 0; i < (itRank->second).size(); i++) {
+                                                       namesToAdd.insert((itRank->second)[i]);
+                                               }
+                                       }
+                               }else if (includeAbunds == "greater") {
+                                       if ((itRank->second).size() > thisRank) {
+                                               //you are more abundant than me
+                                               for (int i = 0; i < (itRank->second).size(); i++) {
+                                                       namesToAdd.insert((itRank->second)[i]);
+                                               }
+                                       }
+                               }else if (includeAbunds == "all") {
+                                       //add everyone
+                                       for (int i = 0; i < (itRank->second).size(); i++) {
+                                               namesToAdd.insert((itRank->second)[i]);
+                                       }
                                }
                        }
                }