X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=counttable.cpp;h=a664228b17c35fff4ce48ca0ea5255b5b99bb1f3;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=c4e2732e8554cd81a934af7f2ee3bfcff7705db6;hpb=fdfbfe59134dd7dd3e49d90609d129128ba2d370;p=mothur.git

diff --git a/counttable.cpp b/counttable.cpp
index c4e2732..a664228 100644
--- a/counttable.cpp
+++ b/counttable.cpp
@@ -42,7 +42,8 @@ int CountTable::readTable(string file) {
             
             if (m->control_pressed) { break; }
             
-            in >> name >> thisTotal; m->gobble(in);
+            in >> name; m->gobble(in); in >> thisTotal; m->gobble(in);
+            if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(thisTotal) + "\n"); }
             
             //if group info, then read it
             vector<int> groupCounts; groupCounts.resize(numGroups, 0);
@@ -157,7 +158,41 @@ int CountTable::getNumSeqs(string seqName) {
 	}
 }
 /************************************************************/
-//returns names of seqs
+//returns unique index for sequence like get in NameAssignment
+int CountTable::get(string seqName) {
+    try {
+        
+        map<string, int>::iterator it = indexNameMap.find(seqName);
+        if (it == indexNameMap.end()) {
+            m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+        }else { return it->second; }
+        
+        return -1;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "CountTable", "get");
+		exit(1);
+	}
+}
+/************************************************************/
+//create ListVector from uniques
+ListVector CountTable::getListVector() {
+    try {
+        ListVector list(indexNameMap.size());
+        for (map<string, int>::iterator it = indexNameMap.begin(); it != indexNameMap.end(); it++) { 
+            if (m->control_pressed) { break; }
+            list.set(it->second, it->first); 
+        }
+        return list;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "CountTable", "getListVector");
+		exit(1);
+	}
+}
+
+/************************************************************/
+//returns the names of all unique sequences in file
 vector<string> CountTable::getNamesOfSeqs() {
     try {
         vector<string> names;
@@ -173,5 +208,37 @@ vector<string> CountTable::getNamesOfSeqs() {
 	}
 }
 /************************************************************/
+//returns names of seqs
+int CountTable::mergeCounts(string seq1, string seq2) {
+    try {
+        map<string, int>::iterator it = indexNameMap.find(seq1);
+        if (it == indexNameMap.end()) {
+            m->mothurOut("[ERROR]: " + seq1 + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+        }else { 
+            map<string, int>::iterator it2 = indexNameMap.find(seq2);
+            if (it2 == indexNameMap.end()) {
+                m->mothurOut("[ERROR]: " + seq2 + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+            }else { 
+                //merge data
+                for (int i = 0; i < groups.size(); i++) {
+                    counts[it->second][i] += counts[it2->second][i];
+                    counts[it2->second][i] = 0;
+                }
+                totals[it->second] += totals[it2->second];
+                totals[it2->second] = 0;
+                uniques--;
+                indexNameMap.erase(it2); 
+            }
+        }
+        
+        return 0;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "CountTable", "getNamesOfSeqs");
+		exit(1);
+	}
+}
+
+/************************************************************/