added countable class to read and store count file. added count parameter to make...

[mothur.git] / counttable.cpp

diff --git a/counttable.cpp b/counttable.cpp
new file mode 100644 (file)
index 0000000..c4e2732
--- /dev/null
+++ b/counttable.cpp
@@ -0,0 +1,177 @@
+//
+//  counttable.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/26/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "counttable.h"
+
+
+/************************************************************/
+int CountTable::readTable(string file) {
+    try {
+        filename = file;
+        ifstream in;
+        m->openInputFile(filename, in);
+        
+        string headers = m->getline(in); m->gobble(in);
+        vector<string> columnHeaders = m->splitWhiteSpace(headers);
+        
+        int numGroups = 0;
+        groups.clear();
+        totalGroups.clear();
+        indexGroupMap.clear();
+        indexNameMap.clear();
+        counts.clear();
+        map<int, string> originalGroupIndexes;
+        if (columnHeaders.size() > 2) { hasGroups = true; numGroups = columnHeaders.size() - 2;  }
+        for (int i = 2; i < columnHeaders.size(); i++) {  groups.push_back(columnHeaders[i]);  originalGroupIndexes[i-2] = columnHeaders[i]; totalGroups.push_back(0); }
+        //sort groups to keep consistent with how we store the groups in groupmap
+        sort(groups.begin(), groups.end());
+        for (int i = 0; i < groups.size(); i++) {  indexGroupMap[groups[i]] = i; }
+        m->setAllGroups(groups);
+        
+        bool error = false;
+        string name;
+        int thisTotal;
+        uniques = 0;
+        total = 0;
+        while (!in.eof()) {
+            
+            if (m->control_pressed) { break; }
+            
+            in >> name >> thisTotal; m->gobble(in);
+            
+            //if group info, then read it
+            vector<int> groupCounts; groupCounts.resize(numGroups, 0);
+            for (int i = 0; i < numGroups; i++) {  int thisIndex = indexGroupMap[originalGroupIndexes[i]]; in >> groupCounts[thisIndex]; m->gobble(in); totalGroups[thisIndex] += groupCounts[thisIndex];  }
+            
+            map<string, int>::iterator it = indexNameMap.find(name);
+            if (it == indexNameMap.end()) {
+                if (hasGroups) {  counts.push_back(groupCounts);  }
+                indexNameMap[name] = uniques;
+                totals.push_back(thisTotal);
+                total += thisTotal;
+                uniques++;
+            }else {
+                error = true;
+                m->mothurOut("[ERROR]: Your count table contains more than 1 sequence named " + name + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); 
+            }
+        }
+        in.close();
+        
+        if (error) { m->control_pressed = true; }
+        
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CountTable", "readTable");
+               exit(1);
+       }
+}
+/************************************************************/
+//group counts for a seq
+vector<int> CountTable::getGroupCounts(string seqName) {
+    try {
+        vector<int> temp;
+        if (hasGroups) {
+            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 { 
+                temp = counts[it->second];
+            }
+        }else{  m->mothurOut("[ERROR]: Your count table does not have group info. Please correct.\n"); m->control_pressed = true; }
+        
+        return temp;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CountTable", "getGroupCounts");
+               exit(1);
+       }
+}
+/************************************************************/
+//total number of sequences for the group
+int CountTable::getGroupCount(string groupName) {
+    try {
+        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;
+            }else { 
+                return totalGroups[it->second];
+            }
+        }else{  m->mothurOut("[ERROR]: Your count table does not have group info. Please correct.\n");  m->control_pressed = true; }
+
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CountTable", "getGroupCount");
+               exit(1);
+       }
+}
+/************************************************************/
+//total number of sequences for the seq for the group
+int CountTable::getGroupCount(string seqName, string groupName) {
+    try {
+        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;
+            }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;
+                }else { 
+                    return counts[it2->second][it->second];
+                }
+            }
+        }else{  m->mothurOut("[ERROR]: Your count table does not have group info. Please correct.\n");  m->control_pressed = true; }
+        
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CountTable", "getGroupCount");
+               exit(1);
+       }
+}
+/************************************************************/
+//total number of seqs represented by seq
+int CountTable::getNumSeqs(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 totals[it->second];
+        }
+
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CountTable", "getNumSeqs");
+               exit(1);
+       }
+}
+/************************************************************/
+//returns names of seqs
+vector<string> CountTable::getNamesOfSeqs() {
+    try {
+        vector<string> names;
+        for (map<string, int>::iterator it = indexNameMap.begin(); it != indexNameMap.end(); it++) {
+            names.push_back(it->first);
+        }
+                
+        return names;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "CountTable", "getNamesOfSeqs");
+               exit(1);
+       }
+}
+/************************************************************/
+
+