added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and OTU001 are...

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index be167d9b9cbb92a8ffea832b8c2eccfb4ed6bf3d..f9784b3ea91e09d1c0d86232b67b70bc5e789b99 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -249,7 +249,7 @@ int BinSeqCommand::execute(){
                
                //if user gave a namesfile then use it
                if (namesfile != "") {  readNamesFile();  }
-        if (countfile != "") {  ct.readTable(countfile, true);  }
+        if (countfile != "") {  ct.readTable(countfile, true, false);  }
                
                input = new InputData(listfile, "list");
                list = input->getListVector();

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index cea481bd22062b7461a06705d08ba4d1c1930451..0547802198960198d9d2a063bc498e79f04bfe33 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -516,7 +516,7 @@ int ChimeraPerseusCommand::execute(){
             
             if (hasCount) {
                 CountTable* ct = new CountTable();
-                ct->readTable(nameFile, true);
+                ct->readTable(nameFile, true, false);
                 
                 if (ct->hasGroupInfo()) {
                     cparser = new SequenceCountParser(fastaFileNames[s], *ct);
@@ -534,7 +534,7 @@ int ChimeraPerseusCommand::execute(){
                     
                     if(processors == 1)        {       numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
                         if (dups) {
-                            CountTable c; c.readTable(nameFile, true);
+                            CountTable c; c.readTable(nameFile, true, false);
                             if (!m->isBlank(newCountFile)) {
                                 ifstream in2;
                                 m->openInputFile(newCountFile, in2);
@@ -559,7 +559,7 @@ int ChimeraPerseusCommand::execute(){
                         numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
                     }else {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile, true);
+                        CountTable c; c.readTable(newCountFile, true, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1070,7 +1070,7 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
                int num = 0;
                
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(name, true); }
+        if (hasCount && dups) { newCount.readTable(name, true, false); }
         
                //sanity check
                if (groups.size() < processors) { processors = groups.size(); }

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index b6d4fc9323f659abe52cd70a1e3598a84d9db936..0d907814e21b2ef48dbd3d1883fb3e8698533189 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -130,7 +130,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
                if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile, true);
+            ct->readTable(pDataArray->namefile, true, false);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index f01bd3ee9d9bb3611b52b38819f98300da9cff39..41661da085060fcd66913f31764232dbbacce342 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -759,7 +759,7 @@ int ChimeraSlayerCommand::execute(){
                                if (processors == 1) {
                     numSeqs = driverGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile);
                     if (hasCount && dups) {
-                        CountTable c; c.readTable(nameFileNames[s], true);
+                        CountTable c; c.readTable(nameFileNames[s], true, false);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -791,7 +791,7 @@ int ChimeraSlayerCommand::execute(){
                     }else {
                         if (hasCount) {
                             set<string> doNotRemove;
-                            CountTable c; c.readTable(newCountFile, true);
+                            CountTable c; c.readTable(newCountFile, true, true);
                             vector<string> namesInTable = c.getNamesOfSeqs();
                             for (int i = 0; i < namesInTable.size(); i++) {
                                 int temp = c.getNumSeqs(namesInTable[i]);
@@ -1551,7 +1551,7 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
                if (fileToPriority.size() < processors) { processors = fileToPriority.size(); }
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(countFile, true); }
+        if (hasCount && dups) { newCount.readTable(countFile, true, false); }
                
                int groupsPerProcessor = fileToPriority.size() / processors;
                int remainder = fileToPriority.size() % processors;
@@ -2161,7 +2161,7 @@ map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string na
         int error;
         if (hasCount) { 
             CountTable ct;
-            ct.readTable(nameFile, true);
+            ct.readTable(nameFile, true, false);
             
             for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
                 int num = ct.getNumSeqs(it->first);

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 422792a68525b495008694360c393e26ba358c09..346afe213b12fab2baab1e4d23102e526f6ecc8c 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -674,7 +674,7 @@ int ChimeraUchimeCommand::execute(){
                 int error;
                 if (hasCount) {
                     CountTable ct;
-                    ct.readTable(nameFile, true);
+                    ct.readTable(nameFile, true, false);
                     for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
                         int num = ct.getNumSeqs(it->first);
                         if (num == 0) { error = 1; }
@@ -725,7 +725,7 @@ int ChimeraUchimeCommand::execute(){
                                if(processors == 1)     {       totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
                     
                     if (hasCount && dups) {
-                        CountTable c; c.readTable(nameFile, true);
+                        CountTable c; c.readTable(nameFile, true, false);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -755,7 +755,7 @@ int ChimeraUchimeCommand::execute(){
                     
                     if (hasCount) {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile, true);
+                        CountTable c; c.readTable(newCountFile, true, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1795,7 +1795,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
                int num = 0;
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(nameFile, true); }
+        if (hasCount && dups) { newCount.readTable(nameFile, true, false); }
                
                //sanity check
                if (groups.size() < processors) { processors = groups.size(); }

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index fadc4a4d401dcf5da93d0d32c56ed9ec8a7ef99a..e98a20d9056b858892d9f4ac69ff2517f2604165 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -175,7 +175,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
                if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile, true);
+            ct->readTable(pDataArray->namefile, true, false);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {

diff --git a/classify.cpp b/classify.cpp
index 5f97c7ec693a97997554683188a013b1054eb3d7..71a9b258e91bf2f527e2e1a8469f2e1e8037d76d 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -295,12 +295,13 @@ int Classify::readTaxonomy(string file) {
                        iss >> name; m->gobble(iss);
             iss >> taxInfo;
             if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
-                       if (m->inUsersGroups(name, names)) {
+            //commented out to save time with large templates. 10/7/13
+                       //if (m->inUsersGroups(name, names)) {
                 taxonomy[name] = taxInfo;
                 phyloTree->addSeqToTree(name, taxInfo);
-            }else {
-                m->mothurOut("[WARNING]: " + name + " is in your taxonomy file and not in your reference file, ignoring.\n");
-            }          
+            //}else {
+            //    m->mothurOut("[WARNING]: " + name + " is in your taxonomy file and not in your reference file, ignoring.\n");
+            //}
         }
                
                MPI_File_close(&inMPI);

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 76d7504aa04b0170629b0f022a882be94ceacfc0..217bc868eb8984c1111ff50fa84f83abeefa2059 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -293,7 +293,7 @@ int ClassifyOtuCommand::execute(){
                if (namefile != "")     {       m->readNames(namefile, nameMap, true);  }
         if (groupfile != "")    {   groupMap = new GroupMap(groupfile);  groupMap->readMap();  groups = groupMap->getNamesOfGroups(); }
         else { groupMap = NULL;  }
-        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile, true);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile, true, false);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
         else {  ct = NULL;    }
         
                //read taxonomy file and save in map for easy access in building bin trees

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index b311821b3e8d293daac13107eb9e6771be360bf0..1b56433073d404e2c7f33513f7362f8306afcb42 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -812,7 +812,7 @@ int ClassifySeqsCommand::execute(){
                 PhyloSummary* taxaSum;
                 if (hasCount) { 
                     ct = new CountTable();
-                    ct->readTable(countfileNames[s], true);
+                    ct->readTable(countfileNames[s], true, false);
                     taxaSum = new PhyloSummary(taxonomyFileName, ct);
                     taxaSum->summarize(tempTaxonomyFile);
                 }else {

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 94129654e1d2b11275e82d3a5da0382b1448efa9..c1ac5bbddd5be05c41e03853c25af4340eab133e 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -315,7 +315,7 @@ int ClusterCommand::execute(){
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile, false);
+            ct->readTable(countfile, false, false);
             read->read(ct);
         }else { read->read(nameMap); }
                

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 08a5938b85b3b40f7a53619766d1a9a3e004a9a5..96bfc5c523be69bcc75dae33e35a209846aa2302 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -226,7 +226,7 @@ int ClusterDoturCommand::execute(){
             delete nameMap;
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile, false);
+            ct->readTable(countfile, false, false);
             cluster->readPhylipFile(phylipfile, ct);
             delete ct;
         }else {

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 9c1408c9a112dcc3ad9ed579026e2528c334a102..4b5c67f8f69bb51160d3d32212cf337719e3b4eb 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -181,7 +181,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
             countfile = validParameter.validFile(parameters, "count", true);
                        if (countfile == "not open") { abort = true; countfile = ""; }  
                        else if (countfile == "not found") { countfile = ""; }
-                       else { ct.readTable(countfile, true); m->setCountTableFile(countfile); }
+                       else { ct.readTable(countfile, true, false); m->setCountTableFile(countfile); }
                        
             if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
                        

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 95693cc420a7e55d5c9a96a102e3d9e55ad0221c..b5dc9692f0f7afefabae27676b9aa61491c048f1 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -1174,7 +1174,7 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
             cluster->readPhylipFile(thisDistFile, nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile, false);
+            ct->readTable(thisNamefile, false, false);
             cluster->readPhylipFile(thisDistFile, ct);
         }
         tag = cluster->getTag();
@@ -1302,7 +1302,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile, false);
+            ct->readTable(thisNamefile, false, false);
             read->read(ct);
         }else { read->read(nameMap); }
                

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 3d671f98420e0fa7cf844aac647bd43feea959e8..fbec746804bcd7257383e99f26e058dfe4df6f25 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -226,7 +226,7 @@ int ConsensusSeqsCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                if (namefile != "") { readNames(); }
-        if (countfile != "") { ct.readTable(countfile, true);  }
+        if (countfile != "") { ct.readTable(countfile, true, false);  }
                
                if (m->control_pressed) { return 0; }
                

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index 83c2d315d0b8f781caa02c04c4fed5e1cb6b6a0d..ce3358ef43b9cee9d7887314fb0378cb203b7ebe 100644 (file)
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -261,7 +261,7 @@ int CountGroupsCommand::execute(){
             m->openOutputFile(outputFileName, out);
             
                        CountTable ct;
-                       ct.readTable(countfile, true);
+                       ct.readTable(countfile, true, false);
             
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all

diff --git a/counttable.cpp b/counttable.cpp
index 0e9eec38234d52215af681b74a00b5713c7113b0..d5720acd386c36cf8cd713dcbc6d1bd5e507609b 100644 (file)
--- a/counttable.cpp
+++ b/counttable.cpp
@@ -211,7 +211,7 @@ int CountTable::createTable(string namefile, string groupfile, bool createGroup)
        }
 }
 /************************************************************/
-int CountTable::readTable(string file, bool readGroups) {
+int CountTable::readTable(string file, bool readGroups, bool mothurRunning) {
     try {
         filename = file;
         ifstream in;
@@ -246,7 +246,7 @@ int CountTable::readTable(string file, bool readGroups) {
             in >> name; m->gobble(in); in >> thisTotal; m->gobble(in);
             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(thisTotal) + "\n"); }
             
-            if (thisTotal == 0) { error=true; m->mothurOut("[ERROR]: Your count table contains a sequence named " + name + " with a total=0. Please correct."); m->mothurOutEndLine();
+            if ((thisTotal == 0) && !mothurRunning) { error=true; m->mothurOut("[ERROR]: Your count table contains a sequence named " + name + " with a total=0. Please correct."); m->mothurOutEndLine();
             }
             
             //if group info, then read it

diff --git a/counttable.h b/counttable.h
index 51d0b4544bc73c7e832826bad702028f0143a549..c0ced354ef8bac6b013105c6bd3fe0fdfb21a3cf 100644 (file)
--- a/counttable.h
+++ b/counttable.h
@@ -50,7 +50,7 @@ class CountTable {
         //reads and creates smart enough to eliminate groups with zero counts 
         int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames 
         int createTable(string, string, bool); //namefile, groupfile, createGroup
-        int readTable(string, bool);
+        int readTable(string, bool, bool);
     
         int printTable(string);
         int printHeaders(ofstream&);

diff --git a/createdatabasecommand.cpp b/createdatabasecommand.cpp
index eab7c8261a55e45abe3f762f86cc46e59c9822a6..235682bfec8fdfc36c43ed25fb78ffd06eef1b4f 100644 (file)
--- a/createdatabasecommand.cpp
+++ b/createdatabasecommand.cpp
@@ -298,7 +298,7 @@ int CreateDatabaseCommand::execute(){
             }
             repNames = tempRepNames;
         }else {
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             numUniqueNamesFile = ct.getNumUniqueSeqs();
             nameMap = ct.getNameMap();
         }
@@ -506,7 +506,7 @@ int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
        try {
         int index = -1;
         for (int i = 0; i < otuLabels.size(); i++) {
-            if (otuLabels[i] == label) { index = i; break; }
+            if (m->isLabelEquivalent(otuLabels[i],label)) { index = i; break; }
         }
                return index;
     }

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51fa43b39f87f06a3054808acb4937e05ae2337f..98109ef33c488a071b04ad5ada84ffcab9d2e1f8 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -209,7 +209,7 @@ int DeconvoluteCommand::execute() {
         }
         CountTable ct;
         if (countfile != "")  {  
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (countfile == outCountFile){
                 //prepare filenames and open files
                 map<string, string> mvariables;

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 45e0a783e393ba828d8bd74c3884fa45779a92f2..15dcbba802d5e850fccbb7bb71b05dba6af38b74 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -370,7 +370,7 @@ int GetGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
                 
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 005a89f2ebbee9e1b4c37567b6ce382979c90226..862aef7a0da6dde200bc387209bdd73d730015f5 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -514,7 +514,7 @@ int GetLineageCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName, true);
+            ct.readTable(outputFileName, true, false);
             ct.printTable(outputFileName);
         }
 
@@ -628,7 +628,7 @@ int GetLineageCommand::readConsList(){
             }
             otuLabel += sbinNumber;
             
-            if (names.count(otuLabel) != 0) {
+            if (names.count(m->getSimpleLabel(otuLabel)) != 0) {
                                selectedCount++;
                 newList.push_back(list->get(i));
             }
@@ -767,7 +767,7 @@ int GetLineageCommand::readShared(){
             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
             
             //is this otu on the list
-            if (names.count(m->currentBinLabels[i]) != 0) {
+            if (names.count(m->getSimpleLabel(m->currentBinLabels[i])) != 0) {
                 numSelected++; wroteSomething = true;
                 newLabels.push_back(m->currentBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
@@ -1241,7 +1241,7 @@ int GetLineageCommand::readConsTax(){
                                        int pos = newtax.find(noConfidenceTaxons[j]);
                     
                                        if (pos != string::npos) { //this sequence contains the taxon the user wants
-                                               names.insert(otuLabel);
+                                               names.insert(m->getSimpleLabel(otuLabel));
                                                out << otuLabel << '\t' << numReps << '\t' << tax << endl;
                                                //since you belong to at least one of the taxons we want you are included so no need to search for other
                                                break;
@@ -1253,7 +1253,7 @@ int GetLineageCommand::readConsTax(){
                                                int pos = newtax.find(noConfidenceTaxons[j]);
                         
                                                if (pos != string::npos) { //this sequence contains the taxon the user wants
-                                                       names.insert(otuLabel);
+                                                       names.insert(m->getSimpleLabel(otuLabel));
                                                        out << otuLabel << '\t' << numReps << '\t' << tax << endl;
                                                        //since you belong to at least one of the taxons we want you are included so no need to search for other
                                                        break;
@@ -1309,7 +1309,7 @@ int GetLineageCommand::readConsTax(){
                             
                                                        //passed the test so add you
                                                        if (good) {
-                                                               names.insert(otuLabel);
+                                                               names.insert(m->getSimpleLabel(otuLabel));
                                                                out << otuLabel << '\t' << numReps << '\t' << tax << endl;
                                                                break;
                                                        }

diff --git a/getotulabelscommand.cpp b/getotulabelscommand.cpp
index b6253b02a64ec25c6a394b59438a79554c3685eb..00297e2d8049be362a991589446544b6c1cf99fc 100644 (file)
--- a/getotulabelscommand.cpp
+++ b/getotulabelscommand.cpp
@@ -234,6 +234,10 @@ int GetOtuLabelsCommand::execute(){
         
         //get labels you want to keep
                labels = m->readAccnos(accnosfile);
+        //simplfy labels
+        set<string> newLabels;
+        for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {  newLabels.insert(m->getSimpleLabel(*it)); }
+        labels = newLabels;
                
                if (m->control_pressed) { return 0; }
                
@@ -302,7 +306,7 @@ int GetOtuLabelsCommand::readClassifyOtu(){
             
             in >> otu >> size >> tax; m->gobble(in);
             
-            if (labels.count(otu) != 0) {
+            if (labels.count(m->getSimpleLabel(otu)) != 0) {
                                wroteSomething = true;
                                selectedCount++;
                 
@@ -357,7 +361,7 @@ int GetOtuLabelsCommand::readOtuAssociation(){
             in >> otu1 >> otu2;
             string line = m->getline(in); m->gobble(in);
             
-            if ((labels.count(otu1) != 0) && (labels.count(otu2) != 0)){
+            if ((labels.count(m->getSimpleLabel(otu1)) != 0) && (labels.count(m->getSimpleLabel(otu2)) != 0)){
                                wroteSomething = true;
                                selectedCount++;
                 
@@ -412,7 +416,7 @@ int GetOtuLabelsCommand::readCorrAxes(){
             in >> otu;
             string line = m->getline(in); m->gobble(in);
             
-            if (labels.count(otu) != 0) {
+            if (labels.count(m->getSimpleLabel(otu)) != 0) {
                                wroteSomething = true;
                                selectedCount++;
                 
@@ -461,7 +465,7 @@ int GetOtuLabelsCommand::readShared(){
             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
             
             //is this otu on the list
-            if (labels.count(m->currentBinLabels[i]) != 0) {
+            if (labels.count(m->getSimpleLabel(m->currentBinLabels[i])) != 0) {
                 numSelected++; wroteSomething = true;
                 newLabels.push_back(m->currentBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
@@ -532,7 +536,7 @@ int GetOtuLabelsCommand::readList(){
             }
             otuLabel += sbinNumber; 
             
-            if (labels.count(otuLabel) != 0) {
+            if (labels.count(m->getSimpleLabel(otuLabel)) != 0) {
                                selectedCount++;
                 newList.push_back(list->get(i));
             }

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index d476cc3499844c88014bcef9e1a005459fab3dda..7e71a1a836b2e6306b40d67f5cdce0d7f35dbcdc 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -261,7 +261,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { hasGroups = true; }
             }
             
@@ -1106,7 +1106,7 @@ int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile, true);
+            thisCt.readTable(countfile, true, false);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
     
@@ -1253,7 +1253,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
         
         CountTable thisCt;
         if (countfile != "") {
-            thisCt.readTable(countfile, true);
+            thisCt.readTable(countfile, true, false);
             if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
         }
         

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index da1bfae2c07f5cb719961dce93324ff8135fbfc4..469117ca7bdf4cfb65553bb45536c93fd06251d2 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -319,7 +319,7 @@ int GetRAbundCommand::execute(){
 int GetRAbundCommand::processList(ofstream& out){
        try {
         CountTable ct;
-        ct.readTable(countfile, false);
+        ct.readTable(countfile, false, false);
         
         InputData input(inputfile, format);
         ListVector* list = input.getListVector();

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index f4838cf8a72a75708085b3917b8828939e43f683..22abde5fade29a689fa88266772f5e3445d5158c 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -307,7 +307,7 @@ int GetSAbundCommand::execute(){
 int GetSAbundCommand::processList(ofstream& out){
        try {
         CountTable ct;
-        ct.readTable(countfile, false);
+        ct.readTable(countfile, false, false);
         
         InputData input(inputfile, format);
         ListVector* list = input.getListVector();

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 83fdf73e9af36fd9826f5a8c2efcc11655ac938e..82f9710e6e40cb84b8fee9f285fca71b3fe0099c 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -589,7 +589,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName, true);
+            ct.readTable(outputFileName, true, false);
             ct.printTable(outputFileName);
         }
                

diff --git a/heatmap.cpp b/heatmap.cpp
index 36665ff7c6402652e2bfa2039ab0023294e1f248..367342c7167451402c5879a1f6efd1f83e7a48a4 100644 (file)
--- a/heatmap.cpp
+++ b/heatmap.cpp
@@ -119,7 +119,8 @@ string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
                }
                
                //sort lookup so shared bins are on top
-               if (sorted != "none") {  sortSharedVectors(lookup);  }
+        vector<string> sortedLabels = m->currentBinLabels;
+               if (sorted != "none") {  sortedLabels = sortSharedVectors(lookup);  }
                
                vector<vector<string> > scaleRelAbund;
                vector<float> maxRelAbund(lookup[0]->size(), 0.0);              
@@ -158,36 +159,46 @@ string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 
                string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
                m->openOutputFile(filenamesvg, outsvg);
+        int binHeight = 20;
+        int labelBump = 100;
+        int binWidth = 300;
                
                //svg image
-               outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((numBinsToDisplay*5 + 120))  + "\">\n";
+               outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * binWidth + labelBump) + " " + toString((numBinsToDisplay*binHeight + 120))  + "\">\n";
                outsvg << "<g>\n";
                
                //white backround
-               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120))  + "\"/>"; 
+               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * binWidth+labelBump) + "\" height=\"" + toString((numBinsToDisplay*binHeight + 120))  + "\"/>";
                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" text-anchor=\"middle\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
                
                //column labels
-               for (int h = 0; h < lookup.size(); h++) {
-                       outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n"; 
+               for (int h = 0; h < lookup.size()+1; h++) {
+            if (h == 0) {
+                string tempLabel = "OTU";
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(labelBump-labelBump/2+1) + "\" y=\"50\">" + tempLabel + "</text>\n";
+            }else {
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((binWidth * h) - 150) - ((int)lookup[h-1]->getGroup().length() / 2)+labelBump/2) + "\" y=\"50\">" + lookup[h-1]->getGroup() + "</text>\n";
+            }
                }
 
                //output legend and color labels
                string color;
                int x = 0;
-               int y = 103 + (numBinsToDisplay*5);
+               int y = 103 + (numBinsToDisplay*binHeight);
                printLegend(y, superMaxRelAbund);
                
                y = 70;
                for (int i = 0; i < numBinsToDisplay; i++) {
+            outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + sortedLabels[i] + "</text>\n";
+            x += labelBump;
                        for (int j = 0; j < scaleRelAbund.size(); j++) {
                                if (m->control_pressed) { outsvg.close(); return "control"; }
                                
-                               outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
-                               x += 300;
+                               outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"" + toString(binWidth) +  "\" height=\"" + toString(binHeight) +  "\"/>\n";
+                               x += binWidth;
                        }
                        x = 0;
-                       y += 5;
+                       y += binHeight;
                }
                
                outsvg << "</g>\n</svg>\n";
@@ -203,12 +214,14 @@ string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 }
 
 //**********************************************************************************************************************
-int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
+vector<string> HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
        try {
                                
                vector<SharedRAbundVector*> looktemp;
                map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
                map<int, int>::iterator it;
+        
+        vector<string> sortedLabels = m->currentBinLabels;
                
                /****************** find order of otus **********************/
                if (sorted == "shared") {
@@ -217,7 +230,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
                        place = orderTopOtu(lookup);    
                }else if (sorted == "topgroup") {
                        place = orderTopGroup(lookup);  
-               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return 1; }
+               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return sortedLabels; }
                                
                
                /******************* create copy of lookup *********************/
@@ -241,6 +254,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
                                int newAbund = looktemp[j]->getAbundance(i);                                                                                            // 1 -> 3
                                lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
                        }
+            sortedLabels[place[i]] = m->currentBinLabels[i];
                }
                
                //delete looktemp -- Sarah look at - this is causing segmentation faults
@@ -248,7 +262,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 //                     delete looktemp[j];
                }
                
-               return 0;
+               return sortedLabels;
                
        }
        catch(exception& e) {
@@ -416,7 +430,8 @@ string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
                }
                
                //sort lookup so shared bins are on top
-               if (sorted != "none") {  sortSharedVectors(lookup);  }
+               vector<string> sortedLabels = m->currentBinLabels;
+               if (sorted != "none") {  sortedLabels = sortSharedVectors(lookup);  }
                
                vector<vector<string> > scaleRelAbund;
                vector<float> maxRelAbund(lookup.size(), 0.0);          
@@ -455,36 +470,47 @@ string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
 
                string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
                m->openOutputFile(filenamesvg, outsvg);
+        
+        int binHeight = 20;
+        int labelBump = 100;
+        int binWidth = 300;
                
                //svg image
-               outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((numBinsToDisplay*5 + 120))  + "\">\n";
+               outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * binWidth + labelBump) + " " + toString((numBinsToDisplay*binHeight + 120))  + "\">\n";
                outsvg << "<g>\n";
                
                //white backround
-               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((numBinsToDisplay*5 + 120))  + "\"/>"; 
+               outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * binWidth+labelBump) + "\" height=\"" + toString((numBinsToDisplay*binHeight + 120))  + "\"/>";
                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" text-anchor=\"middle\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
                
                //column labels
-               for (int h = 0; h < lookup.size(); h++) {
-                       outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n"; 
-               }
-
+               for (int h = 0; h < lookup.size()+1; h++) {
+            if (h == 0) {
+                string tempLabel = "OTU";
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(labelBump-labelBump/2+1) + "\" y=\"50\">" + tempLabel + "</text>\n";
+            }else {
+                outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((binWidth * h) - 150) - ((int)lookup[h-1]->getGroup().length() / 2)+labelBump/2) + "\" y=\"50\">" + lookup[h-1]->getGroup() + "</text>\n";
+            }
+               }
+        
                //output legend and color labels
                string color;
                int x = 0;
-               int y = 103 + (numBinsToDisplay*5);
+               int y = 103 + (numBinsToDisplay*binHeight);
                printLegend(y, superMaxRelAbund);
                
                y = 70;
                for (int i = 0; i < numBinsToDisplay; i++) {
+            outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + sortedLabels[i] + "</text>\n";
+            x += labelBump;
                        for (int j = 0; j < scaleRelAbund.size(); j++) {
                                if (m->control_pressed) { outsvg.close(); return "control"; }
                                
-                               outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
-                               x += 300;
+                               outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"" + toString(binWidth) +  "\" height=\"" + toString(binHeight) +  "\"/>\n";
+                               x += binWidth;
                        }
                        x = 0;
-                       y += 5;
+                       y += binHeight;
                }
                
                outsvg << "</g>\n</svg>\n";
@@ -499,12 +525,14 @@ string HeatMap::getPic(vector<SharedRAbundFloatVector*> lookup) {
        }
 }
 //**********************************************************************************************************************
-int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
+vector<string> HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
        try {
                                
                vector<SharedRAbundFloatVector*> looktemp;
                map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
                map<int, int>::iterator it;
+        
+        vector<string> sortedLabels = m->currentBinLabels;
                
                /****************** find order of otus **********************/
                if (sorted == "shared") {
@@ -513,7 +541,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
                        place = orderTopOtu(lookup);    
                }else if (sorted == "topgroup") {
                        place = orderTopGroup(lookup);  
-               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return 1; }
+               }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return sortedLabels; }
                                
                
                /******************* create copy of lookup *********************/
@@ -536,6 +564,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
                        for (int j = 0; j < looktemp.size(); j++) {                                                                                                             // 3 -> 2
                                float newAbund = looktemp[j]->getAbundance(i);                                                                                          // 1 -> 3
                                lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
+                sortedLabels[place[i]] = m->currentBinLabels[i];
                        }
                }
                
@@ -544,7 +573,7 @@ int HeatMap::sortSharedVectors(vector<SharedRAbundFloatVector*>& lookup){
 //                     delete looktemp[j];
                }
                
-               return 0;
+               return sortedLabels;
                
        }
        catch(exception& e) {

diff --git a/heatmap.h b/heatmap.h
index 2b491767d57e48c4a05728aa6a48cbfc6939b38f..922147ccb62d54f154f34796a7ad7786717841d6 100644 (file)
--- a/heatmap.h
+++ b/heatmap.h
@@ -51,8 +51,8 @@ class HeatMap {
                string getPic(vector<SharedRAbundFloatVector*>);
 
        private:
-               int sortSharedVectors(vector<SharedRAbundVector*>& );
-               int sortSharedVectors(vector<SharedRAbundFloatVector*>& );
+               vector<string> sortSharedVectors(vector<SharedRAbundVector*>& );
+               vector<string> sortSharedVectors(vector<SharedRAbundFloatVector*>& );
                int sortRabund(RAbundVector*&);
                void printLegend(int, float);
 

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 01a60aea3b01ad2ce95584c33280e7dde4d8147f..14c55308852a6e3de86b6747981c160ec9a62723 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -543,7 +543,7 @@ int HeatMapSimCommand::runCommandDist() {
                 }
              }else if (countfile != "") {
                 nameMap = NULL;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 names = ct.getNamesOfSeqs();
             }
                        

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 47d04f9d528ab14053f468f2eacc7e150db736c0..ef54dae941edcf3d8f2720e931d8a9a293574ee3 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -17,7 +17,7 @@ HelpCommand::HelpCommand(string option)  {
 //**********************************************************************************************************************
 int HelpCommand::execute(){
        try {
-               validCommands->printCommands(cout);
+        validCommands->printCommands(cout);
                m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine();
        
                m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.\n");

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index cf884705cb26f341ef08713b118af32fd49c5bdf..343d4fdc6399f8ca9a91c6cac9b31313d7b76bbb 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -415,7 +415,7 @@ int ListSeqsCommand::readGroup(){
 int ListSeqsCommand::readCount(){
        try {
                CountTable ct;
-               ct.readTable(countfile, false);
+               ct.readTable(countfile, false, false);
         
         if (m->control_pressed) { return 0; }
         

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index 7cf8295fb48e02b0dce58b32432d39c736695259..248b3c8194d27e05e9e8b15359cf6de5b9c2395a 100644 (file)
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -596,8 +596,9 @@ vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup,
                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
                     }
                     binLabel += sbinNumber;
+                    binLabel = m->getSimpleLabel(binLabel);
                     labelTaxMap[binLabel] = taxs[i];
-                }else {  labelTaxMap[otuLabels[i]] = taxs[i]; }
+                }else {  labelTaxMap[m->getSimpleLabel(otuLabels[i])] = taxs[i]; }
             }
             
             
@@ -610,7 +611,7 @@ vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup,
                 
                 if (m->control_pressed) { return metadata; }
                 
-                it = labelTaxMap.find(m->currentBinLabels[i]);
+                it = labelTaxMap.find(m->getSimpleLabel(m->currentBinLabels[i]));
                 
                 if (it == labelTaxMap.end()) { m->mothurOut("[ERROR]: can't find taxonomy information for " + m->currentBinLabels[i] + ".\n"); m->control_pressed = true; }
                 else {

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 0bf56e7c2166daf33816de12216d318a5fba466b..87027f4df5e0166f25852fec44cd6cfa120c90a7 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1042,7 +1042,9 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
             
             int oStart = contig.length();
+            //cout << fSeq.getAligned()  << endl; cout << rSeq.getAligned() << endl;
             for (int i = overlapStart; i < overlapEnd; i++) {
+                //cout << seq1[i] << ' ' << seq2[i] << ' ' << scores1[ABaseMap[i]] << ' ' << scores2[BBaseMap[i]] << endl;
                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
                     contig += seq1[i];
                 }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
@@ -1076,7 +1078,8 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             }else { //seq2 ends before seq1 so take from overlap to length from seq1
                 for (int i = overlapEnd; i < length; i++) {  contig += seq1[i]; }
             }
-            
+            //cout << contig << endl;
+            //exit(1);
             if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart);  if (contig.length() == 0) { trashCode += "l"; } }
             
             if(trashCode.length() == 0){

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 97f0afdb366949d39e5af37a96c0211d9df0ca17..85db5e0e8ffc384960f7954d6db1266bac9ea3c1 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -240,7 +240,7 @@ int MGClusterCommand::execute(){
                        nameMap->readMap();
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile, false);
+            ct->readTable(countfile, false, false);
             nameMap= new NameAssignment();
             vector<string> tempNames = ct->getNamesOfSeqs();
             for (int i = 0; i < tempNames.size(); i++) {  nameMap->push_back(tempNames[i]);  }

diff --git a/mothurout.cpp b/mothurout.cpp
index 713bafd0c2a79ec637abdf9d481a0c96c183ee77..3d4504daf761d625ffedd1e11749aa567ca9327b 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -2599,6 +2599,65 @@ int MothurOut::getNumChar(string line, char c){
                exit(1);
        }
 }
+/***********************************************************************/
+string MothurOut::getSimpleLabel(string label){
+       try {
+               string simple = "";
+        
+        //remove OTU or phylo tag
+        string newLabel1 = "";
+        for (int i = 0; i < label.length(); i++) {
+            if(label[i]>47 && label[i]<58) { //is a digit
+                newLabel1 += label[i];
+            }
+        }
+        
+        int num1;
+        mothurConvert(newLabel1, num1);
+        
+        simple = toString(num1);
+        
+               return simple;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "isLabelEquivalent");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+bool MothurOut::isLabelEquivalent(string label1,  string label2){
+       try {
+               bool same = false;
+        
+        //remove OTU or phylo tag
+        string newLabel1 = "";
+        for (int i = 0; i < label1.length(); i++) {
+            if(label1[i]>47 && label1[i]<58) { //is a digit
+                newLabel1 += label1[i];
+            }
+        }
+        
+        string newLabel2 = "";
+        for (int i = 0; i < label2.length(); i++) {
+            if(label2[i]>47 && label2[i]<58) { //is a digit
+                newLabel2 += label2[i];
+            }
+        }
+        
+        int num1, num2;
+        mothurConvert(newLabel1, num1);
+        mothurConvert(newLabel2, num2);
+        
+        if (num1 == num2) { same = true; }
+               
+               return same;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "isLabelEquivalent");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 bool MothurOut::isSubset(vector<string> bigset, vector<string> subset) {
        try {

diff --git a/mothurout.h b/mothurout.h
index 9987374e6c824cafe4aaf343c319d5bca14f209b..f58f4e874a7f72961489d7e2651bda651e3d2bb4 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -138,6 +138,8 @@ class MothurOut {
                bool isTrue(string);
                bool isContainingOnlyDigits(string);
                bool isNumeric1(string);
+        bool isLabelEquivalent(string, string);
+        string getSimpleLabel(string);
         string findEdianness();
        
                

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 5a568f3511d38f56601362d860a9643e702c9a1b..32a7e0828ff143d8f414bacf66c52a205bbf27c7 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -169,7 +169,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (!ct.hasGroupInfo()) { 
                     abort = true;
                     m->mothurOut("[ERROR]: The parse.list command requires group info to be present in your countfile, quitting."); m->mothurOutEndLine();

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 8a8db37612937ee86d7d11adf1b9973d8cba634d..cb8dd490e3a53a40edce7d1d52fffada445fac13 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -1275,7 +1275,7 @@ int PcrSeqsCommand::readCount(set<string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile, true);
+            ct.readTable(goodCountFile, true, false);
             ct.printTable(goodCountFile);
         }
                

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index bd3f172c2bcaa3e13ced0b5c57d92e39c9073969..fbbe4bb3a2fc5c99f77875292849e0a0e95f1043 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }

diff --git a/primerdesigncommand.cpp b/primerdesigncommand.cpp
index 195adf4f716b29bd7c12a2f3529603e4baec6b4d..960da85e8ce7ab4922f6afc38c728f2be5288ca2 100644 (file)
--- a/primerdesigncommand.cpp
+++ b/primerdesigncommand.cpp
@@ -1088,7 +1088,7 @@ map<string, int> PrimerDesignCommand::readCount(unsigned long int& numSeqs){
         map<string, int> nameMap;
         
         CountTable ct;
-        ct.readTable(countfile, false);
+        ct.readTable(countfile, false, false);
         vector<string> namesOfSeqs = ct.getNamesOfSeqs();
         numSeqs = ct.getNumUniqueSeqs();
         

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 64f9ab6822301310e975e6bbe58736e953eed4f2..9eefa43c9f303249c812d27a1ccbc481dc6b7fcf 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -377,7 +377,7 @@ int RemoveGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
             
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 66bbc1779bc16055076d6b1b814233f69e077d6d..01f45ca97329fbbe383c2157f12880ca05671a10 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -665,7 +665,7 @@ int RemoveLineageCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName, true);
+            ct.readTable(outputFileName, true, false);
             ct.printTable(outputFileName);
         }
                
@@ -705,7 +705,7 @@ int RemoveLineageCommand::readConsList(){
             }
             otuLabel += sbinNumber;
             
-            if (names.count(otuLabel) == 0) {
+            if (names.count(m->getSimpleLabel(otuLabel)) == 0) {
                 newList.push_back(list->get(i));
             }else { removedCount++; }
         }
@@ -843,7 +843,7 @@ int RemoveLineageCommand::readShared(){
             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
             
             //is this otu on the list
-            if (names.count(m->currentBinLabels[i]) == 0) {
+            if (names.count(m->getSimpleLabel(m->currentBinLabels[i])) == 0) {
                 wroteSomething = true;
                 newLabels.push_back(m->currentBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
@@ -1242,7 +1242,7 @@ int RemoveLineageCommand::readConsTax(){
                                                //wroteSomething = true;
                                                //out << name << '\t' << tax << endl;
                                        }else{ //this sequence contains the taxon the user wants to remove
-                                               names.insert(otuLabel);
+                                               names.insert(m->getSimpleLabel(otuLabel));
                                                remove=true; break;
                                        }
                                        
@@ -1256,7 +1256,7 @@ int RemoveLineageCommand::readConsTax(){
                                                        //wroteSomething = true;
                                                        //out << name << '\t' << tax << endl;
                                                }else{ //this sequence contains the taxon the user wants to remove
-                                                       names.insert(otuLabel);
+                                                       names.insert(m->getSimpleLabel(otuLabel));
                                                        remove=true; break;
                                                }
                                        }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
@@ -1309,7 +1309,7 @@ int RemoveLineageCommand::readConsTax(){
                                                        
                                                        //passed the test so remove you
                                                        if (remove) {
-                                                               names.insert(otuLabel);
+                                                               names.insert(m->getSimpleLabel(otuLabel));
                                                                remove=true; break;
                                                        }else {
                                                                //wroteSomething = true;

diff --git a/removeotulabelscommand.cpp b/removeotulabelscommand.cpp
index fa98b86dde528f0190129f9b3939148e6d72f9a2..161c4bfb3553d52ceac6fd89b033152cf9fa8e43 100644 (file)
--- a/removeotulabelscommand.cpp
+++ b/removeotulabelscommand.cpp
@@ -234,6 +234,10 @@ int RemoveOtuLabelsCommand::execute(){
         
         //get labels you want to keep
                labels = m->readAccnos(accnosfile);
+        //simplfy labels
+        set<string> newLabels;
+        for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {  newLabels.insert(m->getSimpleLabel(*it)); }
+        labels = newLabels;
         
         if (m->debug) { m->mothurOut("[DEBUG]: numlabels = " + toString(labels.size()) + "\n"); }
                
@@ -305,7 +309,7 @@ int RemoveOtuLabelsCommand::readClassifyOtu(){
             
             if (m->debug) { m->mothurOut("[DEBUG]: " + otu + toString(size) + tax + "\n"); }
             
-            if (labels.count(otu) == 0) {
+            if (labels.count(m->getSimpleLabel(otu)) == 0) {
                                wroteSomething = true;
                 out << otu << '\t' << size << '\t' << tax << endl;
             }else {  removedCount++;  }
@@ -357,7 +361,7 @@ int RemoveOtuLabelsCommand::readOtuAssociation(){
             in >> otu1 >> otu2;
             string line = m->getline(in); m->gobble(in);
             
-            if ((labels.count(otu1) == 0) && (labels.count(otu2) == 0)){
+            if ((labels.count(m->getSimpleLabel(otu1)) == 0) && (labels.count(m->getSimpleLabel(otu2)) == 0)){
                                wroteSomething = true;
                 
                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
@@ -410,7 +414,7 @@ int RemoveOtuLabelsCommand::readCorrAxes(){
             in >> otu;
             string line = m->getline(in); m->gobble(in);
             
-            if (labels.count(otu) == 0) {
+            if (labels.count(m->getSimpleLabel(otu)) == 0) {
                                wroteSomething = true;
                 
                 out << otu << '\t' << line << endl;
@@ -458,7 +462,7 @@ int RemoveOtuLabelsCommand::readShared(){
             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
             
             //is this otu on the list
-            if (labels.count(m->currentBinLabels[i]) == 0) {
+            if (labels.count(m->getSimpleLabel(m->currentBinLabels[i])) == 0) {
                 wroteSomething = true;
                 newLabels.push_back(m->currentBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
@@ -529,7 +533,7 @@ int RemoveOtuLabelsCommand::readList(){
             }
             otuLabel += sbinNumber; 
             
-            if (labels.count(otuLabel) == 0) {
+            if (labels.count(m->getSimpleLabel(otuLabel)) == 0) {
                 newList.push_back(list->get(i));
             }else { removedCount++; }
         }

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index a551681fb6721e4b3670fe912e1b6bfe909dd388..2eb5f63da369828e4e67e0f0b262b1e786b75a88 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -411,7 +411,7 @@ int RemoveRareCommand::processList(){
                        util.setGroups(Groups, namesGroups);
                        m->openOutputFile(outputGroupFileName, outGroup);
                }else if (countfile != "") {
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (ct.hasGroupInfo()) {
                 vector<string> namesGroups = ct.getNamesOfGroups();
                 SharedUtil util;

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index b1bc4fd508576c04126206b4e178798c088cb91d..fa7e6dda2a853d6a0234c1dc92be3bad258118d1 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -557,7 +557,7 @@ int RemoveSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName, true);
+            ct.readTable(outputFileName, true, false);
             ct.printTable(outputFileName);
         }
 

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index e40c41218f5a599d894e0b2cb52f54406635f9ee..a56b0ebb73d1f6188ecd09430e70ed0128abaf31 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -14,7 +14,7 @@
 vector<string> ScreenSeqsCommand::setParameters(){     
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
-        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,true,true); parameters.push_back(pcontigsreport);
+        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,false,true); parameters.push_back(pcontigsreport);
         CommandParameter palignreport("alignreport", "InputTypes", "", "", "report", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
         CommandParameter psummary("summary", "InputTypes", "", "", "report", "none", "none","summary",false,false); parameters.push_back(psummary);
         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
@@ -683,7 +683,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
             getSummary(positions); 
@@ -714,7 +714,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
             getSummaryReport();
@@ -1019,7 +1019,7 @@ int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
                        if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
                        getSummary(positions); 
@@ -2205,7 +2205,7 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile, true);
+            ct.readTable(goodCountFile, true, false);
             ct.printTable(goodCountFile);
         }
                

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 3354665852ce1b5a95b9ecc7cc673d5083b25d8b..fee74a719ce9c4d3a988a0a30647f2f1368ca8f9 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -200,7 +200,7 @@ int AlignCheckCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }
                

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5879241372dd3b60b34683683a0c1edbcbd64d57..41ddf35a7705264445749caf8868d80049ae61ac 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -358,7 +358,7 @@ int SeqErrorCommand::execute(){
                if(namesFileName != "")     {   weights = getWeights();         }
         else if (countfile != "")   {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             weights = ct.getNameMap();
         }
                

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 0e3b70c1db3824084a51fb0db1c88630285878c2..e941b3a9a2ff500dd07e221712757a8b899526d2 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -203,7 +203,7 @@ int SeqSummaryCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }
                

diff --git a/sequencecountparser.cpp b/sequencecountparser.cpp
index 37eb4e7f5256617bd3917428616a897ee14706e4..5349da09ff719a5ac07a85ecb4015c44d41121ee 100644 (file)
--- a/sequencecountparser.cpp
+++ b/sequencecountparser.cpp
@@ -16,7 +16,7 @@ SequenceCountParser::SequenceCountParser(string countfile, string fastafile) {
                
                //read count file
                CountTable countTable;
-               countTable.readTable(countfile, true);
+               countTable.readTable(countfile, true, false);
                
                //initialize maps
                namesOfGroups = countTable.getNamesOfGroups();

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 8d5d89c3a96843b5fd1c8aafa112f25c3b216e1f..1e078b3f82080ec554462a12f2564b5a5f470d04 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -766,7 +766,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
             m->setAllGroups(allGroups);
         }else{
             countTable = new CountTable();
-            countTable->readTable(countfile, true);
+            countTable->readTable(countfile, true, false);
         }
         
         if (m->control_pressed) { return 0; }

diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 0ee2f795cea302bd98a31285b278479f13ef17f3..2ce250ba908b4b45fa200b845275af22c3ca3be6 100644 (file)
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -32,7 +32,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB
             groupmap->readMap(); 
         }else {
             countTable = new CountTable();
-            countTable->readTable(m->getCountTableFile(), true);
+            countTable->readTable(m->getCountTableFile(), true, false);
         }
 
                int hold;

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index c405e38060cec0db4b610c2e6c9e24a8810d7aed..7fa99f1b04fd2632bf4d6e59ab08db6d1a38c1d9 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1414,7 +1414,8 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
         
         RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
         
-        Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); 
+        float adjust = -1.0;
+        Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest", adjust);
         string tag = cluster->getTag();
         
         double clusterCutoff = cutoff;

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 580493b60a1e4d449a71b8689635e8ced4dea397..0fff42804cf702b0ba74cbbe245b51a0f91c1bff 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -212,7 +212,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
             }
             
             if ((namefile != "") && (countfile != "")) {

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 5c0103708bc99daaf6d0046435882c72a6c631a7..88292bd2694e4dd044bcacc8c38d5c2c34a7d204 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -320,7 +320,7 @@ int SplitGroupCommand::runCount(){
        try {
         
         CountTable ct;
-        ct.readTable(countfile, true);
+        ct.readTable(countfile, true, false);
         if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, cannot split by group.\n"); m->control_pressed = true; }
         
         if (m->control_pressed) { return 0; }

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 9e27fae51eca7ef564892e112d8a17d24eba6089..6c0d1bcbe71a3c3c2a7fccda9695f7aef6aec25b 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -273,7 +273,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
             }
             
             if ((namefile != "") && (countfile != "")) {

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index e1e626ea273a650840dd849442e43762e9a100cf..56a6fcb099818b4590e80bff0639193b9bf65767 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -196,7 +196,7 @@ int SummaryQualCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
                else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }
         

diff --git a/summarytaxcommand.cpp b/summarytaxcommand.cpp
index e244863c65de54c6c5133d3901a1dc1bc973c6ac..097983e93f24c853cc4d720eb2b1b82a3261b79c 100644 (file)
--- a/summarytaxcommand.cpp
+++ b/summarytaxcommand.cpp
@@ -223,7 +223,7 @@ int SummaryTaxCommand::execute(){
             groupMap->readMap();
         }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile, true);
+            ct->readTable(countfile, true, false);
         }
                
         PhyloSummary* taxaSum;

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 80698f1b4b0317719421dbe9c4af3c0583bd9d97..753b5cbe3cf7f67ed623bb8d866b848c6c96e5be 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -458,7 +458,7 @@ int TreeGroupCommand::execute(){
                 readMatrix->read(nameMap);
             }else if (countfile != "") {
                 ct = new CountTable();
-                ct->readTable(countfile, true);
+                ct->readTable(countfile, true, false);
                 readMatrix->read(ct);
             }else {
                 readMatrix->read(nameMap);

diff --git a/treereader.cpp b/treereader.cpp
index 8427b562501086e8a9bf13b6e036474348412b0e..249b2b3c3c187c5a62bf5c1cf7aaab88a44bcff2 100644 (file)
--- a/treereader.cpp
+++ b/treereader.cpp
@@ -15,7 +15,7 @@ TreeReader::TreeReader(string tf, string cf) : treefile(tf), countfile(cf)  {
     try {
         m = MothurOut::getInstance();
         ct = new CountTable();
-        ct->readTable(cf, true);
+        ct->readTable(cf, true, false);
         
         //if no groupinfo in count file we need to add it
         if (!ct->hasGroupInfo()) {

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 4128142448b8412314dc2b1d8ce057c6e8527519..0d55d7c4a0b043f811d2d6b9f61ef159952ea1f9 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -422,7 +422,7 @@ int TrimSeqsCommand::execute(){
                
                if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             nameCount = ct.getNameMap();
                        outputNames.push_back(trimCountFile);
                        outputNames.push_back(scrapCountFile);
@@ -540,7 +540,7 @@ int TrimSeqsCommand::execute(){
             
             if (countfile != "") { //create countfile with group info included
                 CountTable* ct = new CountTable();
-                ct->readTable(trimCountFile, true);
+                ct->readTable(trimCountFile, true, false);
                 map<string, int> justTrimmedNames = ct->getNameMap();
                 delete ct;