a few minor things - pds

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 25e6296c919929232721518d587ba9da02c421c4..e6a9c0cc7d46bb0f07a39b0f0ada2936bd0ff287 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -277,12 +277,12 @@
                375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
                377326630FAF16E0007ABB8B /* concensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = concensuscommand.cpp; sourceTree = SOURCE_ROOT; };
                377326640FAF16E0007ABB8B /* concensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = concensuscommand.h; sourceTree = SOURCE_ROOT; };
-               378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = "<group>"; };
-               378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = "<group>"; };
-               378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = "<group>"; };
-               378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = "<group>"; };
-               3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = "<group>"; };
-               3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = "<group>"; };
+               378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; };
+               378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; };
+               378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
+               378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; };
+               3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; };
+               3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; };
                378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = SOURCE_ROOT; };
                378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = SOURCE_ROOT; };
                378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = SOURCE_ROOT; };
@@ -477,8 +477,8 @@
                7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; };
                7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; };
                7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; };
-               7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = "<group>"; };
-               7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = "<group>"; };
+               7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = SOURCE_ROOT; };
+               7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = SOURCE_ROOT; };
                7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; };
                7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; };
                7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; };

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 2811f1fd7e6d404c557dff149cce8860f80f99f0..e628908e07f7994a117ff70585fc6c0e54d2377e 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -34,14 +34,14 @@
 
 AlignCommand::AlignCommand(string option){
        try {
-//             globaldata = GlobalData::getInstance();
+               //              globaldata = GlobalData::getInstance();
                abort = false;
                
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
                else {
-
+                       
                        //valid paramters for this command
                        string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
@@ -50,7 +50,7 @@ AlignCommand::AlignCommand(string option){
                        map<string, string> parameters = parser.getParameters(); 
                        
                        ValidParameters validParameter;
-               
+                       
                        //check to make sure all parameters are valid for command
                        for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
@@ -60,7 +60,7 @@ AlignCommand::AlignCommand(string option){
                        templateFileName = validParameter.validFile(parameters, "template", true);
                        if (templateFileName == "not found") { cout << "template is a required parameter for the align.seqs command." << endl; abort = true; }
                        else if (templateFileName == "not open") { abort = true; }      
-               
+                       
                        candidateFileName = validParameter.validFile(parameters, "candidate", true);
                        if (candidateFileName == "not found") { cout << "candidate is a required parameter for the align.seqs command." << endl; abort = true; }
                        else if (candidateFileName == "not open") { abort = true; }     
@@ -70,27 +70,27 @@ AlignCommand::AlignCommand(string option){
                        string temp;
                        temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
                        convert(temp, kmerSize); 
-               
+                       
                        temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
                        convert(temp, match);  
-
+                       
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
                        convert(temp, misMatch);  
-
-                       temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-1.0";                  }
+                       
+                       temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
                        convert(temp, gapOpen);  
-
-                       temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-2.0";                  }
+                       
+                       temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
                        convert(temp, gapExtend); 
-               
+                       
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
                        convert(temp, processors); 
-
+                       
                        search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
                        
                        align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
                }
-
+               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function AlignCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -114,8 +114,8 @@ AlignCommand::~AlignCommand(){
 void AlignCommand::help(){
        try {
                cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
-               cout << "The align.seqs command parameters are fasta, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.  " << "\n";
-               cout << "The fasta and candidate parameters are required." << "\n";
+               cout << "The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.  " << "\n";
+               cout << "The template and candidate parameters are required." << "\n";
                cout << "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer." << "\n";
                cout << "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman." << "\n";
                cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 7." << "\n";
@@ -124,9 +124,9 @@ void AlignCommand::help(){
                cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n";
                cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -2.0." << "\n";
                cout << "The align.seqs command should be in the following format: " << "\n";
-               cout << "align.seqs(fasta=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
-               cout << "Example align.seqs(candidate=candidate.fasta, fasta=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
-               cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
+               cout << "align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
+               cout << "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -144,10 +144,10 @@ void AlignCommand::help(){
 int AlignCommand::execute(){
        try {
                if (abort == true) {    return 0;       }
-       
+               
                srand( (unsigned)time( NULL ) );  //needed to assign names to temporary files
                
-
+               
                if(search == "kmer")                    {       templateDB = new KmerDB(templateFileName, kmerSize);    }
                else if(search == "suffix")             {       templateDB = new SuffixDB(templateFileName);                    }
                else if(search == "blast")              {       templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch);        }
@@ -155,7 +155,7 @@ int AlignCommand::execute(){
                        cout << search << " is not a valid search option. I will run the command using kmer, ksize=8." << endl; kmerSize = 8;
                        templateDB = new KmerDB(templateFileName, kmerSize);
                }
-       
+               
                if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000);        }
                else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000);                       }
                else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
@@ -184,10 +184,11 @@ int AlignCommand::execute(){
                }
                else{
                        vector<int> positions;
+                       processIDS.resize(0);
                        
                        ifstream inFASTA;
                        openInputFile(candidateFileName, inFASTA);
-
+                       
                        while(!inFASTA.eof()){
                                char c = inFASTA.get();
                                if(c == '>'){   positions.push_back(inFASTA.tellg());   }
@@ -207,20 +208,16 @@ int AlignCommand::execute(){
                                lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                        }
                        createProcesses(alignFileName, reportFileName); 
-
                        
-                       //append and remove temp files
-                       map<int, int>::iterator it = processIDS.begin();
-                       rename((alignFileName + toString(it->second) + ".temp").c_str(), alignFileName.c_str());
-                       rename((reportFileName + toString(it->second) + ".temp").c_str(), alignFileName.c_str());
-                       it++;
+                       rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
+                       rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
                        
-                       for (; it != processIDS.end(); it++) {
-                               appendAlignFiles((alignFileName + toString(it->second) + ".temp"), alignFileName);
-                               remove((alignFileName + toString(it->second) + ".temp").c_str());
-
-                               appendReportFiles((reportFileName + toString(it->second) + ".temp"), reportFileName);
-                               remove((reportFileName + toString(it->second) + ".temp").c_str());
+                       for(int i=1;i<processors;i++){
+                               appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+                               remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+                               
+                               appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
+                               remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
                        }
                }
 #else
@@ -233,12 +230,12 @@ int AlignCommand::execute(){
                
                driver(lines[0], alignFileName, reportFileName);
 #endif
-
+               
                cout << "It took " << time(NULL) - start << " secs to align " << numFastaSeqs << " sequences" << endl;
                cout << endl;
-
-
-                               
+               
+               
+               
                return 0;
        }
        catch(exception& e) {
@@ -282,7 +279,10 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                        
                        delete candidateSeq;            
                }
-                       
+               
+               alignmentFile.close();
+               inFASTA.close();
+               
                return 1;
        }
        catch(exception& e) {
@@ -301,14 +301,14 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName)
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 0;
-               processIDS.clear();
+               //              processIDS.resize(0);
                
                //loop through and create all the processes you want
                while (process != processors) {
                        int pid = fork();
-                                               
+                       
                        if (pid > 0) {
-                               processIDS[lines[process]->numSeqs] = pid;  //create map from line number to pid so you can append files in correct order later
+                               processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
                                driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp");
@@ -317,8 +317,8 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName)
                }
                
                //force parent to wait until all the processes are done
-               for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { 
-                       int temp = it->second;
+               for (int i=0;i<processors;i++) { 
+                       int temp = processIDS[i];
                        wait(&temp);
                }
 #endif         
@@ -381,7 +381,7 @@ void AlignCommand::appendReportFiles(string temp, string filename) {
                ifstream input;
                openInputFile(temp, input);
                while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
-
+               
                string line;
                //read input file and write to output file
                while(input.eof() != true) {

diff --git a/aligncommand.h b/aligncommand.h
index 62bf3dc100297c2c3f089257329a750e2301f598..50e9bffb3ba26790d4b0531605d34cf99f173dbe 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -22,19 +22,19 @@ public:
        ~AlignCommand();
        int execute(); 
        void help();    
-
+       
 private:
        struct linePair {
                int start;
                int numSeqs;
                linePair(int i, int j) : start(i), numSeqs(j) {}
        };
-       map<int, int> processIDS;   //end line, processid
+       vector<int> processIDS;   //processid
        vector<linePair*> lines;
-
+       
        Database* templateDB;
        Alignment* alignment;
-
+       
        int driver(linePair*, string, string);
        void createProcesses(string, string);
        void appendAlignFiles(string, string); 
@@ -43,7 +43,7 @@ private:
        string candidateFileName, templateFileName, distanceFileName, search, align;
        float match, misMatch, gapOpen, gapExtend;
        int processors, kmerSize;
-
+       
        bool abort;
 };
 

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 68076d3dee6e47f40292f63f66d859a24931e569..3b0d7984bc1d0be02cb66c9d816f72df94e48f36 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -81,9 +81,9 @@ HeatMapSimCommand::HeatMapSimCommand(string option){
                        }
                        
                        calc = validParameter.validFile(parameters, "calc", false);                     
-                       if (calc == "not found") { calc = "jclass-thetayc";  }
+                       if (calc == "not found") { calc = "jest-thetayc";  }
                        else { 
-                                if (calc == "default")  {  calc = "jclass-thetayc";  }
+                                if (calc == "default")  {  calc = "jest-thetayc";  }
                        }
                        splitAtDash(calc, Estimators);
                        

diff --git a/nastreport.cpp b/nastreport.cpp
index 0f361f1dc1401848e4a39fc15cd3def8a3f37a2d..d7be4dd57c272b69dc0aa09fd35b7d4c2f9d4f0b 100644 (file)
--- a/nastreport.cpp
+++ b/nastreport.cpp
@@ -27,6 +27,12 @@ NastReport::NastReport(string candidateReportFName) {
 
 /******************************************************************************************************************/
 
+NastReport::~NastReport() {
+       candidateReportFile.close();
+}
+
+/******************************************************************************************************************/
+
 void NastReport::print(){
        
        candidateReportFile << queryName << '\t' << queryLength << '\t' << templateName << '\t' << templateLength << '\t';

diff --git a/nastreport.hpp b/nastreport.hpp
index be75efdd92714e673e9921215e89875eeafd0f3e..2be289c2345df9929949ddc725936adb7ee0c1ab 100644 (file)
--- a/nastreport.hpp
+++ b/nastreport.hpp
@@ -19,6 +19,7 @@ class NastReport {
 
 public:
        NastReport(string);
+       ~NastReport();
        void setCandidate(Sequence*);
        void setTemplate(Sequence*);
        void setSearchParameters(string, float);

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 5789fd0665f849822ec8d8c365de3a26e65b77ef..bc375dee4e36de59fa2e8ae66d3516aa41c9339b 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -51,10 +51,10 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;
-                       temp = validParameter.validFile(parameters, "start", false);                    if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
                        convert(temp, startPos); 
                
-                       temp = validParameter.validFile(parameters, "end", false);                              if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
                        convert(temp, endPos);  
 
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
@@ -63,10 +63,10 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
                        convert(temp, maxHomoP);  
 
-                       temp = validParameter.validFile(parameters, "minlength", false);                if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
                        convert(temp, minLength); 
                        
-                       temp = validParameter.validFile(parameters, "maxlength", false);                if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
                        convert(temp, maxLength); 
                }
 

diff --git a/sequence.cpp b/sequence.cpp
index 580f68ae7706ed15a11f9f460e29a56bd441767b..aa1f1c7eae3c0b1cb08105a070a172169ecf320e 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -89,7 +89,7 @@ void Sequence::setName(string seqName) {
 
 void Sequence::setUnaligned(string sequence){
        
-       if(sequence.find_first_of('-') != string::npos) {
+       if(sequence.find_first_of('.') != string::npos || sequence.find_first_of('-') != string::npos) {
                string temp = "";
                for(int j=0;j<sequence.length();j++) {
                        if(isalpha(sequence[j]))        {       temp += sequence[j];    }