working on current change

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 95604fc4ff4f738dc780de23b01ab65d4f473fe7..5da0ee8d0f091b8ce07acdedd48d2069e53ec1e9 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -224,6 +224,8 @@ AlignCommand::AlignCommand(string option)  {
                                                        //erase from file list
                                                        candidateFileNames.erase(candidateFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(candidateFileNames[i]);
                                                }
                                        }
                                }

diff --git a/amovacommand.cpp b/amovacommand.cpp
index ad5823b15e108396ee1b0e0977167c8e4f1fbb22..141673375fb8bb1a37e67980df9708fe6d2da126 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -122,17 +122,17 @@ AmovaCommand::AmovaCommand(string option) {
                                phylipFileName = m->getPhylipFile(); 
                                if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setPhylipFile(phylipFileName); }
                        
                        //check for required parameters
                        designFileName = validParameter.validFile(parameters, "design", true);
-                       if (designFileName == "not open") { abort = true; }
+                       if (designFileName == "not open") { designFileName = ""; abort = true; }
                        else if (designFileName == "not found") {
                                //if there is a current design file, use it
                                designFileName = m->getDesignFile(); 
                                if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }                           
-                       }       
+                       }else { m->setDesignFile(designFileName); }     
 
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 6f9e53839200ce251b0f607f0b776e075a4dffd4..c5cb4d60c751d6614b82cd961c29d9e645fcbaa8 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -124,17 +124,17 @@ AnosimCommand::AnosimCommand(string option) {
                                if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
                                
-                       }       
+                       }else { m->setPhylipFile(phylipFileName); }     
                        
                        //check for required parameters
                        designFileName = validParameter.validFile(parameters, "design", true);
-                       if (designFileName == "not open") { abort = true; }
+                       if (designFileName == "not open") { designFileName = ""; abort = true; }
                        else if (designFileName == "not found") {
                                //if there is a current design file, use it
                                designFileName = m->getDesignFile(); 
                                if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }                                                           
-                       }       
+                       }else { m->setDesignFile(designFileName); }     
                        
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index c4ef741f80c22bc784df4e6916f4a214fb2feacd..8e8ec2bc51362d8b8876d6e3cbb10ef9ff5e167e 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -138,6 +138,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") {                  
@@ -146,6 +147,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { listfile = ""; abort = true; }       
+                       else { m->setListFile(listfile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -167,10 +169,12 @@ BinSeqCommand::BinSeqCommand(string option) {
                        namesfile = validParameter.validFile(parameters, "name", true);
                        if (namesfile == "not open") { abort = true; }  
                        else if (namesfile == "not found") { namesfile = ""; }
+                       else {  m->setNameFile(namesfile); }
 
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                }
        }

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index f63f2f496d05ac403cc7584db343067771e5ebb7..478821ec861e7b537e6f15b8c44bdab86a8d2c9f 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -113,8 +113,13 @@ BootSharedCommand::BootSharedCommand(string option) {
                        }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
-                       if (sharedfile == "not found") { m->mothurOut("shared is a required parameter.");  m->mothurOutEndLine(); sharedfile = ""; abort = true; }
+                       if (sharedfile == "not found") { 
+                               sharedfile = m->getSharedFile(); 
+                               if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current shared file and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }       
                        else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+                       else { m->setSharedFile(sharedfile); }
                
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 29f2220dcc512d7a5db58bfee3c3767418ff7aa7..fd51664a21ffa6373ebf9fd46d0fe5f586eb288c 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -119,10 +119,12 @@ CatchAllCommand::CatchAllCommand(string option)  {
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }
                        else if (sabundfile == "not found") { sabundfile = "";  }
+                       else { m->setSabundFile(sabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }
                        else if (sharedfile == "not found") { sharedfile = "";   }
+                       else { m->setSharedFile(sharedfile); }
                        
                        string label = validParameter.validFile(parameters, "label", false);                    
                        if (label == "not found") { label = ""; }

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 7a62d5bb447c3c20d155b15a5edf5f6b71b19b37..0031acb15b750823bb8cb3afed79d79f9a07d399 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -171,6 +171,8 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index df4e67db118462e1115857331c7adcc4551a272c..bc96e0530993e63cf099381a1ccd8829f9cc7714 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -185,6 +185,8 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index d82a84a1b86ab5643e0416d8d73091ce16b29e23..5b249d7ff6892a53ce0493c3fa5319468681a8bd 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -183,6 +183,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }
@@ -262,6 +264,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                                        //erase from file list
                                                        nameFileNames.erase(nameFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setNameFile(nameFileNames[i]);
                                                }
                                        }
                                }

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 94c2bf5c1a392a8f12398db3806a503cd099f3bc..482bf7b5c2a67e57aaefc4cf4fc93c76a2b78611 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -205,6 +205,8 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index fed36135db3116567dea8b323f9ec0803cd29da8..636e17536a024f04476fc04ce431bb6524e29839 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -205,6 +205,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }
@@ -279,6 +281,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                                        //erase from file list
                                                        nameFileNames.erase(nameFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setNameFile(nameFileNames[i]);
                                                }
                                        }
                                }

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 33b48bd184ba95f1db5e1db2117a32a64254c664..375964c306651e93c07966d464b02cf24acb187c 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -209,6 +209,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }
@@ -283,6 +285,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                                                        //erase from file list
                                                        nameFileNames.erase(nameFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setNameFile(nameFileNames[i]);
                                                }
                                        }
                                }

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 0e500d4982d372c95436b99e1ead81cb3c02a9c5..fc4327f210d04241b5c1e7a6056759525998c738 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -115,7 +115,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index eaf8cc206cebfe6eb1a60b40ff7042ede86ef6bd..d065b3a37c5ac41f9c6c3b59eb9ca3832f8697a9 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -166,6 +166,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                else {  m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not found") {  //if there is a current list file, use it
@@ -174,6 +175,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (taxfile == "not open") { abort = true; }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        refTaxonomy = validParameter.validFile(parameters, "reftaxonomy", true);
                        if (refTaxonomy == "not found") { refTaxonomy = ""; m->mothurOut("reftaxonomy is not required, but if given will keep the rankIDs in the summary file static."); m->mothurOutEndLine(); }
@@ -182,10 +184,12 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0d5ef61bbf939ce103d38f2ef36473abb01d3efa..72ca1d00fed7815ef68a8f1dc321c8c911eaeff0 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -239,6 +239,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                        
@@ -319,6 +321,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                        //erase from file list
                                                        namefileNames.erase(namefileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setNameFile(namefileNames[i]);
                                                }
                                        }
                                }
@@ -375,6 +379,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                                //erase from file list
                                                groupfileNames.erase(groupfileNames.begin()+i);
                                                i--;
+                                       }else {
+                                               m->setGroupFile(groupfileNames[i]);
                                        }
                                }
                        }

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 04dbc79aa15d3c4b6913a2e8131283b849dd90b9..29a5d725ff121b47b5c8f3132f54776f3e8a34ff 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -155,12 +155,12 @@ ClearcutCommand::ClearcutCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { fastafile = ""; abort = true; }
                        else if (fastafile == "not found") { fastafile = ""; }  
-                       else { inputFile = fastafile;  }
+                       else { inputFile = fastafile;  m->setFastaFile(fastafile); }
                        
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { phylipfile = ""; abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }
-                       else { inputFile = phylipfile;  }
+                       else { inputFile = phylipfile;  m->setPhylipFile(phylipfile); }
                                
                        if ((phylipfile == "") && (fastafile == "")) {  
                                //is there are current file available for either of these?

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 16348c8d324a962ca336c82a2ad303f156cde9e3..fd1f841dacab7ea017f15400766f384f10789cf3 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -135,16 +135,17 @@ ClusterCommand::ClusterCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { phylipfile = ""; abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  distfile = phylipfile;  format = "phylip";      }
+                       else {  distfile = phylipfile;  format = "phylip";      m->setPhylipFile(phylipfile); }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { columnfile = ""; abort = true; }        
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  distfile = columnfile; format = "column";       }
+                       else {  distfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        if ((phylipfile == "") && (columnfile == "")) { 
                                //is there are current file available for either of these?

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 9f51a8cfd07d83887010f2612831f2eb72e323a7..3f629dc09af39d7c9785a18687d9aecb8bee5f58 100644 (file)
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -132,13 +132,14 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
                                        m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine(); 
                                        abort = true; 
                                }       
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
 
                
                        //check for optional parameter and set defaults
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 2e37e7caedc35b67609e7c27e263261abd6f88f9..71ce5eed4e6e21c63210be0e34eb9a6f72dac59b 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -138,6 +138,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { fastafile = ""; abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
@@ -147,7 +148,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
                        else if (namefile == "not open") { abort = true; }      
-                       else {  readNameFile();  }
+                       else {  readNameFile(); m->setNameFile(namefile); }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found"){       temp = "0";                             }

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index bdc8075342de2f484238c4810ee4da5babb0356c..9999eb0fb81e461e9f168c2c81b7531a3774607a 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -183,25 +183,27 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  distfile = phylipfile;  format = "phylip";      }
+                       else {  distfile = phylipfile;  format = "phylip";      m->setPhylipFile(phylipfile); }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  distfile = columnfile; format = "column";       }
+                       else {  distfile = columnfile; format = "column";       m->setColumnFile(columnfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
-                       else if (namefile == "not found") { namefile = ""; }
+                       else if (namefile == "not found") { namefile = "";  }
+                       else { m->setNameFile(namefile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }  
                        else if (fastafile == "not found") { fastafile = ""; }
-                       else { distfile = fastafile;  splitmethod = "fasta";  }
+                       else { distfile = fastafile;  splitmethod = "fasta";  m->setFastaFile(fastafile); }
                        
                        taxFile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxFile == "not open") { abort = true; }    
                        else if (taxFile == "not found") { taxFile = ""; }
+                       else {  m->setTaxonomyFile(taxFile); }
                        
                        if ((phylipfile == "") && (columnfile == "") && (fastafile == "")) { 
                                //is there are current file available for either of these?

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 7b8364b9b25d07e457508dbe5fe0153a4cc3a27f..5bd9fd75c474aeafdf632d8800b9c184916ccc83 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -211,22 +211,22 @@ CollectCommand::CollectCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
-                       else {  format = "sabund"; inputfile = sabundfile; }
+                       else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
-                       else {  format = "rabund"; inputfile = rabundfile; }
+                       else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "sharedfile"; inputfile = sharedfile; }
+                       else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index d72dd7139735f16b8fcd8b02aa39058a5f4a3110..202883e201561f8851d77c5e6569df33280143c3 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -238,7 +238,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 9d817a212cc2ad2ee3a330b982d96cffe251bdce..9172819bd78f39dfee97b94c4c4b24c79bd080ae 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -139,15 +139,17 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
-                       else if (namefile == "not found") { namefile = ""; }    
+                       else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = "";  }   
+                       else { m->setListFile(listfile); }
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 791ec4978fd82d2fb692723fc105dfd5b6c041f0..cd188b8a921a33aaac255852b5ab22d6008f605e 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -140,12 +140,12 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; }
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else { inputFileName = sharedfile; }
+                       else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { abort = true; }
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else { inputFileName = relabundfile; }
+                       else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        metadatafile = validParameter.validFile(parameters, "metadata", true);
                        if (metadatafile == "not open") { abort = true; }

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index a4464692607df14d08384f3cfdf112a4e18debb8..a9bffc6eca25d3ad78ce7b01d96e196ba6308bfb 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -117,11 +117,12 @@ CountSeqsCommand::CountSeqsCommand(string option)  {
                                namefile = m->getNameFile(); 
                                if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all"; }

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 6f7657f3da640514fb5125527b17cfd779a5cad0..5888feedcf5f6d6c01438d5acecc5e65ba897c54 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -116,7 +116,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                                inFastaName = m->getFastaFile(); 
                                if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(inFastaName); } 
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -127,6 +127,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option)  {
                        oldNameMapFName = validParameter.validFile(parameters, "name", true);
                        if (oldNameMapFName == "not open") { abort = true; }
                        else if (oldNameMapFName == "not found"){       oldNameMapFName = "";   }
+                       else { m->setNameFile(oldNameMapFName); }
                }
 
        }

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 940672c1bef7f6ab2004a9b374011cd1f8420e85..f590d8b3baaf67091f59a741a87a23e09c8873b0 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -156,7 +156,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
-                                               }
+                                               }else { m->setFastaFile(fastaFileNames[i]); }
                                        }
                                }
                                

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index aed53037c152ded2b13e00b1dfbf30ff739d341d..2ba6f3d2363d86cc49108e2cb3db71fddd1ae879 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -114,7 +114,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                                fastaFile = m->getFastaFile(); 
                                if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastaFile); }   
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -128,7 +128,7 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option)  {
                                nameFile = m->getNameFile(); 
                                if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setNameFile(nameFile); }
                }
 
        }

diff --git a/deuniquetreecommand.cpp b/deuniquetreecommand.cpp
index 7f33ad65e13a44ed77dc2fab585cbded550475ad..f39a182ed863893c66f9b22a25c4c6765c04d165 100644 (file)
--- a/deuniquetreecommand.cpp
+++ b/deuniquetreecommand.cpp
@@ -116,7 +116,7 @@ DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
                                treefile = m->getTreeFile(); 
                                if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }                                                               
-                       }       
+                       }else { m->setTreeFile(treefile); }     
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
@@ -124,7 +124,7 @@ DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
                                namefile = m->getNameFile(); 
                                if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }                                                               
-                       }
+                       }else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(treefile);       }
                }

diff --git a/distancecommand.cpp b/distancecommand.cpp
index b73cd7c751176c386a95931b0887c6790f046583..4bdeaaeb5d9b388ac56fc2553f57dc10c0d598d9 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -152,6 +152,7 @@ DistanceCommand::DistanceCommand(string option) {
                                m->openInputFile(fastafile, inFASTA);
                                alignDB = SequenceDB(inFASTA); 
                                inFASTA.close();
+                               m->setFastaFile(fastafile);
                        }
                        
                        oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
@@ -161,6 +162,7 @@ DistanceCommand::DistanceCommand(string option) {
                        column = validParameter.validFile(parameters, "column", true);
                        if (column == "not found") { column = ""; }
                        else if (column == "not open") { abort = true; }        
+                       else { m->setColumnFile(column); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 167dd3ce835f071e70c187ba9507fb2931a2e548..1204663a52c73a3a98af34c42c4a93ec044e7200 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -190,6 +190,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                                                }else{  
                                                        string simpleName = m->getSimpleName(fastafileNames[i]);
                                                        filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+                                                       m->setFastaFile(fastafileNames[i]);
                                                }
                                                in.close();
                                        }

diff --git a/getcommandinfocommand.cpp b/getcommandinfocommand.cpp
index 283cd405eed10282df0ded886c616cb003b7847a..52559b3c064f6437affcbdc5dcd3d0b174089b42 100644 (file)
--- a/getcommandinfocommand.cpp
+++ b/getcommandinfocommand.cpp
@@ -113,6 +113,14 @@ int GetCommandInfoCommand::execute(){
                                }
                                out << "help=" << newHelpString << endl;
                                
+                               //remove /n from citation string since gui reads line by line
+                               string mycitationString = thisCommand->getCitation();
+                               string newCitationString = "";
+                               for (int i = 0; i < mycitationString.length(); i++) { 
+                                       if (mycitationString[i] != '\n') { newCitationString += mycitationString[i]; }
+                               }
+                               out << "citation=" << newCitationString << endl;
+                               
                                //outputTypes - makes something like outputTypes=fasta-name-qfile
                                map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
                                map<string, vector<string> >::iterator itTypes;

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index b39fb645154f97252e7d928c9862cde01553ab6b..1190f49d41036c3d3034d8555544725014ee49f0 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -103,7 +103,7 @@ GetgroupCommand::GetgroupCommand(string option)  {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 

diff --git a/qualityscores.cpp b/qualityscores.cpp
index c9c65042843bffddf5c6d3d7acca4ab38754ac5e..520d0bb56eae9c66a936311ca71aa5330bf29aa1 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,20 +44,22 @@ QualityScores::QualityScores(ifstream& qFile){
                else{
                        seqName = seqName.substr(1);
                }
+               
                string qScoreString = m->getline(qFile);
                while(qFile.peek() != '>' && qFile.peek() != EOF){
-                       qScoreString += ' ' + m->getline(qFile);
+                       qScoreString +=  ' ' + m->getline(qFile);
                }
                
                istringstream qScoreStringStream(qScoreString);
                int count = 0;
                while(!qScoreStringStream.eof()){
                        if (m->control_pressed) { break; }
-                       qScoreStringStream >> score;
+                       qScoreStringStream >> score;  m->gobble(qScoreStringStream);
+
                        qScores.push_back(score);
                        count++;
                }
-               qScores.pop_back();
+               //qScores.pop_back();
                
 //             string scores = "";
 //             
@@ -102,7 +104,7 @@ QualityScores::QualityScores(ifstream& qFile){
 //             qScores.pop_back();
 
                seqLength = qScores.size();
-               
+               //cout << "seqlenght = " <<     seqLength << '\t' << count << endl;
                
        }
        catch(exception& e) {
@@ -151,7 +153,10 @@ void QualityScores::printQScores(ofstream& qFile){
 void QualityScores::trimQScores(int start, int end){
        try {
                vector<int> hold;
-                       
+               
+
+               //cout << seqName << '\t' << start << '\t' << end << '\t' << qScores.size() << endl;
+               //for (int i = 0; i < qScores.size(); i++) { cout << qScores[i] << end; }
                if(end == -1){          
                        hold = vector<int>(qScores.begin()+start, qScores.end());
                        qScores = hold;         

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5efb1ce78c659577c520defc124c48e60b848dc8..6ce944ef21189948519310e372907580d8ac1400 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -24,7 +24,6 @@ vector<string> SeqErrorCommand::setParameters(){
                CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
                CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pfilter("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfilter);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -204,9 +203,6 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        temp = validParameter.validFile(parameters, "ignorechimeras", false);   if (temp == "not found") { temp = "T"; }
                        ignoreChimeras = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "filter", false);   if (temp == "not found") { temp = "T"; }
-                       filter = m->isTrue(temp);  
-                       
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        convert(temp, processors); 
@@ -230,25 +226,6 @@ int SeqErrorCommand::execute(){
                maxLength = 2000;
                totalBases = 0;
                totalMatches = 0;
-
-               //run vertical filter on query and reference files.
-               if (filter) {
-                       string inputString = "fasta=" + queryFileName + "-" + referenceFileName;
-                       m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
-                       m->mothurOut("Running command: filter.seqs(" + inputString + ") to improve processing time."); m->mothurOutEndLine(); 
-                       
-                       Command* filterCommand = new FilterSeqsCommand(inputString);
-                       filterCommand->execute();
-                       
-                       map<string, vector<string> > filenames = filterCommand->getOutputFiles();
-                       
-                       delete filterCommand;
-                       
-                       m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
-                       
-                       queryFileName = filenames["fasta"][0];
-                       referenceFileName = filenames["fasta"][1];
-               }
                
                string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
                outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index cb715ce05bc1edad8f2790cd78b67a356eafd7c3..3fdd66930a3078114b28d6f2f126de3da70f7da5 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -84,7 +84,7 @@ private:
 
        string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
        double threshold;
-       bool ignoreChimeras, filter;
+       bool ignoreChimeras;
        int numRefs, processors;
        int maxLength, totalBases, totalMatches;
        //ofstream errorSummaryFile, errorSeqFile;

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 765dc78e68a2ac12034853c008055b87d58abc03..77af9e647be61a96ba83bf4929156aa7554633e8 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -283,7 +283,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        }
                        
                        if ((sfftxtFilename == "") && (filenames.size() == 0)) {  
-                               //if there is a current fasta file, use it
+                               //if there is a current sff file, use it
                                string filename = m->getSFFFile(); 
                                if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
@@ -901,13 +901,20 @@ int SffInfoCommand::parseSffTxt() {
                //output file names
                ofstream outFasta, outQual, outFlow;
                string outFastaFileName, outQualFileName;
-               string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "flow";
+               string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
+               if (fileRoot.length() > 0) {
+                       //rip off last .
+                       fileRoot = fileRoot.substr(0, fileRoot.length()-1);
+                       fileRoot = m->getRootName(fileRoot);
+               }
+               
+               string outFlowFileName = outputDir + fileRoot + "flow";
                if (trim) {
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "fasta";
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "qual";
+                       outFastaFileName = outputDir + fileRoot + "fasta";
+                       outQualFileName = outputDir + fileRoot + "qual";
                }else{
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.fasta";
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.qual";
+                       outFastaFileName = outputDir + fileRoot + "raw.fasta";
+                       outQualFileName = outputDir + fileRoot + "raw.qual";
                }
                
                if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 5ace75e3a2d152f27e6483aab2ad4a697f952c79..ab9674f6836cafb373af0b89e43f4f7519476ae4 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -96,7 +96,7 @@ int SystemCommand::execute(){
                
                ifstream in;
                string filename = "./commandScreen.output";
-               m->openInputFile(filename, in);
+               m->openInputFile(filename, in, "no error");
                
                string output = "";
                while(char c = in.get()){

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 4d6b45da96664677f61908874d79b8d847f0e74c..6410c8f4cb39a32efad1f8a18e4876cec6080b9f 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -559,7 +559,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);
                        }
-
+                       //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
                                
@@ -1316,7 +1316,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group
                        if (alignment != NULL) {  delete alignment;  }
                        
                }
-               
+       
                return success;
                
        }