working on current change

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index 37e5d404b4c39765ff17be9a087c03183abff391..1ba8aa7bd6d2e8df8fbc513272c7784cafd3bc67 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -164,15 +164,18 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
-                       else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else if (accnosfile == "not found") {  accnosfile = ""; }
+                       else { m->setAccnosFile(accnosfile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        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; }
@@ -181,15 +184,17 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all"; }

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index aba8e8a128f6299feabfee18a8118384974fa206..8535db3203c6da354ce55e1a4f095f07b6d4e487 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -113,17 +113,17 @@ GetlabelCommand::GetlabelCommand(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); }
                        
                        if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index fc173100942199c9f5f5ea1b400d0cb0ad978303..0d836130d31124298a13c3a388267144cf5538ff 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -169,15 +169,18 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        //check for required parameters                 
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        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); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -186,6 +189,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
@@ -193,7 +197,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
                                taxfile = m->getTaxonomyFile(); 
                                if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setTaxonomyFile(taxfile); }
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 4dc20634c1e53d774348559447c736f736ff4e69..57afd85943e956b6bf4364d0b7c0b8bf27657cc3 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -114,6 +114,7 @@ GetListCountCommand::GetListCountCommand(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") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                
                        //check for optional parameter and set defaults

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index ce4b8950c3f1946054c7b24c82445a9ea1bc1cec..3e31691e6c8340d3ff7f02c0f316085f246f1b6b 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -203,6 +203,7 @@ GetOTURepCommand::GetOTURepCommand(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") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") {                  
@@ -211,20 +212,22 @@ GetOTURepCommand::GetOTURepCommand(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") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not found") { phylipfile = "";  }
                        else if (phylipfile == "not open") { abort = true; }    
-                       else { distFile = phylipfile; format = "phylip";   }
+                       else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);   }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not found") { columnfile = ""; }
                        else if (columnfile == "not open") { abort = true; }    
-                       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?
                                //give priority to column, then phylip
@@ -263,7 +266,8 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
-                                               
+                       else { m->setGroupFile(groupfile); }
+                       
                        sorted = validParameter.validFile(parameters, "sorted", false);         if (sorted == "not found"){     sorted = "";    }
                        if (sorted == "none") { sorted=""; }
                        if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index 681deb7646540d663560ed68d5da61deadea0f44..d29773ca340cf1119f04c312f897a0e5f2d7d4e8 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -134,7 +134,8 @@ GetOtusCommand::GetOtusCommand(string option)  {
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
-                       else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else if (accnosfile == "not found") {  accnosfile = ""; }
+                       else { m->setAccnosFile(accnosfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
@@ -142,7 +143,7 @@ GetOtusCommand::GetOtusCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
@@ -150,7 +151,7 @@ GetOtusCommand::GetOtusCommand(string option)  {
                                listfile = m->getListFile(); 
                                if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setListFile(listfile); }     
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index f886c2369a87d757532b68456af89753f72bb9c6..9c89f7f82f1f93cbaadfa1277d2b1002a7fa3f0b 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -116,12 +116,12 @@ GetRAbundCommand::GetRAbundCommand(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); }
                        
                        
                        //check for optional parameter and set defaults

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index d4caf5b59a758899606cfc316b20cb386679307c..693e36d000891339b843115fa11bd338dbc7a103 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -111,7 +111,7 @@ GetRelAbundCommand::GetRelAbundCommand(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/getsabundcommand.cpp b/getsabundcommand.cpp
index 3f6413606193afed8b5e2b7f6e89d77c20ef4ce4..799d8dced192019f65a633e946262db92c1e615f 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -114,12 +114,12 @@ GetSAbundCommand::GetSAbundCommand(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); }
                        
                        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); }
                        
                
                                                //check for optional parameter and set defaults

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index a4697ca3fded8c34ec5320630a588e243601373d..71a2db9723c32a39ea8e158074fbfac8a29de1ca 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -201,21 +201,24 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                        m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); 
                                        abort = true;
                                } 
-                       }       
+                       }else { m->setAccnosFile(accnosfile); } 
                        
                        if (accnosfile2 == "not found") { accnosfile2 = ""; }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        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); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -224,14 +227,17 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; }
                        else if (qualfile == "not found") {  qualfile = "";  }
+                       else { m->setQualFile(qualfile); }
                        
                        accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
                        if (accnosfile2 == "not open") { abort = true; }

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 99687701436dc5ffac7e71a444d97b42f4b6815a..06e199f7a93c96e71ba5cb15f1cafd21c8ca2d8e 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -148,7 +148,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                        m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
                                        abort = true;
                                }
-                       }else {  format = "list";       }
+                       }else {  format = "list";       m->setListFile(listfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -159,7 +159,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                        m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); 
                                        abort = true;
                                }
-                       }
+                       }else { m->setGroupFile(groupfile); }
                                                
                        if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
                        
@@ -197,7 +197,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
-                               
+                       else { m->setFastaFile(fastafile); }
                }
 
        }

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 3e99473bb6d742cd759c6a5a3eed55373df58549..d98f5c69926f795cb75510853184197676647ab9 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -135,16 +135,17 @@ HClusterCommand::HClusterCommand(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 { m->setNameFile(namefile); }
                        
                        if ((phylipfile == "") && (columnfile == "")) { 
                                //is there are current file available for either of these?

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index cf5140a1c7a03db5603cd2358ea7797ea80701f6..0d8c5b03df532dc83e23f030e93d906c727842e3 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -153,27 +153,27 @@ HeatMapCommand::HeatMapCommand(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); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { relabundfile = ""; abort = true; }    
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else {  format = "relabund"; inputfile = relabundfile; }
+                       else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        
                        if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) { 

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 92271d9dad6d3532e3463fd7e0be4ad9dcbf395c..38e344dfea67fdcfe89ce80a0476300d8ff50e3a 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -158,21 +158,22 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  format = "phylip";      inputfile = phylipfile; if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
+                       else {  format = "phylip";      inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  format = "column";      inputfile = columnfile; if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
+                       else {  format = "column";      inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; } 
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "shared";      inputfile = sharedfile;  if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
+                       else {  format = "shared";      inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        
                        //error checking on files                       

diff --git a/homovacommand.cpp b/homovacommand.cpp
index a8d2786f085ef584ba5f18069dfea2c5a51da572..22fd1bff1b0af5ac23532423f7b42471e1b6b3b3 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -125,7 +125,7 @@ HomovaCommand::HomovaCommand(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);
@@ -135,7 +135,7 @@ HomovaCommand::HomovaCommand(string option) {
                                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/indicatorcommand.cpp b/indicatorcommand.cpp
index ac7efcf5a40846dd8fcf6a2166dbc773f18d2b34..ab9e275279e0399182d458b7a6a64b81ba56c205 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -147,21 +147,22 @@ IndicatorCommand::IndicatorCommand(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); }     
                        
                        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); }
                        
                        designfile = validParameter.validFile(parameters, "design", true);
                        if (designfile == "not open") { abort = true; }
                        else if (designfile == "not found") { designfile = ""; }
+                       else { m->setDesignFile(designfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "";  Groups.push_back("all"); }

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 11430117dd1df9c9e2696010324eb3c51b4f2fe6..c993a06282d4abec617318d87ec9ec18bb64c5e2 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -138,7 +138,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
                                        m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine(); 
                                        abort = true;
                                } 
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
@@ -150,7 +150,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
                                        m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); 
                                        abort = true;
                                } 
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        //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/listseqscommand.cpp b/listseqscommand.cpp
index 902ac87286e302977d2fe555754a632487e6e43b..3fe8360e3241477b869c26f5b1892541e28d84a4 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -150,15 +150,18 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        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); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -167,10 +170,12 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
-
+                       else { m->setListFile(listfile); }
+                       
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 2dd45a542665c71a1221adca4eed77d9c1bb65f5..82f730159c000888e544308ddfb58289a3363fc2 100644 (file)
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -116,7 +116,7 @@ MakeFastQCommand::MakeFastQCommand(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); }   
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; qualfile = ""; }
@@ -124,7 +124,7 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
                                qualfile = m->getQualFile(); 
                                if (qualfile != "") {  m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setQualFile(qualfile); }     
                        
                        //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/makegroupcommand.cpp b/makegroupcommand.cpp
index e7704642874d050a3de7625a28ed3fae390fe653..2cab212cf94a0a9908b764facdd55669ff222cc9 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -159,7 +159,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
-                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  }
+                                               }else{  filename += m->getRootName(m->getSimpleName(fastaFileNames[i]));  m->setFastaFile(fastaFileNames[i]); }
                                        }
                                }
                                

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 3b5d87368914b0feb70eda6c354d5b81a4cdb071..780091027a66340b5ac94ff9480c792cba18281b 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -157,6 +157,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                                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 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/mergegroupscommand.cpp b/mergegroupscommand.cpp
index f62bb0ca8bcf0e0cd5b63ca080208af0b1a5d00d..a01441ed7ad6db77aa26b1a147755cd7eaa354bc 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -126,7 +126,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                                designfile = m->getDesignFile(); 
                                if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setDesignFile(designfile); } 
                        
                        //make sure the user has already run the read.otu command
                        sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -136,7 +136,7 @@ MergeGroupsCommand::MergeGroupsCommand(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); } 
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 99a3043995b429bf4661a776f25f050262905412..0704f55896e835f331eda28446012e62c790904e 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -134,7 +134,7 @@ MetaStatsCommand::MetaStatsCommand(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); }
                        
                        //check for required parameters
                        designfile = validParameter.validFile(parameters, "design", true);
@@ -144,7 +144,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                designfile = m->getDesignFile(); 
                                if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setDesignFile(designfile); }
                        
                        //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/mgclustercommand.cpp b/mgclustercommand.cpp
index 5a790afd45bbfcc2c92d23827aa58a184f257cee..fd2671750afa59b42fb3015c182df778b8871583 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -141,6 +141,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
                        

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 4567dbba1e7b0b16e88f496307ef3cb7ff3a8650..946aa68ab24ed5a10800d6d5c9e2ca32f4fd2ade 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -128,7 +128,7 @@ NMDSCommand::NMDSCommand(string option)  {
                                phylipfile = m->getPhylipFile(); 
                                if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " 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(phylipfile); } 
                        
                        axesfile = validParameter.validFile(parameters, "axes", true);
                        if (axesfile == "not open") { axesfile = ""; abort = true; }

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 07c353af3c33847978638fd71d1e220d34c090d4..a4bdd47099c350e77cfe238bcf34e254d1db9341 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -122,12 +122,12 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
                        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); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { relabundfile = ""; abort = true; }    
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else {  format = "relabund"; inputfile = relabundfile; }
+                       else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        
                        if ((sharedfile == "") && (relabundfile == "")) { 

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index cc5703223c7db32f31a2bf6db21d256145100f06..b1f05398963ec330aa4a9409299715a02e25600e 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -110,6 +110,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                                        abort = true;
                                }
                        }else if (listFile == "not open") { 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"){  

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index db032516e69e631147dbe3f2179a99a53ea2a1e2..75a1388694284e7dedb1caee31c577cb7ce29d04 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -198,6 +198,8 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index b791be7efcbffa74c7aa2e7f325cc4e8d39e00fb..e2c3e011c028a71bf79585519a7bbd9e25439c74 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -123,7 +123,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                        abort = true;
                                                
                                }
-                       }       
+                       }else { m->setListFile(listfile); }     
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
@@ -137,6 +137,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                        if (error == 1) { abort = true; }
                                }else { m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();  abort = true; } 
                        }else {  
+                               m->setGroupFile(groupfile);
                                groupMap = new GroupMap(groupfile);
                                
                                int error = groupMap->readMap();

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 403b2b86d9addf1f9291e7f87fac63ef1755c002..6e69cad4f8dbde50541a8daad71dbcce712b8953 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -144,16 +144,18 @@ ParsimonyCommand::ParsimonyCommand(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); }     
                                
                                //check for required parameters
                                groupfile = validParameter.validFile(parameters, "group", true);
                                if (groupfile == "not open") { abort = true; }
                                else if (groupfile == "not found") { groupfile = ""; }
+                               else { m->setGroupFile(groupfile); }
                                
                                namefile = validParameter.validFile(parameters, "name", true);
                                if (namefile == "not open") { abort = true; }
                                else if (namefile == "not found") { namefile = ""; }
+                               else { m->setNameFile(namefile); }
                        }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 

diff --git a/pcacommand.cpp b/pcacommand.cpp
index e273e5fe7079ffab790ccf5498e69675a0fafeef..5eed4566a74565c5641720dd519ae4df77e90b31 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -117,12 +117,12 @@ PCACommand::PCACommand(string option)  {
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  mode = "sharedfile"; inputFile = sharedfile; }
+                       else {  mode = "sharedfile"; inputFile = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { relabundfile = ""; abort = true; }    
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else {  mode = "relabund"; inputFile = relabundfile; }
+                       else {  mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        
                        if ((sharedfile == "") && (relabundfile == "")) { 

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 5d917372e5f88a5a45b762efc57ab388d80a4ebc..20e8e1be712765513c1f581b4e94536207f4f773 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -111,7 +111,7 @@ PCOACommand::PCOACommand(string option)  {
                                phylipfile = m->getPhylipFile(); 
                                if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " 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(phylipfile); } 
                        
                        filename = phylipfile;  
                        

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 8e8c7b67715ae9fb262fe4a41f7c9ef121dc2bff..abb12435b0a414cf3bcea5f69505ba263fe733de 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -150,16 +150,18 @@ PhyloDiversityCommand::PhyloDiversityCommand(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); }     
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(treefile);       }
                        

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index c03fcc1ac133572fc7d821816edadc0b1fc32ecb..ef23375df9425f11816acbf8594f46e613e9e148 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -129,11 +129,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                        abort = true; 
                                }
                        }else if (taxonomyFileName == "not open") { abort = true; }     
+                       else { m->setTaxonomyFile(taxonomyFileName); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
-                       else { readNamesFile(); }       
+                       else { readNamesFile(); m->setNameFile(namefile); }     
                        
                        //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/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 7a9d53089cd1b59b7fd278936c28e3f231bea005..898ad9b72640a4f5c9050f98b399e23efeafd58d 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -188,6 +188,7 @@ PipelineCommand::PipelineCommand(string option) {
                                sffFile = validParameter.validFile(parameters, "sff", true);
                                if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true;  }
                                else if (sffFile == "not open") { sffFile = ""; abort = true; }
+                               else { m->setSFFFile(sffFile); }
                                        
                                oligosFile = validParameter.validFile(parameters, "oligos", true);
                                if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true;  }

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 9299a6c6fc26e222869d515eb3fc362d0671bced..f13b29cc7307595460876dc482e510d2996c8d2d 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -124,6 +124,7 @@ PreClusterCommand::PreClusterCommand(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") { 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"){  
@@ -136,7 +137,7 @@ PreClusterCommand::PreClusterCommand(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     = validParameter.validFile(parameters, "diffs", false);                         if(temp == "not found"){        temp = "1"; }
                        convert(temp, diffs); 

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 82251c4a8fad67ea36fea2d7232b2f9171d5e3f5..b9007f4c430de320ba2a63d32c98cd30a08fcb83 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -184,22 +184,22 @@ RareFactCommand::RareFactCommand(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 ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index fe92f97038eea51cd87a05608bad0e2525070c58..717fec2fea1fc1ba23564fc683149e38d177496e 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -124,7 +124,7 @@ RareFactSharedCommand::RareFactSharedCommand(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/removegroupscommand.cpp b/removegroupscommand.cpp
index 7034941e73e6a02ae07a02ab11631e8a7b752f3d..9b537281b4abef7ecb9f270e1438993fca198e22 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -166,14 +166,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
                        else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else { m->setAccnosFile(accnosfile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
+                       else { m->setFastaFile(fastafile); }
                        
                        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; }
@@ -182,15 +185,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 5f5435f8679a9b65bb4799dae9dff30555818d3c..d1db13f685f0c965b89b60d78ea26deb9616b81e 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -171,14 +171,17 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
+                       else { m->setFastaFile(fastafile); }
                        
                        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); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -187,6 +190,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
@@ -194,7 +198,7 @@ RemoveLineageCommand::RemoveLineageCommand(string option)  {
                                taxfile = m->getTaxonomyFile(); 
                                if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setTaxonomyFile(taxfile); }
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 30f337bf7fffc90bcdf7d9ebb8cc97611c6ebd29..0fbed18b8be943fc4134cc18555c5a25cbd25b74 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -134,7 +134,8 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
-                       else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else if (accnosfile == "not found") {  accnosfile = ""; }
+                       else { m->setAccnosFile(accnosfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
@@ -142,7 +143,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
@@ -150,7 +151,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                                listfile = m->getListFile(); 
                                if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setListFile(listfile); }     
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index 255448ece9d1ed6eb5c8d65b4d562644ddf73051..c320fa4d8854f003486bc71c8e6b0806ec7ae0e3 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -160,23 +160,28 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
                        //check for file parameters
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
-                       else if (listfile == "not found") {  listfile = "";  }  
+                       else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { abort = true; }
                        else if (sabundfile == "not found") {  sabundfile = "";  }      
+                       else { m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { abort = true; }
                        else if (rabundfile == "not found") {  rabundfile = "";  }                              
+                       else { m->setRabundFile(rabundfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = "";  abort = true; }
                        else if (sharedfile == "not found") {  sharedfile = "";  }
+                       else { m->setSharedFile(sharedfile); }
                        
                        if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index c7dd5c227622cb3fe0cbf764ff266fdbdea21271..b8bb46433cab982d8f29ef79adbd34dd5fa243b0 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -191,19 +191,22 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                                        m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); 
                                        abort = true;
                                }  
-                       }       
+                       }else { m->setAccnosFile(accnosfile); } 
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }        
-                       
+                       else { m->setFastaFile(fastafile); }
+                                                                  
                        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 if (groupfile == "not found") {  groupfile = "";  }
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -212,15 +215,17 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; }
                        else if (qualfile == "not found") {  qualfile = "";  }                  
-
+                       else { m->setQualFile(qualfile); }
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 17924c9669b6b5338d15824b2920410fcf305af4..ea2ddeb8e718b44363409f0b332827feec41d6a9 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -113,11 +113,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                        fastaFileName = validParameter.validFile(parameters, "fasta", true);
                        if (fastaFileName == "not open") { abort = true; }
                        else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }    
+                       else { m->setFastaFile(fastaFileName); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if (qualFileName == "not open") { abort = true; }
                        else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }      
-
+                       else { m->setQualFile(qualFileName); }
+                       
                        if((fastaFileName == "") && (qualFileName == "")){
                                fastaFileName = m->getFastaFile(); 
                                if (fastaFileName != "") {  m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index b68a8cc8ea0042d53222da781770627c58ff3966..9f7aa40b3cc6786388a4e9eb8e47326661460e2d 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -173,20 +173,24 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                                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 if (fastafile == "not open") { abort = true; }     
+                       else if (fastafile == "not open") { abort = true; }
+                       else { m->setFastaFile(fastafile); }
        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; }   
                        else if (qualfile == "not found") { qualfile = ""; }
+                       else { m->setQualFile(qualfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-
+                       else { m->setNameFile(namefile); }
+                       
                        alignreport = validParameter.validFile(parameters, "alignreport", true);
                        if (alignreport == "not open") { abort = true; }
                        else if (alignreport == "not found") { alignreport = ""; }      

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 2b84cc365d4796363bd3e4c5612abb246cfc5aab..cc53ee0f02741cbe0fc6358a3a08cd56e891cd09 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -127,11 +127,12 @@ AlignCheckCommand::AlignCheckCommand(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") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = "";  }   
+                       else { m->setNameFile(namefile); }
                        
                        //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/sensspeccommand.cpp b/sensspeccommand.cpp
index 213a2ca99da988257a46ba8e91cb5e4123b5bb0e..726c9045b20dfd7ac907b5e73f0692e3d0835c69 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -134,16 +134,17 @@ SensSpecCommand::SensSpecCommand(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") { abort = true; }      
+                       else { m->setListFile(listFile); }
                        
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not found") { phylipfile = "";  }
                        else if (phylipfile == "not open") { abort = true; }    
-                       else { distFile = phylipfile; format = "phylip";   }
+                       else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);  }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not found") { columnfile = ""; }
                        else if (columnfile == "not open") { abort = true; }    
-                       else { distFile = columnfile; format = "column";   }
+                       else { distFile = columnfile; format = "column";   m->setColumnFile(columnfile); }
                        
                        if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
                                //give priority to column, then phylip

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 6ce944ef21189948519310e372907580d8ac1400..564e412ea95f1421b1d3cc72761c2ac98fe61c44 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -164,6 +164,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (queryFileName == "not open") { abort = true; } 
+                       else { m->setFastaFile(queryFileName); }
                        
                        referenceFileName = validParameter.validFile(parameters, "reference", true);
                        if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
@@ -174,11 +175,13 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        namesFileName = validParameter.validFile(parameters, "name", true);
                        if(namesFileName == "not found"){       namesFileName = "";     }
                        else if (namesFileName == "not open") { namesFileName = ""; abort = true; }     
+                       else { m->setNameFile(namesFileName); }
                        
                        qualFileName = validParameter.validFile(parameters, "qfile", true);
                        if(qualFileName == "not found"){        qualFileName = "";      }
                        else if (qualFileName == "not open") { qualFileName = ""; abort = true; }       
-
+                       else { m->setQualFile(qualFileName); }
+                       
                        reportFileName = validParameter.validFile(parameters, "report", true);
                        if(reportFileName == "not found"){      reportFileName = "";    }
                        else if (reportFileName == "not open") { reportFileName = ""; abort = true; }   

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 620de95c333cdee1360157f7aa7068f3ce1f1f62..8c7b9b69525abe705d432069043b4288c9830e23 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -116,11 +116,12 @@ SeqSummaryCommand::SeqSummaryCommand(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") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = "";  }   
+                       else { m->setNameFile(namefile); }
                        
                        //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/sffinfocommand.cpp b/sffinfocommand.cpp
index 77af9e647be61a96ba83bf4929156aa7554633e8..207328203a24088c111054de2b157fae9235876c 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -170,7 +170,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                                                        //erase from file list
                                                        filenames.erase(filenames.begin()+i);
                                                        i--;
-                                               }
+                                               }else { m->setSFFFile(filenames[i]); }
                                        }
                                }
                                

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index b322007bc5e8ef6cba50d4c6d2ff5fce0b87a0fa..38bc480836ba114e3ed55d0c1aa65f4e33d4218a 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -131,7 +131,7 @@ SharedCommand::SharedCommand(string option)  {
                                 listfile = m->getListFile(); 
                                 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
                                 else {         m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-                        }      
+                        }else { m->setListFile(listfile); }    
                                                        
                         ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
                         if (ordergroupfile == "not open") { abort = true; }    

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index ba59dfe66e1b333f88317542e3a17844ac6d558e..aa47940a030f968e02686b915d26e84c29584b8d 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -152,12 +152,12 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else{ inputFile = listfile; }   
+                       else{ inputFile = listfile; m->setListFile(listfile); } 
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-                       else{ inputFile = namefile; }   
+                       else{ inputFile = namefile; m->setNameFile(namefile); } 
                
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
@@ -165,7 +165,7 @@ SplitAbundCommand::SplitAbundCommand(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); }   
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") {  groupfile = ""; abort = true; } 
@@ -175,7 +175,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                
                                int error = groupMap->readMap();
                                if (error == 1) { abort = true; }
-       
+                               m->setGroupFile(groupfile);
                        }
                        
                        groups = validParameter.validFile(parameters, "groups", false);         

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 220c7cc680b1729880001c5bf94ad1fc284a85e9..6dd6206084fbe7ea81b9ad254ac2aedf28031407 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -126,6 +126,7 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
+                       else { m->setNameFile(namefile); }
                
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
@@ -133,7 +134,7 @@ SplitGroupCommand::SplitGroupCommand(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); }   
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") {  groupfile = ""; abort = true; } 
@@ -141,7 +142,7 @@ SplitGroupCommand::SplitGroupCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else {  m->setGroupFile(groupfile); }
                        
                        groups = validParameter.validFile(parameters, "groups", false);         
                        if (groups == "not found") { groups = ""; }

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 0f7bdec57cc94e1b721c8cee65c57eb01a5e6124..95a0442d6c970bd74a383c1e13765af305eeac57 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -182,32 +182,38 @@ SubSampleCommand::SubSampleCommand(string option) {
                        //check for required parameters
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
-                       else if (listfile == "not found") { listfile = ""; }    
+                       else if (listfile == "not found") { listfile = ""; }
+                       else { m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
+                       else { m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
+                       else { m->setRabundFile(rabundfile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { fastafile = ""; abort = true; }  
                        else if (fastafile == "not found") { fastafile = ""; }
+                       else { m->setFastaFile(fastafile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
+                       else { m->setSharedFile(sharedfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }    
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; 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/summarycommand.cpp b/summarycommand.cpp
index 4d71c07511d711ec10baad3b94ca724cbf1e320f..2bb88770ec37651df7ff9da2954926abf3bf5153 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -164,22 +164,22 @@ SummaryCommand::SummaryCommand(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 ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index cc1a374ba96496a96a17bd4626f689b25ea1ed7f..b3b4b1869f4368c3c7555d5a711e95acb54c9283 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -161,7 +161,7 @@ SummarySharedCommand::SummarySharedCommand(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/treegroupscommand.cpp b/treegroupscommand.cpp
index 9c56d2228092a25779cd0431c5a3a5ef06f81563..902b9a253b0aa7e5515b74adf464b7fe17a65e2c 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -179,21 +179,22 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { phylipfile = ""; abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  inputfile = phylipfile;  format = "phylip";     }
+                       else {  inputfile = 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 {  inputfile = columnfile; format = "column";      }
+                       else {  inputfile = columnfile; format = "column";      m->setColumnFile(columnfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  inputfile = sharedfile; format = "sharedfile";  }
+                       else {  inputfile = sharedfile; format = "sharedfile";  m->setSharedFile(sharedfile); }
                        
                        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 == "") && (sharedfile == "")) { 
                                //is there are current file available for either of these?

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 77377a47c34e51bf13e97bef11f7966ba2cb6199..ec043360ad1cd553d782d1d67ab531c9a4610778 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -157,7 +157,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found")        {       oligoFileName = "";             }
                        else if(temp == "not open")     {       abort = true;                   } 
-                       else                                            {       oligoFileName = temp;   }
+                       else                                            {       oligoFileName = temp;   m->setOligosFile(oligoFileName); }
                        
                        temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
                        else if(m->isTrue(temp))        {       fasta = 1;      }

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6410c8f4cb39a32efad1f8a18e4876cec6080b9f..082bc7950c590d9251100c3a6cb45dd18af6d2aa 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -189,6 +189,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                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 if (fastaFile == "not open") { 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"){  
@@ -207,7 +208,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found"){       oligoFile = "";         }
                        else if(temp == "not open"){    abort = true;   } 
-                       else                                    {       oligoFile = temp;               }
+                       else                                    {       oligoFile = temp; m->setOligosFile(oligoFile);          }
                        
                        
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
@@ -236,12 +237,12 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "qfile", true);     
                        if (temp == "not found")        {       qFileName = "";         }
                        else if(temp == "not open")     {       abort = true;           }
-                       else                                            {       qFileName = temp;       }
+                       else                                            {       qFileName = temp;       m->setQualFile(qFileName); }
                        
                        temp = validParameter.validFile(parameters, "name", true);      
                        if (temp == "not found")        {       nameFile = "";          }
                        else if(temp == "not open")     {       nameFile = "";  abort = true;           }
-                       else                                            {       nameFile = temp;        }
+                       else                                            {       nameFile = temp;        m->setNameFile(nameFile); }
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
                        convert(temp, qThreshold);

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 8ec2d06e75d3980b42cb9980ca1631a978418429..058555eeb26ef7608cd4a337e492cca135c3c55c 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -146,16 +146,18 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(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); }     
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 0570945b71d9c8962c46bec2a58525a1e37a5e6f..00bb5d6c39eb0894389be1e5fecaba838d4303bd 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -146,16 +146,18 @@ UnifracWeightedCommand::UnifracWeightedCommand(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); }     
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        

diff --git a/venncommand.cpp b/venncommand.cpp
index cae041704c52e7caf6c4368ca393d441a69065c9..6d4c2a0616880aee92f5fec430f63df51606e929 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -129,12 +129,12 @@ VennCommand::VennCommand(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); }
                        
                        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 ((sharedfile == "") && (listfile == "")) { 
                                //is there are current file available for any of these?