*** empty log message ***

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 728d4d27303a3c3b9d9ad602693ba4b309a36202..eaf49dfe6937c4201330981cacf8cb5bfbf198cc 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -23,6 +23,7 @@ ErrorCheck::ErrorCheck() {
 /******************************************************/
 
 void ErrorCheck::refresh() {
+
        //columnfile = globaldata->getColumnFile();
        //phylipfile = globaldata->getPhylipFile();
        //listfile = globaldata->getListFile();
@@ -38,6 +39,7 @@ void ErrorCheck::refresh() {
        //method = globaldata->getMethod();
        //randomtree = globaldata->getRandomTree();
        //sharedfile = globaldata->getSharedFile();
+
 }
 
 /*******************************************************/
@@ -74,7 +76,6 @@ bool ErrorCheck::checkInput(string input) {
                
                //is it a valid command
                if (validCommand->isValidCommand(commandName) != true) { return false; }
-               
                string parameter, value;
                
                //reads in parameters and values
@@ -94,9 +95,11 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "name" )               { namefile = value; }
                                if (parameter == "order" )              { orderfile = value; }
                                if (parameter == "fasta" )              { fastafile = value; }
+                               if (parameter == "nexus" )              { nexusfile = value; }
+                               if (parameter == "clustal" )    { clustalfile = value; }
                                if (parameter == "tree" )               { treefile = value; }
-                               if (parameter == "group" )              { groupfile = value; }
-                               if (parameter == "shared" )             { sharedfile = value; }
+                               if (parameter == "group" )                      { groupfile = value; }
+                               if (parameter == "shared" )                     { sharedfile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
                                if (parameter == "iters" )                      { iters = value; }
@@ -107,10 +110,13 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "line" )                       { line = value; }
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "abund" )          { abund = value; }
-                               if (parameter == "random" )                     { randomtree = value;   }
-                               if (parameter == "sorted" )                     { sorted = value;       }
+                               if (parameter == "random" )                     { randomtree = value; }
+                               if (parameter == "sorted" )                     { sorted = value; }
+                               if (parameter == "trump" )          { trump = value; }
+                               if (parameter == "soft" )                       { soft = value; }
+                               if (parameter == "filter" )         { filter = value; }
                                if (parameter == "scale" )                      { scale = value;        }
-                               
+
                        }
                        
                        //gets the last parameter and value
@@ -131,6 +137,8 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "group" )              { groupfile = value; }
                                if (parameter == "shared" )             { sharedfile = value; }
                                if (parameter == "fasta" )              { fastafile = value; }
+                               if (parameter == "nexus" )              { nexusfile = value; }
+                               if (parameter == "clustal" )    { clustalfile = value; }
                                if (parameter == "tree" )               { treefile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
@@ -144,7 +152,11 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "random" )                     { randomtree = value;   }
                                if (parameter == "abund" )          { abund = value; }
                                if (parameter == "sorted" )                     { sorted = value;       }
+                               if (parameter == "trump" )          { trump = value; }
+                               if (parameter == "soft" )                       { soft = value; }
+                               if (parameter == "filter" )         { filter = value; }
                                if (parameter == "scale" )                      { scale = value;        }
+
                        }
                }
                
@@ -172,6 +184,8 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }else if (commandName == "read.tree") { 
                        validateTreeFiles(); //checks the treefile and groupfile parameters
+               }else if (commandName == "read.seqs") {
+                       if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) { cout << "You must enter a fastafile, nexusfile, or clustalfile with the read.seqs() command." << endl; return false; }
                }else if (commandName == "deconvolute") {
                        if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
                        validateReadFiles();
@@ -230,6 +244,12 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
+               if (commandName == "filter.seqs"){ 
+                       if ((globaldata->getFastaFile() == "") && (globaldata->getNexusFile() == "") && (globaldata->getClustalFile() == "") && (globaldata->getPhylipFile() == "")) {
+                                cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false; 
+                       }
+               }
+               
                if ((commandName == "bin.seqs")) { 
                        if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
                        validateBinFiles();
@@ -551,6 +571,9 @@ void ErrorCheck::clear() {
        groupfile               =       ""; 
        orderfile               =       "";
        sharedfile              =       "";
+       fastafile       =   "";
+       nexusfile       =   "";
+       clustalfile     =   "";
        line                    =       "";
        label                   =       "";
        method                  =   "furthest";