changed name of distance command to dist.seqs

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index aa223a20379d1fd590908fbb5aa92c7a38cbf03b..c866ca0060960ab20f50f53ffbd774c066ffc628 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 +110,15 @@ 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;        }
-                               
+                               if (parameter == "ends" )                       { ends = value; }
+                               if (parameter == "processors" )         { processors = value;   }
+
                        }
                        
                        //gets the last parameter and value
@@ -131,6 +139,8 @@ 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 +154,13 @@ 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;        }
+                               if (parameter == "ends" )                       { ends = value; }
+                               if (parameter == "processors" )         { processors = value;   }
+
                        }
                }
                
@@ -177,7 +193,7 @@ bool ErrorCheck::checkInput(string input) {
                        validateReadFiles();
                }
                
-               //are you trying to cluster before you have read something                      
+               //are you trying to cluster before you have read something      
                if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
                        ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
                                cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
@@ -196,9 +212,9 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
-               if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
+               if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) {
                        if (globaldata->gTree.size() == 0) {//no trees were read
-                               cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false;  }
+                               cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false;  }
                }
                
                //check for valid method
@@ -230,6 +246,13 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
+               if ((commandName == "filter.seqs") || (commandName == "dist.seq")) { 
+                       if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
+                                cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false; 
+                       }
+                       validateSeqsFiles();
+               }
+               
                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();
@@ -486,6 +509,71 @@ void ErrorCheck::validateReadPhil() {
 }
 /*******************************************************/
 
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a distfile read
+void ErrorCheck::validateSeqsFiles() {
+       try {
+               ifstream filehandle;
+               int ableToOpen;
+               
+               //checks to make sure only one file type is given
+               if (phylipfile != "") { 
+                       if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) { 
+                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+                       else {
+                               ableToOpen = openInputFile(phylipfile, filehandle);
+                               filehandle.close();
+                               if (ableToOpen == 1) { //unable to open
+                                       errorFree = false;
+                               }
+                       }
+               }else if (nexusfile != "") { 
+                       if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) { 
+                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+                       else {
+                               ableToOpen = openInputFile(nexusfile, filehandle);
+                               filehandle.close();
+                               if (ableToOpen == 1) { //unable to open
+                                       errorFree = false;
+                               }
+                       }
+               }else if (fastafile != "") { 
+                       if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) { 
+                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+                       else {
+                               ableToOpen = openInputFile(fastafile, filehandle);
+                               filehandle.close();
+                               if (ableToOpen == 1) { //unable to open
+                                       errorFree = false;
+                               }
+                       }
+               }else if (clustalfile != "") { 
+                       if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) { 
+                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
+                       else {
+                               ableToOpen = openInputFile(clustalfile, filehandle);
+                               filehandle.close();
+                               if (ableToOpen == 1) { //unable to open
+                                       errorFree = false;
+                               }
+                       }
+
+               }
+               
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/*******************************************************/
+
 /******************************************************/
 //This function checks to make sure the user entered appropriate
 // format parameters on a bin.seq command
@@ -551,6 +639,9 @@ void ErrorCheck::clear() {
        groupfile               =       ""; 
        orderfile               =       "";
        sharedfile              =       "";
+       fastafile       =   "";
+       nexusfile       =   "";
+       clustalfile     =   "";
        line                    =       "";
        label                   =       "";
        method                  =   "furthest";