fixed bugs for 1.8

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 1697ff7a0d57534b81e9b1f135cf494ae55c2d34..d97ffc7934484c3b7ba29a3674418c672b77133a 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -74,7 +74,7 @@ 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();  }
                        
                        string temp     = validParameter.validFile(parameters, "diffs", false);                         if(temp == "not found"){        temp = "1"; }
                        convert(temp, diffs); 
@@ -116,7 +116,7 @@ int PreClusterCommand::execute(){
                if (abort == true) { return 0; }
                
                //reads fasta file and return number of seqs
-               int numSeqs = readNamesFASTA(); //fills alignSeqs and makes all seqs active
+               int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
        
                if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0;  }
                if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); return 0;  }
@@ -179,7 +179,7 @@ int PreClusterCommand::execute(){
                exit(1);
        }
 }
-/**************************************************************************************************/
+/**************************************************************************************************
 int PreClusterCommand::readFASTA(){
        try {
 //             ifstream inFasta;
@@ -216,44 +216,55 @@ int PreClusterCommand::readFASTA(){
 }
 /**************************************************************************************************/
 //this seems to require the names and fasta file to be in the same order???
-int PreClusterCommand::readNamesFASTA(){
+int PreClusterCommand::readFASTA(){
        try {
-               ifstream inNames;
+               //ifstream inNames;
                ifstream inFasta;
                
-               openInputFile(namefile, inNames);
+               //openInputFile(namefile, inNames);
                openInputFile(fastafile, inFasta);
                
-               string firstCol, secondCol, nameString;
+               //string firstCol, secondCol, nameString;
                length = 0;
                
-               while (inFasta && inNames) {
+               while (!inFasta.eof()) {
        
-                       inNames >> firstCol >> secondCol;
-                       nameString = secondCol;
+                       //inNames >> firstCol >> secondCol;
+                       //nameString = secondCol;
                        
-                       gobble(inNames);
-                       int size = 1;
-                       while (secondCol.find_first_of(',') != -1) { 
-                               size++;
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-                       }
+                       //gobble(inNames);
+                       //int size = 1;
+                       //while (secondCol.find_first_of(',') != -1) { 
+                       //      size++;
+                       //      secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
+                       //}
                        
                        Sequence seq(inFasta);  gobble(inFasta);
-                       if (seq.getName() != firstCol) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
-                       else{
-                               seqPNode tempNode(size, seq, nameString);
-                               alignSeqs.push_back(tempNode);
-                               if (seq.getAligned().length() > length) {  length = alignSeqs[0].seq.getAligned().length();  }
-                       }                       
+                       
+                       if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
+                               if (namefile != "") {
+                                       itSize = sizes.find(seq.getName());
+                                       
+                                       if (itSize == sizes.end()) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
+                                       else{
+                                               seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
+                                               alignSeqs.push_back(tempNode);
+                                               if (seq.getAligned().length() > length) {  length = alignSeqs[0].seq.getAligned().length();  }
+                                       }       
+                               }else { //no names file, you are identical to yourself 
+                                       seqPNode tempNode(1, seq, seq.getName());
+                                       alignSeqs.push_back(tempNode);
+                                       if (seq.getAligned().length() > length) {  length = alignSeqs[0].seq.getAligned().length();  }
+                               }
+                       }
                }
                inFasta.close();
-               inNames.close();
+               //inNames.close();
                return alignSeqs.size();
        }
        
        catch(exception& e) {
-               errorOut(e, "PreClusterCommand", "readNamesFASTA");
+               errorOut(e, "PreClusterCommand", "readFASTA");
                exit(1);
        }
 }
@@ -305,6 +316,30 @@ void PreClusterCommand::printData(string newfasta, string newname){
                exit(1);
        }
 }
+/**************************************************************************************************/
+void PreClusterCommand::readNameFile(){
+       try {
+               ifstream in;
+               openInputFile(namefile, in);
+               string firstCol, secondCol;
+                               
+               while (!in.eof()) {
+                       in >> firstCol >> secondCol; gobble(in);
+                       names[firstCol] = secondCol;
+                       int size = 1;
+                       while (secondCol.find_first_of(',') != -1) { 
+                               size++;
+                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
+                       }
+                       sizes[firstCol] = size;
+               }
+               in.close();
+       }
+       catch(exception& e) {
+               errorOut(e, "PreClusterCommand", "readNameFile");
+               exit(1);
+       }
+}
 
 /**************************************************************************************************/