changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index e2302d38bf02f5c58daae759713deb28a1a75b6b..dc40611711062150b7046e1be665a34c87d87818 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -12,10 +12,11 @@
 
 //**********************************************************************************************************************
 
-AlignCheckCommand::AlignCheckCommand(string option){
+AlignCheckCommand::AlignCheckCommand(string option)  {
        try {
                abort = false;
-               
+               haderror = 0;
+                       
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
@@ -60,11 +61,11 @@ AlignCheckCommand::AlignCheckCommand(string option){
                        //check for required parameters
                        mapfile = validParameter.validFile(parameters, "map", true);
                        if (mapfile == "not open") { abort = true; }
-                       else if (mapfile == "not found") {  mapfile = "";  mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; }      
+                       else if (mapfile == "not found") {  mapfile = "";  m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }        
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true;  }       
+                       else if (fastafile == "not found") {  fastafile = "";  m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true;  } 
                        
                        //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"){  
@@ -76,7 +77,7 @@ AlignCheckCommand::AlignCheckCommand(string option){
 
        }
        catch(exception& e) {
-               errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
+               m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
                exit(1);
        }
 }
@@ -84,15 +85,15 @@ AlignCheckCommand::AlignCheckCommand(string option){
 
 void AlignCheckCommand::help(){
        try {
-               mothurOut("The align.check command reads a fasta file and map file.\n");
-               mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
-               mothurOut("The align.check command parameters are fasta and map, both are required.\n");
-               mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
-               mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+               m->mothurOut("The align.check command reads a fasta file and map file.\n");
+               m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
+               m->mothurOut("The align.check command parameters are fasta and map, both are required.\n");
+               m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
+               m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "AlignCheckCommand", "help");
+               m->errorOut(e, "AlignCheckCommand", "help");
                exit(1);
        }
 }
@@ -119,11 +120,14 @@ int AlignCheckCommand::execute(){
 
                
                while(!in.eof()){
+                       if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
                        
                        Sequence seq(in);  gobble(in);
                        if (seq.getName() != "") {
                                statData data = getStats(seq.getAligned());
                                
+                               if (haderror == 1) { break; }
+                               
                                out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
                                out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
                        }
@@ -132,11 +136,18 @@ int AlignCheckCommand::execute(){
                in.close();
                out.close();
                
+               if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(outfile); m->mothurOutEndLine();   
+               m->mothurOutEndLine();
+               
                return 0;               
        }
 
        catch(exception& e) {
-               errorOut(e, "AlignCheckCommand", "execute");
+               m->errorOut(e, "AlignCheckCommand", "execute");
                exit(1);
        }
 }
@@ -164,7 +175,7 @@ void AlignCheckCommand::readMap(){
                for(int i=0;i<seqLength;i++){
                        if(structMap[i] != 0){
                                if(structMap[structMap[i]] != i){
-                                       mothurOut("Your map file contains an error:  line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); mothurOutEndLine();
+                                       m->mothurOut("Your map file contains an error:  line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine();
                                }
                        }
                }
@@ -172,7 +183,7 @@ void AlignCheckCommand::readMap(){
                
        }
        catch(exception& e) {
-               errorOut(e, "AlignCheckCommand", "readMap");
+               m->errorOut(e, "AlignCheckCommand", "readMap");
                exit(1);
        }
 }
@@ -184,8 +195,11 @@ statData AlignCheckCommand::getStats(string sequence){
                statData data;
                sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
                
-               int seqLength = sequence.length();
-               for(int i=1;i<seqLength;i++){
+               int length = sequence.length();
+               
+               if (length != seqLength) { m->mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); m->mothurOutEndLine(); haderror = 1; return data;  }
+               
+               for(int i=1;i<length;i++){
                        if(structMap[i] != 0){
                                if(sequence[i] == 'A'){
                                        if(sequence[structMap[i]] == 'T')               {       data.tilde++;   }
@@ -236,7 +250,7 @@ statData AlignCheckCommand::getStats(string sequence){
                
        }
        catch(exception& e) {
-               errorOut(e, "AlignCheckCommand", "getStats");
+               m->errorOut(e, "AlignCheckCommand", "getStats");
                exit(1);
        }
 }