added name, group and count files to chop.seqs. added intelligent warnings for when...

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 80dd8561ef286fb862c01e99089eaea534f92884..96d7ae641b8b956694fe5ad12b9671c0279b302c 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -9,11 +9,15 @@
 
 #include "chopseqscommand.h"
 #include "sequence.hpp"
+#include "removeseqscommand.h"
 
 //**********************************************************************************************************************
 vector<string> ChopSeqsCommand::setParameters(){       
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
         CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
                CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
@@ -36,8 +40,9 @@ string ChopSeqsCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
-               helpString += "The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
+               helpString += "The chop.seqs command parameters are fasta, name, group, count, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
                helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
+        helpString += "If you provide a name, group or count file any sequences removed from the fasta file will also be removed from those files.\n";
                helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
                helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
                helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
@@ -58,7 +63,10 @@ string ChopSeqsCommand::getOutputPattern(string type) {
     try {
         string pattern = "";
         
-        if (type == "fasta") {  pattern = "[filename],chop.fasta"; } 
+        if (type == "fasta") {  pattern = "[filename],chop.fasta"; }
+        else if (type == "name") {  pattern = "[filename],chop.names"; }
+        else if (type == "group") {  pattern = "[filename],chop.groups"; }
+        else if (type == "count") {  pattern = "[filename],chop.count_table"; } 
         else if (type == "accnos") {  pattern = "[filename],chop.accnos"; } 
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
@@ -77,6 +85,9 @@ ChopSeqsCommand::ChopSeqsCommand(){
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
+        outputTypes["name"] = tempOutNames;
+        outputTypes["group"] = tempOutNames;
+        outputTypes["count"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
@@ -110,6 +121,9 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
                        outputTypes["accnos"] = tempOutNames;
+            outputTypes["name"] = tempOutNames;
+            outputTypes["group"] = tempOutNames;
+            outputTypes["count"] = tempOutNames;
                
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -123,6 +137,30 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
                                }
+                
+                it = parameters.find("name");
+                               //user has given a template file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["name"] = inputDir + it->second;             }
+                               }
+                
+                it = parameters.find("group");
+                               //user has given a template file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["group"] = inputDir + it->second;            }
+                               }
+                
+                it = parameters.find("count");
+                               //user has given a template file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["count"] = inputDir + it->second;            }
+                               }
                        }
 
                        //check for required parameters
@@ -134,8 +172,31 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                                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); }
+                       
+                       groupfile = validParameter.validFile(parameters, "group", true);
+                       if (groupfile == "not open") { groupfile = ""; abort = true; }
+                       else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
+                               
+            countfile = validParameter.validFile(parameters, "count", true);
+                       if (countfile == "not open") { countfile = ""; abort = true; }
+                       else if (countfile == "not found") { countfile = "";  }
+                       else { m->setCountTableFile(countfile); }
+            
+            if ((namefile != "") && (countfile != "")) {
+                m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+            }
+                       
+            if ((groupfile != "") && (countfile != "")) {
+                m->mothurOut("[ERROR]: you may only use one of the following: group or count."); 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"){  outputDir = m->hasPath(fastafile);      }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        
                        string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; } 
                        m->mothurConvert(temp, numbases);   
@@ -168,9 +229,12 @@ int ChopSeqsCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-        map<string, string> variables; 
-        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+        map<string, string> variables;
+        string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
         string outputFileName = getOutputFileName("fasta", variables);
+        outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
         string outputFileNameAccnos = getOutputFileName("accnos", variables);        
         
         vector<unsigned long long> positions; 
@@ -198,29 +262,95 @@ int ChopSeqsCommand::execute(){
         
         if (m->control_pressed) {  return 0; }
                
-               m->mothurOutEndLine();
-               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
-               
-               if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
+        if (wroteAccnos) {
+            outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos);
+            
+             //use remove.seqs to create new name, group and count file
+            if ((countfile != "") || (namefile != "") || (groupfile != "")) {
+                string inputString = "accnos=" + outputFileNameAccnos;
+                
+                if (countfile != "") {  inputString += ", count=" + countfile;  }
+                else{
+                    if (namefile != "") {  inputString += ", name=" + namefile;  }
+                    if (groupfile != "") {  inputString += ", group=" + groupfile;  }
+                }
+                
+                m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+                m->mothurOut("Running command: remove.seqs(" + inputString + ")"); m->mothurOutEndLine();
+                m->mothurCalling = true;
+                
+                Command* removeCommand = new RemoveSeqsCommand(inputString);
+                removeCommand->execute();
+                
+                map<string, vector<string> > filenames = removeCommand->getOutputFiles();
+                
+                delete removeCommand;
+                m->mothurCalling = false;
+                m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+                
+                if (groupfile != "") {
+                    thisOutputDir = outputDir;
+                    if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
+                    variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+                    string outGroup = getOutputFileName("group", variables);
+                    m->renameFile(filenames["group"][0], outGroup);
+                    outputNames.push_back(outGroup); outputTypes["group"].push_back(outGroup);
+                }
+                
+                if (namefile != "") {
+                    thisOutputDir = outputDir;
+                    if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
+                    variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+                    string outName = getOutputFileName("name", variables);
+                    m->renameFile(filenames["name"][0], outName);
+                    outputNames.push_back(outName); outputTypes["name"].push_back(outName);
+                }
+                
+                if (countfile != "") {
+                    thisOutputDir = outputDir;
+                    if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
+                    variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+                    string outCount = getOutputFileName("count", variables);
+                    m->renameFile(filenames["count"][0], outCount);
+                    outputNames.push_back(outCount); outputTypes["count"].push_back(outCount);
+                }
+            }
+        }
                else {  m->mothurRemove(outputFileNameAccnos);  }
                
-               m->mothurOutEndLine();
-               
                //set fasta file as new current fastafile
                string current = "";
                itTypes = outputTypes.find("fasta");
                if (itTypes != outputTypes.end()) {
                        if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
                }
-               
+        
                if (wroteAccnos) { //set accnos file as new current accnosfile
                        itTypes = outputTypes.find("accnos");
                        if (itTypes != outputTypes.end()) {
                                if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
                        }
+            
+            itTypes = outputTypes.find("name");
+            if (itTypes != outputTypes.end()) {
+                if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+            }
+            
+            itTypes = outputTypes.find("group");
+            if (itTypes != outputTypes.end()) {
+                if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+            }
+            
+            itTypes = outputTypes.find("count");
+            if (itTypes != outputTypes.end()) {
+                if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+            }
                }
                
+        m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOutEndLine();
                
                return 0;               
        }

diff --git a/chopseqscommand.h b/chopseqscommand.h
index c9a4962c96fe9e548b50db1e4c0d6f63d1cdfff4..a9cfc102fb957ea775b14211db4e1f1e1118c50f 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -27,7 +27,7 @@ class ChopSeqsCommand : public Command {
                string getCommandCategory()             { return "Sequence Processing"; }
                
         string getHelpString();        
-    string getOutputPattern(string);   
+        string getOutputPattern(string);       
                string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
                string getDescription()         { return "trim sequence length"; }
        
@@ -41,7 +41,7 @@ class ChopSeqsCommand : public Command {
             linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
         };
     
-               string fastafile, outputDir, keep;
+               string fastafile, outputDir, keep, namefile, groupfile, countfile;
                bool abort, countGaps, Short;
                int numbases, processors;
                vector<string> outputNames;

diff --git a/counttable.cpp b/counttable.cpp
index c16bf9227a51580cac00de78a215b89e2a93e001..48b52d98e76e6da585c862682c3906bdf4ad0f67 100644 (file)
--- a/counttable.cpp
+++ b/counttable.cpp
@@ -40,7 +40,13 @@ int CountTable::createTable(set<string>& n, map<string, string>& g, set<string>&
             if (itGroup != g.end()) {   
                 groupCounts[indexGroupMap[itGroup->second]] = 1; 
                 totalGroups[indexGroupMap[itGroup->second]]++;
-            }else { m->mothurOut("[ERROR]: Your group file does not contain " + seqName + ". Please correct."); m->mothurOutEndLine(); }
+            }else {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(seqName, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
+                m->mothurOut("[ERROR]: Your group file does not contain " + seqName + ". Please correct."); m->mothurOutEndLine();
+            }
             
             map<string, int>::iterator it2 = indexNameMap.find(seqName);
             if (it2 == indexNameMap.end()) {
@@ -360,6 +366,10 @@ vector<int> CountTable::getGroupCounts(string seqName) {
         if (hasGroups) {
             map<string, int>::iterator it = indexNameMap.find(seqName);
             if (it == indexNameMap.end()) {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(seqName, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
                 m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
             }else { 
                 temp = counts[it->second];
@@ -404,6 +414,10 @@ int CountTable::getGroupCount(string seqName, string groupName) {
             }else { 
                 map<string, int>::iterator it2 = indexNameMap.find(seqName);
                 if (it2 == indexNameMap.end()) {
+                    //look for it in names of groups to see if the user accidently used the wrong file
+                    if (m->inUsersGroups(seqName, groups)) {
+                        m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                    }
                     m->mothurOut("[ERROR]: seq " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
                 }else { 
                     return counts[it2->second][it->second];
@@ -429,6 +443,10 @@ int CountTable::setAbund(string seqName, string groupName, int num) {
             }else { 
                 map<string, int>::iterator it2 = indexNameMap.find(seqName);
                 if (it2 == indexNameMap.end()) {
+                    //look for it in names of groups to see if the user accidently used the wrong file
+                    if (m->inUsersGroups(seqName, groups)) {
+                        m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                    }
                     m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
                 }else { 
                     int oldCount = counts[it2->second][it->second];
@@ -576,6 +594,12 @@ int CountTable::renameSeq(string oldSeqName, string newSeqName) {
         
         map<string, int>::iterator it = indexNameMap.find(oldSeqName);
         if (it == indexNameMap.end()) {
+            if (hasGroupInfo()) {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(oldSeqName, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + oldSeqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
+            }
             m->mothurOut("[ERROR]: " + oldSeqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
         }else {  
             int index = it->second;
@@ -598,6 +622,12 @@ int CountTable::getNumSeqs(string seqName) {
                 
         map<string, int>::iterator it = indexNameMap.find(seqName);
         if (it == indexNameMap.end()) {
+            if (hasGroupInfo()) {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(seqName, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
+            }
             m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
         }else { 
             return totals[it->second];
@@ -617,6 +647,12 @@ int CountTable::get(string seqName) {
         
         map<string, int>::iterator it = indexNameMap.find(seqName);
         if (it == indexNameMap.end()) {
+            if (hasGroupInfo()) {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(seqName, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
+            }
             m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
         }else { return it->second; }
         
@@ -663,6 +699,12 @@ int CountTable::remove(string seqName) {
             total -= thisTotal;
             indexNameMap.erase(it);
         }else {
+            if (hasGroupInfo()) {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(seqName, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + seqName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
+            }
             m->mothurOut("[ERROR]: Your count table contains does not include " + seqName + ", cannot remove."); m->mothurOutEndLine(); m->control_pressed = true;
         }
         
@@ -799,10 +841,22 @@ int CountTable::mergeCounts(string seq1, string seq2) {
     try {
         map<string, int>::iterator it = indexNameMap.find(seq1);
         if (it == indexNameMap.end()) {
+            if (hasGroupInfo()) {
+                //look for it in names of groups to see if the user accidently used the wrong file
+                if (m->inUsersGroups(seq1, groups)) {
+                    m->mothurOut("[WARNING]: Your group or design file contains a group named " + seq1 + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                }
+            }
             m->mothurOut("[ERROR]: " + seq1 + " is not in your count table. Please correct.\n"); m->control_pressed = true;
         }else { 
             map<string, int>::iterator it2 = indexNameMap.find(seq2);
             if (it2 == indexNameMap.end()) {
+                if (hasGroupInfo()) {
+                    //look for it in names of groups to see if the user accidently used the wrong file
+                    if (m->inUsersGroups(seq2, groups)) {
+                        m->mothurOut("[WARNING]: Your group or design file contains a group named " + seq2 + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
+                    }
+                }
                 m->mothurOut("[ERROR]: " + seq2 + " is not in your count table. Please correct.\n"); m->control_pressed = true;
             }else { 
                 //merge data

diff --git a/groupmap.cpp b/groupmap.cpp
index e5d8427200aed0a61aaf04a0e7084ed0e17a0a78..8e2139db771010d1b372ccfdc0a6a0523c6e4849 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -317,6 +317,10 @@ string GroupMap::getGroup(string sequenceName) {
        if (it != groupmap.end()) { //sequence name was in group file
                return it->second;      
        }else {
+        //look for it in names of groups to see if the user accidently used the wrong file
+        if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+            m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine(); 
+        }
                return "not found";
        }
 }

diff --git a/readtree.cpp b/readtree.cpp
index 4c9def84dcb08fb28084b52c8464f2fc98f0da85..b9c38e973f2cea531c03c17071ed65a155bf65a3 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -115,8 +115,10 @@ int ReadNewickTree::read(CountTable* ct) {
                
                //if you are not a nexus file 
                if ((c = filehandle.peek()) != '#') {  
-                       while((c = filehandle.peek()) != EOF) { 
+                       while((c = filehandle.peek()) != EOF) {
+                if (m->control_pressed) {  filehandle.close(); return 0; }
                                while ((c = filehandle.peek()) != EOF) {
+                    if (m->control_pressed) {  filehandle.close(); return 0; }
                                        // get past comments
                                        if(c == '[') {
                                                comment = 1;
@@ -146,9 +148,11 @@ int ReadNewickTree::read(CountTable* ct) {
                        Tree* temp = new Tree(ct);  delete temp;
                        
                        nexusTranslation(ct);  //reads file through the translation and updates treemap
-                       while((c = filehandle.peek()) != EOF) { 
+                       while((c = filehandle.peek()) != EOF) {
+                if (m->control_pressed) {  filehandle.close(); return 0; }
                                // get past comments
-                               while ((c = filehandle.peek()) != EOF) {        
+                               while ((c = filehandle.peek()) != EOF) {
+                    if (m->control_pressed) {  filehandle.close(); return 0; }
                                        if(holder == "[" || holder == "[!"){
                                                comment = 1;
                                        }
@@ -242,7 +246,7 @@ int ReadNewickTree::readTreeString(CountTable* ct) {
                        n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 
                        lc = readNewickInt(filehandle, n, T, ct);
-                       if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+                       if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); m->control_pressed = true; return -1; } //reports an error in reading
        
                        if(filehandle.peek()==','){                                                     
                                readSpecialChar(filehandle,',',"comma");
@@ -254,7 +258,7 @@ int ReadNewickTree::readTreeString(CountTable* ct) {
                
                        if(rooted != 1){                                                                
                                rc = readNewickInt(filehandle, n, T, ct);
-                               if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+                               if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); m->control_pressed = true; return -1; } //reports an error in reading
                                if(filehandle.peek() == ')'){                                   
                                        readSpecialChar(filehandle,')',"right parenthesis");
                                }                                                                                       

diff --git a/tree.cpp b/tree.cpp
index 6b799f479d12dd13da3e1579c19167dda056ba43..745893471e065abee12e7752b91c71bb37c1a635 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -1233,7 +1233,7 @@ void Tree::printTree() {
 
 /*****************************************************************/
 //this code is a mess and should be rethought...-slw
-void Tree::parseTreeFile() {
+int Tree::parseTreeFile() {
        
        //only takes names from the first tree and assumes that all trees use the same names.
        try {
@@ -1246,8 +1246,10 @@ void Tree::parseTreeFile() {
                
                //ifyou are not a nexus file 
                if((c = filehandle.peek()) != '#') {  
-                       while((c = filehandle.peek()) != ';') { 
+                       while((c = filehandle.peek()) != ';') {
+                if (m->control_pressed) {  filehandle.close(); return 0; }
                                while ((c = filehandle.peek()) != ';') {
+                    if (m->control_pressed) {  filehandle.close(); return 0; }
                                        // get past comments
                                        if(c == '[') {
                                                comment = 1;
@@ -1267,7 +1269,8 @@ void Tree::parseTreeFile() {
                        string holder = "";
                                        
                        // get past comments
-                       while(holder != "translate" && holder != "Translate"){  
+                       while(holder != "translate" && holder != "Translate"){
+                if (m->control_pressed) {  filehandle.close(); return 0; }
                                if(holder == "[" || holder == "[!"){
                                        comment = 1;
                                }
@@ -1296,7 +1299,8 @@ void Tree::parseTreeFile() {
 
                                string number, name, h;
                                h = ""; // so it enters the loop the first time
-                               while((h != ";") && (number != ";")) { 
+                               while((h != ";") && (number != ";")) {
+                    if (m->control_pressed) {  filehandle.close(); return 0; }
                                        filehandle >> number;
                                        filehandle >> name;
        
@@ -1309,7 +1313,7 @@ void Tree::parseTreeFile() {
                        }
                }
                filehandle.close();
-               
+               return 0;
                //for (int i = 0; i < globaldata->Treenames.size(); i++) {
 //cout << globaldata->Treenames[i] << endl; }
 //cout << globaldata->Treenames.size() << endl;
@@ -1327,7 +1331,8 @@ int Tree::readTreeString(ifstream& filehandle)    {
                int c;
                string name;  //, k
                
-               while((c = filehandle.peek()) != ';') { 
+               while((c = filehandle.peek()) != ';') {
+            if (m->control_pressed) {  return 0; }
 //k = c;
 //cout << " at beginning of while " <<  k << endl;                     
                        if(c == ')')  {    

diff --git a/tree.h b/tree.h
index 88e49c0d0372c16371e7c9f8254a0717ab93ae12..c8e8478edb8f313ab16d4dbeebf0a3d60a0a2698 100644 (file)
--- a/tree.h
+++ b/tree.h
@@ -69,7 +69,7 @@ private:
        //void randomLabels(string, string);
        void printBranch(int, ostream&, map<string, string>);  //recursively print out tree
     void printBranch(int, ostream&, string);
-       void parseTreeFile();   //parses through tree file to find names of nodes and number of them
+       int parseTreeFile();    //parses through tree file to find names of nodes and number of them
                                                        //this is required in case user has sequences in the names file that are
                                                        //not included in the tree. 
                                                        //only takes names from the first tree in the tree file and assumes that all trees use the same names.