From: pschloss Date: Thu, 30 Jul 2009 15:27:29 +0000 (+0000) Subject: pat's changes after generating wiki pages for 1.5 X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=143ce9d26deb936202317b52f6af473542c7df78 pat's changes after generating wiki pages for 1.5 --- diff --git a/getseqscommand.cpp b/getseqscommand.cpp index ae242b6..8406b81 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -21,7 +21,7 @@ GetSeqsCommand::GetSeqsCommand(string option){ else { //valid paramters for this command - string Array[] = {"fasta","name", "group", "align", "accnos" }; + string Array[] = {"fasta","name", "group", "alignreport", "accnos" }; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -51,13 +51,13 @@ GetSeqsCommand::GetSeqsCommand(string option){ if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } - alignfile = validParameter.validFile(parameters, "align", true); + alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } else if (alignfile == "not found") { alignfile = ""; } - if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, align."); mothurOutEndLine(); abort = true; } + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, alignreport."); mothurOutEndLine(); abort = true; } - if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, align."); mothurOutEndLine(); abort = true; } + if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport."); mothurOutEndLine(); abort = true; } } } @@ -72,7 +72,7 @@ void GetSeqsCommand::help(){ try { mothurOut("The get.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n"); mothurOut("It outputs a file containing only the sequences in the .accnos file.\n"); - mothurOut("The get.seqs command parameters are accnos, fasta, name, group and align. You must provide accnos and one of the other parameters.\n"); + mothurOut("The get.seqs command parameters are accnos, fasta, name, group and alignreport. You must provide accnos and one of the other parameters.\n"); mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"); mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); @@ -111,7 +111,7 @@ int GetSeqsCommand::execute(){ //********************************************************************************************************************** void GetSeqsCommand::readFasta(){ try { - string outputFileName = getRootName(fastafile) + "pick"; + string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile); ofstream out; openOutputFile(outputFileName, out); @@ -155,7 +155,7 @@ void GetSeqsCommand::readFasta(){ void GetSeqsCommand::readName(){ try { - string outputFileName = getRootName(namefile) + "pick"; + string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);; ofstream out; openOutputFile(outputFileName, out); @@ -240,7 +240,7 @@ void GetSeqsCommand::readName(){ void GetSeqsCommand::readGroup(){ try { - string outputFileName = getRootName(groupfile) + "pick"; + string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile); ofstream out; openOutputFile(outputFileName, out); @@ -285,7 +285,7 @@ void GetSeqsCommand::readGroup(){ //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name void GetSeqsCommand::readAlign(){ try { - string outputFileName = getRootName(alignfile) + "pick"; + string outputFileName = getRootName(alignfile) + "pick" + getExtension(alignfile);; ofstream out; openOutputFile(outputFileName, out); @@ -346,6 +346,7 @@ void GetSeqsCommand::readAlign(){ } } //********************************************************************************************************************** + void GetSeqsCommand::readAccnos(){ try { diff --git a/listseqscommand.cpp b/listseqscommand.cpp index a7d79f3..efc88e9 100644 --- a/listseqscommand.cpp +++ b/listseqscommand.cpp @@ -21,7 +21,7 @@ ListSeqsCommand::ListSeqsCommand(string option){ else { //valid paramters for this command - string Array[] = {"fasta","name", "group", "align" }; + string Array[] = {"fasta","name", "group", "alignreport" }; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -47,7 +47,7 @@ ListSeqsCommand::ListSeqsCommand(string option){ if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } - alignfile = validParameter.validFile(parameters, "align", true); + alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } else if (alignfile == "not found") { alignfile = ""; } @@ -67,7 +67,7 @@ ListSeqsCommand::ListSeqsCommand(string option){ void ListSeqsCommand::help(){ try { mothurOut("The list.seqs command reads a fasta, name, group or alignreport file and outputs a .accnos file containing sequence names.\n"); - mothurOut("The list.seqs command parameters are fasta, name, group and align. You must provide one of these parameters.\n"); + mothurOut("The list.seqs command parameters are fasta, name, group and alignreport. You must provide one of these parameters.\n"); mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n"); mothurOut("Example list.seqs(fasta=amazon.fasta).\n"); mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp index d3d12cc..a49d41a 100644 --- a/removeseqscommand.cpp +++ b/removeseqscommand.cpp @@ -21,7 +21,7 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){ else { //valid paramters for this command - string Array[] = {"fasta","name", "group", "align", "accnos" }; + string Array[] = {"fasta","name", "group", "alignreport", "accnos" }; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -51,13 +51,13 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){ if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } - alignfile = validParameter.validFile(parameters, "align", true); + alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } else if (alignfile == "not found") { alignfile = ""; } - if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, align."); mothurOutEndLine(); abort = true; } + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, alignreport."); mothurOutEndLine(); abort = true; } - if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, align."); mothurOutEndLine(); abort = true; } + if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport."); mothurOutEndLine(); abort = true; } } } @@ -72,7 +72,7 @@ void RemoveSeqsCommand::help(){ try { mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group or alignreport file.\n"); mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n"); - mothurOut("The remove.seqs command parameters are accnos, fasta, name, group and align. You must provide accnos and one of the other parameters.\n"); + mothurOut("The remove.seqs command parameters are accnos, fasta, name, group and alignreport. You must provide accnos and one of the other parameters.\n"); mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"); mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); @@ -111,7 +111,7 @@ int RemoveSeqsCommand::execute(){ //********************************************************************************************************************** void RemoveSeqsCommand::readFasta(){ try { - string outputFileName = getRootName(fastafile) + "pick"; + string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile); ofstream out; openOutputFile(outputFileName, out); @@ -153,7 +153,7 @@ void RemoveSeqsCommand::readFasta(){ void RemoveSeqsCommand::readName(){ try { - string outputFileName = getRootName(namefile) + "pick"; + string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile); ofstream out; openOutputFile(outputFileName, out); @@ -236,7 +236,7 @@ void RemoveSeqsCommand::readName(){ void RemoveSeqsCommand::readGroup(){ try { - string outputFileName = getRootName(groupfile) + "pick"; + string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile); ofstream out; openOutputFile(outputFileName, out); @@ -278,7 +278,7 @@ void RemoveSeqsCommand::readGroup(){ //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name void RemoveSeqsCommand::readAlign(){ try { - string outputFileName = getRootName(alignfile) + "pick"; + string outputFileName = getRootName(alignfile) + "pick" + getExtension(alignfile); ofstream out; openOutputFile(outputFileName, out);