--- /dev/null
+/*
+ Copyright by Matthias Hoechsmann (C) 2002-2004
+ =====================================
+ You may use, copy and distribute this file freely as long as you
+ - do not change the file,
+ - leave this copyright notice in the file,
+ - do not make any profit with the distribution of this file
+ - give credit where credit is due
+ You are not allowed to copy or distribute this file otherwise
+ The commercial usage and distribution of this file is prohibited
+ Please report bugs and suggestions to <mhoechsm@TechFak.Uni-Bielefeld.DE>
+*/
+
+#include <iostream>
+#include <sstream>
+
+#ifndef WIN32
+#include "config.h"
+#endif
+
+#ifndef HAVE_LIBRNA
+#undef HAVE_LIBG2
+#endif
+
+#include "rnaforester_options.h"
+
+RNAforesterOptions::RNAforesterOptions(int argc, const char **argv)
+: m_argv(argv)
+{
+ nrArgs = argc;
+ m_options=new OptionsInfo[NumberOfOptions];
+
+ setOption(Help, "--help",""," ","shows this help info",false);
+ setOption(Version, "--version",""," ","shows version information",false);
+ setOption(OutputAlignmentDotFormat, "-dot","=file"," ","show alignment forest in dot format",true);
+ setOption(CalculateDistance, "-d",""," ","calculate distance instead of similarity",false);
+ setOption(RelativeScore, "-r",""," ","calculate relative score",false);
+ setOption(LocalSimilarity, "-l",""," ","local similarity",false);
+ setOption(LocalSubopts, "-so","=int"," ","local suboptimal alignments within int%",false);
+ setOption(SmallInLarge, "-s",""," ","small-in-large similarity",false);
+ setOption(Multiple, "-m",""," ","multiple alignment mode",false);
+ setOption(ClusterThreshold, "-mt","=double"," ","clustering threshold",false);
+ setOption(ClusterJoinCutoff, "-mc","=double"," ","clustering cutoff",false);
+#ifdef HAVE_LIBRNA // This features require the ViennaRNA library
+ setOption(PredictProfile, "-p",""," ","predict structures from sequences",false);
+ setOption(PredictMinPairProb, "-pmin","=double"," ","minimum basepair frequency for prediction",false);
+#endif
+ setOption(SaveProfile, "-sp","=file"," ","save profile",false);
+ setOption(ProfileSearch, "-ps","=file"," ","profile search",false);
+
+ setOption(TreeEdit, "-e",""," ","use tree edit model to calculate distance and similarity",true);
+ setOption(GlobalAlignment, "-g",""," ","calculate global alignment in its original version",true);
+ setOption(BpRepScore, "-pm","=int"," ","basepair(bond) match score",false);
+ setOption(BpDelScore, "-pd","=int"," ","basepair bond indel score",false);
+ setOption(BMatchScore, "-bm","=int"," ","base match score",false);
+ setOption(BRepScore, "-br","=int"," ","base mismatch score",false);
+ setOption(BDelScore, "-bd","=int"," ","base indel score",false);
+ setOption(RIBOSUMScore, "--RIBOSUM",""," ","RIBOSUM85-60 scoring matrix (base-pair substitutions)",false);
+ setOption(ConsensusMinPairProb, "-cmin","=double"," ","minimum basepair frequency for consensus structure",false);
+#ifdef HAVE_LIBG2 // This features require the g2 library
+ setOption(MakeSquigglePlot, "-2d",""," ","generate alignment 2D plots in postscript format",false);
+ setOption(SquiggleHideBaseNumbers, "--2d_hidebasenum",""," ","hide base numbers in 2D plot",false);
+ setOption(SquiggleBaseNumberInterval,"--2d_basenuminterval","=n"," ","show every n-th base number",false);
+ setOption(SquiggleGreyColors, "--2d_grey",""," ","use only grey colors in 2D plots",false);
+ setOption(SquiggleScaleFactor, "--2d_scale","=double"," ","scale factor for the 2d plots",false);
+ setOption(SquiggleGenerateFIG, "--2d_fig",""," ","generate additional fig file of 2d plot",false);
+#ifdef HAVE_LIBGD // This features require the gd library
+ setOption(SquiggleGeneratePNG, "--2d_png",""," ","generate additional png file of 2d plot",false);
+ setOption(SquiggleGenerateJPG, "--2d_jpg",""," ","generate additional jpg file of 2d plot",false);
+#endif
+#endif
+ setOption(ReadFromFile, "-f","=file"," ","read input from file",false);
+ // setOption(SaveMultipleAliFile, "-sm","=file"," ","save multiple alignment as binary file",true);
+ setOption(NoScale, "--noscale",""," ","suppress output of scale",false);
+ setOption(MakeDotForInputTrees, "-idot",""," ","make dot files for the input trees",true);
+#ifdef HAVE_LIBRNA // This features require the ViennaRNA library and the libxml++ library
+#ifdef HAVE_LIBXMLPLUSPLUS
+#ifdef HAVE_LIBXML2
+ setOption(GenerateXML, "--xml",""," ","generate xml file in RNAStructAlignmentML format",false);
+ setOption(XmlOutputFile, "--xml_output",""," ","name of xml output file",false);
+#endif
+#endif
+#endif
+ setOption(SecretHelp, "--shelp",""," ","shows this help info",true);
+ setOption(ShowOnlyScore, "--score",""," ","compute only scores, no alignment",false);
+ setOption(FastaOutput, "--fasta",""," ","generate fasta output of alignments",false);
+
+ setOption(SpaceTimeInfo, "--spacetime",""," ","space and time measurements",true);
+
+ // set the arguments that can be seperated by spaces
+ stringstream ss;
+ for(int i=0;i<NumberOfOptions;i++)
+ {
+ if(!m_options[i].parameter.empty())
+ ss << m_options[i].tag << "|";
+ }
+
+ Arguments::setArgumentsWithSpaces(ss.str());
+ m_args = new Arguments(argc,argv);
+
+ // check options for compatibility
+ //exclude(LocalSimilarity,Multiple);
+ exclude(LocalSimilarity,SmallInLarge);
+ //exclude(SmallInLarge,Multiple);
+
+#ifdef HAVE_LIBG2 // This features require the g2 library
+ exclude(SquiggleHideBaseNumbers,Multiple);
+ exclude(SquiggleBaseNumberInterval,Multiple);
+#endif
+ exclude(CalculateDistance,LocalSimilarity);
+ exclude(CalculateDistance,RIBOSUMScore);
+ exclude(CalculateDistance,RelativeScore);
+ exclude(CalculateDistance,Multiple);
+ exclude(CalculateDistance,SmallInLarge);
+ exclude(Multiple,RIBOSUMScore);
+ exclude(RIBOSUMScore,BpRepScore);
+ exclude(RIBOSUMScore,BMatchScore);
+ exclude(RIBOSUMScore,BDelScore);
+
+ requires(LocalSubopts,LocalSimilarity);
+ requires(ClusterThreshold,Multiple);
+ requires(ClusterJoinCutoff,Multiple);
+#ifdef HAVE_LIBRNA // This features require the ViennaRNA library
+ requires(PredictProfile,Multiple);
+ requires(PredictMinPairProb,PredictProfile);
+#endif
+
+
+ // exclude(TreeEdit,Multiple);
+ // exclude(TreeEdit,LocalSimilarity);
+ // exclude(TreeEdit,RIBOSUMScore);
+ // exclude(GlobalAlignment,Multiple);
+ // exclude(GlobalAlignment,LocalSimilarity);
+ // exclude(GlobalAlignment,RIBOSUMScore);
+ // exclude(GlobalAlignment,TreeEdit);
+}
+
+RNAforesterOptions::~RNAforesterOptions()
+{
+ delete[] m_options;
+ delete m_args;
+}
+
+inline void RNAforesterOptions::setOption(RNAforesterOption i,string tag, string parameter, string filler, string description, bool hidden)
+{
+ m_options[i].tag=tag;
+ m_options[i].parameter=parameter;
+ m_options[i].filler=filler;
+ m_options[i].description=description;
+ m_options[i].hidden=hidden;
+}
+
+bool RNAforesterOptions::has(RNAforesterOption option) const
+{
+ return m_args->has(m_options[option].tag);
+}
+
+const char** RNAforesterOptions::getArgs() const
+{
+ return m_argv;
+}
+
+const unsigned int RNAforesterOptions::getNrOfOptions() const
+{
+ return nrArgs;
+}
+
+void RNAforesterOptions::help()
+{
+ cout << "Usage: " << m_argv[0] << " [options]" << endl;
+
+ for(int i=0;i<NumberOfOptions;i++)
+ {
+ if(!m_options[i].hidden)
+ cout << m_options[i].tag << m_options[i].parameter << m_options[i].filler << m_options[i].description << endl;
+ }
+}
+
+void RNAforesterOptions::secretHelp()
+{
+ cout << "Usage: " << m_argv[0] << " [options]" << endl;
+ cout << "help including hidden parameters" << endl;
+
+ for(int i=0;i<NumberOfOptions;i++)
+ {
+ cout << m_options[i].tag << m_options[i].parameter << m_options[i].filler << m_options[i].description;
+ if(m_options[i].hidden)
+ cout << " *";
+ cout << endl;
+ }
+}
+
+string RNAforesterOptions::generateFilename(RNAforesterOption option, const string &suffix, const string &defName, Uint count) const
+{
+ string s;
+
+ get(option,s,string(""));
+ if(s=="")
+ {
+ if(has(ReadFromFile))
+ {
+ ostringstream ss;
+
+ get(ReadFromFile,s,defName);
+ ss << s;
+ if(count)
+ ss << "_" << count;
+
+ ss << suffix << '\0';
+
+ s=ss.str();
+ }
+ else
+ {
+ s=defName;
+ }
+ }
+
+ return s;
+}
+
+void RNAforesterOptions::exclude(RNAforesterOption opt1, RNAforesterOption opt2)
+{
+ if(has(opt1) && has(opt2))
+ throw IncompatibleException(m_options[opt1].tag,m_options[opt2].tag);
+}
+
+void RNAforesterOptions::requires(RNAforesterOption opt1, RNAforesterOption opt2)
+{
+ if(has(opt1) && !has(opt2))
+ throw RequiresException(m_options[opt1].tag,m_options[opt2].tag);
+}
+
+// ************************************************
+
+void RNAforesterOptions::IncompatibleException::showError()
+{
+ cerr << "The options " << m_tag1 << " and " << m_tag2 << " exclude each other." << endl;
+}
+
+void RNAforesterOptions::RequiresException::showError()
+{
+ cerr << "The options " << m_tag1 << " requires option " << m_tag2 << "." << endl;
+}
git://source.jalview.org / jabaws.git / blobdiff