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#include <QApplication>
#include <gsl/gsl_rng.h>
#include "mainwindowimpl.h"
#include "../warg/src/rng.h"
#include "../warg/src/mpiutils.h"
#include "mainapplicationdbusadaptor.h"
#include <QDBusConnection>
bool verbose=false;
namespace weakarg
{
//void opt() {};
ProgramOptions& opt() {static ProgramOptions po;return po;}
}
static const char * help=
"\n\
Usage: gui [OPTIONS] <filename>\n\
For graphical use, no options are necessary. \n\
To pre-run a limited set of functions, or use batch \n\
mode, the following options can be used.\n\
NOTE: They are processed IN ORDER, so be sure to open\n\
the file before using it, and set output names before\n\
producing the output!\n\
\n\
Options:\n\
-b Batch mode. Perform operations then quit \n\
without displaying the gui.\n\
-o <filename> Open the specified input XML file.\n\
-c <filename><:num> \n\
Write a csv file of the main features. If\n\
:num is provided then it changes the variables\n\
in the output (default 2):\n\
:1 - Parameters only\n\
:2 - Parameters + Number of recedges\n\
:3 - Parameters + Clonal Pairwise Distances\n\
:4 - All of the above.\n\
-T <filename> Redirect the batch processed output \n\
from stdout to the file specified.\n\
Specify "" to display to the gui.\n\
-t <list> Perform a convergence of trees test \n\
between the open file and the set of \n\
specified files (separated by commas).\n\
-g <list><:num> Perform a gelman-rubin test \n\
between the open file and the set of \n\
specified files (separated by commas). \n\
<num> takes the same meaning as for -c.\n\
-S <filename> Redirect the Score against true tree output \n\
from stdout to the file specified.\n\
Specify "" to display to the gui.\n\
-s <filename> Perform a score against true tree test\n\
against the newick-format file specified.\n\
-C <i> Performs a consensus-of-trees either with\n\
the specified cutoff (integer i=0-100) or \n\
an extended consensus if i<0.\n\
-H 0/1/2/3 Extract the heatmap. Pass 0 for no prior correction,\n\
1 for correction in number of std, 2 for correction\n\
measured in proportion or 3 for prior only.\n\
-d 0/1/2/3 Extract the pairwise clonal tree heatmap. Pass 0 for \n\
no prior correction,\n\
1 for correction in number of std, 2 for correction\n\
measured in proportion or 3 for prior only.\n\
-e <operation>:<value>:<filename>\n\
Extract iterations and thin. <operation> is either\n\
either \"thin\" with value \"x\" to thin every\n\
x'th iteration, or \"extract\" with value \"x-y\" to extract\n\
iterations between x and y. The outputfile is after\n\
the final colon.\n\
-E <filenames>:<filename>\n\
Combines the list of output files specified NOT \n\
including the current one, separated by commas, and\n\
outputs to the file after the colon.\n\
-n Start in the display mode without recombination (You must\n\
specify the outputfile with -o).\n\
-h This help message.\n\
\n\
Examples:\n\
\n\
-o test1.xml -t test2.xml -b:\n\
Performs a convergence of tree test between files\n\
test1.xml and test2.xml, printing the results to\n\
stdout and exiting the program.\n\
-o test1.xml -t test2.xml:\n\
As above, but leave the gui window open.\n\
-o test1.xml -T "" -t test2.xml:\n\
As above, but opens the results in the gui \n\
and with the gui window open.\n\
-o test1.xml -t test2.xml,test3.xml -b:\n\
Performs a convergence of tree test between files\n\
test1.xml, test2.xml and test3.xml.\n\
-t test1.xml -o test2.xml -b:\n\
Fails.\n\
";
int main(int argc, char *argv[])
{
srand(time(NULL));
QApplication app(argc, argv);
MainWindowImpl mainwindowimpl;
// register a DBus adaptor for communication with genome browser apps
MainApplicationAdaptor* maa = new MainApplicationAdaptor(&mainwindowimpl);
// connect to D-BUS and register as an object:
QDBusConnection qdbc = QDBusConnection::connectToBus(QDBusConnection::SessionBus, "org.gel.mauve.remote.WargInterface");
qdbc.registerService("org.gel.mauve.remote.WargInterface");
qdbc.registerObject("/weakarg", maa, QDBusConnection::ExportAllContents);
int grmode=2;
int expmode=2;
optind=0;
bool batch=false;
int priorcorrectHM=0;
int priorcorrectPD=0;
int recstart=0;
QString sof("COUT"),tof("COUT"),tmp;
int c;
QStringList ts,ts2;
while ((c = getopt (argc, argv, "c:o:s:d:C:S:T:t:g:be:E:H:hn")) != -1)
switch (c)
{
cout<<c<<endl;
case('o'): ts.push_back(QString(optarg));mainwindowimpl.openXMLFile(ts);break;
case('b'):batch=true;break;
case('c'):tmp=QString(optarg);ts=tmp.split(":");if(ts.size()>1){expmode=ts[1].toInt();}mainwindowimpl.on_actionExport_in_CSV_format_activated(ts[0],expmode);break;
case('S'):sof=QString(optarg);break;
case('s'):mainwindowimpl.on_actionScore_against_true_tree_activated(QString(optarg),sof);break;
case('C'):if(atoi(optarg)<0) { mainwindowimpl.on_actionExtended_consensus_of_trees_activated(tof); }else { mainwindowimpl.on_actionMajority_rule_consensus_of_trees_activated(atoi(optarg),tof);}; break;
case('T'):tof=QString(optarg);break;
case('t'):tmp=QString(optarg);ts=tmp.split(",");
mainwindowimpl.on_actionTest_convergence_of_trees_activated(ts,tof);break;
case('g'):tmp=QString(optarg);ts=tmp.split(":");if(ts.size()>1){grmode=ts[1].toInt();}
ts=ts[0].split(",");
mainwindowimpl.on_actionGelman_Rubin_test_activated(ts,tof,grmode);break;
case('H'):priorcorrectHM=atoi(optarg);
mainwindowimpl.on_actionHeat_map_activated(priorcorrectHM,tof);break;
case('d'):priorcorrectPD=atoi(optarg);
mainwindowimpl.on_actionPheat_map_activated(priorcorrectPD,tof);break;
case('e'):tmp=QString(optarg);ts2=tmp.split(":");
if(ts2.size()!=3){cout<<"Wrong arguments: Need to specify <operation>:<value>:<outputfile> for -e"<<endl<<optarg<<endl<<help<<endl;};
if(ts2[0].compare(QString("thin"),Qt::CaseInsensitive)==0){
mainwindowimpl.on_actionThinIterations_activated(ts2[2],ts2[1].toInt());
}else if(ts2[0].compare(QString("extract"),Qt::CaseInsensitive)==0){
ts=ts2[1].split("-");
mainwindowimpl.on_actionExtractIterations_activated(ts2[2],ts[0].toInt(),ts[1].toInt());
}else{ cout<<"Wrong arguments: Invalid <operation> for -e"<<endl<<optarg<<endl<<help<<endl;};
break;
case('E'):tmp=QString(optarg);ts2=tmp.split(":");
if(ts2.size()<=1){cout<<"Wrong arguments: Need to specify inputfiles and outputfile separated by \":\" to combine with -E"<<endl<<optarg<<endl<<help<<endl;};
ts=ts2[0].split(",");if(ts.size()<=1){cout<<"Need multiple inputfiles to combine with -E"<<optarg<<endl<<help<<endl;};
mainwindowimpl.on_actionCombine_output_files_activated(ts,ts2[1]);break;
case('n'):recstart=2;break;
case('h'):cout<<help<<endl;return 0;
case '?':cout<<"Wrong arguments: did not recognise "<<c<<" "<<optarg<<endl<<help<<endl;return 1;
default:
cout<<"Wrong arguments: did not recognise "<<c<<" "<<optarg<<endl<<help<<endl;return 1;
abort ();
}
if (argc-optind>=1) {
QStringList qstrs;
for (int i=1;i<argc;i++) qstrs.push_back(QString(argv[i]));
mainwindowimpl.openXMLFile(qstrs);
}
if(batch) {
return(0);
}
else {
mainwindowimpl.setRecView(recstart);
mainwindowimpl.show();
return app.exec();
}
}
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