Compiling a C++ 'Hello world' program using the #NCBI C++ toolbox: my notebook.

This post is my notebook for compiling a simple C++ application using the NCBI C++ toolbox (http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/).

This application prints 'Hello world' and takes two arguments:

• '-o' to specificiy the output filename (default is standard output)
• '-n' to set the name to be printed (default: "Word !")

The code I used is the one containing in the distribution of blast 2.2.30

The program itself is a C++ Class, it extends the class CNcbiApplication

(...)
class HelloApp : public CNcbiApplication
    {
    (...)
    }

In the constructor, we just set the name and the version of the program:

HelloApp::HelloApp()
    {
    CRef<CVersion> version(new CVersion());
    version->SetVersionInfo(1, 0, 0);
    this->SetFullVersion(version);
    }

The destructor is void

HelloApp::~HelloApp()
    {
    }

an HelloApp::Init() method is used to register the command line arguments.

void HelloApp::Init()
    {
    CArgDescriptions* arg_desc = new CArgDescriptions ;
    arg_desc->SetUsageContext(
        GetArguments().GetProgramBasename(),
        "Hello NCBI"
        );
    (...)

in HelloApp::Init() we register the '-o' argument:

arg_desc->AddDefaultKey(
    "o",/* name */
    "output_file_name",/* synopsis */
    "output file name",/* comment */
    CArgDescriptions::eOutputFile, /* argument type */
    "-" /* default value*/
    );

and the '-n' argument:

arg_desc->AddDefaultKey(
    "n",/* name */
    "name",/* synopsis */
    "Name",/* comment */
    CArgDescriptions::eString, /* argument type */
    "World !" /* default value*/
    );

once the two arguments have been registered, the new command line is pushed in the application:

SetupArgDescriptions( arg_desc );

the HelloApp::Run() method is the workhorse of the program. Here, we get the output stream and we print the name.

int HelloApp::Run()
    {
    /* get output stream */
    CNcbiOstream& out =  this->GetArgs()["o"].AsOutputFile();
    out << "Hello " << this->GetArgs()["n"].AsString() << endl;
    return 0;
    }

All in one:

#include <memory>
#include <limits>
#include "corelib/ncbiapp.hpp"
#include <ctype.h>



USING_NCBI_SCOPE;

/**
 * Hello NCBI
 *      testing NCBI C++ toolbox
 *  Motivation:
 *      filter sequences on size
 *  Author:
 *      Pierre Lindenbaum PhD 2015
 *
 */
class HelloApp : public CNcbiApplication /* extends a basic NCBI application defined in c++/include/corelib/ncbiapp.hpp */
    {
    public:

        /* constructor, just set the version to '1.0.0'*/
        HelloApp()
            {
            CRef<CVersion> version(new CVersion());
            version->SetVersionInfo(1, 0, 0);
            this->SetFullVersion(version);
            }
            
            
        /* called to initialize rge program.
        *  The default behavior of this in 'CNcbiApplication' is "do nothing".
        *  Here, we set the command line arguments.
        */
        virtual void Init()
            {
            CArgDescriptions* arg_desc = new CArgDescriptions ; /* defined in /c++/include/corelib/ncbiargs.hpp */
            arg_desc->SetUsageContext(
                GetArguments().GetProgramBasename(),
                "Hello NCBI"
                );
            
           /* argument for output file */
           arg_desc->AddDefaultKey(
                    "o",/* name */
                    "output_file_name",/* synopsis */
                    "output file name",/* comment */
                    CArgDescriptions::eOutputFile, /* argument type */
                    "-" /* default value*/
                    );
            /* argument for name */
           arg_desc->AddDefaultKey(
                    "n",/* name */
                    "name",/* synopsis */
                    "Name",/* comment */
                    CArgDescriptions::eString, /* argument type */
                    "World !" /* default value*/
                    );
            
            /* push this command args */
            SetupArgDescriptions( arg_desc );
            }   
        
        /* class destructor */
        virtual ~HelloApp()
            {
            }
        
        /* workhorse of the program */
        virtual int Run()
            {
            /* get output stream */
            CNcbiOstream& out =  this->GetArgs()["o"].AsOutputFile();
            out << "Hello " << this->GetArgs()["n"].AsString() << endl;
            return 0;
            }
    };

int main(int argc,char** argv)
    {
    return HelloApp().AppMain(
        argc,
        argv,
        0, /* envp Environment pointer */
        eDS_ToStderr,/* log message. In /c++/include/corelib/ncbidiag.hpp  */
        0, /* Specify registry to load, as per LoadConfig() */
        "hello" /* Specify application name */
        );
    }

Compiling

there is a bunch of libaries available under ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib and it's hard to know which are the one required for linking. I put everything in my command line. All in one it looks like:

g++  -std=gnu++11  -finline-functions -fstrict-aliasing -fomit-frame-pointer    
-Iblast2.2.30/ncbi-blast-2.2.30+-src/c++/include -Iblast2.2.30/ncbi-blast-2.2.30
+-src/c++/ReleaseMT/inc  -Wno-deprecated -Wno-deprecated-declarations -o hello h
ello.cpp -Lblast2.2.30/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lblast_app_util
 -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb_rmt-st
atic -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_forma
t-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lblastxml2-stati
c -lxcgi-static -lxhtml-static -lxblast-static -lxalgoblastdbindex-static -lcomp
osition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmask
s_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjread-
static -lvariation-static -lcreaders-static -lsubmit-static -lxnetblastcli-stati
c -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmg
r-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_
id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldba
pi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-static -lid1
-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgen
ome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseqcode-st
atic -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-st
atic -lxser-static -lxutil-static -lxncbi-static -lgomp -lz -lbz2 -ldl -lnsl -lr
t -lm -lpthread -Lblast2.2.30/ncbi-blast-2.2.30+-src/c++/ReleaseMT/lib -lblast_a
pp_util -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb
_rmt-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastd
b_format-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lblastxml
2-static -lxcgi-static -lxhtml-static -lxblast-static -lxalgoblastdbindex-static
 -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -l
seqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxo
bjread-static -lvariation-static -lcreaders-static -lsubmit-static -lxnetblastcl
i-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -
lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_x
reader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-stati
c -ldbapi_driver-static -lncbi_xreader-static -lxconnext-static -lxconnect-stati
c -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-stati
c -lgenome_collection-static -lseqedit-static -lseqset-static -lseq-static -lseq
code-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgen
eral-static -lxser-static -lxutil-static -lxncbi-static -lgomp -lz -lbz2 -ldl -l
nsl -lrt -lm -lpthread

Testing

run without arguments:

$ ./hello 
Hello World !

run with arguments:

$ ./hello -n Pierre
Hello Pierre
$ ./hello -n Pierre -o test.txt && cat test.txt 
Hello Pierre

errors:

$ ./hello -x Pierre
USAGE
  hello [-h] [-help] [-xmlhelp] [-o output_file_name] [-n name]
    [-logfile File_Name] [-conffile File_Name] [-version] [-version-full]
    [-dryrun]

DESCRIPTION
   Hello NCBI

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Unknown argument: "x"

get help:

$ ./hello -help
USAGE
  hello [-h] [-help] [-xmlhelp] [-o output_file_name] [-n name]
    [-logfile File_Name] [-conffile File_Name] [-version] [-version-full]
    [-dryrun]

DESCRIPTION
   Hello NCBI

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -xmlhelp
   Print USAGE, DESCRIPTION and ARGUMENTS in XML format; ignore all other
   parameters
 -o <File_Out>
   output file name
   Default = `-'
 -n <String>
   Name
   Default = `World !'
 -logfile <File_Out>
   File to which the program log should be redirected
 -conffile <File_In>
   Program's configuration (registry) data file
 -version
   Print version number;  ignore other arguments
 -version-full
   Print extended version data;  ignore other arguments
 -dryrun
   Dry run the application: do nothing, only test all preconditions

get xml help:

$ ./hello -xmlhelp | xmllint --format -
<?xml version="1.0"?>
<ncbi_application xmlns="ncbi:application" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:schemaLocation="ncbi:application ncbi_application.xsd">
  <program type="regular">
    <name>hello</name>
    <version>1.0.0</version>
    <description>Hello NCBI</description>
  </program>
  <arguments>
    <key name="conffile" type="File_In" optional="true">
      <description>Program's configuration (registry) data file</description>
      <synopsis>File_Name</synopsis>
    </key>
    <key name="logfile" type="File_Out" optional="true">
      <description>File to which the program log should be redirected</description>
      <synopsis>File_Name</synopsis>
    </key>
    <key name="n" type="String" optional="true">
      <description>Name</description>
      <synopsis>name</synopsis>
      <default>World !</default>
    </key>
    <key name="o" type="File_Out" optional="true">
      <description>output file name</description>
      <synopsis>output_file_name</synopsis>
      <default>-</default>
    </key>
    <flag name="dryrun" optional="true">
      <description>Dry run the application: do nothing, only test all preconditions</description>
    </flag>
    <flag name="h" optional="true">
      <description>Print USAGE and DESCRIPTION;  ignore all other parameters</description>
    </flag>
    <flag name="help" optional="true">
      <description>Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters</description>
    </flag>
    <flag name="version" optional="true">
      <description>Print version number;  ignore other arguments</description>
    </flag>
    <flag name="version-full" optional="true">
      <description>Print extended version data;  ignore other arguments</description>
    </flag>
    <flag name="xmlhelp" optional="true">
      <description>Print USAGE, DESCRIPTION and ARGUMENTS in XML format; ignore all other parameters</description>
    </flag>
  </arguments>
</ncbi_application>

That's it,
Pierre

Playing with the Gimp server: my notebook

In the following post, I'll show how the Gimp can be used as a server that will read and execute some statements in the scheme programming language. The scheme script will be used to downlad, resize and filter an image from the web.

Starting the Gimp Server

Go in menu Filters→Script-Fu→Start Server

The original image

(3156 x 2538)Barbara McClintock in the lab at Cold Spring Harbor in 1947

The script

Here is the scheme script:

The java client

The following java client will send the previous scheme script to the gimp server. The simple protocol used by GIMP is described on this page.

>javac GimpClient.java
>java GimpClient input.scm
Success

The result

That's it,


Pierre