/******************************COPYRIGHT NOTICE*******************************/
/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  30 Nov 2019 - 10:22.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
/*                                                                                          */
/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
/*    it under the terms of the GNU General Public License as published by                  */
/*    the Free Software Foundation; either version 2 of the License, or                     */
/*    (at your option) any later version.                                                   */
/*                                                                                          */
/*    T-COFFEE is distributed in the hope that it will be useful,                           */
/*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
/*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
/*    GNU General Public License for more details.                                          */
/*                                                                                          */
/*    You should have received a copy of the GNU General Public License                     */
/*    along with Foobar; if not, write to the Free Software                                 */
/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
/*...............................................                                           */
/*  If you need some more information                                                       */
/*  cedric.notredame@gmail.com                                                             */
/*...............................................                                           */
/******************************COPYRIGHT NOTICE*******************************/
/* PROGRAM PATH - DO NOT CHANGE MANUALLY THIS FILE -- It is generated automatically by the build process -- See the 'update' target in the 'makefile' for more details */

//ERROR MESSAGES


#define ADDRESS_BUILT_IN "built_in"
#define PROGRAM_BUILT_IN "t_coffee"
#define TEST_WWWSITE_4_TCOFFEE "www.google.com"


//TclinkdbStart
/********************************************/
/*            Predictions                    */
/********************************************/
#define RNAPLFOLD_4_TCOFFEE "RNAplfold"
#define RNAPLFOLD_ADDRESS "http://www.tbi.univie.ac.at/~ivo/RNA/"

#define HMMTOP_4_TCOFFEE "hmmtop"
#define HMMTOP_ADDRESS "www.enzim.hu/hmmtop/"

#define GOR4_4_TCOFFEE "gorIV"
#define GOR4_ADDRESS "http://mig.jouy.inra.fr/logiciels/gorIV/"


/********************************************/
/*            SEQUENCE ALIGNMENT            */
/********************************************/

/*MSA Methods*/
#define CLUSTALW_4_TCOFFEE "clustalw"
#define CLUSTALW_ADDRESS "ftp://www.ebi.ac.uk/pub/clustalw"

#define CLUSTALW2_4_TCOFFEE "clustalw2"
#define CLUSTALW2_ADDRESS "http://www.clustal.org"

#define CLUSTALO_ADDRESS "http://www.clustal.org/omega/"
#define CLUSTALO_4_TCOFFEE "clustalo"

#define POA_4_TCOFFEE "poa"
#define POA_ADDRESS "http://www.bioinformatics.ucla.edu/poa/"
#define POA_DIR  "/usr/share/"
#define POA_FILE1 "blosum80.mat"

#define PROBCONS_4_TCOFFEE "probcons"
#define PROBCONSRNA_4_TCOFFEE "probconsRNA"
#define PROBCONS_ADDRESS  "http://probcons.stanford.edu/"


#define MSAPROBS_4_TCOFFEE "probcons"
#define MSAPROBS_4_TCOFFEE "probconsRNA"
#define MSAPROBS_ADDRESS   "http://msaprobs.sourceforge.net/homepage.htm#latest"




#define DIALIGNT_4_TCOFFEE "dialign-t"
#define DIALIGNT_ADDRESS "http://dialign-t.gobics.de/"
#define DIALIGNT_DIR "/usr/share/dialign-t/"

#define DIALIGNTX_4_TCOFFEE "dialign-tx"
#define DIALIGNTX_ADDRESS  "http://dialign-tx.gobics.de/"
#define DIALIGNTX_DIR "/usr/share/dialign-tx/"

#define MSA_4_TCOFFEE "msa.pl"
#define MSA_ADDRESS "https://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html"

#define DCA_4_TCOFFEE "dca.pl"
#define DCA_ADDRESS "https://bibiserv2.cebitec.uni-bielefeld.de/applications/dca/resources/downloads/dca-1.1-src.tar.gz"

#define MAFFT_4_TCOFFEE "mafft"
#define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/"

#define MUSCLE_4_TCOFFEE "muscle"
#define MUSCLE_ADDRESS "http://www.drive5.com/muscle/"

#define TCOFFEE_4_TCOFFEE "t_coffee"
#define TCOFFEE_ADDRESS "http://www.tcoffee.org"


#define PCMA_4_TCOFFEE "pcma"
#define PCMA_ADDRESS "ftp://iole.swmed.edu/pub/PCMA/"

#define KALIGN_4_TCOFFEE "kalign"
#define KALIGN_ADDRESS "http://msa.cgb.ki.se"

#define AMAP_4_TCOFFEE "amap"
#define AMAP_ADDRESS "http://bio.math.berkeley.edu/amap/"

#define PRODA_4_TCOFFEE "proda"
#define PRODA_ADDRESS   "http://proda.stanford.edu/"

#define PRANK_4_TCOFFEE "prank"
#define PRANK_ADDRESS   "http://www.ebi.ac.uk/goldman-srv/prank/"

#define CONSAN_4_TCOFFEE "sfold"
#define CONSAN_ADDRESS "http://selab.janelia.org/software/consan/"



/********************************************/
/*           BLAST CLIEENTS                     */
/********************************************/
#define EBIWUBLASTc_4_TCOFFEE "wublast.pl"
#define EBIWUBLASTc_ADDRESS "built_in"
//#define EBIWUBLASTc_ADDRESS "http://www.ebi.ac.uk/Tools/webservices/services/wublast"


#define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl"
#define EBIBLASTPGPc_ADDRESS "built_in"

#define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
#define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"


//coffee_pot_dbEnd
/*Blast Server*/

          /* BLAST_4_TCOFFEE
	     can take the following values: 
	         NCBI  ->use blastcl3 ftp://ftp.ncbi.nih.gov/blast/network/netblast/
		 SIB   ->contact the sib
		 LOCAL ->you must have blast installed
	  */





/********************************************/
/*            STRUCTURE ALIGNMENT           */
/********************************************/
#define DALILITEc_4_TCOFFEE "dalilite.pl"
#define DALILITEc_ADDRESS "built_in"
/*Sap*/
#define SAP_4_TCOFFEE         "sap"
#define SAP_ADDRESS           "http://mathbio.nimr.mrc.ac.uk/wiki/Software"
/*TM-Align*/
#define TMALIGN_4_TCOFFEE         "TMalign"
#define TMALIGN_ADDRESS           "http://zhang.bioinformatics.ku.edu/TM-align/"
/*Mustang*/
#define MUSTANG_4_TCOFFEE         "mustang"
#define MUSTANG_ADDRESS           "http://www.cs.mu.oz.au/~arun/mustang/"

#define LSQMAN_4_TCOFFEE      "lsqman"

/*Align_pdb*/
#define ALIGN_PDB_4_TCOFFEE   "align_pdb"

/*Fugue*/
#define FUGUE_4_TCOFFEE   "fugueali"
#define FUGUE_ADDRESS     "http://www-cryst.bioc.cam.ac.uk/fugue/download.html"

//TclinkdbEnd
/*New Methods*/
/********************************************/
/*            Various Methoids              */
/********************************************/
#define METHODS_4_TCOFFEE  "~/.t_coffee/methods/"
#define METHOD_4_MSA_WEIGHTS "petra_weight"
/********************************************/
/*            SEQAN LIBRARY                  */
/********************************************/
#define SEQAN_TCOFFEE_4_TCOFFEE "seqan_tcoffee"
/********************************************/
/*            REFORMATING  AND UTILITIES                 */
/********************************************/
#define WGET_4_TCOFFEE "wget"
#define WGET_ADDRESS "http://www.gnu.org/software/wget/"

#define CURL_4_TCOFFEE "curl"
#define CURL_ADDRESS "http://curl.haxx.se/"

#define SEQ_REFORMAT_4_TCOFFEE          "seq_reformat"
#define PS2PDF                          "ps2pdf"
#define EXTRACT_FROM_PDB_4_TCOFFEE      "extract_from_pdb"
#define BLAST_ALN2FASTA_ALN             "blast_aln2fasta_aln.pl"
#define FASTA_ALN2FASTA_ALN_UNIQUE_NAME "fasta_aln2fasta_aln_unique_name.pl"
#define MSF_ALN2FASTA_ALN               "msf_aln2fasta_aln.pl"
#define SEQ2MSA_WEIGHT        "seq2msa_weight"
/********************************************/
/*            DEPRECATED DEF                */
/********************************************/
//Deprecated definitions
#define SIB_BLAST_4_TCOFFEE "blastall.remote"
#define LOCAL_BLAST_4_TCOFFEE "blastall"
#define BLAST_DB_4_TCOFFEE "nr"
#define NCBI_BLAST_4_TCOFFEE ""
/********************************************/
/*            PARAMETER_FILE                */
/********************************************/




/*               PARAMETER FILES               */
#define COLOR_FILE         "seq_reformat.color"
/*This file specifies the 10 colors available to seq_reformat.
If the file is not on the system, hard coded defaults will be used.
The format is as follow:

-------------------------------------------------------------------------------------------
<Your comments (as many lines as needed >
*
<number in the range 0-9> <HTML code> <R value (float)> <G value (float)> <B value (float)>
-------------------------------------------------------------------------------------------
the RGB values are used for the post-script generation, the html code is used in html documents.
*/
