--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*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@europe.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 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 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.
+*/
git://source.jalview.org / jabaws.git / blobdiff