--- /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
+
+#define TCOFFEE_4_TCOFFEE "t_coffee"
+#define TCOFFEE_type "sequence_multiple_aligner"
+#define TCOFFEE_ADDRESS "http://www.tcoffee.org"
+#define TCOFFEE_language "C++"
+#define TCOFFEE_language2 "CXX"
+#define TCOFFEE_source "http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz"
+#define TCOFFEE_update_action "always"
+#define TCOFFEE_mode "tcoffee,mcoffee,rcoffee,expresso,3dcoffee"
+#define CLUSTALO_4_TCOFFEE "clustalo"
+#define CLUSTALO_type "sequence_multiple_aligner"
+#define CLUSTALO_ADDRESS "http://www.clustal.org/omega/"
+#define CLUSTALO_language "C++"
+#define CLUSTALO_language2 "C++"
+#define CLUSTALO_source "http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz"
+#define CLUSTALO_mode "mcoffee"
+#define CLUSTALO_version "1.1.0"
+#define STRIKE_4_TCOFFEE "strike"
+#define STRIKE_type "sequence_alignment_scoring"
+#define STRIKE_ADDRESS "http://www.tcoffee.org/Projects/strike/index.html"
+#define STRIKE_language "C++"
+#define STRIKE_language2 "CXX"
+#define STRIKE_source "http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2"
+#define STRIKE_mode "tcoffee,expresso"
+#define STRIKE_version "1.2"
+#define CLUSTALW2_4_TCOFFEE "clustalw2"
+#define CLUSTALW2_type "sequence_multiple_aligner"
+#define CLUSTALW2_ADDRESS "http://www.clustal.org"
+#define CLUSTALW2_language "C++"
+#define CLUSTALW2_language2 "CXX"
+#define CLUSTALW2_source "http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz"
+#define CLUSTALW2_mode "mcoffee,rcoffee"
+#define CLUSTALW2_version "2.0.10"
+#define CLUSTALW_4_TCOFFEE "clustalw"
+#define CLUSTALW_type "sequence_multiple_aligner"
+#define CLUSTALW_ADDRESS "http://www.clustal.org"
+#define CLUSTALW_language "C"
+#define CLUSTALW_language2 "C"
+#define CLUSTALW_source "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz"
+#define CLUSTALW_mode "mcoffee,rcoffee"
+#define CLUSTALW_version "1.82"
+#define DIALIGNT_4_TCOFFEE "dialign-t"
+#define DIALIGNT_type "sequence_multiple_aligner"
+#define DIALIGNT_ADDRESS "http://dialign-tx.gobics.de/"
+#define DIALIGNT_DIR "/usr/share/dialign-tx/"
+#define DIALIGNT_language "C"
+#define DIALIGNT_language2 "C"
+#define DIALIGNT_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz"
+#define DIALIGNT_mode "mcoffee"
+#define DIALIGNT_binary "dialign-t"
+#define DIALIGNT_version "1.0.2"
+#define DIALIGNTX_4_TCOFFEE "dialign-tx"
+#define DIALIGNTX_type "sequence_multiple_aligner"
+#define DIALIGNTX_ADDRESS "http://dialign-tx.gobics.de/"
+#define DIALIGNTX_DIR "/usr/share/dialign-tx/"
+#define DIALIGNTX_language "C"
+#define DIALIGNTX_language2 "C"
+#define DIALIGNTX_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz"
+#define DIALIGNTX_mode "mcoffee"
+#define DIALIGNTX_binary "dialign-tx"
+#define DIALIGNTX_version "1.0.2"
+#define POA_4_TCOFFEE "poa"
+#define POA_type "sequence_multiple_aligner"
+#define POA_ADDRESS "http://www.bioinformatics.ucla.edu/poa/"
+#define POA_language "C"
+#define POA_language2 "C"
+#define POA_source "http://downloads.sourceforge.net/poamsa/poaV2.tar.gz"
+#define POA_DIR "/usr/share/"
+#define POA_FILE1 "blosum80.mat"
+#define POA_mode "mcoffee"
+#define POA_binary "poa"
+#define POA_version "2.0"
+#define PROBCONS_4_TCOFFEE "probcons"
+#define PROBCONS_type "sequence_multiple_aligner"
+#define PROBCONS_ADDRESS "http://probcons.stanford.edu/"
+#define PROBCONS_language2 "CXX"
+#define PROBCONS_language "C++"
+#define PROBCONS_source "http://probcons.stanford.edu/probcons_v1_12.tar.gz"
+#define PROBCONS_mode "mcoffee"
+#define PROBCONS_binary "probcons"
+#define PROBCONS_version "1.12"
+#define MAFFT_4_TCOFFEE "mafft"
+#define MAFFT_type "sequence_multiple_aligner"
+#define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/"
+#define MAFFT_language "C"
+#define MAFFT_language "C"
+#define MAFFT_source "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz"
+#define MAFFT_windows "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar"
+#define MAFFT_mode "mcoffee,rcoffee"
+#define MAFFT_binary "mafft.tar.gz"
+#define MAFFT_version "6.603"
+#define MUSCLE_4_TCOFFEE "muscle"
+#define MUSCLE_type "sequence_multiple_aligner"
+#define MUSCLE_ADDRESS "http://www.drive5.com/muscle/"
+#define MUSCLE_language "C++"
+#define MUSCLE_language2 "GPP"
+#define MUSCLE_source "http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz"
+#define MUSCLE_windows "http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip"
+#define MUSCLE_linux "http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz"
+#define MUSCLE_mode "mcoffee,rcoffee"
+#define MUSCLE_version "3.7"
+#define MUS4_4_TCOFFEE "mus4"
+#define MUS4_type "sequence_multiple_aligner"
+#define MUS4_ADDRESS "http://www.drive5.com/muscle/"
+#define MUS4_language "C++"
+#define MUS4_language2 "GPP"
+#define MUS4_source "http://www.drive5.com/muscle/muscle4.0_src.tar.gz"
+#define MUS4_mode "mcoffee,rcoffee"
+#define MUS4_version "4.0"
+#define PCMA_4_TCOFFEE "pcma"
+#define PCMA_type "sequence_multiple_aligner"
+#define PCMA_ADDRESS "ftp://iole.swmed.edu/pub/PCMA/"
+#define PCMA_language "C"
+#define PCMA_language2 "C"
+#define PCMA_source "ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz"
+#define PCMA_mode "mcoffee"
+#define PCMA_version "1.0"
+#define KALIGN_4_TCOFFEE "kalign"
+#define KALIGN_type "sequence_multiple_aligner"
+#define KALIGN_ADDRESS "http://msa.cgb.ki.se"
+#define KALIGN_language "C"
+#define KALIGN_language2 "C"
+#define KALIGN_source "http://msa.cgb.ki.se/downloads/kalign/current.tar.gz"
+#define KALIGN_mode "mcoffee"
+#define KALIGN_version "1.0"
+#define AMAP_4_TCOFFEE "amap"
+#define AMAP_type "sequence_multiple_aligner"
+#define AMAP_ADDRESS "http://bio.math.berkeley.edu/amap/"
+#define AMAP_language "C++"
+#define AMAP_language2 "CXX"
+#define AMAP_source "http://amap-align.googlecode.com/files/amap.2.0.tar.gz"
+#define AMAP_mode "mcoffee"
+#define AMAP_version "2.0"
+#define PRODA_4_TCOFFEE "proda"
+#define PRODA_type "sequence_multiple_aligner"
+#define PRODA_ADDRESS "http://proda.stanford.edu"
+#define PRODA_language "C++"
+#define PRODA_language2 "CXX"
+#define PRODA_source "http://proda.stanford.edu/proda_1_0.tar.gz"
+#define PRODA_mode "mcoffee"
+#define PRODA_version "1.0"
+#define FSA_4_TCOFFEE "fsa"
+#define FSA_type "sequence_multiple_aligner"
+#define FSA_ADDRESS "http://fsa.sourceforge.net/"
+#define FSA_language "C++"
+#define FSA_language2 "CXX"
+#define FSA_source "http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/"
+#define FSA_mode "mcoffee"
+#define FSA_version "1.15.3"
+#define PRANK_4_TCOFFEE "prank"
+#define PRANK_type "sequence_multiple_aligner"
+#define PRANK_ADDRESS "http://www.ebi.ac.uk/goldman-srv/prank/"
+#define PRANK_language "C++"
+#define PRANK_language2 "CXX"
+#define PRANK_source "http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100802.tgz"
+#define PRANK_mode "mcoffee"
+#define PRANK_version "100303"
+#define SAP_4_TCOFFEE "sap"
+#define SAP_type "structure_pairwise_aligner"
+#define SAP_ADDRESS "http://mathbio.nimr.mrc.ac.uk/wiki/Software"
+#define SAP_language "C"
+#define SAP_language2 "C"
+#define SAP_source "http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.3.tar.gz"
+#define SAP_mode "expresso,3dcoffee"
+#define SAP_version "1.1.3"
+#define TMALIGN_4_TCOFFEE "TMalign"
+#define TMALIGN_type "structure_pairwise_aligner"
+#define TMALIGN_ADDRESS "http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f"
+#define TMALIGN_language "Fortran"
+#define TMALIGN_language2 "Fortran"
+#define TMALIGN_source "http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f"
+#define TMALIGN_linux "http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign_32.gz"
+#define TMALIGN_mode "expresso,3dcoffee"
+#define TMALIGN_version "2013.05.11"
+#define MUSTANG_4_TCOFFEE "mustang"
+#define MUSTANG_type "structure_pairwise_aligner"
+#define MUSTANG_ADDRESS "http://www.cs.mu.oz.au/~arun/mustang"
+#define MUSTANG_language "C++"
+#define MUSTANG_language2 "CXX"
+#define MUSTANG_source "http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz"
+#define MUSTANG_mode "expresso,3dcoffee"
+#define MUSTANG_version "3.2.1"
+#define LSQMAN_4_TCOFFEE "lsqman"
+#define LSQMAN_type "structure_pairwise_aligner"
+#define LSQMAN_ADDRESS "empty"
+#define LSQMAN_language "empty"
+#define LSQMAN_language2 "empty"
+#define LSQMAN_source "empty"
+#define LSQMAN_update_action "never"
+#define LSQMAN_mode "expresso,3dcoffee"
+#define ALIGN_PDB_4_TCOFFEE "align_pdb"
+#define ALIGN_PDB_type "structure_pairwise_aligner"
+#define ALIGN_PDB_ADDRESS "empty"
+#define ALIGN_PDB_language "empty"
+#define ALIGN_PDB_language2 "empty"
+#define ALIGN_PDB_source "empty"
+#define ALIGN_PDB_update_action "never"
+#define ALIGN_PDB_mode "expresso,3dcoffee"
+#define FUGUE_4_TCOFFEE "fugueali"
+#define FUGUE_type "structure_pairwise_aligner"
+#define FUGUE_ADDRESS "http://www-cryst.bioc.cam.ac.uk/fugue/download.html"
+#define FUGUE_language "empty"
+#define FUGUE_language2 "empty"
+#define FUGUE_source "empty"
+#define FUGUE_update_action "never"
+#define FUGUE_mode "expresso,3dcoffee"
+#define DALILITEc_4_TCOFFEE "dalilite.pl"
+#define DALILITEc_type "structure_pairwise_aligner"
+#define DALILITEc_ADDRESS "built_in"
+#define DALILITEc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/dalilite"
+#define DALILITEc_language "Perl"
+#define DALILITEc_language2 "Perl"
+#define DALILITEc_source "empty"
+#define DALILITEc_update_action "never"
+#define DALILITEc_mode "expresso,3dcoffee"
+#define PROBCONSRNA_4_TCOFFEE "probconsRNA"
+#define PROBCONSRNA_type "RNA_multiple_aligner"
+#define PROBCONSRNA_ADDRESS "http://probcons.stanford.edu/"
+#define PROBCONSRNA_language "C++"
+#define PROBCONSRNA_language2 "CXX"
+#define PROBCONSRNA_source "http://probcons.stanford.edu/probconsRNA.tar.gz"
+#define PROBCONSRNA_mode "mcoffee,rcoffee"
+#define PROBCONSRNA_version "1.0"
+#define CONSAN_4_TCOFFEE "sfold"
+#define CONSAN_type "RNA_pairwise_aligner"
+#define CONSAN_ADDRESS "http://selab.janelia.org/software/consan/"
+#define CONSAN_language "empty"
+#define CONSAN_language2 "empty"
+#define CONSAN_source "empty"
+#define CONSAN_update_action "never"
+#define CONSAN_mode "rcoffee"
+#define RNAPLFOLD_4_TCOFFEE "RNAplfold"
+#define RNAPLFOLD_type "RNA_secondarystructure_predictor"
+#define RNAPLFOLD_ADDRESS "http://www.tbi.univie.ac.at/~ivo/RNA/"
+#define RNAPLFOLD_language "C"
+#define RNAPLFOLD_language2 "C"
+#define RNAPLFOLD_source "http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz"
+#define RNAPLFOLD_mode "rcoffee,"
+#define RNAPLFOLD_version "1.7.2"
+#define PHYLIP_4_TCOFFEE "retree"
+#define PHYLIP_type "RNA_secondarystructure_predictor"
+#define PHYLIP_ADDRESS "http://evolution.gs.washington.edu/phylip/"
+#define PHYLIP_language "C"
+#define PHYLIP_language2 "C"
+#define PHYLIP_source "http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz"
+#define PHYLIP_mode "trmsd,"
+#define PHYLIP_version "3.69"
+#define HMMTOP_4_TCOFFEE "hmmtop"
+#define HMMTOP_type "protein_secondarystructure_predictor"
+#define HMMTOP_ADDRESS "www.enzim.hu/hmmtop/"
+#define HMMTOP_language "C"
+#define HMMTOP_language2 "C"
+#define HMMTOP_source "empty"
+#define HMMTOP_binary "hmmtop"
+#define HMMTOP_update_action "never"
+#define HMMTOP_mode "tcoffee"
+#define HMMTOP_version "2.1"
+#define GOR4_4_TCOFFEE "gorIV"
+#define GOR4_type "protein_secondarystructure_predictor"
+#define GOR4_ADDRESS "http://mig.jouy.inra.fr/logiciels/gorIV/"
+#define GOR4_language "C"
+#define GOR4_language2 "C"
+#define GOR4_source "http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz"
+#define GOR4_update_action "never"
+#define GOR4_mode "tcoffee"
+#define EBIWUBLASTc_4_TCOFFEE "wublast.pl"
+#define EBIWUBLASTc_type "protein_homology_predictor"
+#define EBIWUBLASTc_ADDRESS "built_in"
+#define EBIWUBLASTc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/wublast"
+#define EBIWUBLASTc_language "Perl"
+#define EBIWUBLASTc_language2 "Perl"
+#define EBIWUBLASTc_source "empty"
+#define EBIWUBLASTc_update_action "never"
+#define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
+#define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl"
+#define EBIBLASTPGPc_type "protein_homology_predictor"
+#define EBIBLASTPGPc_ADDRESS "built_in"
+#define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
+#define EBIBLASTPGPc_language "Perl"
+#define EBIBLASTPGPc_language2 "Perl"
+#define EBIBLASTPGPc_source "empty"
+#define EBIBLASTPGPc_update_action "never"
+#define EBIBLASTPGPc_mode "psicoffee,expresso,accurate"
+#define blastall_4_TCOFFEE "blastall"
+#define blastall_type "protein_homology_predictor"
+#define blastall_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
+#define blastall_language "C"
+#define blastall_language2 "C"
+#define blastall_source "empty"
+#define blastall_update_action "never"
+#define blastall_mode "psicoffee,expresso,3dcoffee"
+#define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
+#define NCBIBLAST_type "protein_homology_predictor"
+#define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
+#define NCBIBLAST_language "C"
+#define NCBIBLAST_language2 "C"
+#define NCBIBLAST_source "empty"
+#define NCBIBLAST_update_action "never"
+#define NCBIBLAST_mode "psicoffee,expresso,3dcoffee"
+#define SOAPLITE_4_TCOFFEE "SOAP::Lite"
+#define SOAPLITE_type "library"
+#define SOAPLITE_ADDRESS "http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL"
+#define SOAPLITE_language "Perl"
+#define SOAPLITE_language2 "Perl"
+#define SOAPLITE_source "empty"
+#define _update_action "never"
+#define SOAPLITE_mode "none"
+#define XMLSIMPLE_4_TCOFFEE "XML::Simple"
+#define XMLSIMPLE_type "library"
+#define XMLSIMPLE_ADDRESS "http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm"
+#define XMLSIMPLE_language "Perl"
+#define XMLSIMPLE_language2 "Perl"
+#define XMLSIMPLE_source "empty"
+#define XMLSIMPLE_mode "psicoffee,expresso,accurate"
+//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