Author: mok0-guest Date: 2008-08-04 13:35:29 +0000 (Mon, 04 Aug 2008) New Revision: 2386
Removed: trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch Modified: trunk/packages/mustang/trunk/debian/changelog trunk/packages/mustang/trunk/debian/control trunk/packages/mustang/trunk/debian/patches/00list trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch Log: Removed patch 01-upstream which was a reverse patch to a previous version. Updated patch 02-main.cpp so it works with upstream's distributed tarball. debian/control, debian/changelog: new email address for me: [EMAIL PROTECTED] -> [EMAIL PROTECTED] Modified: trunk/packages/mustang/trunk/debian/changelog =================================================================== --- trunk/packages/mustang/trunk/debian/changelog 2008-08-04 10:52:06 UTC (rev 2385) +++ trunk/packages/mustang/trunk/debian/changelog 2008-08-04 13:35:29 UTC (rev 2386) @@ -19,7 +19,7 @@ [ Andreas Tille ] * Maintainer: Debian-Med Packaging Team - Uploaders: Morten Kjeldgaard <[EMAIL PROTECTED]> + Uploaders: Morten Kjeldgaard <[EMAIL PROTECTED]> * XS-DM-Upload-Allowed: Yes * Vcs-Browser, Vcs-Svn @@ -29,7 +29,7 @@ * debian/control has less redundany and easier working, added ref to paper. * changed debian watch to reflect version mangling in debian/changelog - -- Morten Kjeldgaard <[EMAIL PROTECTED]> Mon, 04 Aug 2008 10:42:14 +0200 + -- Morten Kjeldgaard <[EMAIL PROTECTED]> Mon, 04 Aug 2008 10:42:14 +0200 mustang (3.0-0ubuntu1) gutsy; urgency=low Modified: trunk/packages/mustang/trunk/debian/control =================================================================== --- trunk/packages/mustang/trunk/debian/control 2008-08-04 10:52:06 UTC (rev 2385) +++ trunk/packages/mustang/trunk/debian/control 2008-08-04 13:35:29 UTC (rev 2386) @@ -2,7 +2,7 @@ Section: science Priority: optional Maintainer: Debian-Med Packaging Team <[EMAIL PROTECTED]> -Uploaders: Morten Kjeldgaard <[EMAIL PROTECTED]> +Uploaders: Morten Kjeldgaard <[EMAIL PROTECTED]> DM-Upload-Allowed: yes Homepage: http://www.cs.mu.oz.au/~arun/mustang/ Build-Depends: debhelper (>= 5), dpatch Modified: trunk/packages/mustang/trunk/debian/patches/00list =================================================================== --- trunk/packages/mustang/trunk/debian/patches/00list 2008-08-04 10:52:06 UTC (rev 2385) +++ trunk/packages/mustang/trunk/debian/patches/00list 2008-08-04 13:35:29 UTC (rev 2386) @@ -1,4 +1,3 @@ -01-upstream.dpatch -02-main.cpp.dpatch -03-test_zf-cchh.dpatch +02-main.cpp +03-test_zf-cchh 04-gcc-4.3-exit Deleted: trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch =================================================================== --- trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch 2008-08-04 10:52:06 UTC (rev 2385) +++ trunk/packages/mustang/trunk/debian/patches/01-upstream.dpatch 2008-08-04 13:35:29 UTC (rev 2386) @@ -1,359 +0,0 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## upstream.dpatch by Morten Kjeldgaard <[EMAIL PROTECTED]> -## -## DP: This is a patch that upstream distributes from his website. - [EMAIL PROTECTED]@ - -# Arun S. Konagurthu -# 15 January 2008 -# -diff --recursive -c --new-file src/./CmdLineParser_2.cpp ../old/MUSTANG_v.3/src/./CmdLineParser_2.cpp -*** foo/src/./CmdLineParser_2.cpp 2008-01-15 13:34:17.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./CmdLineParser_2.cpp 2006-10-19 12:28:31.000000000 -0400 -*************** -*** 387,393 **** - static int cntr = 0 ; - if( cntr == 0 ) - { -! cerr << "MUSTANG v.3 Command Line error!\n" ; - } - - cerr << "::" << setw(2) << cntr+1 <<"::" << " invalid option: " << o << endl ; ---- 387,393 ---- - static int cntr = 0 ; - if( cntr == 0 ) - { -! cerr << "MUSTANG vO.2 Command Line error!\n" ; - } - - cerr << "::" << setw(2) << cntr+1 <<"::" << " invalid option: " << o << endl ; -*************** -*** 786,792 **** - cerr << "Try \'mustang --help\' for more information.\n" ; - exit(0) ; - } -! //cerr << "MUSTANG v.3: MUltiple STructural Alignment alNGorithm.\n" ; - //cerr << "Authors: A.S. Konagurthu, J.C. Whisstock, and P.J. Stuckey, A.M. Lesk\n" ; - //cerr << "Written by : A.S. Konagurthu\n" ; - exit(0); ---- 786,792 ---- - cerr << "Try \'mustang --help\' for more information.\n" ; - exit(0) ; - } -! //cerr << "MUSTANG v0.3: MUltiple STructural Alignment alNGorithm.\n" ; - //cerr << "Authors: A.S. Konagurthu, J.C. Whisstock, and P.J. Stuckey, A.M. Lesk\n" ; - //cerr << "Written by : A.S. Konagurthu\n" ; - exit(0); -diff --recursive -c --new-file src/./ew_2.cpp ../old/MUSTANG_v.3/src/./ew_2.cpp -*** foo/src/./ew_2.cpp 2008-01-15 13:18:34.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./ew_2.cpp 2005-11-15 19:19:56.000000000 -0500 -*************** -*** 1033,1039 **** - int start_pos ; - - //dealing with left-hand terminal -! if( I > 5 || J > 5 ) // Nterminal- NO cut - { - start_pos = ( NEQUIV-(2*EXAMINATION_SIZE) ) >= 4 ? 4 : ( NEQUIV-(2*EXAMINATION_SIZE) ) ; - CORESIZE = start_pos ; ---- 1033,1039 ---- - int start_pos ; - - //dealing with left-hand terminal -! if( I > 5 || J == 5 ) // Nterminal- NO cut - { - start_pos = ( NEQUIV-(2*EXAMINATION_SIZE) ) >= 4 ? 4 : ( NEQUIV-(2*EXAMINATION_SIZE) ) ; - CORESIZE = start_pos ; -diff --recursive -c --new-file src/./extended_lib_gen_3.cpp ../old/MUSTANG_v.3/src/./extended_lib_gen_3.cpp -*** foo/src/./extended_lib_gen_3.cpp 2008-01-15 13:18:34.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./extended_lib_gen_3.cpp 2005-11-15 19:19:56.000000000 -0500 -*************** -*** 32,40 **** - #include "macros.h" - #include "extended_lib_gen.h" - #include "de_alloc_routines.h" -- -- int Aminus1, Aminus2, Aminus3, Aminus4, Aplus1, Aplus2, Aplus3, Aplus4 ; -- int Bmprime1, Bmprime2, Bmprime3, Bmprime4, Bpprime1, Bpprime2, Bpprime3, Bpprime4 ; - /* ******************************************* - * GLOBAL FUNCTION DEFINITION * - * ******************************************* */ ---- 32,37 ---- -*************** -*** 213,218 **** ---- 210,216 ---- - { - float AAA, BBB ; - AAA = Edge_Weights[ind][A][B] ; -+ BBB = Edge_Weights[ind][A][B_orig] ; - - /* - The paln here is not to extended an arc between A and B thro' C if -*************** -*** 223,244 **** - This helps to stop random drift aways in the final multiple alignment. - at the same time allow those that are continuous. - */ -! Aminus1 = A-1 ; Aminus2 = A-2 ; Aminus3 = A-3 ; Aminus4 = A-4 ; -! if(Aminus1>=0) Bmprime1 = merge_trav->mates[0][Aminus1] ; else Bmprime1 = -1 ; -! if(Aminus2>=0) Bmprime2 = merge_trav->mates[0][Aminus2] ; else Bmprime2 = -1 ; -! if(Aminus3>=0) Bmprime3 = merge_trav->mates[0][Aminus3] ; else Bmprime3 = -1 ; -! if(Aminus4>=0) Bmprime4 = merge_trav->mates[0][Aminus4] ; else Bmprime4 = -1 ; -! - int cntm = 0; - if( Bmprime1 == B-1 ) cntm++ ; - if( Bmprime2 == B-2 ) cntm++ ; - if( Bmprime3 == B-3 ) cntm++ ; - if( Bmprime4 == B-4 ) cntm++ ; -! Aplus1 = A+1 ; Aplus2 = A+2 ; Aplus3 = A+3 ; Aplus4 = A+4 ; -! if(Aplus1<merge_trav->sizes[0]) Bpprime1 = merge_trav->mates[0][Aplus1] ; else Bpprime1 = -1 ; -! if(Aplus2<merge_trav->sizes[0]) Bpprime2 = merge_trav->mates[0][Aplus2] ; else Bpprime2 = -1 ; -! if(Aplus3<merge_trav->sizes[0]) Bpprime3 = merge_trav->mates[0][Aplus3] ; else Bpprime3 = -1 ; -! if(Aplus4<merge_trav->sizes[0]) Bpprime4 = merge_trav->mates[0][Aplus4] ; else Bpprime4 = -1 ; - int cntp = 0; - if( Bpprime1 == B+1 ) cntp++ ; - if( Bpprime2 == B+2 ) cntp++ ; ---- 221,241 ---- - This helps to stop random drift aways in the final multiple alignment. - at the same time allow those that are continuous. - */ -! int Aminus1 = A-1 ; int Aminus2 = A-2 ; int Aminus3 = A-3 ; int Aminus4 = A-4 ; -! int Bmprime1 = merge_trav->mates[0][Aminus1] ; -! int Bmprime2 = merge_trav->mates[0][Aminus2] ; -! int Bmprime3 = merge_trav->mates[0][Aminus3] ; -! int Bmprime4 = merge_trav->mates[0][Aminus4] ; - int cntm = 0; - if( Bmprime1 == B-1 ) cntm++ ; - if( Bmprime2 == B-2 ) cntm++ ; - if( Bmprime3 == B-3 ) cntm++ ; - if( Bmprime4 == B-4 ) cntm++ ; -! int Aplus1 = A+1 ; int Aplus2 = A+2 ; int Aplus3 = A+3 ; int Aplus4 = A+4 ; -! int Bpprime1 = merge_trav->mates[0][Aplus1] ; -! int Bpprime2 = merge_trav->mates[0][Aplus2] ; -! int Bpprime3 = merge_trav->mates[0][Aplus3] ; -! int Bpprime4 = merge_trav->mates[0][Aplus4] ; - int cntp = 0; - if( Bpprime1 == B+1 ) cntp++ ; - if( Bpprime2 == B+2 ) cntp++ ; -*************** -*** 263,274 **** - //if( B_orig != -99 || merge_trav->mates[1][B] != -99 || cntm >= 3 ||cntp >=3 ) - if( extend_flag == YES ) - { - -! if( Extended_Edge_Weights[ind][A][B] >= 0 ) - Extended_Edge_Weights[ind][A][B] ++ ; - else - Extended_Edge_Weights[ind][A][B] = 1 ; - } - } - temp_merge_trav_CB= temp_merge_trav_CB->link ; - } ---- 260,321 ---- - //if( B_orig != -99 || merge_trav->mates[1][B] != -99 || cntm >= 3 ||cntp >=3 ) - if( extend_flag == YES ) - { -+ float min = AAA < BBB ? AAA : BBB ; - -! if( Extended_Edge_Weights[ind][A][B] >= BBB && BBB >= 0 ) - Extended_Edge_Weights[ind][A][B] ++ ; -+ else if( BBB >= 0 ) -+ { -+ Extended_Edge_Weights[ind][A][B] = -+ Edge_Weights[ind][A][B_orig]+1 ; -+ } - else - Extended_Edge_Weights[ind][A][B] = 1 ; - } -+ -+ /* -+ int ZZZ_ind1 , ZZZ_ind2; -+ if( intermediate > I) -+ ZZZ_ind1 = (NSTRUCTS-1)*I + intermediate - ( I*(I+1)/2+1); -+ else -+ ZZZ_ind1 = (NSTRUCTS-1)*intermediate + I - ( intermediate*(intermediate+1)/2+1); -+ if( intermediate > J) -+ ZZZ_ind2 = (NSTRUCTS-1)*J + intermediate - ( J*(J+1)/2+1); -+ else -+ ZZZ_ind2 = (NSTRUCTS-1)*intermediate + J - ( intermediate*(intermediate+1)/2+1); -+ */ -+ -+ /* -+ AAA = (intermediate > I) ? -+ ((Edge_Weights[ZZZ_ind1][A][C]*tot_max)/ -+ max_edge_weights[ZZZ_ind1]) : -+ ((Edge_Weights[ZZZ_ind1][C][A]*tot_max)/ -+ max_edge_weights[ZZZ_ind1]) ; -+ BBB = (intermediate < J) ? -+ ((Edge_Weights[ZZZ_ind2][C][B]*tot_max)/ -+ max_edge_weights[ZZZ_ind2]) : -+ ((Edge_Weights[ZZZ_ind2][B][C]*tot_max)/ -+ max_edge_weights[ZZZ_ind2]) ; -+ float min = AAA < BBB ? AAA : BBB ; -+ Extended_Edge_Weights[ind][A][B]+=min ; -+ */ -+ /* -+ if( B_orig != -99 ) -+ { -+ //AAA = ((Edge_Weights[ind][A][B_orig]*tot_max)/ -+ // max_edge_weights[ZZZ_ind1]) ; -+ //BBB = ((Edge_Weights[ind][A][B]*tot_max)/ -+ // max_edge_weights[ZZZ_ind1]) ; -+ //float min = AAA < BBB ? AAA : BBB ; -+ //float max = AAA > BBB ? AAA : BBB ; -+ Extended_Edge_Weights[ind][A][B] ++ ; -+ } -+ else -+ Extended_Edge_Weights[ind][A][B] ++ ; -+ //Extended_Edge_Weights[ind][A][B] += -+ // ((Edge_Weights[ind][A][B]*tot_max)/ -+ // max_edge_weights[ZZZ_ind1]); -+ */ - } - temp_merge_trav_CB= temp_merge_trav_CB->link ; - } -diff --recursive -c --new-file src/./main.cpp ../old/MUSTANG_v.3/src/./main.cpp -*** foo/src/./main.cpp 2008-01-15 13:35:04.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./main.cpp 2006-10-19 12:39:45.000000000 -0400 -*************** -*** 65,71 **** - { - cout << "\n" ; - cout << "\t\t\t\t\033[0;37;1;41m"; -! cout << " MUSTANG (v.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ; - //cout << "\033[0;49m" ; - cout << "\t\t\t\t\033[1;33;4;1;46m"; - cout << "Authors: " ; ---- 65,71 ---- - { - cout << "\n" ; - cout << "\t\t\t\t\033[0;37;1;41m"; -! cout << " MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ; - //cout << "\033[0;49m" ; - cout << "\t\t\t\t\033[1;33;4;1;46m"; - cout << "Authors: " ; -*************** -*** 421,427 **** - DE_ALLOC_MERGE_LIB(); - DE_ALLOC_2D( ALGN , NSTRUCTS ) ; - DE_ALLOC_2D( I_ALGN , NSTRUCTS ) ; -! DE_ALLOC_2D( ALGN_QUALITY , NSTRUCTS ) ; - DE_ALLOC_1D( STRUCT_PATH ) ; - DE_ALLOC_2D( struct_names, NSTRUCTS ) ; - DE_ALLOC_2D( struct_paths, NSTRUCTS ) ; ---- 421,427 ---- - DE_ALLOC_MERGE_LIB(); - DE_ALLOC_2D( ALGN , NSTRUCTS ) ; - DE_ALLOC_2D( I_ALGN , NSTRUCTS ) ; -! if(param_D_flag) DE_ALLOC_2D( ALGN_QUALITY , NSTRUCTS ) ; - DE_ALLOC_1D( STRUCT_PATH ) ; - DE_ALLOC_2D( struct_names, NSTRUCTS ) ; - DE_ALLOC_2D( struct_paths, NSTRUCTS ) ; -diff --recursive -c --new-file src/./output_algn.cpp ../old/MUSTANG_v.3/src/./output_algn.cpp -*** foo/src/./output_algn.cpp 2008-01-15 13:39:07.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./output_algn.cpp 2005-11-15 19:19:57.000000000 -0500 -*************** -*** 331,337 **** - outfile2 << "<PRE>\n" ; - // Header starts - outfile2 << "################################################################################################\n" ; -! outfile2 << "# Program: <font color=\"Red\">MUSTANG v.3: A Multiple structural alignment algorithm</font>\n"; - outfile2 << "# Authors: <font color=\"Red\">A. S. Konagurthu, J. C. Whisstock, and P. J. Stuckey, A. M. Lesk</font>\n"; - - outfile2 << "# Rundate: <font color=\"Brown\">" << asctime(localtime(&rundate)) << "</font>"; ---- 331,337 ---- - outfile2 << "<PRE>\n" ; - // Header starts - outfile2 << "################################################################################################\n" ; -! outfile2 << "# Program: <font color=\"Red\">MUSTANG v0.3: A Multiple structural alignment algorithm</font>\n"; - outfile2 << "# Authors: <font color=\"Red\">A. S. Konagurthu, J. C. Whisstock, and P. J. Stuckey, A. M. Lesk</font>\n"; - - outfile2 << "# Rundate: <font color=\"Brown\">" << asctime(localtime(&rundate)) << "</font>"; -*************** -*** 576,582 **** - } - - outfile_ps << "\%!PS-Adobe-\n" ; -! outfile_ps << "\%\%Creator: MUSTANG v.3\n" ; - outfile_ps << "\%\%CreationDate:" << asctime(localtime(&rundate)) << "\n" ; - outfile_ps << "\%\%EndComments\n\n\n" ; - ---- 576,582 ---- - } - - outfile_ps << "\%!PS-Adobe-\n" ; -! outfile_ps << "\%\%Creator: MUSTANG v0.3\n" ; - outfile_ps << "\%\%CreationDate:" << asctime(localtime(&rundate)) << "\n" ; - outfile_ps << "\%\%EndComments\n\n\n" ; - -*************** -*** 610,616 **** - - pscolor_indx = 3 ; - line_cont = YES ; -! strcpy(strbuffer , "MUSTANG v.3: A Multiple structural alignment algorithm") ; - PSPRINT( strbuffer , bold_boolean, pscolor_indx , line_cntr++ , outfile_ps , line_cont ) ; - - ---- 610,616 ---- - - pscolor_indx = 3 ; - line_cont = YES ; -! strcpy(strbuffer , "MUSTANG-Lite v0.3: A Multiple structural alignment algorithm") ; - PSPRINT( strbuffer , bold_boolean, pscolor_indx , line_cntr++ , outfile_ps , line_cont ) ; - - -diff --recursive -c --new-file src/./pairwise_global_structalgn.cpp ../old/MUSTANG_v.3/src/./pairwise_global_structalgn.cpp -*** foo/src/./pairwise_global_structalgn.cpp 2008-01-15 13:18:34.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./pairwise_global_structalgn.cpp 2005-11-15 19:19:57.000000000 -0500 -*************** -*** 56,62 **** - //cout << "Exe_Time:" << (end -start) << endl ; - //exit(0); - void COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( int , int , float ** ) ; -! //COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( a , b, edge_weights ) ; - //if( gibberish ) - if( 0 ) - { ---- 56,62 ---- - //cout << "Exe_Time:" << (end -start) << endl ; - //exit(0); - void COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( int , int , float ** ) ; -! COPY_EDGE_WEIGHTS_TO_GLOBAL_DEFINITION( a , b, edge_weights ) ; - //if( gibberish ) - if( 0 ) - { -diff --recursive -c --new-file src/./pdb_ripper_2.cpp ../old/MUSTANG_v.3/src/./pdb_ripper_2.cpp -*** foo/src/./pdb_ripper_2.cpp 2008-01-15 13:18:34.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./pdb_ripper_2.cpp 2005-11-15 19:19:57.000000000 -0500 -*************** -*** 598,602 **** - pdb_trav -> occupancy = temp_occupancy ; - pdb_trav -> B_factor = temp_bfactor ; - } -- pdb.close() ; - } ---- 598,601 ---- -diff --recursive -c --new-file src/./superpose_on_core_2.cpp ../old/MUSTANG_v.3/src/./superpose_on_core_2.cpp -*** foo/src/./superpose_on_core_2.cpp 2008-01-15 13:41:23.000000000 -0500 ---- ../old/MUSTANG_v.3/src/./superpose_on_core_2.cpp 2006-10-19 12:37:57.000000000 -0400 -*************** -*** 139,146 **** - // Fill Headers - transf.unsetf(ios::left); - transf.unsetf(ios::right); -! transf << "REMARK Produced by MUSTANG v.3" << "\n" ; -! transf << "REMARK Authors: A S Konagurthu, J C Whisstock, P J Stuckey, and A M Lesk\n" ; - transf << "REMARK\n" ; - transf << "REMARK Structures: "; - int temp_cntr = 0 ; ---- 139,146 ---- - // Fill Headers - transf.unsetf(ios::left); - transf.unsetf(ios::right); -! transf << "REMARK Produced by MUSTANG_Lite VER. 0.2" << "\n" ; -! transf << "REMARK Authors: A S Konagurthu, P J Stuckey, J C Whisstock, and A M Lesk\n" ; - transf << "REMARK\n" ; - transf << "REMARK Structures: "; - int temp_cntr = 0 ; Modified: trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch =================================================================== --- trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch 2008-08-04 10:52:06 UTC (rev 2385) +++ trunk/packages/mustang/trunk/debian/patches/02-main.cpp.dpatch 2008-08-04 13:35:29 UTC (rev 2386) @@ -12,9 +12,9 @@ { cout << "\n" ; - cout << "\t\t\t\t\033[0;37;1;41m"; -- cout << " MUSTANG (v0.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ; +- cout << " MUSTANG (v.3): A MUltiple STuructural AligNment alGorithm. \033[0;0m\n" ; + cout << "\033[0;37;1;41m"; -+ cout << " MUSTANG (v0.3): A MUltiple STructural AligNment alGorithm. \033[0;0m\n" ; ++ cout << " MUSTANG (v.3): A MUltiple STructural AligNment alGorithm. \033[0;0m\n" ; //cout << "\033[0;49m" ; - cout << "\t\t\t\t\033[1;33;4;1;46m"; + cout << "\033[1;33;4;1;46m"; _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
