[med-svn] r2386 - in trunk/packages/mustang/trunk/debian: . patches
mok0-guest at alioth.debian.org
mok0-guest at alioth.debian.org
Mon Aug 4 13:35:30 UTC 2008
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: mok at bioxray.dk -> mok at bioxray.au.dk
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 <mok at bioxray.dk>
+ Uploaders: Morten Kjeldgaard <mok at bioxray.au.dk>
* 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 <mok at bioxray.dk> Mon, 04 Aug 2008 10:42:14 +0200
+ -- Morten Kjeldgaard <mok at bioxray.au.dk> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Morten Kjeldgaard <mok at bioxray.dk>
+Uploaders: Morten Kjeldgaard <mok at bioxray.au.dk>
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 <mok at bioxray.au.dk>
-##
-## DP: This is a patch that upstream distributes from his website.
-
- at DPATCH@
-
-# 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";
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