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Viewing changes to ARBDB/gb_aci.h

  • Committer: Package Import Robot
  • Author(s): Elmar Pruesse, Andreas Tille, Elmar Pruesse
  • Date: 2014-09-02 15:15:06 UTC
  • mfrom: (1.1.6)
  • Revision ID: package-import@ubuntu.com-20140902151506-jihq58b3iz342wif
Tags: 6.0.2-1
http://bugs.debian.org/741890
http://bugs.debian.org/757497
[ Andreas Tille ]
* New upstream version
  Closes: #741890
* debian/upstream -> debian/upstream/metadata
* debian/control:
   - Build-Depends: added libglib2.0-dev
   - Depends: added mafft, mrbayes
* debian/rules
   - Add explicite --remove-section=.comment option to manual strip call
* cme fix dpkg-control
* arb-common.dirs: Do not create unneeded lintian dir
* Add turkish debconf translation (thanks for the patch to Mert Dirik
  <mertdirik@gmail.com>)
  Closes: #757497

[ Elmar Pruesse ]
* patches removed:
   - 10_config.makefiles.patch,
     80_no_GL.patch
       removed in favor of creating file from config.makefile.template via 
       sed in debian/control
   - 20_Makefile_main.patch
       merged upstream
   - 21_Makefiles.patch
       no longer needed
   - 30_tmpfile_CVE-2008-5378.patch: 
       merged upstream
   - 50_fix_gcc-4.8.patch:
       merged upstream
   - 40_add_libGLU.patch:
       libGLU not needed for arb_ntree)
   - 60_use_debian_packaged_raxml.patch:
       merged upstream
   - 70_hardening.patch
       merged upstream
   - 72_add_math_lib_to_linker.patch
       does not appear to be needed
* patches added:
   - 10_upstream_r12793__show_db_load_progress:
       backported patch showing progress while ARB is loading a database
       (needed as indicator/splash screen while ARB is launching)
   - 20_upstream_r12794__socket_permissions:
       backported security fix
   - 30_upstream_r12814__desktop_keywords:
       backported add keywords to desktop (fixes lintian warning)
   - 40_upstream_r12815__lintian_spelling:
       backported fix for lintian reported spelling errors
   - 50_private_nameservers
       change configuration to put nameservers into users home dirs
       (avoids need for shared writeable directory)
   - 60_use_debian_phyml
       use phyml from debian package for both interfaces in ARB
* debian/rules:
   - create config.makefile from override_dh_configure target
   - use "make tarfile" in override_dh_install
   - remove extra cleaning not needed for ARB 6
   - use "dh_install --list-missing" to avoid missing files
   - added override_dh_fixperms target
* debian/control:
   - added libarb-dev package
   - Depends: added phyml, xdg-utils
   - Suggests: removed phyml
   - fix lintian duplicate-short-description (new descriptions)
* debian/*.install:
   - "unrolled" confusing globbing to select files
   - pick files from debian/tmp
   - moved all config files to /etc/arb
* debian/arb-common.templates: updated
* scripts:
   - removed arb-add-pt-server
   - launch-wrapper: 
     - only add demo.arb to newly created $ARBUSERDATA
     - pass commandline arguments through bin/arb wrapper
   - preinst: removing old PT server index files on upgrade from 5.5*
   - postinst: set setgid on shared PT dir
* rewrote arb.1 manfile
* added file icon for ARB databases
* using upstream arb_tcp.dat

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Lines of Context:
ARBDB/gb_aci.h
 
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// =============================================================== //
 
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//                                                                 //
 
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//   File      : gb_aci.h                                          //
 
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//   Purpose   :                                                   //
 
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//                                                                 //
 
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//   Institute of Microbiology (Technical University Munich)       //
 
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//   http://www.arb-home.de/                                       //
 
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//                                                                 //
 
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// =============================================================== //
 
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#ifndef GB_ACI_H
 
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#define GB_ACI_H
 
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#ifndef ARBDBT_H
 
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#include "arbdbt.h"
 
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#endif
 
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#ifndef _GLIBCXX_VECTOR
 
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#include <vector>
 
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#endif
 
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#define gb_assert(cond) arb_assert(cond)
 
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typedef SmartMallocPtr(char) GBL;
 
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class GBL_reference {
 
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    GBDATA     *gb_ref;            // the database entry on which the command is applied (may be species, gene, experiment, group and maybe more)
 
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    const char *default_tree_name; // if we have a default tree, its name is specified here (NULL otherwise)
 
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public:
 
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    GBL_reference(GBDATA *gbd, const char *treeName)
 
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        : gb_ref(gbd), default_tree_name(treeName) {}
 
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    GBDATA *get_main() const { return GB_get_root(gb_ref); }
 
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    GBDATA *get_ref() const { return gb_ref; }
 
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    const char *get_tree_name() const { return default_tree_name; }
 
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};
 
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class GBL_streams {
 
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    std::vector<GBL> content;
 
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public:
 
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    void insert(char *copy) { content.push_back(copy); }
 
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    void insert(GBL smartie) { content.push_back(smartie); }
 
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    const char *get(int idx) const { gb_assert(idx<size()); return &*content[idx]; }
 
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    GBL get_smart(int idx) const { gb_assert(idx<size()); return content[idx]; }
 
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    int size() const { return content.size(); }
 
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    void erase() { content.clear(); }
 
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    char *concatenated() const;
 
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    void swap(GBL_streams& other) { std::swap(content, other.content); }
 
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};
 
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struct GBL_command_arguments : public GBL_reference {
 
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    GBL_command_arguments(GBDATA       *gbd,
 
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                          const char   *treeName,
 
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                          GBL_streams&  input_,
 
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                          GBL_streams&  param_,
 
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                          GBL_streams&  output_)
 
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        : GBL_reference(gbd, treeName),
 
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          input(input_),
 
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          param(param_),
 
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          output(output_)
 
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    {}
 
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    const char *command; // the name of the current command
 
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    GBL_streams &input;
 
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    GBL_streams &param;
 
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    GBL_streams &output;
 
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};
 
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typedef GB_ERROR (*GBL_COMMAND)(GBL_command_arguments *args);
 
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struct GBL_command_table {
 
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    const char *command_identifier;
 
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    GBL_COMMAND function;
 
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};
 
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#else
 
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#error gb_aci.h included twice
 
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#endif // GB_ACI_H
 
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