ChangeLog

+2017-02-21  Nicolas Joly  <njoly@pasteur.fr>
+
+	* configure.ac: Bump version to 0.99d.
+
+2017-02-21  Nicolas Joly  <njoly@pasteur.fr>
+
+	* test/embl.sh: Exercize long sequence name.
+
+2017-02-21  Nicolas Joly  <njoly@pasteur.fr>
+
+	* test/genbank.sh: Exercize long sequence name.
+
+2017-02-21  Nicolas Joly  <njoly@pasteur.fr>
+
+	* lib/sequence/sprotl.l: Allow long sequence names (up to 75
+	characters).
+	* test/sprot.sh: Exercize it.
+
+2017-02-21  Nicolas Joly  <njoly@pasteur.fr>
+
+	* lib/sequence/embl*.[ly]: Reject sequence names that are followed
+	by a space character.
+	* test/embl.sh: Exercize it.
+
 2015-12-02  Nicolas Joly  <njoly@pasteur.fr>
 
 	* lib/sequence/sprotl.l: Adjust TrEmbl allowed entry names.

Makefile.in

@@ -161,7 +161,7 @@ CSCOPE = cscope
 DIST_SUBDIRS = $(SUBDIRS)
 am__DIST_COMMON = $(srcdir)/Makefile.in AUTHORS COPYING ChangeLog \
 	INSTALL NEWS README TODO compile config.guess config.sub \
-	install-sh ltmain.sh missing mkinstalldirs ylwrap
+	depcomp install-sh ltmain.sh missing mkinstalldirs ylwrap
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for squizz 0.99c.
+# Generated by GNU Autoconf 2.69 for squizz 0.99d.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -587,8 +587,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='squizz'
 PACKAGE_TARNAME='squizz'
-PACKAGE_VERSION='0.99c'
-PACKAGE_STRING='squizz 0.99c'
+PACKAGE_VERSION='0.99d'
+PACKAGE_STRING='squizz 0.99d'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -765,6 +765,7 @@ with_aix_soname
 with_gnu_ld
 with_sysroot
 enable_libtool_lock
+enable_largefile
 '
       ac_precious_vars='build_alias
 host_alias
@@ -1318,7 +1319,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures squizz 0.99c to adapt to many kinds of systems.
+\`configure' configures squizz 0.99d to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1388,7 +1389,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of squizz 0.99c:";;
+     short | recursive ) echo "Configuration of squizz 0.99d:";;
    esac
   cat <<\_ACEOF
 
@@ -1407,6 +1408,7 @@ Optional Features:
   --enable-fast-install[=PKGS]
                           optimize for fast installation [default=yes]
   --disable-libtool-lock  avoid locking (might break parallel builds)
+  --disable-largefile     omit support for large files
 
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -1504,7 +1506,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-squizz configure 0.99c
+squizz configure 0.99d
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2160,7 +2162,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by squizz $as_me 0.99c, which was
+It was created by squizz $as_me 0.99d, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -3023,7 +3025,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='squizz'
- VERSION='0.99c'
+ VERSION='0.99d'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -12801,8 +12803,6 @@ $as_echo "#define HAVE_FSEEKO 1" >>confdefs.h
 
 fi
 
-#AC_FUNC_MALLOC
-#AC_FUNC_REALLOC
 for ac_func in strftime
 do :
   ac_fn_c_check_func "$LINENO" "strftime" "ac_cv_func_strftime"
@@ -12872,8 +12872,205 @@ done
 
 
 # Add 64-bits file support on some hosts
+# Check whether --enable-largefile was given.
+if test "${enable_largefile+set}" = set; then :
+  enableval=$enable_largefile;
+fi
+
+if test "$enable_largefile" != no; then
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for special C compiler options needed for large files" >&5
+$as_echo_n "checking for special C compiler options needed for large files... " >&6; }
+if ${ac_cv_sys_largefile_CC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_cv_sys_largefile_CC=no
+     if test "$GCC" != yes; then
+       ac_save_CC=$CC
+       while :; do
+	 # IRIX 6.2 and later do not support large files by default,
+	 # so use the C compiler's -n32 option if that helps.
+	 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+	 if ac_fn_c_try_compile "$LINENO"; then :
+  break
+fi
+rm -f core conftest.err conftest.$ac_objext
+	 CC="$CC -n32"
+	 if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_sys_largefile_CC=' -n32'; break
+fi
+rm -f core conftest.err conftest.$ac_objext
+	 break
+       done
+       CC=$ac_save_CC
+       rm -f conftest.$ac_ext
+    fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_largefile_CC" >&5
+$as_echo "$ac_cv_sys_largefile_CC" >&6; }
+  if test "$ac_cv_sys_largefile_CC" != no; then
+    CC=$CC$ac_cv_sys_largefile_CC
+  fi
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for _FILE_OFFSET_BITS value needed for large files" >&5
+$as_echo_n "checking for _FILE_OFFSET_BITS value needed for large files... " >&6; }
+if ${ac_cv_sys_file_offset_bits+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  while :; do
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_sys_file_offset_bits=no; break
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#define _FILE_OFFSET_BITS 64
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_sys_file_offset_bits=64; break
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  ac_cv_sys_file_offset_bits=unknown
+  break
+done
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_file_offset_bits" >&5
+$as_echo "$ac_cv_sys_file_offset_bits" >&6; }
+case $ac_cv_sys_file_offset_bits in #(
+  no | unknown) ;;
+  *)
+cat >>confdefs.h <<_ACEOF
+#define _FILE_OFFSET_BITS $ac_cv_sys_file_offset_bits
+_ACEOF
+;;
+esac
+rm -rf conftest*
+  if test $ac_cv_sys_file_offset_bits = unknown; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for _LARGE_FILES value needed for large files" >&5
+$as_echo_n "checking for _LARGE_FILES value needed for large files... " >&6; }
+if ${ac_cv_sys_large_files+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  while :; do
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
 
-$as_echo "#define _FILE_OFFSET_BITS 64" >>confdefs.h
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_sys_large_files=no; break
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+#define _LARGE_FILES 1
+#include <sys/types.h>
+ /* Check that off_t can represent 2**63 - 1 correctly.
+    We can't simply define LARGE_OFF_T to be 9223372036854775807,
+    since some C++ compilers masquerading as C compilers
+    incorrectly reject 9223372036854775807.  */
+#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+  int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
+		       && LARGE_OFF_T % 2147483647 == 1)
+		      ? 1 : -1];
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_sys_large_files=1; break
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+  ac_cv_sys_large_files=unknown
+  break
+done
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_sys_large_files" >&5
+$as_echo "$ac_cv_sys_large_files" >&6; }
+case $ac_cv_sys_large_files in #(
+  no | unknown) ;;
+  *)
+cat >>confdefs.h <<_ACEOF
+#define _LARGE_FILES $ac_cv_sys_large_files
+_ACEOF
+;;
+esac
+rm -rf conftest*
+  fi
+
+
+fi
 
 
 # Compatibility
@@ -13413,7 +13610,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by squizz $as_me 0.99c, which was
+This file was extended by squizz $as_me 0.99d, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -13479,7 +13676,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-squizz config.status 0.99c
+squizz config.status 0.99d
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

 # Process this file with autoconf to produce a configure script.
-AC_INIT([squizz],[0.99c])
+AC_INIT([squizz],[0.99d])
 AM_INIT_AUTOMAKE
 AC_CONFIG_HEADERS([lib/config.h])
 AC_CONFIG_MACRO_DIR([m4])
@@ -33,14 +33,11 @@ AC_TYPE_UINT64_T
 
 # Checks for library functions.
 AC_FUNC_FSEEKO
-#AC_FUNC_MALLOC
-#AC_FUNC_REALLOC
 AC_FUNC_STRFTIME
 AC_CHECK_FUNCS([localtime_r strcasecmp strchr strdup strerror])
 
 # Add 64-bits file support on some hosts
-AC_DEFINE([_FILE_OFFSET_BITS], [64],
-          [Define to 64 for large file support on some hosts])
+AC_SYS_LARGEFILE
 
 # Compatibility
 test $ac_cv_header_err_h != yes && \

debian/changelog

-squizz (0.99c+dfsg-1) UNRELEASED; urgency=medium
+squizz (0.99d+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * cme fix dpkg-control
+  * Realise that debian/compat > 9 will break tests due to not set $srcdir
+    variable
+
+ -- Andreas Tille <tille@debian.org>  Sun, 18 Feb 2018 15:22:13 +0100
+
+squizz (0.99c+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Moved packaging to Git
   * cme fix dpkg-control
   * xz compression and repack in d/watch
+  * add versioned Depends from libsquizz
+  * remove broken symbols file - feel free to re-add a corrected one
+  * hardening=+all
+  * drop breaks itself
 
- -- Andreas Tille <tille@debian.org>  Fri, 09 Sep 2016 11:46:00 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 09 Sep 2016 12:09:45 +0200
 
 squizz (0.99b+dfsg-3) unstable; urgency=low
 

debian/control

@@ -6,7 +6,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                dh-autoreconf
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/squizz.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/squizz.git
 Homepage: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/
@@ -15,7 +15,6 @@ Package: squizz
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
-Breaks: squizz (<= 0.99a)
 Description: Converter for genetic sequences and alignments
  Squizz is a sequence/alignment format checker, but it has some
  conversion capabilities too.
@@ -30,7 +29,6 @@ Architecture: any
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
-Breaks: squizz (<= 0.99a)
 Description: Conversion libs used by squizz genetic sequence converter
  Squizz is a sequence/alignment format checker, but it has some
  conversion capabilities too.
@@ -47,8 +45,7 @@ Architecture: any
 Section: libdevel
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libsquizz
-Breaks: squizz (<= 0.99a)
+         libsquizz  (= ${binary:Version})
 Description: development tools for squizz genetic sequence converter
  Squizz is a sequence/alignment format checker, but it has some
  conversion capabilities too.

debian/libsquizz.symbols

-libbioali.so.0 libsquizz #MINVER#
- align_check@Base 0.99a
- align_format@Base 0.99a
- align_free@Base 0.99a
- align_new@Base 0.99a
- align_parse@Base 0.99a
- align_print@Base 0.99a
- align_strict@Base 0.99a
- clustal_check@Base 0.99a
- clustal_conserv@Base 0.99a
- clustal_create_buffer@Base 0.99a
- clustal_delete_buffer@Base 0.99a
- clustal_flex_debug@Base 0.99a
- clustal_flush_buffer@Base 0.99a
- clustal_parse@Base 0.99a
- clustal_print@Base 0.99a
- clustal_scan_buffer@Base 0.99a
- clustal_scan_bytes@Base 0.99a
- clustal_scan_string@Base 0.99a
- clustal_switch_to_buffer@Base 0.99a
- clustalalloc@Base 0.99a
- clustalfree@Base 0.99a
- clustalget_debug@Base 0.99a
- clustalget_in@Base 0.99a
- clustalget_leng@Base 0.99a
- clustalget_lineno@Base 0.99a
- clustalget_out@Base 0.99a
- clustalget_text@Base 0.99a
- clustalin@Base 0.99a
- clustalleng@Base 0.99a
- clustallex@Base 0.99a
- clustallex_destroy@Base 0.99a
- clustallineno@Base 0.99a
- clustalout@Base 0.99a
- clustalparse@Base 0.99a
- clustalpop_buffer_state@Base 0.99a
- clustalpush_buffer_state@Base 0.99a
- clustalrealloc@Base 0.99a
- clustalrestart@Base 0.99a
- clustalset_debug@Base 0.99a
- clustalset_in@Base 0.99a
- clustalset_lineno@Base 0.99a
- clustalset_out@Base 0.99a
- clustaltext@Base 0.99a
- clustaly_check@Base 0.99a
- clustaly_parse@Base 0.99a
- fasta2_check@Base 0.99a
- fasta2_parse@Base 0.99a
- fasta2_print@Base 0.99a
- mega_check@Base 0.99a
- mega_create_buffer@Base 0.99a
- mega_delete_buffer@Base 0.99a
- mega_flex_debug@Base 0.99a
- mega_flush_buffer@Base 0.99a
- mega_parse@Base 0.99a
- mega_print@Base 0.99a
- mega_scan_buffer@Base 0.99a
- mega_scan_bytes@Base 0.99a
- mega_scan_string@Base 0.99a
- mega_switch_to_buffer@Base 0.99a
- megaalloc@Base 0.99a
- megafree@Base 0.99a
- megaget_debug@Base 0.99a
- megaget_in@Base 0.99a
- megaget_leng@Base 0.99a
- megaget_lineno@Base 0.99a
- megaget_out@Base 0.99a
- megaget_text@Base 0.99a
- megain@Base 0.99a
- megaleng@Base 0.99a
- megalex@Base 0.99a
- megalex_destroy@Base 0.99a
- megalineno@Base 0.99a
- megaout@Base 0.99a
- megaparse@Base 0.99a
- megapop_buffer_state@Base 0.99a
- megapush_buffer_state@Base 0.99a
- megarealloc@Base 0.99a
- megarestart@Base 0.99a
- megaset_debug@Base 0.99a
- megaset_in@Base 0.99a
- megaset_lineno@Base 0.99a
- megaset_out@Base 0.99a
- megatext@Base 0.99a
- megay_check@Base 0.99a
- megay_parse@Base 0.99a
- msf_check@Base 0.99a
- msf_crc@Base 0.99a
- msf_create_buffer@Base 0.99a
- msf_delete_buffer@Base 0.99a
- msf_flex_debug@Base 0.99a
- msf_flush_buffer@Base 0.99a
- msf_parse@Base 0.99a
- msf_print@Base 0.99a
- msf_scan_buffer@Base 0.99a
- msf_scan_bytes@Base 0.99a
- msf_scan_string@Base 0.99a
- msf_switch_to_buffer@Base 0.99a
- msfalloc@Base 0.99a
- msffree@Base 0.99a
- msfget_debug@Base 0.99a
- msfget_in@Base 0.99a
- msfget_leng@Base 0.99a
- msfget_lineno@Base 0.99a
- msfget_out@Base 0.99a
- msfget_text@Base 0.99a
- msfin@Base 0.99a
- msfleng@Base 0.99a
- msflex@Base 0.99a
- msflex_destroy@Base 0.99a
- msflineno@Base 0.99a
- msfout@Base 0.99a
- msfparse@Base 0.99a
- msfpop_buffer_state@Base 0.99a
- msfpush_buffer_state@Base 0.99a
- msfrealloc@Base 0.99a
- msfrestart@Base 0.99a
- msfset_debug@Base 0.99a
- msfset_in@Base 0.99a
- msfset_lineno@Base 0.99a
- msfset_out@Base 0.99a
- msftext@Base 0.99a
- msfy_check@Base 0.99a
- msfy_parse@Base 0.99a
- nexusi_check@Base 0.99a
- nexusi_create_buffer@Base 0.99a
- nexusi_delete_buffer@Base 0.99a
- nexusi_flex_debug@Base 0.99a
- nexusi_flush_buffer@Base 0.99a
- nexusi_parse@Base 0.99a
- nexusi_print@Base 0.99a
- nexusi_scan_buffer@Base 0.99a
- nexusi_scan_bytes@Base 0.99a
- nexusi_scan_string@Base 0.99a
- nexusi_switch_to_buffer@Base 0.99a
- nexusialloc@Base 0.99a
- nexusifree@Base 0.99a
- nexusiget_debug@Base 0.99a
- nexusiget_in@Base 0.99a
- nexusiget_leng@Base 0.99a
- nexusiget_lineno@Base 0.99a
- nexusiget_out@Base 0.99a
- nexusiget_text@Base 0.99a
- nexusiin@Base 0.99a
- nexusileng@Base 0.99a
- nexusilex@Base 0.99a
- nexusilex_destroy@Base 0.99a
- nexusilineno@Base 0.99a
- nexusiout@Base 0.99a
- nexusiparse@Base 0.99a
- nexusipop_buffer_state@Base 0.99a
- nexusipush_buffer_state@Base 0.99a
- nexusirealloc@Base 0.99a
- nexusirestart@Base 0.99a
- nexusiset_debug@Base 0.99a
- nexusiset_in@Base 0.99a
- nexusiset_lineno@Base 0.99a
- nexusiset_out@Base 0.99a
- nexusitext@Base 0.99a
- nexusiy_check@Base 0.99a
- nexusiy_parse@Base 0.99a
- parse_seqnew@Base 0.99a
- parse_seqnxt@Base 0.99a
- parse_seqrst@Base 0.99a
- parse_sequpd@Base 0.99a
- parse_tmpupd@Base 0.99a
- phylip_fixnam@Base 0.99a
- phylipi_check@Base 0.99a
- phylipi_create_buffer@Base 0.99a
- phylipi_delete_buffer@Base 0.99a
- phylipi_flex_debug@Base 0.99a
- phylipi_flush_buffer@Base 0.99a
- phylipi_parse@Base 0.99a
- phylipi_print@Base 0.99a
- phylipi_scan_buffer@Base 0.99a
- phylipi_scan_bytes@Base 0.99a
- phylipi_scan_string@Base 0.99a
- phylipi_switch_to_buffer@Base 0.99a
- phylipialloc@Base 0.99a
- phylipifree@Base 0.99a
- phylipiget_debug@Base 0.99a
- phylipiget_in@Base 0.99a
- phylipiget_leng@Base 0.99a
- phylipiget_lineno@Base 0.99a
- phylipiget_out@Base 0.99a
- phylipiget_text@Base 0.99a
- phylipiin@Base 0.99a
- phylipileng@Base 0.99a
- phylipilex@Base 0.99a
- phylipilex_destroy@Base 0.99a
- phylipilineno@Base 0.99a
- phylipiout@Base 0.99a
- phylipiparse@Base 0.99a
- phylipipop_buffer_state@Base 0.99a
- phylipipush_buffer_state@Base 0.99a
- phylipirealloc@Base 0.99a
- phylipirestart@Base 0.99a
- phylipiset_debug@Base 0.99a
- phylipiset_in@Base 0.99a
- phylipiset_lineno@Base 0.99a
- phylipiset_out@Base 0.99a
- phylipitext@Base 0.99a
- phylipiy_check@Base 0.99a
- phylipiy_parse@Base 0.99a
- phylips_check@Base 0.99a
- phylips_create_buffer@Base 0.99a
- phylips_delete_buffer@Base 0.99a
- phylips_flex_debug@Base 0.99a
- phylips_flush_buffer@Base 0.99a
- phylips_parse@Base 0.99a
- phylips_print@Base 0.99a
- phylips_scan_buffer@Base 0.99a
- phylips_scan_bytes@Base 0.99a
- phylips_scan_string@Base 0.99a
- phylips_switch_to_buffer@Base 0.99a
- phylipsalloc@Base 0.99a
- phylipsfree@Base 0.99a
- phylipsget_debug@Base 0.99a
- phylipsget_in@Base 0.99a
- phylipsget_leng@Base 0.99a
- phylipsget_lineno@Base 0.99a
- phylipsget_out@Base 0.99a
- phylipsget_text@Base 0.99a
- phylipsin@Base 0.99a
- phylipsleng@Base 0.99a
- phylipslex@Base 0.99a
- phylipslex_destroy@Base 0.99a
- phylipslineno@Base 0.99a
- phylipsout@Base 0.99a
- phylipsparse@Base 0.99a
- phylipspop_buffer_state@Base 0.99a
- phylipspush_buffer_state@Base 0.99a
- phylipsrealloc@Base 0.99a
- phylipsrestart@Base 0.99a
- phylipsset_debug@Base 0.99a
- phylipsset_in@Base 0.99a
- phylipsset_lineno@Base 0.99a
- phylipsset_out@Base 0.99a
- phylipstext@Base 0.99a
- phylipsy_check@Base 0.99a
- phylipsy_parse@Base 0.99a
- stock_check@Base 0.99a
- stock_create_buffer@Base 0.99a
- stock_delete_buffer@Base 0.99a
- stock_flex_debug@Base 0.99a
- stock_flush_buffer@Base 0.99a
- stock_parse@Base 0.99a
- stock_print@Base 0.99a
- stock_scan_buffer@Base 0.99a
- stock_scan_bytes@Base 0.99a
- stock_scan_string@Base 0.99a
- stock_switch_to_buffer@Base 0.99a
- stockalloc@Base 0.99a
- stockfree@Base 0.99a
- stockget_debug@Base 0.99a
- stockget_in@Base 0.99a
- stockget_leng@Base 0.99a
- stockget_lineno@Base 0.99a
- stockget_out@Base 0.99a
- stockget_text@Base 0.99a
- stockin@Base 0.99a
- stockleng@Base 0.99a
- stocklex@Base 0.99a
- stocklex_destroy@Base 0.99a
- stocklineno@Base 0.99a
- stockout@Base 0.99a
- stockparse@Base 0.99a
- stockpop_buffer_state@Base 0.99a
- stockpush_buffer_state@Base 0.99a
- stockrealloc@Base 0.99a
- stockrestart@Base 0.99a
- stockset_debug@Base 0.99a
- stockset_in@Base 0.99a
- stockset_lineno@Base 0.99a
- stockset_out@Base 0.99a
- stocktext@Base 0.99a
- stocky_check@Base 0.99a
- stocky_parse@Base 0.99a
-libbioseq.so.0 libsquizz #MINVER#
- codata_check@Base 0.99b+dfsg
- codata_checksum@Base 0.99b+dfsg
- codata_create_buffer@Base 0.99b+dfsg
- codata_delete_buffer@Base 0.99b+dfsg
- codata_flex_debug@Base 0.99b+dfsg
- codata_flush_buffer@Base 0.99b+dfsg
- codata_parse@Base 0.99b+dfsg
- codata_print@Base 0.99b+dfsg
- codata_scan_buffer@Base 0.99b+dfsg
- codata_scan_bytes@Base 0.99b+dfsg
- codata_scan_string@Base 0.99b+dfsg
- codata_switch_to_buffer@Base 0.99b+dfsg
- codataalloc@Base 0.99b+dfsg
- codatafree@Base 0.99b+dfsg
- codataget_debug@Base 0.99b+dfsg
- codataget_in@Base 0.99b+dfsg
- codataget_leng@Base 0.99b+dfsg
- codataget_lineno@Base 0.99b+dfsg
- codataget_out@Base 0.99b+dfsg
- codataget_text@Base 0.99b+dfsg
- codatain@Base 0.99b+dfsg
- codataleng@Base 0.99b+dfsg
- codatalex@Base 0.99b+dfsg
- codatalex_destroy@Base 0.99b+dfsg
- codatalineno@Base 0.99b+dfsg
- codataout@Base 0.99b+dfsg
- codataparse@Base 0.99b+dfsg
- codatapop_buffer_state@Base 0.99b+dfsg
- codatapush_buffer_state@Base 0.99b+dfsg
- codatarealloc@Base 0.99b+dfsg
- codatarestart@Base 0.99b+dfsg
- codataset_debug@Base 0.99b+dfsg
- codataset_in@Base 0.99b+dfsg
- codataset_lineno@Base 0.99b+dfsg
- codataset_out@Base 0.99b+dfsg
- codatatext@Base 0.99b+dfsg
- codatay_check@Base 0.99b+dfsg
- codatay_parse@Base 0.99b+dfsg
- embl_check@Base 0.99a
- embl_create_buffer@Base 0.99a
- embl_delete_buffer@Base 0.99a
- embl_flex_debug@Base 0.99a
- embl_flush_buffer@Base 0.99a
- embl_parse@Base 0.99a
- embl_print@Base 0.99a
- embl_scan_buffer@Base 0.99a
- embl_scan_bytes@Base 0.99a
- embl_scan_string@Base 0.99a
- embl_switch_to_buffer@Base 0.99a
- emblalloc@Base 0.99a
- emblfree@Base 0.99a
- emblget_debug@Base 0.99a
- emblget_in@Base 0.99a
- emblget_leng@Base 0.99a
- emblget_lineno@Base 0.99a
- emblget_out@Base 0.99a
- emblget_text@Base 0.99a
- emblin@Base 0.99a
- emblleng@Base 0.99a
- embllex@Base 0.99a
- embllex_destroy@Base 0.99a
- embllineno@Base 0.99a
- emblout@Base 0.99a
- emblparse@Base 0.99a
- emblpop_buffer_state@Base 0.99a
- emblpush_buffer_state@Base 0.99a
- emblrealloc@Base 0.99a
- emblrestart@Base 0.99a
- emblset_debug@Base 0.99a
- emblset_in@Base 0.99a
- emblset_lineno@Base 0.99a
- emblset_out@Base 0.99a
- embltext@Base 0.99a
- embly_check@Base 0.99a
- embly_parse@Base 0.99a
-#MISSING: 0.99b+dfsg# error_fatal@Base 0.99a
-#MISSING: 0.99b+dfsg# error_warn@Base 0.99a
- fasta_check@Base 0.99a
- fasta_create_buffer@Base 0.99a
- fasta_delete_buffer@Base 0.99a
- fasta_flex_debug@Base 0.99a
- fasta_flush_buffer@Base 0.99a
- fasta_parse@Base 0.99a
- fasta_print@Base 0.99a
- fasta_scan_buffer@Base 0.99a
- fasta_scan_bytes@Base 0.99a
- fasta_scan_string@Base 0.99a
- fasta_switch_to_buffer@Base 0.99a
- fastaalloc@Base 0.99a
- fastafree@Base 0.99a
- fastaget_debug@Base 0.99a
- fastaget_in@Base 0.99a
- fastaget_leng@Base 0.99a
- fastaget_lineno@Base 0.99a
- fastaget_out@Base 0.99a
- fastaget_text@Base 0.99a
- fastain@Base 0.99a
- fastaleng@Base 0.99a
- fastalex@Base 0.99a
- fastalex_destroy@Base 0.99a
- fastalineno@Base 0.99a
- fastaout@Base 0.99a
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- fastapop_buffer_state@Base 0.99a
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- fastarestart@Base 0.99a
- fastaset_debug@Base 0.99a
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- fastaset_lineno@Base 0.99a
- fastaset_out@Base 0.99a
- fastatext@Base 0.99a
- fastay_check@Base 0.99a
- fastay_parse@Base 0.99a
- file_locate@Base 0.99a
- gcg_check@Base 0.99a
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- gcg_create_buffer@Base 0.99a
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- gcg_flex_debug@Base 0.99a
- gcg_flush_buffer@Base 0.99a
- gcg_parse@Base 0.99a
- gcg_print@Base 0.99a
- gcg_scan_buffer@Base 0.99a
- gcg_scan_bytes@Base 0.99a
- gcg_scan_string@Base 0.99a
- gcg_switch_to_buffer@Base 0.99a
- gcgalloc@Base 0.99a
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- gcgget_debug@Base 0.99a
- gcgget_in@Base 0.99a
- gcgget_leng@Base 0.99a
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- gcglineno@Base 0.99a
- gcgout@Base 0.99a
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- gcgrestart@Base 0.99a
- gcgset_debug@Base 0.99a
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- gcgset_lineno@Base 0.99a
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- gde_parse@Base 0.99a
- gde_print@Base 0.99a
- gde_scan_buffer@Base 0.99a
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- gde_scan_string@Base 0.99a
- gde_switch_to_buffer@Base 0.99a
- gdealloc@Base 0.99a
- gdefree@Base 0.99a
- gdeget_debug@Base 0.99a
- gdeget_in@Base 0.99a
- gdeget_leng@Base 0.99a
- gdeget_lineno@Base 0.99a
- gdeget_out@Base 0.99a
- gdeget_text@Base 0.99a
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- gderestart@Base 0.99a
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- gdeset_out@Base 0.99a
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- genbank_delete_buffer@Base 0.99a
- genbank_flex_debug@Base 0.99a
- genbank_flush_buffer@Base 0.99a
- genbank_parse@Base 0.99a
- genbank_print@Base 0.99a
- genbank_scan_buffer@Base 0.99a
- genbank_scan_bytes@Base 0.99a
- genbank_scan_string@Base 0.99a
- genbank_switch_to_buffer@Base 0.99a
- genbankalloc@Base 0.99a
- genbankfree@Base 0.99a
- genbankget_debug@Base 0.99a
- genbankget_in@Base 0.99a
- genbankget_leng@Base 0.99a
- genbankget_lineno@Base 0.99a
- genbankget_out@Base 0.99a
- genbankget_text@Base 0.99a
- genbankin@Base 0.99a
- genbankleng@Base 0.99a
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- genbanklex_destroy@Base 0.99a
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- genbankout@Base 0.99a
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- genbankrestart@Base 0.99a
- genbankset_debug@Base 0.99a
- genbankset_in@Base 0.99a
- genbankset_lineno@Base 0.99a
- genbankset_out@Base 0.99a
- genbanktext@Base 0.99a
- genbanky_check@Base 0.99a
- genbanky_parse@Base 0.99a
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- ig_scan_bytes@Base 0.99a
- ig_scan_string@Base 0.99a
- ig_switch_to_buffer@Base 0.99a
- igalloc@Base 0.99a
- igfree@Base 0.99a
- igget_debug@Base 0.99a
- igget_in@Base 0.99a
- igget_leng@Base 0.99a
- igget_lineno@Base 0.99a
- igget_out@Base 0.99a
- igget_text@Base 0.99a
- igin@Base 0.99a
- igleng@Base 0.99a
- iglex@Base 0.99a
- iglex_destroy@Base 0.99a
- iglineno@Base 0.99a
- igout@Base 0.99a
- igparse@Base 0.99a
- igpop_buffer_state@Base 0.99a
- igpush_buffer_state@Base 0.99a
- igrealloc@Base 0.99a
- igrestart@Base 0.99a
- igset_debug@Base 0.99a
- igset_in@Base 0.99a
- igset_lineno@Base 0.99a
- igset_out@Base 0.99a
- igtext@Base 0.99a
- igy_check@Base 0.99a
- igy_parse@Base 0.99a
- nbrf_check@Base 0.99a
- nbrf_create_buffer@Base 0.99a
- nbrf_delete_buffer@Base 0.99a
- nbrf_flex_debug@Base 0.99a
- nbrf_flush_buffer@Base 0.99a
- nbrf_parse@Base 0.99a
- nbrf_print@Base 0.99a
- nbrf_scan_buffer@Base 0.99a
- nbrf_scan_bytes@Base 0.99a
- nbrf_scan_string@Base 0.99a
- nbrf_switch_to_buffer@Base 0.99a
- nbrfalloc@Base 0.99a
- nbrffree@Base 0.99a
- nbrfget_debug@Base 0.99a
- nbrfget_in@Base 0.99a
- nbrfget_leng@Base 0.99a
- nbrfget_lineno@Base 0.99a
- nbrfget_out@Base 0.99a
- nbrfget_text@Base 0.99a
- nbrfin@Base 0.99a
- nbrfleng@Base 0.99a
- nbrflex@Base 0.99a
- nbrflex_destroy@Base 0.99a
- nbrflineno@Base 0.99a
- nbrfout@Base 0.99a
- nbrfparse@Base 0.99a
- nbrfpop_buffer_state@Base 0.99a
- nbrfpush_buffer_state@Base 0.99a
- nbrfrealloc@Base 0.99a
- nbrfrestart@Base 0.99a
- nbrfset_debug@Base 0.99a
- nbrfset_in@Base 0.99a
- nbrfset_lineno@Base 0.99a
- nbrfset_out@Base 0.99a
- nbrftext@Base 0.99a
- nbrfy_check@Base 0.99a
- nbrfy_parse@Base 0.99a
- parse_accadd@Base 0.99a
- parse_dscadd1@Base 0.99a
- parse_dscadd2@Base 0.99a
- parse_giadd@Base 0.99a
- parse_kwdadd@Base 0.99a
- parse_kwdupd@Base 0.99a
- parse_namadd@Base 0.99a
- parse_nuladd@Base 0.99a
- parse_stradd@Base 0.99a
- parse_veradd@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_check@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_checksum@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_create_buffer@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_delete_buffer@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_flex_debug@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_flush_buffer@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_parse@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_print@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_scan_buffer@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_scan_bytes@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_scan_string@Base 0.99a
-#MISSING: 0.99b+dfsg# pir_switch_to_buffer@Base 0.99a
-#MISSING: 0.99b+dfsg# piralloc@Base 0.99a
-#MISSING: 0.99b+dfsg# pirfree@Base 0.99a
-#MISSING: 0.99b+dfsg# pirget_debug@Base 0.99a
-#MISSING: 0.99b+dfsg# pirget_in@Base 0.99a
-#MISSING: 0.99b+dfsg# pirget_leng@Base 0.99a
-#MISSING: 0.99b+dfsg# pirget_lineno@Base 0.99a
-#MISSING: 0.99b+dfsg# pirget_out@Base 0.99a
-#MISSING: 0.99b+dfsg# pirget_text@Base 0.99a
-#MISSING: 0.99b+dfsg# pirin@Base 0.99a
-#MISSING: 0.99b+dfsg# pirleng@Base 0.99a
-#MISSING: 0.99b+dfsg# pirlex@Base 0.99a
-#MISSING: 0.99b+dfsg# pirlex_destroy@Base 0.99a
-#MISSING: 0.99b+dfsg# pirlineno@Base 0.99a
-#MISSING: 0.99b+dfsg# pirout@Base 0.99a
-#MISSING: 0.99b+dfsg# pirparse@Base 0.99a
-#MISSING: 0.99b+dfsg# pirpop_buffer_state@Base 0.99a
-#MISSING: 0.99b+dfsg# pirpush_buffer_state@Base 0.99a
-#MISSING: 0.99b+dfsg# pirrealloc@Base 0.99a
-#MISSING: 0.99b+dfsg# pirrestart@Base 0.99a
-#MISSING: 0.99b+dfsg# pirset_debug@Base 0.99a
-#MISSING: 0.99b+dfsg# pirset_in@Base 0.99a
-#MISSING: 0.99b+dfsg# pirset_lineno@Base 0.99a
-#MISSING: 0.99b+dfsg# pirset_out@Base 0.99a
-#MISSING: 0.99b+dfsg# pirtext@Base 0.99a
-#MISSING: 0.99b+dfsg# piry_check@Base 0.99a
-#MISSING: 0.99b+dfsg# piry_parse@Base 0.99a
- protein_weight@Base 0.99a
- raw_check@Base 0.99a
- raw_create_buffer@Base 0.99a
- raw_delete_buffer@Base 0.99a
- raw_flex_debug@Base 0.99a
- raw_flush_buffer@Base 0.99a
- raw_parse@Base 0.99a
- raw_print@Base 0.99a
- raw_scan_buffer@Base 0.99a
- raw_scan_bytes@Base 0.99a
- raw_scan_string@Base 0.99a
- raw_switch_to_buffer@Base 0.99a
- rawalloc@Base 0.99a
- rawfree@Base 0.99a
- rawget_debug@Base 0.99a
- rawget_in@Base 0.99a
- rawget_leng@Base 0.99a
- rawget_lineno@Base 0.99a
- rawget_out@Base 0.99a
- rawget_text@Base 0.99a
- rawin@Base 0.99a
- rawleng@Base 0.99a
- rawlex@Base 0.99a
- rawlex_destroy@Base 0.99a
- rawlineno@Base 0.99a
- rawout@Base 0.99a
- rawparse@Base 0.99a
- rawpop_buffer_state@Base 0.99a
- rawpush_buffer_state@Base 0.99a
- rawrealloc@Base 0.99a
- rawrestart@Base 0.99a
- rawset_debug@Base 0.99a
- rawset_in@Base 0.99a
- rawset_lineno@Base 0.99a
- rawset_out@Base 0.99a
- rawtext@Base 0.99a
- rawy_check@Base 0.99a
- rawy_parse@Base 0.99a
- sequence_check@Base 0.99a
- sequence_fixnam@Base 0.99a
- sequence_format@Base 0.99a
- sequence_free@Base 0.99a
- sequence_new@Base 0.99a
- sequence_parse@Base 0.99a
- sequence_print@Base 0.99a
- sequence_strict@Base 0.99a
- sequence_type@Base 0.99a
- sprot_check@Base 0.99a
- sprot_create_buffer@Base 0.99a
- sprot_delete_buffer@Base 0.99a
- sprot_flex_debug@Base 0.99a
- sprot_flush_buffer@Base 0.99a
- sprot_parse@Base 0.99a
- sprot_print@Base 0.99a
- sprot_scan_buffer@Base 0.99a
- sprot_scan_bytes@Base 0.99a
- sprot_scan_string@Base 0.99a
- sprot_switch_to_buffer@Base 0.99a
- sprotalloc@Base 0.99a
- sprotfree@Base 0.99a
- sprotget_debug@Base 0.99a
- sprotget_in@Base 0.99a
- sprotget_leng@Base 0.99a
- sprotget_lineno@Base 0.99a
- sprotget_out@Base 0.99a
- sprotget_text@Base 0.99a
- sprotin@Base 0.99a
- sprotleng@Base 0.99a
- sprotlex@Base 0.99a
- sprotlex_destroy@Base 0.99a
- sprotlineno@Base 0.99a
- sprotout@Base 0.99a
- sprotparse@Base 0.99a
- sprotpop_buffer_state@Base 0.99a
- sprotpush_buffer_state@Base 0.99a
- sprotrealloc@Base 0.99a
- sprotrestart@Base 0.99a
- sprotset_debug@Base 0.99a
- sprotset_in@Base 0.99a
- sprotset_lineno@Base 0.99a
- sprotset_out@Base 0.99a
- sprottext@Base 0.99a
- sproty_check@Base 0.99a
- sproty_parse@Base 0.99a
- text_keyadd@Base 0.99a
- text_keyupd@Base 0.99a
- text_strupd@Base 0.99a
- text_strupds@Base 0.99a

debian/rules

@@ -6,5 +6,7 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@ --with autoreconf

lib/align.h

 /* align.h - Generic alignment functions */
 
-#ifndef __ALIGN_H_
-#define __ALIGN_H_
+#ifndef SQUIZZ_ALIGN_H_
+#define SQUIZZ_ALIGN_H_
 
 #include <stdio.h>
 
@@ -35,5 +35,5 @@ void align_print(FILE *, align_t *, alifmt_t);
 
 alifmt_t align_format(FILE *);
 
-#endif /* __ALIGN_H_ */
+#endif /* SQUIZZ_ALIGN_H_ */
 

lib/align/clustal.h

 /* clustal.h - CLUSTAL alignment functions */
 
-#ifndef __ALIGN_CLUSTAL_H_
-#define __ALIGN_CLUSTAL_H_
+#ifndef SQUIZZ_ALIGN_CLUSTAL_H_
+#define SQUIZZ_ALIGN_CLUSTAL_H_
 
 #include <stdio.h>
 
@@ -13,4 +13,4 @@ int clustal_check(FILE *);
 align_t *clustal_parse(FILE *);
 void clustal_print(FILE *, align_t *);
 
-#endif /* __ALIGN_CLUSTAL_H_ */
+#endif /* SQUIZZ_ALIGN_CLUSTAL_H_ */

lib/align/fasta2.h

 /* fasta2.h - FASTA alignment functions */
 
-#ifndef __ALIGN_FASTA2_H_
-#define __ALIGN_FASTA2_H_
+#ifndef SQUIZZ_ALIGN_FASTA2_H_
+#define SQUIZZ_ALIGN_FASTA2_H_
 
 #include <stdio.h>
 
@@ -13,4 +13,4 @@ int fasta2_check(FILE *);
 align_t *fasta2_parse(FILE *);
 void fasta2_print(FILE *, align_t *);
 
-#endif /* __ALIGN_FASTA2_H_ */
+#endif /* SQUIZZ_ALIGN_FASTA2_H_ */

lib/align/mega.h

 /* mega.h - MEGA alignment functions */
 
-#ifndef __ALIGN_MEGA_H_
-#define __ALIGN_MEGA_H_
+#ifndef SQUIZZ_ALIGN_MEGA_H_
+#define SQUIZZ_ALIGN_MEGA_H_
 
 #include <stdio.h>
 
@@ -13,4 +13,4 @@ int mega_check(FILE *);
 align_t *mega_parse(FILE *);
 void mega_print(FILE *, align_t *);
 
-#endif /* __ALIGN_MEGA_H_ */
+#endif /* SQUIZZ_ALIGN_MEGA_H_ */

lib/align/msf.h

 /* msf.h - MSF alignment functions */
 
-#ifndef __ALIGN_MSF_H_
-#define __ALIGN_MSF_H_
+#ifndef SQUIZZ_ALIGN_MSF_H_
+#define SQUIZZ_ALIGN_MSF_H_
 
 #include <stdio.h>
 
@@ -13,4 +13,4 @@ int msf_check(FILE *);
 align_t *msf_parse(FILE *);
 void msf_print(FILE *, align_t *);
 
-#endif /* __ALIGN_MSF_H_ */
+#endif /* SQUIZZ_ALIGN_MSF_H_ */

lib/align/nexusi.h

 /* nexusi.h - NEXUSI alignment functions */
 
-#ifndef __ALIGN_NEXUSI_H_
-#define __ALIGN_NEXUSI_H_
+#ifndef SQUIZZ_ALIGN_NEXUSI_H_
+#define SQUIZZ_ALIGN_NEXUSI_H_
 
 #include <stdio.h>
 
@@ -13,4 +13,4 @@ int nexusi_check(FILE *);
 align_t *nexusi_parse(FILE *);
 void nexusi_print(FILE *, align_t *);
 
-#endif /* __ALIGN_NEXUSI_H_ */
+#endif /* SQUIZZ_ALIGN_NEXUSI_H_ */

lib/align/parse.h

 /* parse.h - Alignment parsing helper functions */
 
-#ifndef __ALIGN_PARSE_H_
-#define __ALIGN_PARSE_H_
+#ifndef SQUIZZ_ALIGN_PARSE_H_
+#define SQUIZZ_ALIGN_PARSE_H_
 
 #include "align.h"
 
@@ -15,4 +15,4 @@ int parse_seqnew(align_t *);
 int parse_seqrst(align_t *);
 int parse_seqnxt(align_t *);
 
-#endif /* __ALIGN_PARSE_H_ */
+#endif /* SQUIZZ_ALIGN_PARSE_H_ */

lib/align/phylip.h

 /* phylip.h - PHYLIP common alignment functions */
 
-#ifndef __ALIGN_PHYLIP_H_
-#define __ALIGN_PHYLIP_H_
+#ifndef SQUIZZ_ALIGN_PHYLIP_H_
+#define SQUIZZ_ALIGN_PHYLIP_H_
 
 #include "align.h"
 
@@ -9,4 +9,4 @@
 
 char *phylip_fixnam(const char *);
 
-#endif /* __ALIGN_PHYLIPI_H_ */
+#endif /* SQUIZZ_ALIGN_PHYLIPI_H_ */

lib/align/phylipi.h

 /* phylipi.h - PHYLIPI alignment functions */
 
-#ifndef __ALIGN_PHYLIPI_H_
-#define __ALIGN_PHYLIPI_H_
+#ifndef SQUIZZ_ALIGN_PHYLIPI_H_
+#define SQUIZZ_ALIGN_PHYLIPI_H_
 
 #include <stdio.h>
 
@@ -14,4 +14,4 @@ int phylipi_check(FILE *);
 align_t *phylipi_parse(FILE *);
 void phylipi_print(FILE *, align_t *);
 
-#endif /* __ALIGN_PHYLIPI_H_ */
+#endif /* SQUIZZ_ALIGN_PHYLIPI_H_ */

lib/align/phylips.h

 /* phylips.h - PHYLIPS alignment functions */
 
-#ifndef __ALIGN_PHYLIPS_H_
-#define __ALIGN_PHYLIPS_H_
+#ifndef SQUIZZ_ALIGN_PHYLIPS_H_
+#define SQUIZZ_ALIGN_PHYLIPS_H_
 
 #include <stdio.h>
 
@@ -14,4 +14,4 @@ int phylips_check(FILE *);
 align_t *phylips_parse(FILE *);
 void phylips_print(FILE *, align_t *);
 
-#endif /* __ALIGN_PHYLIPS_H_ */
+#endif /* SQUIZZ_ALIGN_PHYLIPS_H_ */

lib/align/stock.h

 /* stock.h - STOCKHOLM alignment functions */
 
-#ifndef __ALIGN_STOCK_H_
-#define __ALIGN_STOCK_H_
+#ifndef SQUIZZ_ALIGN_STOCK_H_
+#define SQUIZZ_ALIGN_STOCK_H_
 
 #include <stdio.h>
 
@@ -13,4 +13,4 @@ int stock_check(FILE *);
 align_t *stock_parse(FILE *);
 void stock_print(FILE *, align_t *);
 
-#endif /* __ALIGN_STOCK_H_ */
+#endif /* SQUIZZ_ALIGN_STOCK_H_ */

lib/compat.h

 /* compat.h - Compatibility stuff */
 
-#ifndef __COMPAT_H_
-#define __COMPAT_H_
+#ifndef SQUIZZ_COMPAT_H_
+#define SQUIZZ_COMPAT_H_
 
 #ifndef PRIu64
 # ifdef _LP64
@@ -25,4 +25,4 @@
 # endif
 #endif /* PRIsiz */
 
-#endif /* __COMPAT_H_ */
+#endif /* SQUIZZ_COMPAT_H_ */