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v2.2.13 done

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commit 426295fb5463efc4048e74bd938c57d6fcbdf7a6 1 parent 6371ca9
THIPBPK authored
22 Makefile
View
@@ -103,11 +103,11 @@ DIST_ARCHIVES = $(distdir).tar.gz
GZIP_ENV = --best
distuninstallcheck_listfiles = find . -type f -print
distcleancheck_listfiles = find . -type f -print
-ACLOCAL = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run aclocal-1.11
-AMTAR = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run tar
-AUTOCONF = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoconf
-AUTOHEADER = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoheader
-AUTOMAKE = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run automake-1.11
+ACLOCAL = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run aclocal-1.11
+AMTAR = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run tar
+AUTOCONF = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoconf
+AUTOHEADER = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoheader
+AUTOMAKE = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run automake-1.11
AWK = awk
CC = gcc
CCDEPMODE = depmode=gcc3
@@ -163,7 +163,7 @@ LIBOBJS =
LIBS = -lm
LTLIBINTL =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run makeinfo
+MAKEINFO = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run makeinfo
MKDIR_P = ./install-sh -c -d
NEXT_UNISTD_H = <unistd.h>
OBJEXT = o
@@ -186,10 +186,10 @@ SET_MAKE =
SHELL = /bin/sh
STRIP =
VERSION = 2.2.13
-abs_builddir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models
-abs_srcdir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models
-abs_top_builddir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models
-abs_top_srcdir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models
+abs_builddir = /Users/cstrope/git/indel-seq-gen
+abs_srcdir = /Users/cstrope/git/indel-seq-gen
+abs_top_builddir = /Users/cstrope/git/indel-seq-gen
+abs_top_srcdir = /Users/cstrope/git/indel-seq-gen
ac_ct_CC = gcc
ac_ct_CXX = g++
am__include = include
@@ -213,7 +213,7 @@ host_alias =
htmldir = ${docdir}
includedir = ${prefix}/include
infodir = ${datarootdir}/info
-install_sh = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/install-sh
+install_sh = ${SHELL} /Users/cstrope/git/indel-seq-gen/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
22 autom4te.cache/output.1
View
@@ -1,6 +1,6 @@
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.68 for indel-seq-gen 2.1.03.
+@%:@ Generated by GNU Autoconf 2.68 for indel-seq-gen 2.2.13.
@%:@
@%:@ Report bugs to <corystrope@gmail.com>.
@%:@
@@ -560,12 +560,12 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='indel-seq-gen'
PACKAGE_TARNAME='indel-seq-gen'
-PACKAGE_VERSION='2.1.03'
-PACKAGE_STRING='indel-seq-gen 2.1.03'
+PACKAGE_VERSION='2.2.13'
+PACKAGE_STRING='indel-seq-gen 2.2.13'
PACKAGE_BUGREPORT='corystrope@gmail.com'
PACKAGE_URL=''
-ac_unique_file="src/aamodels.cpp"
+ac_unique_file="src/model.cpp"
# Factoring default headers for most tests.
ac_includes_default="\
#include <stdio.h>
@@ -1294,7 +1294,7 @@ if test "$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 indel-seq-gen 2.1.03 to adapt to many kinds of systems.
+\`configure' configures indel-seq-gen 2.2.13 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1360,7 +1360,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of indel-seq-gen 2.1.03:";;
+ short | recursive ) echo "Configuration of indel-seq-gen 2.2.13:";;
esac
cat <<\_ACEOF
@@ -1449,7 +1449,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-indel-seq-gen configure 2.1.03
+indel-seq-gen configure 2.2.13
generated by GNU Autoconf 2.68
Copyright (C) 2010 Free Software Foundation, Inc.
@@ -1956,7 +1956,7 @@ 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 indel-seq-gen $as_me 2.1.03, which was
+It was created by indel-seq-gen $as_me 2.2.13, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -2773,7 +2773,7 @@ fi
# Define the identity of the package.
PACKAGE='indel-seq-gen'
- VERSION='2.1.03'
+ VERSION='2.2.13'
cat >>confdefs.h <<_ACEOF
@@ -6192,7 +6192,7 @@ cat >>$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 indel-seq-gen $as_me 2.1.03, which was
+This file was extended by indel-seq-gen $as_me 2.2.13, which was
generated by GNU Autoconf 2.68. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -6258,7 +6258,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-indel-seq-gen config.status 2.1.03
+indel-seq-gen config.status 2.2.13
configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
22 autom4te.cache/output.2
View
@@ -1,6 +1,6 @@
@%:@! /bin/sh
@%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.68 for indel-seq-gen 2.1.03.
+@%:@ Generated by GNU Autoconf 2.68 for indel-seq-gen 2.2.13.
@%:@
@%:@ Report bugs to <corystrope@gmail.com>.
@%:@
@@ -560,12 +560,12 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='indel-seq-gen'
PACKAGE_TARNAME='indel-seq-gen'
-PACKAGE_VERSION='2.1.03'
-PACKAGE_STRING='indel-seq-gen 2.1.03'
+PACKAGE_VERSION='2.2.13'
+PACKAGE_STRING='indel-seq-gen 2.2.13'
PACKAGE_BUGREPORT='corystrope@gmail.com'
PACKAGE_URL=''
-ac_unique_file="src/aamodels.cpp"
+ac_unique_file="src/model.cpp"
# Factoring default headers for most tests.
ac_includes_default="\
#include <stdio.h>
@@ -1294,7 +1294,7 @@ if test "$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 indel-seq-gen 2.1.03 to adapt to many kinds of systems.
+\`configure' configures indel-seq-gen 2.2.13 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1360,7 +1360,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of indel-seq-gen 2.1.03:";;
+ short | recursive ) echo "Configuration of indel-seq-gen 2.2.13:";;
esac
cat <<\_ACEOF
@@ -1449,7 +1449,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-indel-seq-gen configure 2.1.03
+indel-seq-gen configure 2.2.13
generated by GNU Autoconf 2.68
Copyright (C) 2010 Free Software Foundation, Inc.
@@ -1956,7 +1956,7 @@ 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 indel-seq-gen $as_me 2.1.03, which was
+It was created by indel-seq-gen $as_me 2.2.13, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -2773,7 +2773,7 @@ fi
# Define the identity of the package.
PACKAGE='indel-seq-gen'
- VERSION='2.1.03'
+ VERSION='2.2.13'
cat >>confdefs.h <<_ACEOF
@@ -6192,7 +6192,7 @@ cat >>$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 indel-seq-gen $as_me 2.1.03, which was
+This file was extended by indel-seq-gen $as_me 2.2.13, which was
generated by GNU Autoconf 2.68. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -6258,7 +6258,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-indel-seq-gen config.status 2.1.03
+indel-seq-gen config.status 2.2.13
configured by $0, generated by GNU Autoconf 2.68,
with options \\"\$ac_cs_config\\"
112 autom4te.cache/requests
View
@@ -14,55 +14,55 @@
'configure.ac'
],
{
- '_LT_AC_TAGCONFIG' => 1,
'AM_PROG_F77_C_O' => 1,
- 'AC_INIT' => 1,
+ '_LT_AC_TAGCONFIG' => 1,
'm4_pattern_forbid' => 1,
- '_AM_COND_IF' => 1,
+ 'AC_INIT' => 1,
'AC_CANONICAL_TARGET' => 1,
- 'AC_SUBST' => 1,
+ '_AM_COND_IF' => 1,
'AC_CONFIG_LIBOBJ_DIR' => 1,
- 'AC_FC_SRCEXT' => 1,
+ 'AC_SUBST' => 1,
'AC_CANONICAL_HOST' => 1,
+ 'AC_FC_SRCEXT' => 1,
'AC_PROG_LIBTOOL' => 1,
'AM_INIT_AUTOMAKE' => 1,
- 'AM_PATH_GUILE' => 1,
'AC_CONFIG_SUBDIRS' => 1,
+ 'AM_PATH_GUILE' => 1,
'AM_AUTOMAKE_VERSION' => 1,
'LT_CONFIG_LTDL_DIR' => 1,
- 'AC_REQUIRE_AUX_FILE' => 1,
'AC_CONFIG_LINKS' => 1,
- 'm4_sinclude' => 1,
+ 'AC_REQUIRE_AUX_FILE' => 1,
'LT_SUPPORTED_TAG' => 1,
+ 'm4_sinclude' => 1,
'AM_MAINTAINER_MODE' => 1,
'AM_NLS' => 1,
'AM_GNU_GETTEXT_INTL_SUBDIR' => 1,
- 'AM_MAKEFILE_INCLUDE' => 1,
'_m4_warn' => 1,
+ 'AM_MAKEFILE_INCLUDE' => 1,
'AM_PROG_CXX_C_O' => 1,
- '_AM_COND_ENDIF' => 1,
'_AM_MAKEFILE_INCLUDE' => 1,
+ '_AM_COND_ENDIF' => 1,
'AM_ENABLE_MULTILIB' => 1,
'AM_SILENT_RULES' => 1,
'AM_PROG_MOC' => 1,
'AC_CONFIG_FILES' => 1,
- 'include' => 1,
'LT_INIT' => 1,
- 'AM_PROG_AR' => 1,
+ 'include' => 1,
'AM_GNU_GETTEXT' => 1,
+ 'AM_PROG_AR' => 1,
'AC_LIBSOURCE' => 1,
- 'AM_PROG_FC_C_O' => 1,
'AC_CANONICAL_BUILD' => 1,
+ 'AM_PROG_FC_C_O' => 1,
'AC_FC_FREEFORM' => 1,
'AH_OUTPUT' => 1,
- '_AM_SUBST_NOTMAKE' => 1,
'AC_CONFIG_AUX_DIR' => 1,
- 'sinclude' => 1,
- 'AM_PROG_CC_C_O' => 1,
+ '_AM_SUBST_NOTMAKE' => 1,
'm4_pattern_allow' => 1,
- 'AM_XGETTEXT_OPTION' => 1,
- 'AC_CANONICAL_SYSTEM' => 1,
+ 'AM_PROG_CC_C_O' => 1,
+ 'sinclude' => 1,
'AM_CONDITIONAL' => 1,
+ 'AC_CANONICAL_SYSTEM' => 1,
+ 'AM_XGETTEXT_OPTION' => 1,
'AC_CONFIG_HEADERS' => 1,
'AC_DEFINE_TRACE_LITERAL' => 1,
'AM_POT_TOOLS' => 1,
@@ -106,64 +106,64 @@
],
{
'gl_GETOPT' => 1,
- 'm4_pattern_forbid' => 1,
'gltests_LIBSOURCES' => 1,
+ 'm4_pattern_forbid' => 1,
'AM_SET_CURRENT_AUTOMAKE_VERSION' => 1,
- 'gltests_REPLACE_FUNCS' => 1,
'_AM_SET_OPTION' => 1,
+ 'gltests_REPLACE_FUNCS' => 1,
'AC_DEFUN' => 1,
'AM_PROG_MKDIR_P' => 1,
- 'gl_UNISTD_MODULE_INDICATOR' => 1,
'AM_INIT_AUTOMAKE' => 1,
+ 'gl_UNISTD_MODULE_INDICATOR' => 1,
'AM_AUTOMAKE_VERSION' => 1,
'AM_MISSING_HAS_RUN' => 1,
- 'gl_PREREQ_GETOPT' => 1,
'AC_PROG_MKDIR_P' => 1,
+ 'gl_PREREQ_GETOPT' => 1,
'AM_SUBST_NOTMAKE' => 1,
'AM_MISSING_PROG' => 1,
'AM_OUTPUT_DEPENDENCY_COMMANDS' => 1,
'gl_COMMON_BODY' => 1,
'gl_CHECK_NEXT_HEADERS' => 1,
'AC_DEFUN_ONCE' => 1,
- 'gl_GETOPT_SUBSTITUTE_HEADER' => 1,
'AC_C_RESTRICT' => 1,
- 'gl_INCLUDE_NEXT' => 1,
+ 'gl_GETOPT_SUBSTITUTE_HEADER' => 1,
'gl_GETOPT_IFELSE' => 1,
- 'gl_EARLY' => 1,
+ 'gl_INCLUDE_NEXT' => 1,
'AM_PROG_INSTALL_STRIP' => 1,
- '_m4_warn' => 1,
- 'gl_MODULE_INDICATOR' => 1,
+ 'gl_EARLY' => 1,
'gl_COMMON' => 1,
+ 'gl_MODULE_INDICATOR' => 1,
+ '_m4_warn' => 1,
'gl_REPLACE_FUNCS' => 1,
'AM_SANITY_CHECK' => 1,
- 'AM_SILENT_RULES' => 1,
- 'gl_UNISTD_H' => 1,
'gl_FILE_LIST' => 1,
+ 'gl_UNISTD_H' => 1,
+ 'AM_SILENT_RULES' => 1,
'gl_GETOPT_SUBSTITUTE' => 1,
- 'include' => 1,
'gl_LIBSOURCES' => 1,
- 'gltests_LIBOBJ' => 1,
+ 'include' => 1,
'_AM_PROG_TAR' => 1,
+ 'gltests_LIBOBJ' => 1,
'AM_AUX_DIR_EXPAND' => 1,
'AM_DEP_TRACK' => 1,
'gl_LIBOBJ' => 1,
'_AM_SET_OPTIONS' => 1,
- 'AM_RUN_LOG' => 1,
'_AM_OUTPUT_DEPENDENCY_COMMANDS' => 1,
+ 'AM_RUN_LOG' => 1,
'_AM_IF_OPTION' => 1,
- 'gl_GETOPT_CHECK_HEADERS' => 1,
'_AM_SUBST_NOTMAKE' => 1,
- 'm4_pattern_allow' => 1,
+ 'gl_GETOPT_CHECK_HEADERS' => 1,
'_AM_AUTOCONF_VERSION' => 1,
+ 'm4_pattern_allow' => 1,
'_AM_MANGLE_OPTION' => 1,
- 'AM_SET_LEADING_DOT' => 1,
'AM_CONDITIONAL' => 1,
- 'gl_UNISTD_H_DEFAULTS' => 1,
- 'gl_INIT' => 1,
+ 'AM_SET_LEADING_DOT' => 1,
'AM_SET_DEPDIR' => 1,
+ 'gl_INIT' => 1,
+ 'gl_UNISTD_H_DEFAULTS' => 1,
'_AM_DEPENDENCIES' => 1,
- 'm4_include' => 1,
'AM_PROG_INSTALL_SH' => 1,
+ 'm4_include' => 1,
'_AC_AM_CONFIG_HEADER_HOOK' => 1,
'AU_DEFUN' => 1,
'AM_MAKE_INCLUDE' => 1
@@ -181,55 +181,55 @@
'configure.ac'
],
{
- 'AM_PROG_F77_C_O' => 1,
'_LT_AC_TAGCONFIG' => 1,
- 'AC_INIT' => 1,
+ 'AM_PROG_F77_C_O' => 1,
'm4_pattern_forbid' => 1,
- 'AC_CANONICAL_TARGET' => 1,
+ 'AC_INIT' => 1,
'_AM_COND_IF' => 1,
- 'AC_CONFIG_LIBOBJ_DIR' => 1,
+ 'AC_CANONICAL_TARGET' => 1,
'AC_SUBST' => 1,
- 'AC_CANONICAL_HOST' => 1,
+ 'AC_CONFIG_LIBOBJ_DIR' => 1,
'AC_FC_SRCEXT' => 1,
+ 'AC_CANONICAL_HOST' => 1,
'AC_PROG_LIBTOOL' => 1,
'AM_INIT_AUTOMAKE' => 1,
- 'AC_CONFIG_SUBDIRS' => 1,
'AM_PATH_GUILE' => 1,
+ 'AC_CONFIG_SUBDIRS' => 1,
'AM_AUTOMAKE_VERSION' => 1,
'LT_CONFIG_LTDL_DIR' => 1,
- 'AC_CONFIG_LINKS' => 1,
'AC_REQUIRE_AUX_FILE' => 1,
- 'LT_SUPPORTED_TAG' => 1,
+ 'AC_CONFIG_LINKS' => 1,
'm4_sinclude' => 1,
+ 'LT_SUPPORTED_TAG' => 1,
'AM_MAINTAINER_MODE' => 1,
'AM_NLS' => 1,
'AM_GNU_GETTEXT_INTL_SUBDIR' => 1,
- '_m4_warn' => 1,
'AM_MAKEFILE_INCLUDE' => 1,
+ '_m4_warn' => 1,
'AM_PROG_CXX_C_O' => 1,
- '_AM_MAKEFILE_INCLUDE' => 1,
'_AM_COND_ENDIF' => 1,
+ '_AM_MAKEFILE_INCLUDE' => 1,
'AM_ENABLE_MULTILIB' => 1,
'AM_SILENT_RULES' => 1,
'AM_PROG_MOC' => 1,
'AC_CONFIG_FILES' => 1,
- 'include' => 1,
'LT_INIT' => 1,
- 'AM_GNU_GETTEXT' => 1,
+ 'include' => 1,
'AM_PROG_AR' => 1,
+ 'AM_GNU_GETTEXT' => 1,
'AC_LIBSOURCE' => 1,
- 'AC_CANONICAL_BUILD' => 1,
'AM_PROG_FC_C_O' => 1,
+ 'AC_CANONICAL_BUILD' => 1,
'AC_FC_FREEFORM' => 1,
'AH_OUTPUT' => 1,
- 'AC_CONFIG_AUX_DIR' => 1,
'_AM_SUBST_NOTMAKE' => 1,
- 'm4_pattern_allow' => 1,
- 'AM_PROG_CC_C_O' => 1,
+ 'AC_CONFIG_AUX_DIR' => 1,
'sinclude' => 1,
- 'AM_CONDITIONAL' => 1,
- 'AC_CANONICAL_SYSTEM' => 1,
+ 'AM_PROG_CC_C_O' => 1,
+ 'm4_pattern_allow' => 1,
'AM_XGETTEXT_OPTION' => 1,
+ 'AC_CANONICAL_SYSTEM' => 1,
+ 'AM_CONDITIONAL' => 1,
'AC_CONFIG_HEADERS' => 1,
'AC_DEFINE_TRACE_LITERAL' => 1,
'AM_POT_TOOLS' => 1,
2  autom4te.cache/traces.2
View
@@ -3,7 +3,7 @@ m4trace:aclocal.m4:953: -1- m4_include([m4/gnulib-common.m4])
m4trace:aclocal.m4:954: -1- m4_include([m4/gnulib-comp.m4])
m4trace:aclocal.m4:955: -1- m4_include([m4/include_next.m4])
m4trace:aclocal.m4:956: -1- m4_include([m4/unistd_h.m4])
-m4trace:configure.ac:6: -1- AC_INIT([indel-seq-gen], [2.1.03], [corystrope@gmail.com])
+m4trace:configure.ac:6: -1- AC_INIT([indel-seq-gen], [2.2.13], [corystrope@gmail.com])
m4trace:configure.ac:6: -1- m4_pattern_forbid([^_?A[CHUM]_])
m4trace:configure.ac:6: -1- m4_pattern_forbid([_AC_])
m4trace:configure.ac:6: -1- m4_pattern_forbid([^LIBOBJS$], [do not use LIBOBJS directly, use AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS'])
55 config.log
View
@@ -30,8 +30,8 @@ Kernel configured for up to 16 processors.
Processor type: i486 (Intel 80486)
Processors active: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Primary memory available: 8.00 gigabytes
-Default processor set: 103 tasks, 509 threads, 16 processors
-Load average: 3.35, Mach factor: 12.63
+Default processor set: 89 tasks, 463 threads, 16 processors
+Load average: 0.26, Mach factor: 15.73
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
@@ -586,6 +586,7 @@ config.status:928: creating data/Makefile
config.status:928: creating doc/Makefile
config.status:928: creating src/Makefile
config.status:928: creating config.h
+config.status:1109: config.h is unchanged
config.status:1157: executing depfiles commands
## ---------------- ##
@@ -665,14 +666,14 @@ gl_cv_next_unistd_h='<unistd.h>'
## Output variables. ##
## ----------------- ##
-ACLOCAL='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run aclocal-1.11'
+ACLOCAL='${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
-AMTAR='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run tar'
-AUTOCONF='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoconf'
-AUTOHEADER='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoheader'
-AUTOMAKE='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run automake-1.11'
+AMTAR='${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run tar'
+AUTOCONF='${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoconf'
+AUTOHEADER='${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoheader'
+AUTOMAKE='${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run automake-1.11'
AWK='awk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
@@ -729,7 +730,7 @@ LIBOBJS=''
LIBS='-lm '
LTLIBINTL=''
LTLIBOBJS=''
-MAKEINFO='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run makeinfo'
+MAKEINFO='${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run makeinfo'
MKDIR_P='./install-sh -c -d'
NEXT_UNISTD_H='<unistd.h>'
OBJEXT='o'
@@ -781,7 +782,7 @@ host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
-install_sh='${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/install-sh'
+install_sh='${SHELL} /Users/cstrope/git/indel-seq-gen/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
@@ -840,3 +841,39 @@ target_alias=''
#define HAVE_SQRT 1
configure: exit 0
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by indel-seq-gen config.status 2.2.13, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status config.h
+
+on stropemac.statgen.ncsu.edu
+
+config.status:928: creating config.h
+config.status:1109: config.h is unchanged
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by indel-seq-gen config.status 2.2.13, which was
+generated by GNU Autoconf 2.68. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status src/Makefile depfiles
+
+on stropemac.statgen.ncsu.edu
+
+config.status:928: creating src/Makefile
+config.status:1157: executing depfiles commands
16 config.status
View
@@ -449,7 +449,7 @@ Copyright (C) 2010 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
-ac_pwd='/Users/cstrope/iSG/indel-seq-gen/branches/codon_models'
+ac_pwd='/Users/cstrope/git/indel-seq-gen'
srcdir='.'
INSTALL='/usr/bin/install -c'
MKDIR_P='./install-sh -c -d'
@@ -703,7 +703,7 @@ S["CFLAGS"]="-g -O2"
S["CC"]="gcc"
S["am__untar"]="${AMTAR} xf -"
S["am__tar"]="${AMTAR} chof - \"$$tardir\""
-S["AMTAR"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run tar"
+S["AMTAR"]="${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run tar"
S["am__leading_dot"]="."
S["SET_MAKE"]=""
S["AWK"]="awk"
@@ -711,12 +711,12 @@ S["mkdir_p"]="$(top_builddir)/./install-sh -c -d"
S["MKDIR_P"]="./install-sh -c -d"
S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s"
S["STRIP"]=""
-S["install_sh"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/install-sh"
-S["MAKEINFO"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run makeinfo"
-S["AUTOHEADER"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoheader"
-S["AUTOMAKE"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run automake-1.11"
-S["AUTOCONF"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoconf"
-S["ACLOCAL"]="${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run aclocal-1.11"
+S["install_sh"]="${SHELL} /Users/cstrope/git/indel-seq-gen/install-sh"
+S["MAKEINFO"]="${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run makeinfo"
+S["AUTOHEADER"]="${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoheader"
+S["AUTOMAKE"]="${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run automake-1.11"
+S["AUTOCONF"]="${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoconf"
+S["ACLOCAL"]="${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run aclocal-1.11"
S["VERSION"]="2.2.13"
S["PACKAGE"]="indel-seq-gen"
S["CYGPATH_W"]="echo"
22 data/Makefile
View
@@ -48,11 +48,11 @@ CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run aclocal-1.11
-AMTAR = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run tar
-AUTOCONF = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoconf
-AUTOHEADER = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run autoheader
-AUTOMAKE = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run automake-1.11
+ACLOCAL = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run aclocal-1.11
+AMTAR = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run tar
+AUTOCONF = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoconf
+AUTOHEADER = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoheader
+AUTOMAKE = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run automake-1.11
AWK = awk
CC = gcc
CCDEPMODE = depmode=gcc3
@@ -108,7 +108,7 @@ LIBOBJS =
LIBS = -lm
LTLIBINTL =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/missing --run makeinfo
+MAKEINFO = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run makeinfo
MKDIR_P = .././install-sh -c -d
NEXT_UNISTD_H = <unistd.h>
OBJEXT = o
@@ -131,10 +131,10 @@ SET_MAKE =
SHELL = /bin/sh
STRIP =
VERSION = 2.2.13
-abs_builddir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/data
-abs_srcdir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/data
-abs_top_builddir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models
-abs_top_srcdir = /Users/cstrope/iSG/indel-seq-gen/branches/codon_models
+abs_builddir = /Users/cstrope/git/indel-seq-gen/data
+abs_srcdir = /Users/cstrope/git/indel-seq-gen/data
+abs_top_builddir = /Users/cstrope/git/indel-seq-gen
+abs_top_srcdir = /Users/cstrope/git/indel-seq-gen
ac_ct_CC = gcc
ac_ct_CXX = g++
am__include = include
@@ -158,7 +158,7 @@ host_alias =
htmldir = ${docdir}
includedir = ${prefix}/include
infodir = ${datarootdir}/info
-install_sh = ${SHELL} /Users/cstrope/iSG/indel-seq-gen/branches/codon_models/install-sh
+install_sh = ${SHELL} /Users/cstrope/git/indel-seq-gen/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
28 doc/Makefile
View
@@ -48,11 +48,11 @@ CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run aclocal-1.11
-AMTAR = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run tar
-AUTOCONF = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run autoconf
-AUTOHEADER = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run autoheader
-AUTOMAKE = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run automake-1.11
+ACLOCAL = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run aclocal-1.11
+AMTAR = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run tar
+AUTOCONF = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoconf
+AUTOHEADER = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoheader
+AUTOMAKE = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run automake-1.11
AWK = awk
CC = gcc
CCDEPMODE = depmode=gcc3
@@ -108,17 +108,17 @@ LIBOBJS =
LIBS = -lm
LTLIBINTL =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run makeinfo
+MAKEINFO = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run makeinfo
MKDIR_P = .././install-sh -c -d
NEXT_UNISTD_H = <unistd.h>
OBJEXT = o
PACKAGE = indel-seq-gen
PACKAGE_BUGREPORT = corystrope@gmail.com
PACKAGE_NAME = indel-seq-gen
-PACKAGE_STRING = indel-seq-gen 2.1.03
+PACKAGE_STRING = indel-seq-gen 2.2.13
PACKAGE_TARNAME = indel-seq-gen
PACKAGE_URL =
-PACKAGE_VERSION = 2.1.03
+PACKAGE_VERSION = 2.2.13
PATH_SEPARATOR = :
RANLIB = ranlib
REPLACE_CHOWN = 0
@@ -130,11 +130,11 @@ REPLACE_LSEEK = 0
SET_MAKE =
SHELL = /bin/sh
STRIP =
-VERSION = 2.1.03
-abs_builddir = /Users/cstrope/git/indel-Seq-Gen/doc
-abs_srcdir = /Users/cstrope/git/indel-Seq-Gen/doc
-abs_top_builddir = /Users/cstrope/git/indel-Seq-Gen
-abs_top_srcdir = /Users/cstrope/git/indel-Seq-Gen
+VERSION = 2.2.13
+abs_builddir = /Users/cstrope/git/indel-seq-gen/doc
+abs_srcdir = /Users/cstrope/git/indel-seq-gen/doc
+abs_top_builddir = /Users/cstrope/git/indel-seq-gen
+abs_top_srcdir = /Users/cstrope/git/indel-seq-gen
ac_ct_CC = gcc
ac_ct_CXX = g++
am__include = include
@@ -158,7 +158,7 @@ host_alias =
htmldir = ${docdir}
includedir = ${prefix}/include
infodir = ${datarootdir}/info
-install_sh = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/install-sh
+install_sh = ${SHELL} /Users/cstrope/git/indel-seq-gen/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
28 lib/Makefile
View
@@ -82,11 +82,11 @@ HEADERS = $(noinst_HEADERS)
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run aclocal-1.11
-AMTAR = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run tar
-AUTOCONF = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run autoconf
-AUTOHEADER = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run autoheader
-AUTOMAKE = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run automake-1.11
+ACLOCAL = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run aclocal-1.11
+AMTAR = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run tar
+AUTOCONF = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoconf
+AUTOHEADER = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run autoheader
+AUTOMAKE = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run automake-1.11
AWK = awk
CC = gcc
CCDEPMODE = depmode=gcc3
@@ -142,17 +142,17 @@ LIBOBJS =
LIBS = -lm
LTLIBINTL =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/missing --run makeinfo
+MAKEINFO = ${SHELL} /Users/cstrope/git/indel-seq-gen/missing --run makeinfo
MKDIR_P = .././install-sh -c -d
NEXT_UNISTD_H = <unistd.h>
OBJEXT = o
PACKAGE = indel-seq-gen
PACKAGE_BUGREPORT = corystrope@gmail.com
PACKAGE_NAME = indel-seq-gen
-PACKAGE_STRING = indel-seq-gen 2.1.03
+PACKAGE_STRING = indel-seq-gen 2.2.13
PACKAGE_TARNAME = indel-seq-gen
PACKAGE_URL =
-PACKAGE_VERSION = 2.1.03
+PACKAGE_VERSION = 2.2.13
PATH_SEPARATOR = :
RANLIB = ranlib
REPLACE_CHOWN = 0
@@ -164,11 +164,11 @@ REPLACE_LSEEK = 0
SET_MAKE =
SHELL = /bin/sh
STRIP =
-VERSION = 2.1.03
-abs_builddir = /Users/cstrope/git/indel-Seq-Gen/lib
-abs_srcdir = /Users/cstrope/git/indel-Seq-Gen/lib
-abs_top_builddir = /Users/cstrope/git/indel-Seq-Gen
-abs_top_srcdir = /Users/cstrope/git/indel-Seq-Gen
+VERSION = 2.2.13
+abs_builddir = /Users/cstrope/git/indel-seq-gen/lib
+abs_srcdir = /Users/cstrope/git/indel-seq-gen/lib
+abs_top_builddir = /Users/cstrope/git/indel-seq-gen
+abs_top_srcdir = /Users/cstrope/git/indel-seq-gen
ac_ct_CC = gcc
ac_ct_CXX = g++
am__include = include
@@ -192,7 +192,7 @@ host_alias =
htmldir = ${docdir}
includedir = ${prefix}/include
infodir = ${datarootdir}/info
-install_sh = ${SHELL} /Users/cstrope/git/indel-Seq-Gen/install-sh
+install_sh = ${SHELL} /Users/cstrope/git/indel-seq-gen/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
153 src/.deps/eigen.Po
View
@@ -13,21 +13,12 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/time.h /usr/include/_structs.h /usr/include/math.h \
- /usr/include/architecture/i386/math.h \
- /opt/local/include/gcc46/c++/iostream \
+ /usr/include/architecture/i386/math.h eigen.h \
+ /opt/local/include/gcc46/c++/vector \
+ /opt/local/include/gcc46/c++/bits/stl_algobase.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++config.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/os_defines.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/cpu_defines.h \
- /opt/local/include/gcc46/c++/ostream /opt/local/include/gcc46/c++/ios \
- /opt/local/include/gcc46/c++/iosfwd \
- /opt/local/include/gcc46/c++/bits/stringfwd.h \
- /opt/local/include/gcc46/c++/bits/postypes.h \
- /opt/local/include/gcc46/c++/cwchar /usr/include/wchar.h \
- /opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdarg.h \
- /usr/include/_wctype.h /usr/include/ctype.h /usr/include/runetype.h \
- /opt/local/include/gcc46/c++/exception \
- /opt/local/include/gcc46/c++/bits/char_traits.h \
- /opt/local/include/gcc46/c++/bits/stl_algobase.h \
/opt/local/include/gcc46/c++/bits/functexcept.h \
/opt/local/include/gcc46/c++/bits/exception_defines.h \
/opt/local/include/gcc46/c++/bits/cpp_type_traits.h \
@@ -40,6 +31,26 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++/bits/stl_iterator_base_funcs.h \
/opt/local/include/gcc46/c++/bits/stl_iterator.h \
/opt/local/include/gcc46/c++/debug/debug.h \
+ /opt/local/include/gcc46/c++/bits/allocator.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++allocator.h \
+ /opt/local/include/gcc46/c++/ext/new_allocator.h \
+ /opt/local/include/gcc46/c++/new /opt/local/include/gcc46/c++/exception \
+ /opt/local/include/gcc46/c++/bits/stl_construct.h \
+ /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
+ /opt/local/include/gcc46/c++/bits/stl_vector.h \
+ /opt/local/include/gcc46/c++/initializer_list \
+ /opt/local/include/gcc46/c++/bits/stl_bvector.h \
+ /opt/local/include/gcc46/c++/bits/range_access.h \
+ /opt/local/include/gcc46/c++/bits/vector.tcc \
+ /opt/local/include/gcc46/c++/iostream \
+ /opt/local/include/gcc46/c++/ostream /opt/local/include/gcc46/c++/ios \
+ /opt/local/include/gcc46/c++/iosfwd \
+ /opt/local/include/gcc46/c++/bits/stringfwd.h \
+ /opt/local/include/gcc46/c++/bits/postypes.h \
+ /opt/local/include/gcc46/c++/cwchar /usr/include/wchar.h \
+ /opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdarg.h \
+ /usr/include/_wctype.h /usr/include/ctype.h /usr/include/runetype.h \
+ /opt/local/include/gcc46/c++/bits/char_traits.h \
/opt/local/include/gcc46/c++/bits/localefwd.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++locale.h \
/opt/local/include/gcc46/c++/clocale /usr/include/locale.h \
@@ -54,17 +65,11 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/atomic_word.h \
/opt/local/include/gcc46/c++/bits/locale_classes.h \
/opt/local/include/gcc46/c++/string \
- /opt/local/include/gcc46/c++/bits/allocator.h \
- /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++allocator.h \
- /opt/local/include/gcc46/c++/ext/new_allocator.h \
- /opt/local/include/gcc46/c++/new \
/opt/local/include/gcc46/c++/bits/ostream_insert.h \
/opt/local/include/gcc46/c++/bits/cxxabi_forced.h \
/opt/local/include/gcc46/c++/bits/stl_function.h \
/opt/local/include/gcc46/c++/backward/binders.h \
- /opt/local/include/gcc46/c++/bits/range_access.h \
/opt/local/include/gcc46/c++/bits/basic_string.h \
- /opt/local/include/gcc46/c++/initializer_list \
/opt/local/include/gcc46/c++/bits/basic_string.tcc \
/opt/local/include/gcc46/c++/bits/locale_classes.tcc \
/opt/local/include/gcc46/c++/streambuf \
@@ -79,13 +84,7 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++/bits/basic_ios.tcc \
/opt/local/include/gcc46/c++/bits/ostream.tcc \
/opt/local/include/gcc46/c++/istream \
- /opt/local/include/gcc46/c++/bits/istream.tcc \
- /opt/local/include/gcc46/c++/vector \
- /opt/local/include/gcc46/c++/bits/stl_construct.h \
- /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
- /opt/local/include/gcc46/c++/bits/stl_vector.h \
- /opt/local/include/gcc46/c++/bits/stl_bvector.h \
- /opt/local/include/gcc46/c++/bits/vector.tcc eigen.h
+ /opt/local/include/gcc46/c++/bits/istream.tcc
/usr/include/stdio.h:
@@ -149,7 +148,11 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/usr/include/architecture/i386/math.h:
-/opt/local/include/gcc46/c++/iostream:
+eigen.h:
+
+/opt/local/include/gcc46/c++/vector:
+
+/opt/local/include/gcc46/c++/bits/stl_algobase.h:
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++config.h:
@@ -157,57 +160,79 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/cpu_defines.h:
-/opt/local/include/gcc46/c++/ostream:
+/opt/local/include/gcc46/c++/bits/functexcept.h:
-/opt/local/include/gcc46/c++/ios:
+/opt/local/include/gcc46/c++/bits/exception_defines.h:
-/opt/local/include/gcc46/c++/iosfwd:
+/opt/local/include/gcc46/c++/bits/cpp_type_traits.h:
-/opt/local/include/gcc46/c++/bits/stringfwd.h:
+/opt/local/include/gcc46/c++/ext/type_traits.h:
-/opt/local/include/gcc46/c++/bits/postypes.h:
+/opt/local/include/gcc46/c++/ext/numeric_traits.h:
-/opt/local/include/gcc46/c++/cwchar:
+/opt/local/include/gcc46/c++/bits/stl_pair.h:
-/usr/include/wchar.h:
+/opt/local/include/gcc46/c++/bits/move.h:
-/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdarg.h:
+/opt/local/include/gcc46/c++/bits/concept_check.h:
-/usr/include/_wctype.h:
+/opt/local/include/gcc46/c++/bits/stl_iterator_base_types.h:
-/usr/include/ctype.h:
+/opt/local/include/gcc46/c++/bits/stl_iterator_base_funcs.h:
-/usr/include/runetype.h:
+/opt/local/include/gcc46/c++/bits/stl_iterator.h:
+
+/opt/local/include/gcc46/c++/debug/debug.h:
+
+/opt/local/include/gcc46/c++/bits/allocator.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++allocator.h:
+
+/opt/local/include/gcc46/c++/ext/new_allocator.h:
+
+/opt/local/include/gcc46/c++/new:
/opt/local/include/gcc46/c++/exception:
-/opt/local/include/gcc46/c++/bits/char_traits.h:
+/opt/local/include/gcc46/c++/bits/stl_construct.h:
-/opt/local/include/gcc46/c++/bits/stl_algobase.h:
+/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
-/opt/local/include/gcc46/c++/bits/functexcept.h:
+/opt/local/include/gcc46/c++/bits/stl_vector.h:
-/opt/local/include/gcc46/c++/bits/exception_defines.h:
+/opt/local/include/gcc46/c++/initializer_list:
-/opt/local/include/gcc46/c++/bits/cpp_type_traits.h:
+/opt/local/include/gcc46/c++/bits/stl_bvector.h:
-/opt/local/include/gcc46/c++/ext/type_traits.h:
+/opt/local/include/gcc46/c++/bits/range_access.h:
-/opt/local/include/gcc46/c++/ext/numeric_traits.h:
+/opt/local/include/gcc46/c++/bits/vector.tcc:
-/opt/local/include/gcc46/c++/bits/stl_pair.h:
+/opt/local/include/gcc46/c++/iostream:
-/opt/local/include/gcc46/c++/bits/move.h:
+/opt/local/include/gcc46/c++/ostream:
-/opt/local/include/gcc46/c++/bits/concept_check.h:
+/opt/local/include/gcc46/c++/ios:
-/opt/local/include/gcc46/c++/bits/stl_iterator_base_types.h:
+/opt/local/include/gcc46/c++/iosfwd:
-/opt/local/include/gcc46/c++/bits/stl_iterator_base_funcs.h:
+/opt/local/include/gcc46/c++/bits/stringfwd.h:
-/opt/local/include/gcc46/c++/bits/stl_iterator.h:
+/opt/local/include/gcc46/c++/bits/postypes.h:
-/opt/local/include/gcc46/c++/debug/debug.h:
+/opt/local/include/gcc46/c++/cwchar:
+
+/usr/include/wchar.h:
+
+/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdarg.h:
+
+/usr/include/_wctype.h:
+
+/usr/include/ctype.h:
+
+/usr/include/runetype.h:
+
+/opt/local/include/gcc46/c++/bits/char_traits.h:
/opt/local/include/gcc46/c++/bits/localefwd.h:
@@ -251,14 +276,6 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++/string:
-/opt/local/include/gcc46/c++/bits/allocator.h:
-
-/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++allocator.h:
-
-/opt/local/include/gcc46/c++/ext/new_allocator.h:
-
-/opt/local/include/gcc46/c++/new:
-
/opt/local/include/gcc46/c++/bits/ostream_insert.h:
/opt/local/include/gcc46/c++/bits/cxxabi_forced.h:
@@ -267,12 +284,8 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++/backward/binders.h:
-/opt/local/include/gcc46/c++/bits/range_access.h:
-
/opt/local/include/gcc46/c++/bits/basic_string.h:
-/opt/local/include/gcc46/c++/initializer_list:
-
/opt/local/include/gcc46/c++/bits/basic_string.tcc:
/opt/local/include/gcc46/c++/bits/locale_classes.tcc:
@@ -304,17 +317,3 @@ eigen.o: eigen.cpp /usr/include/stdio.h /usr/include/_types.h \
/opt/local/include/gcc46/c++/istream:
/opt/local/include/gcc46/c++/bits/istream.tcc:
-
-/opt/local/include/gcc46/c++/vector:
-
-/opt/local/include/gcc46/c++/bits/stl_construct.h:
-
-/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
-
-/opt/local/include/gcc46/c++/bits/stl_vector.h:
-
-/opt/local/include/gcc46/c++/bits/stl_bvector.h:
-
-/opt/local/include/gcc46/c++/bits/vector.tcc:
-
-eigen.h:
66 src/.deps/evolve.Po
View
@@ -95,24 +95,32 @@ evolve.o: evolve.cpp evolve.h /opt/local/include/gcc46/c++/exception \
/opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
- /opt/local/include/gcc46/c++/backward/auto_ptr.h aamodels.h \
+ /opt/local/include/gcc46/c++/backward/auto_ptr.h gamma.h \
/opt/local/include/gcc46/c++/vector \
/opt/local/include/gcc46/c++/bits/stl_vector.h \
/opt/local/include/gcc46/c++/bits/stl_bvector.h \
- /opt/local/include/gcc46/c++/bits/vector.tcc eigen.h inClade.h tree.h \
- /opt/local/include/gcc46/c++/limits gamma.h inTree.h \
+ /opt/local/include/gcc46/c++/bits/vector.tcc insert_freqs.h \
+ /opt/local/include/gcc46/c++/cstdlib model.h eigen.h inTree.h \
/opt/local/include/gcc46/c++/map \
/opt/local/include/gcc46/c++/bits/stl_tree.h \
/opt/local/include/gcc46/c++/bits/stl_map.h \
/opt/local/include/gcc46/c++/bits/stl_multimap.h \
- /opt/local/include/gcc46/c++/cstdlib /opt/local/include/gcc46/c++/cmath \
- model.h nucmodels.h motif.h /opt/local/include/gcc46/c++/set \
+ /opt/local/include/gcc46/c++/cmath inClade.h tree.h \
+ /opt/local/include/gcc46/c++/limits twister.h motif.h \
+ /opt/local/include/gcc46/c++/set \
/opt/local/include/gcc46/c++/bits/stl_set.h \
/opt/local/include/gcc46/c++/bits/stl_multiset.h /usr/include/assert.h \
- seqGenOptions.h ../config.h insert_freqs.h treefile.h twister.h random.h \
+ seqGenOptions.h ../config.h propose_path.h stats.h \
+ /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h treefile.h \
+ forward_simulation.h trace.h random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- /usr/include/sys/types.h trace.h
+ /usr/include/sys/types.h
evolve.h:
@@ -376,7 +384,7 @@ evolve.h:
/opt/local/include/gcc46/c++/backward/auto_ptr.h:
-aamodels.h:
+gamma.h:
/opt/local/include/gcc46/c++/vector:
@@ -386,15 +394,13 @@ aamodels.h:
/opt/local/include/gcc46/c++/bits/vector.tcc:
-eigen.h:
-
-inClade.h:
+insert_freqs.h:
-tree.h:
+/opt/local/include/gcc46/c++/cstdlib:
-/opt/local/include/gcc46/c++/limits:
+model.h:
-gamma.h:
+eigen.h:
inTree.h:
@@ -406,13 +412,15 @@ inTree.h:
/opt/local/include/gcc46/c++/bits/stl_multimap.h:
-/opt/local/include/gcc46/c++/cstdlib:
-
/opt/local/include/gcc46/c++/cmath:
-model.h:
+inClade.h:
-nucmodels.h:
+tree.h:
+
+/opt/local/include/gcc46/c++/limits:
+
+twister.h:
motif.h:
@@ -428,11 +436,27 @@ seqGenOptions.h:
../config.h:
-insert_freqs.h:
+propose_path.h:
+
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility:
+
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
treefile.h:
-twister.h:
+forward_simulation.h:
+
+trace.h:
random.h:
@@ -441,5 +465,3 @@ random.h:
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h:
/usr/include/sys/types.h:
-
-trace.h:
312 src/.deps/gamma.Po
View
@@ -1,6 +1,90 @@
gamma.o: gamma.cpp /usr/include/math.h \
- /usr/include/architecture/i386/math.h /usr/include/sys/cdefs.h twister.h \
- gamma.h
+ /usr/include/architecture/i386/math.h /usr/include/sys/cdefs.h \
+ /opt/local/include/gcc46/c++/iostream \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++config.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/os_defines.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/cpu_defines.h \
+ /opt/local/include/gcc46/c++/ostream /opt/local/include/gcc46/c++/ios \
+ /opt/local/include/gcc46/c++/iosfwd \
+ /opt/local/include/gcc46/c++/bits/stringfwd.h \
+ /opt/local/include/gcc46/c++/bits/postypes.h \
+ /opt/local/include/gcc46/c++/cwchar /usr/include/wchar.h \
+ /usr/include/_types.h /usr/include/sys/_types.h \
+ /usr/include/machine/_types.h /usr/include/i386/_types.h \
+ /opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdarg.h \
+ /usr/include/stdio.h /usr/include/time.h /usr/include/_structs.h \
+ /usr/include/sys/_structs.h /usr/include/_wctype.h /usr/include/ctype.h \
+ /usr/include/runetype.h /opt/local/include/gcc46/c++/exception \
+ /opt/local/include/gcc46/c++/bits/char_traits.h \
+ /opt/local/include/gcc46/c++/bits/stl_algobase.h \
+ /opt/local/include/gcc46/c++/bits/functexcept.h \
+ /opt/local/include/gcc46/c++/bits/exception_defines.h \
+ /opt/local/include/gcc46/c++/bits/cpp_type_traits.h \
+ /opt/local/include/gcc46/c++/ext/type_traits.h \
+ /opt/local/include/gcc46/c++/ext/numeric_traits.h \
+ /opt/local/include/gcc46/c++/bits/stl_pair.h \
+ /opt/local/include/gcc46/c++/bits/move.h \
+ /opt/local/include/gcc46/c++/bits/concept_check.h \
+ /opt/local/include/gcc46/c++/bits/stl_iterator_base_types.h \
+ /opt/local/include/gcc46/c++/bits/stl_iterator_base_funcs.h \
+ /opt/local/include/gcc46/c++/bits/stl_iterator.h \
+ /opt/local/include/gcc46/c++/debug/debug.h \
+ /opt/local/include/gcc46/c++/bits/localefwd.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++locale.h \
+ /opt/local/include/gcc46/c++/clocale /usr/include/locale.h \
+ /usr/include/_locale.h /opt/local/include/gcc46/c++/cctype \
+ /opt/local/include/gcc46/c++/bits/ios_base.h \
+ /opt/local/include/gcc46/c++/ext/atomicity.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/gthr.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/pthread_impl.h /usr/include/sched.h \
+ ../lib/unistd.h /usr/include/unistd.h /usr/include/sys/unistd.h \
+ /usr/include/sys/select.h /usr/include/sys/appleapiopts.h \
+ /usr/include/sys/_select.h /usr/include/stdlib.h \
+ /usr/include/Availability.h /usr/include/AvailabilityInternal.h \
+ /usr/include/sys/wait.h /usr/include/sys/signal.h \
+ /usr/include/machine/signal.h /usr/include/i386/signal.h \
+ /usr/include/i386/_structs.h /usr/include/machine/_structs.h \
+ /usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
+ /usr/include/machine/endian.h /usr/include/i386/endian.h \
+ /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
+ /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
+ /usr/include/machine/types.h /usr/include/i386/types.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/atomic_word.h \
+ /opt/local/include/gcc46/c++/bits/locale_classes.h \
+ /opt/local/include/gcc46/c++/string \
+ /opt/local/include/gcc46/c++/bits/allocator.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++allocator.h \
+ /opt/local/include/gcc46/c++/ext/new_allocator.h \
+ /opt/local/include/gcc46/c++/new \
+ /opt/local/include/gcc46/c++/bits/ostream_insert.h \
+ /opt/local/include/gcc46/c++/bits/cxxabi_forced.h \
+ /opt/local/include/gcc46/c++/bits/stl_function.h \
+ /opt/local/include/gcc46/c++/backward/binders.h \
+ /opt/local/include/gcc46/c++/bits/range_access.h \
+ /opt/local/include/gcc46/c++/bits/basic_string.h \
+ /opt/local/include/gcc46/c++/initializer_list \
+ /opt/local/include/gcc46/c++/bits/basic_string.tcc \
+ /opt/local/include/gcc46/c++/bits/locale_classes.tcc \
+ /opt/local/include/gcc46/c++/streambuf \
+ /opt/local/include/gcc46/c++/bits/streambuf.tcc \
+ /opt/local/include/gcc46/c++/bits/basic_ios.h \
+ /opt/local/include/gcc46/c++/bits/locale_facets.h \
+ /opt/local/include/gcc46/c++/cwctype /usr/include/wctype.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/ctype_base.h \
+ /opt/local/include/gcc46/c++/bits/streambuf_iterator.h \
+ /opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/ctype_inline.h \
+ /opt/local/include/gcc46/c++/bits/locale_facets.tcc \
+ /opt/local/include/gcc46/c++/bits/basic_ios.tcc \
+ /opt/local/include/gcc46/c++/bits/ostream.tcc \
+ /opt/local/include/gcc46/c++/istream \
+ /opt/local/include/gcc46/c++/bits/istream.tcc twister.h gamma.h \
+ /opt/local/include/gcc46/c++/vector \
+ /opt/local/include/gcc46/c++/bits/stl_construct.h \
+ /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
+ /opt/local/include/gcc46/c++/bits/stl_vector.h \
+ /opt/local/include/gcc46/c++/bits/stl_bvector.h \
+ /opt/local/include/gcc46/c++/bits/vector.tcc
/usr/include/math.h:
@@ -8,6 +92,230 @@ gamma.o: gamma.cpp /usr/include/math.h \
/usr/include/sys/cdefs.h:
+/opt/local/include/gcc46/c++/iostream:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++config.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/os_defines.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/cpu_defines.h:
+
+/opt/local/include/gcc46/c++/ostream:
+
+/opt/local/include/gcc46/c++/ios:
+
+/opt/local/include/gcc46/c++/iosfwd:
+
+/opt/local/include/gcc46/c++/bits/stringfwd.h:
+
+/opt/local/include/gcc46/c++/bits/postypes.h:
+
+/opt/local/include/gcc46/c++/cwchar:
+
+/usr/include/wchar.h:
+
+/usr/include/_types.h:
+
+/usr/include/sys/_types.h:
+
+/usr/include/machine/_types.h:
+
+/usr/include/i386/_types.h:
+
+/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdarg.h:
+
+/usr/include/stdio.h:
+
+/usr/include/time.h:
+
+/usr/include/_structs.h:
+
+/usr/include/sys/_structs.h:
+
+/usr/include/_wctype.h:
+
+/usr/include/ctype.h:
+
+/usr/include/runetype.h:
+
+/opt/local/include/gcc46/c++/exception:
+
+/opt/local/include/gcc46/c++/bits/char_traits.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algobase.h:
+
+/opt/local/include/gcc46/c++/bits/functexcept.h:
+
+/opt/local/include/gcc46/c++/bits/exception_defines.h:
+
+/opt/local/include/gcc46/c++/bits/cpp_type_traits.h:
+
+/opt/local/include/gcc46/c++/ext/type_traits.h:
+
+/opt/local/include/gcc46/c++/ext/numeric_traits.h:
+
+/opt/local/include/gcc46/c++/bits/stl_pair.h:
+
+/opt/local/include/gcc46/c++/bits/move.h:
+
+/opt/local/include/gcc46/c++/bits/concept_check.h:
+
+/opt/local/include/gcc46/c++/bits/stl_iterator_base_types.h:
+
+/opt/local/include/gcc46/c++/bits/stl_iterator_base_funcs.h:
+
+/opt/local/include/gcc46/c++/bits/stl_iterator.h:
+
+/opt/local/include/gcc46/c++/debug/debug.h:
+
+/opt/local/include/gcc46/c++/bits/localefwd.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++locale.h:
+
+/opt/local/include/gcc46/c++/clocale:
+
+/usr/include/locale.h:
+
+/usr/include/_locale.h:
+
+/opt/local/include/gcc46/c++/cctype:
+
+/opt/local/include/gcc46/c++/bits/ios_base.h:
+
+/opt/local/include/gcc46/c++/ext/atomicity.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/gthr.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/gthr-default.h:
+
+/usr/include/pthread.h:
+
+/usr/include/pthread_impl.h:
+
+/usr/include/sched.h:
+
+../lib/unistd.h:
+
+/usr/include/unistd.h:
+
+/usr/include/sys/unistd.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/sys/appleapiopts.h:
+
+/usr/include/sys/_select.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/Availability.h:
+
+/usr/include/AvailabilityInternal.h:
+
+/usr/include/sys/wait.h:
+
+/usr/include/sys/signal.h:
+
+/usr/include/machine/signal.h:
+
+/usr/include/i386/signal.h:
+
+/usr/include/i386/_structs.h:
+
+/usr/include/machine/_structs.h:
+
+/usr/include/mach/i386/_structs.h:
+
+/usr/include/sys/resource.h:
+
+/usr/include/machine/endian.h:
+
+/usr/include/i386/endian.h:
+
+/usr/include/sys/_endian.h:
+
+/usr/include/libkern/_OSByteOrder.h:
+
+/usr/include/libkern/i386/_OSByteOrder.h:
+
+/usr/include/alloca.h:
+
+/usr/include/machine/types.h:
+
+/usr/include/i386/types.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/atomic_word.h:
+
+/opt/local/include/gcc46/c++/bits/locale_classes.h:
+
+/opt/local/include/gcc46/c++/string:
+
+/opt/local/include/gcc46/c++/bits/allocator.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++allocator.h:
+
+/opt/local/include/gcc46/c++/ext/new_allocator.h:
+
+/opt/local/include/gcc46/c++/new:
+
+/opt/local/include/gcc46/c++/bits/ostream_insert.h:
+
+/opt/local/include/gcc46/c++/bits/cxxabi_forced.h:
+
+/opt/local/include/gcc46/c++/bits/stl_function.h:
+
+/opt/local/include/gcc46/c++/backward/binders.h:
+
+/opt/local/include/gcc46/c++/bits/range_access.h:
+
+/opt/local/include/gcc46/c++/bits/basic_string.h:
+
+/opt/local/include/gcc46/c++/initializer_list:
+
+/opt/local/include/gcc46/c++/bits/basic_string.tcc:
+
+/opt/local/include/gcc46/c++/bits/locale_classes.tcc:
+
+/opt/local/include/gcc46/c++/streambuf:
+
+/opt/local/include/gcc46/c++/bits/streambuf.tcc:
+
+/opt/local/include/gcc46/c++/bits/basic_ios.h:
+
+/opt/local/include/gcc46/c++/bits/locale_facets.h:
+
+/opt/local/include/gcc46/c++/cwctype:
+
+/usr/include/wctype.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/ctype_base.h:
+
+/opt/local/include/gcc46/c++/bits/streambuf_iterator.h:
+
+/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/ctype_inline.h:
+
+/opt/local/include/gcc46/c++/bits/locale_facets.tcc:
+
+/opt/local/include/gcc46/c++/bits/basic_ios.tcc:
+
+/opt/local/include/gcc46/c++/bits/ostream.tcc:
+
+/opt/local/include/gcc46/c++/istream:
+
+/opt/local/include/gcc46/c++/bits/istream.tcc:
+
twister.h:
gamma.h:
+
+/opt/local/include/gcc46/c++/vector:
+
+/opt/local/include/gcc46/c++/bits/stl_construct.h:
+
+/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
+
+/opt/local/include/gcc46/c++/bits/stl_vector.h:
+
+/opt/local/include/gcc46/c++/bits/stl_bvector.h:
+
+/opt/local/include/gcc46/c++/bits/vector.tcc:
44 src/.deps/inClade.Po
View
@@ -99,9 +99,9 @@ inClade.o: inClade.cpp inClade.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/iomanip /opt/local/include/gcc46/c++/memory \
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
- /opt/local/include/gcc46/c++/backward/auto_ptr.h aamodels.h eigen.h \
- gamma.h insert_freqs.h /opt/local/include/gcc46/c++/cstdlib model.h \
- inTree.h /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/backward/auto_ptr.h gamma.h insert_freqs.h \
+ /opt/local/include/gcc46/c++/cstdlib model.h eigen.h inTree.h \
+ /opt/local/include/gcc46/c++/map \
/opt/local/include/gcc46/c++/bits/stl_tree.h \
/opt/local/include/gcc46/c++/bits/stl_map.h \
/opt/local/include/gcc46/c++/bits/stl_multimap.h \
@@ -110,10 +110,16 @@ inClade.o: inClade.cpp inClade.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/bits/stl_set.h \
/opt/local/include/gcc46/c++/bits/stl_multiset.h /usr/include/assert.h \
tree.h /opt/local/include/gcc46/c++/limits seqGenOptions.h ../config.h \
- nucmodels.h treefile.h twister.h random.h \
+ propose_path.h stats.h /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h treefile.h twister.h \
+ forward_simulation.h trace.h random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- /usr/include/sys/types.h trace.h
+ /usr/include/sys/types.h
inClade.h:
@@ -387,10 +393,6 @@ evolve.h:
/opt/local/include/gcc46/c++/backward/auto_ptr.h:
-aamodels.h:
-
-eigen.h:
-
gamma.h:
insert_freqs.h:
@@ -399,6 +401,8 @@ insert_freqs.h:
model.h:
+eigen.h:
+
inTree.h:
/opt/local/include/gcc46/c++/map:
@@ -429,12 +433,30 @@ seqGenOptions.h:
../config.h:
-nucmodels.h:
+propose_path.h:
+
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility:
+
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
treefile.h:
twister.h:
+forward_simulation.h:
+
+trace.h:
+
random.h:
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h:
@@ -442,5 +464,3 @@ random.h:
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h:
/usr/include/sys/types.h:
-
-trace.h:
51 src/.deps/inTree.Po
View
@@ -99,19 +99,26 @@ inTree.o: inTree.cpp inTree.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/sstream \
/opt/local/include/gcc46/c++/bits/sstream.tcc \
/opt/local/include/gcc46/c++/cstdlib /opt/local/include/gcc46/c++/cmath \
- /usr/include/math.h /usr/include/architecture/i386/math.h aamodels.h \
- eigen.h evolve.h /opt/local/include/gcc46/c++/bitset \
- /opt/local/include/gcc46/c++/iomanip /opt/local/include/gcc46/c++/memory \
+ /usr/include/math.h /usr/include/architecture/i386/math.h evolve.h \
+ /opt/local/include/gcc46/c++/bitset /opt/local/include/gcc46/c++/iomanip \
+ /opt/local/include/gcc46/c++/memory \
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
/opt/local/include/gcc46/c++/backward/auto_ptr.h gamma.h insert_freqs.h \
- model.h nucmodels.h motif.h /opt/local/include/gcc46/c++/set \
+ model.h eigen.h tree.h /opt/local/include/gcc46/c++/limits motif.h \
+ /opt/local/include/gcc46/c++/set \
/opt/local/include/gcc46/c++/bits/stl_set.h \
/opt/local/include/gcc46/c++/bits/stl_multiset.h /usr/include/assert.h \
- tree.h /opt/local/include/gcc46/c++/limits random.h \
+ random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- trace.h treefile.h twister.h inClade.h seqGenOptions.h ../config.h
+ trace.h treefile.h twister.h inClade.h seqGenOptions.h ../config.h \
+ propose_path.h stats.h /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h forward_simulation.h
inTree.h:
@@ -383,10 +390,6 @@ inTree.h:
/usr/include/architecture/i386/math.h:
-aamodels.h:
-
-eigen.h:
-
evolve.h:
/opt/local/include/gcc46/c++/bitset:
@@ -407,7 +410,11 @@ insert_freqs.h:
model.h:
-nucmodels.h:
+eigen.h:
+
+tree.h:
+
+/opt/local/include/gcc46/c++/limits:
motif.h:
@@ -419,10 +426,6 @@ motif.h:
/usr/include/assert.h:
-tree.h:
-
-/opt/local/include/gcc46/c++/limits:
-
random.h:
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h:
@@ -440,3 +443,21 @@ inClade.h:
seqGenOptions.h:
../config.h:
+
+propose_path.h:
+
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility:
+
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
+
+forward_simulation.h:
74 src/.deps/main.Po
View
@@ -98,23 +98,29 @@ main.o: main.cpp /opt/local/include/gcc46/c++/cstdio \
/opt/local/include/gcc46/c++/bits/stl_vector.h \
/opt/local/include/gcc46/c++/bits/stl_bvector.h \
/opt/local/include/gcc46/c++/bits/vector.tcc gamma.h seqGenOptions.h \
- ../config.h model.h evolve.h /opt/local/include/gcc46/c++/bitset \
+ ../config.h model.h eigen.h evolve.h /opt/local/include/gcc46/c++/bitset \
/opt/local/include/gcc46/c++/memory \
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
- /opt/local/include/gcc46/c++/backward/auto_ptr.h aamodels.h eigen.h \
- inClade.h inTree.h /opt/local/include/gcc46/c++/map \
- /opt/local/include/gcc46/c++/bits/stl_tree.h \
- /opt/local/include/gcc46/c++/bits/stl_map.h \
- /opt/local/include/gcc46/c++/bits/stl_multimap.h \
- /opt/local/include/gcc46/c++/cmath motif.h \
+ /opt/local/include/gcc46/c++/backward/auto_ptr.h insert_freqs.h motif.h \
/opt/local/include/gcc46/c++/set \
+ /opt/local/include/gcc46/c++/bits/stl_tree.h \
/opt/local/include/gcc46/c++/bits/stl_set.h \
/opt/local/include/gcc46/c++/bits/stl_multiset.h /usr/include/assert.h \
- treefile.h twister.h insert_freqs.h random.h \
+ inTree.h /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/bits/stl_map.h \
+ /opt/local/include/gcc46/c++/bits/stl_multimap.h \
+ /opt/local/include/gcc46/c++/cmath inClade.h twister.h treefile.h \
+ propose_path.h stats.h /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h forward_simulation.h \
+ trace.h random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- /usr/include/sys/types.h trace.h nucmodels.h progress.h
+ /usr/include/sys/types.h paleo.h dependency.h
/opt/local/include/gcc46/c++/cstdio:
@@ -390,6 +396,8 @@ seqGenOptions.h:
model.h:
+eigen.h:
+
evolve.h:
/opt/local/include/gcc46/c++/bitset:
@@ -402,39 +410,55 @@ evolve.h:
/opt/local/include/gcc46/c++/backward/auto_ptr.h:
-aamodels.h:
+insert_freqs.h:
-eigen.h:
+motif.h:
-inClade.h:
+/opt/local/include/gcc46/c++/set:
+
+/opt/local/include/gcc46/c++/bits/stl_tree.h:
+
+/opt/local/include/gcc46/c++/bits/stl_set.h:
+
+/opt/local/include/gcc46/c++/bits/stl_multiset.h:
+
+/usr/include/assert.h:
inTree.h:
/opt/local/include/gcc46/c++/map:
-/opt/local/include/gcc46/c++/bits/stl_tree.h:
-
/opt/local/include/gcc46/c++/bits/stl_map.h:
/opt/local/include/gcc46/c++/bits/stl_multimap.h:
/opt/local/include/gcc46/c++/cmath:
-motif.h:
+inClade.h:
-/opt/local/include/gcc46/c++/set:
+twister.h:
-/opt/local/include/gcc46/c++/bits/stl_set.h:
+treefile.h:
-/opt/local/include/gcc46/c++/bits/stl_multiset.h:
+propose_path.h:
-/usr/include/assert.h:
+stats.h:
-treefile.h:
+/opt/local/include/gcc46/c++/algorithm:
-twister.h:
+/opt/local/include/gcc46/c++/utility:
-insert_freqs.h:
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
+
+forward_simulation.h:
+
+trace.h:
random.h:
@@ -444,8 +468,6 @@ random.h:
/usr/include/sys/types.h:
-trace.h:
-
-nucmodels.h:
+paleo.h:
-progress.h:
+dependency.h:
124 src/.deps/model.Po
View
@@ -59,8 +59,13 @@ model.o: model.cpp model.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/initializer_list \
/opt/local/include/gcc46/c++/bits/basic_string.tcc \
/opt/local/include/gcc46/c++/cstring /usr/include/string.h \
- /usr/include/math.h /usr/include/architecture/i386/math.h evolve.h \
- /opt/local/include/gcc46/c++/bitset \
+ /usr/include/math.h /usr/include/architecture/i386/math.h eigen.h \
+ /opt/local/include/gcc46/c++/vector \
+ /opt/local/include/gcc46/c++/bits/stl_construct.h \
+ /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
+ /opt/local/include/gcc46/c++/bits/stl_vector.h \
+ /opt/local/include/gcc46/c++/bits/stl_bvector.h \
+ /opt/local/include/gcc46/c++/bits/vector.tcc \
/opt/local/include/gcc46/c++/iostream \
/opt/local/include/gcc46/c++/ostream /opt/local/include/gcc46/c++/ios \
/opt/local/include/gcc46/c++/bits/ios_base.h \
@@ -78,8 +83,8 @@ model.o: model.cpp model.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/bits/basic_ios.tcc \
/opt/local/include/gcc46/c++/bits/ostream.tcc \
/opt/local/include/gcc46/c++/istream \
- /opt/local/include/gcc46/c++/bits/istream.tcc \
- /opt/local/include/gcc46/c++/fstream \
+ /opt/local/include/gcc46/c++/bits/istream.tcc evolve.h \
+ /opt/local/include/gcc46/c++/bitset /opt/local/include/gcc46/c++/fstream \
/opt/local/include/gcc46/c++/bits/codecvt.h \
/opt/local/include/gcc46/c++/cstdio \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/basic_file.h \
@@ -91,29 +96,30 @@ model.o: model.cpp model.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/bits/stl_list.h \
/opt/local/include/gcc46/c++/bits/list.tcc \
/opt/local/include/gcc46/c++/iomanip /opt/local/include/gcc46/c++/memory \
- /opt/local/include/gcc46/c++/bits/stl_construct.h \
- /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
- /opt/local/include/gcc46/c++/backward/auto_ptr.h aamodels.h \
- /opt/local/include/gcc46/c++/vector \
- /opt/local/include/gcc46/c++/bits/stl_vector.h \
- /opt/local/include/gcc46/c++/bits/stl_bvector.h \
- /opt/local/include/gcc46/c++/bits/vector.tcc eigen.h inClade.h tree.h \
- /opt/local/include/gcc46/c++/limits gamma.h inTree.h \
- /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/backward/auto_ptr.h gamma.h insert_freqs.h \
+ /opt/local/include/gcc46/c++/cstdlib motif.h \
+ /opt/local/include/gcc46/c++/set \
/opt/local/include/gcc46/c++/bits/stl_tree.h \
- /opt/local/include/gcc46/c++/bits/stl_map.h \
- /opt/local/include/gcc46/c++/bits/stl_multimap.h \
- /opt/local/include/gcc46/c++/cstdlib /opt/local/include/gcc46/c++/cmath \
- motif.h /opt/local/include/gcc46/c++/set \
/opt/local/include/gcc46/c++/bits/stl_set.h \
/opt/local/include/gcc46/c++/bits/stl_multiset.h /usr/include/assert.h \
- seqGenOptions.h ../config.h nucmodels.h insert_freqs.h treefile.h \
- twister.h random.h \
+ inTree.h /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/bits/stl_map.h \
+ /opt/local/include/gcc46/c++/bits/stl_multimap.h \
+ /opt/local/include/gcc46/c++/cmath inClade.h tree.h \
+ /opt/local/include/gcc46/c++/limits twister.h seqGenOptions.h \
+ ../config.h propose_path.h stats.h \
+ /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h treefile.h \
+ forward_simulation.h trace.h random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- /usr/include/sys/types.h trace.h
+ /usr/include/sys/types.h
model.h:
@@ -299,9 +305,19 @@ model.h:
/usr/include/architecture/i386/math.h:
-evolve.h:
+eigen.h:
-/opt/local/include/gcc46/c++/bitset:
+/opt/local/include/gcc46/c++/vector:
+
+/opt/local/include/gcc46/c++/bits/stl_construct.h:
+
+/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
+
+/opt/local/include/gcc46/c++/bits/stl_vector.h:
+
+/opt/local/include/gcc46/c++/bits/stl_bvector.h:
+
+/opt/local/include/gcc46/c++/bits/vector.tcc:
/opt/local/include/gcc46/c++/iostream:
@@ -343,6 +359,10 @@ evolve.h:
/opt/local/include/gcc46/c++/bits/istream.tcc:
+evolve.h:
+
+/opt/local/include/gcc46/c++/bitset:
+
/opt/local/include/gcc46/c++/fstream:
/opt/local/include/gcc46/c++/bits/codecvt.h:
@@ -369,71 +389,73 @@ evolve.h:
/opt/local/include/gcc46/c++/memory:
-/opt/local/include/gcc46/c++/bits/stl_construct.h:
-
-/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
-
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h:
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h:
/opt/local/include/gcc46/c++/backward/auto_ptr.h:
-aamodels.h:
-
-/opt/local/include/gcc46/c++/vector:
+gamma.h:
-/opt/local/include/gcc46/c++/bits/stl_vector.h:
+insert_freqs.h:
-/opt/local/include/gcc46/c++/bits/stl_bvector.h:
+/opt/local/include/gcc46/c++/cstdlib:
-/opt/local/include/gcc46/c++/bits/vector.tcc:
+motif.h:
-eigen.h:
+/opt/local/include/gcc46/c++/set:
-inClade.h:
+/opt/local/include/gcc46/c++/bits/stl_tree.h:
-tree.h:
+/opt/local/include/gcc46/c++/bits/stl_set.h:
-/opt/local/include/gcc46/c++/limits:
+/opt/local/include/gcc46/c++/bits/stl_multiset.h:
-gamma.h:
+/usr/include/assert.h:
inTree.h:
/opt/local/include/gcc46/c++/map:
-/opt/local/include/gcc46/c++/bits/stl_tree.h:
-
/opt/local/include/gcc46/c++/bits/stl_map.h:
/opt/local/include/gcc46/c++/bits/stl_multimap.h:
-/opt/local/include/gcc46/c++/cstdlib:
-
/opt/local/include/gcc46/c++/cmath:
-motif.h:
-
-/opt/local/include/gcc46/c++/set:
+inClade.h:
-/opt/local/include/gcc46/c++/bits/stl_set.h:
+tree.h:
-/opt/local/include/gcc46/c++/bits/stl_multiset.h:
+/opt/local/include/gcc46/c++/limits:
-/usr/include/assert.h:
+twister.h:
seqGenOptions.h:
../config.h:
-nucmodels.h:
+propose_path.h:
-insert_freqs.h:
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility:
+
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
treefile.h:
-twister.h:
+forward_simulation.h:
+
+trace.h:
random.h:
@@ -442,5 +464,3 @@ random.h:
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h:
/usr/include/sys/types.h:
-
-trace.h:
63 src/.deps/motif.Po
View
@@ -103,17 +103,24 @@ motif.o: motif.cpp motif.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++/bits/sstream.tcc \
/opt/local/include/gcc46/c++/list \
/opt/local/include/gcc46/c++/bits/stl_list.h \
- /opt/local/include/gcc46/c++/bits/list.tcc aamodels.h eigen.h inClade.h \
- tree.h /opt/local/include/gcc46/c++/limits gamma.h inTree.h \
+ /opt/local/include/gcc46/c++/bits/list.tcc gamma.h insert_freqs.h \
+ /opt/local/include/gcc46/c++/cstdlib model.h eigen.h inTree.h \
/opt/local/include/gcc46/c++/map \
/opt/local/include/gcc46/c++/bits/stl_map.h \
/opt/local/include/gcc46/c++/bits/stl_multimap.h \
- /opt/local/include/gcc46/c++/cstdlib /opt/local/include/gcc46/c++/cmath \
- model.h nucmodels.h seqGenOptions.h ../config.h insert_freqs.h \
- treefile.h twister.h random.h \
+ /opt/local/include/gcc46/c++/cmath inClade.h tree.h \
+ /opt/local/include/gcc46/c++/limits twister.h seqGenOptions.h \
+ ../config.h propose_path.h stats.h \
+ /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h treefile.h \
+ forward_simulation.h trace.h random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- /usr/include/sys/types.h trace.h
+ /usr/include/sys/types.h
motif.h:
@@ -397,17 +404,15 @@ evolve.h:
/opt/local/include/gcc46/c++/bits/list.tcc:
-aamodels.h:
-
-eigen.h:
+gamma.h:
-inClade.h:
+insert_freqs.h:
-tree.h:
+/opt/local/include/gcc46/c++/cstdlib:
-/opt/local/include/gcc46/c++/limits:
+model.h:
-gamma.h:
+eigen.h:
inTree.h:
@@ -417,23 +422,41 @@ inTree.h:
/opt/local/include/gcc46/c++/bits/stl_multimap.h:
-/opt/local/include/gcc46/c++/cstdlib:
-
/opt/local/include/gcc46/c++/cmath:
-model.h:
+inClade.h:
-nucmodels.h:
+tree.h:
+
+/opt/local/include/gcc46/c++/limits:
+
+twister.h:
seqGenOptions.h:
../config.h:
-insert_freqs.h:
+propose_path.h:
+
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility:
+
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
treefile.h:
-twister.h:
+forward_simulation.h:
+
+trace.h:
random.h:
@@ -442,5 +465,3 @@ random.h:
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h:
/usr/include/sys/types.h:
-
-trace.h:
144 src/.deps/seqGenOptions.Po
View
@@ -58,10 +58,18 @@ seqGenOptions.o: seqGenOptions.cpp seqGenOptions.h ../config.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/atomic_word.h \
/opt/local/include/gcc46/c++/initializer_list \
- /opt/local/include/gcc46/c++/bits/basic_string.tcc model.h \
+ /opt/local/include/gcc46/c++/bits/basic_string.tcc \
+ /opt/local/include/gcc46/c++/list \
+ /opt/local/include/gcc46/c++/bits/stl_list.h \
+ /opt/local/include/gcc46/c++/bits/list.tcc model.h \
/opt/local/include/gcc46/c++/cstring /usr/include/string.h \
- /usr/include/math.h /usr/include/architecture/i386/math.h evolve.h \
- /opt/local/include/gcc46/c++/bitset \
+ /usr/include/math.h /usr/include/architecture/i386/math.h eigen.h \
+ /opt/local/include/gcc46/c++/vector \
+ /opt/local/include/gcc46/c++/bits/stl_construct.h \
+ /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
+ /opt/local/include/gcc46/c++/bits/stl_vector.h \
+ /opt/local/include/gcc46/c++/bits/stl_bvector.h \
+ /opt/local/include/gcc46/c++/bits/vector.tcc \
/opt/local/include/gcc46/c++/iostream \
/opt/local/include/gcc46/c++/ostream /opt/local/include/gcc46/c++/ios \
/opt/local/include/gcc46/c++/bits/ios_base.h \
@@ -79,8 +87,8 @@ seqGenOptions.o: seqGenOptions.cpp seqGenOptions.h ../config.h \
/opt/local/include/gcc46/c++/bits/basic_ios.tcc \
/opt/local/include/gcc46/c++/bits/ostream.tcc \
/opt/local/include/gcc46/c++/istream \
- /opt/local/include/gcc46/c++/bits/istream.tcc \
- /opt/local/include/gcc46/c++/fstream \
+ /opt/local/include/gcc46/c++/bits/istream.tcc evolve.h \
+ /opt/local/include/gcc46/c++/bitset /opt/local/include/gcc46/c++/fstream \
/opt/local/include/gcc46/c++/bits/codecvt.h \
/opt/local/include/gcc46/c++/cstdio \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/basic_file.h \
@@ -88,32 +96,30 @@ seqGenOptions.o: seqGenOptions.cpp seqGenOptions.h ../config.h \
/opt/local/include/gcc46/c++/bits/fstream.tcc \
/opt/local/include/gcc46/c++/sstream \
/opt/local/include/gcc46/c++/bits/sstream.tcc \
- /opt/local/include/gcc46/c++/list \
- /opt/local/include/gcc46/c++/bits/stl_list.h \
- /opt/local/include/gcc46/c++/bits/list.tcc \
/opt/local/include/gcc46/c++/iomanip /opt/local/include/gcc46/c++/memory \
- /opt/local/include/gcc46/c++/bits/stl_construct.h \
- /opt/local/include/gcc46/c++/bits/stl_uninitialized.h \
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
- /opt/local/include/gcc46/c++/backward/auto_ptr.h aamodels.h \
- /opt/local/include/gcc46/c++/vector \
- /opt/local/include/gcc46/c++/bits/stl_vector.h \
- /opt/local/include/gcc46/c++/bits/stl_bvector.h \
- /opt/local/include/gcc46/c++/bits/vector.tcc eigen.h inClade.h tree.h \
- /opt/local/include/gcc46/c++/limits gamma.h inTree.h \
- /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/backward/auto_ptr.h gamma.h insert_freqs.h \
+ /opt/local/include/gcc46/c++/cstdlib motif.h \
+ /opt/local/include/gcc46/c++/set \
/opt/local/include/gcc46/c++/bits/stl_tree.h \
- /opt/local/include/gcc46/c++/bits/stl_map.h \
- /opt/local/include/gcc46/c++/bits/stl_multimap.h \
- /opt/local/include/gcc46/c++/cstdlib /opt/local/include/gcc46/c++/cmath \
- motif.h /opt/local/include/gcc46/c++/set \
/opt/local/include/gcc46/c++/bits/stl_set.h \
/opt/local/include/gcc46/c++/bits/stl_multiset.h /usr/include/assert.h \
- treefile.h twister.h insert_freqs.h random.h \
+ inTree.h /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/bits/stl_map.h \
+ /opt/local/include/gcc46/c++/bits/stl_multimap.h \
+ /opt/local/include/gcc46/c++/cmath inClade.h tree.h \
+ /opt/local/include/gcc46/c++/limits twister.h treefile.h propose_path.h \
+ stats.h /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h forward_simulation.h \
+ trace.h random.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
/opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
- /usr/include/sys/types.h trace.h nucmodels.h ../lib/getopt.h
+ /usr/include/sys/types.h ../lib/getopt.h
seqGenOptions.h:
@@ -293,6 +299,12 @@ seqGenOptions.h:
/opt/local/include/gcc46/c++/bits/basic_string.tcc:
+/opt/local/include/gcc46/c++/list:
+
+/opt/local/include/gcc46/c++/bits/stl_list.h:
+
+/opt/local/include/gcc46/c++/bits/list.tcc:
+
model.h:
/opt/local/include/gcc46/c++/cstring:
@@ -303,9 +315,19 @@ model.h:
/usr/include/architecture/i386/math.h:
-evolve.h:
+eigen.h:
-/opt/local/include/gcc46/c++/bitset:
+/opt/local/include/gcc46/c++/vector:
+
+/opt/local/include/gcc46/c++/bits/stl_construct.h:
+
+/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
+
+/opt/local/include/gcc46/c++/bits/stl_vector.h:
+
+/opt/local/include/gcc46/c++/bits/stl_bvector.h:
+
+/opt/local/include/gcc46/c++/bits/vector.tcc:
/opt/local/include/gcc46/c++/iostream:
@@ -347,6 +369,10 @@ evolve.h:
/opt/local/include/gcc46/c++/bits/istream.tcc:
+evolve.h:
+
+/opt/local/include/gcc46/c++/bitset:
+
/opt/local/include/gcc46/c++/fstream:
/opt/local/include/gcc46/c++/bits/codecvt.h:
@@ -363,75 +389,73 @@ evolve.h:
/opt/local/include/gcc46/c++/bits/sstream.tcc:
-/opt/local/include/gcc46/c++/list:
-
-/opt/local/include/gcc46/c++/bits/stl_list.h:
-
-/opt/local/include/gcc46/c++/bits/list.tcc:
-
/opt/local/include/gcc46/c++/iomanip:
/opt/local/include/gcc46/c++/memory:
-/opt/local/include/gcc46/c++/bits/stl_construct.h:
-
-/opt/local/include/gcc46/c++/bits/stl_uninitialized.h:
-
/opt/local/include/gcc46/c++/bits/stl_tempbuf.h:
/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h:
/opt/local/include/gcc46/c++/backward/auto_ptr.h:
-aamodels.h:
-
-/opt/local/include/gcc46/c++/vector:
+gamma.h:
-/opt/local/include/gcc46/c++/bits/stl_vector.h:
+insert_freqs.h:
-/opt/local/include/gcc46/c++/bits/stl_bvector.h:
+/opt/local/include/gcc46/c++/cstdlib:
-/opt/local/include/gcc46/c++/bits/vector.tcc:
+motif.h:
-eigen.h:
+/opt/local/include/gcc46/c++/set:
-inClade.h:
+/opt/local/include/gcc46/c++/bits/stl_tree.h:
-tree.h:
+/opt/local/include/gcc46/c++/bits/stl_set.h:
-/opt/local/include/gcc46/c++/limits:
+/opt/local/include/gcc46/c++/bits/stl_multiset.h:
-gamma.h:
+/usr/include/assert.h:
inTree.h:
/opt/local/include/gcc46/c++/map:
-/opt/local/include/gcc46/c++/bits/stl_tree.h:
-
/opt/local/include/gcc46/c++/bits/stl_map.h:
/opt/local/include/gcc46/c++/bits/stl_multimap.h:
-/opt/local/include/gcc46/c++/cstdlib:
-
/opt/local/include/gcc46/c++/cmath:
-motif.h:
-
-/opt/local/include/gcc46/c++/set:
+inClade.h:
-/opt/local/include/gcc46/c++/bits/stl_set.h:
+tree.h:
-/opt/local/include/gcc46/c++/bits/stl_multiset.h:
+/opt/local/include/gcc46/c++/limits:
-/usr/include/assert.h:
+twister.h:
treefile.h:
-twister.h:
+propose_path.h:
-insert_freqs.h:
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility:
+
+/opt/local/include/gcc46/c++/bits/stl_relops.h:
+
+/opt/local/include/gcc46/c++/bits/stl_algo.h:
+
+/opt/local/include/gcc46/c++/bits/algorithmfwd.h:
+
+/opt/local/include/gcc46/c++/bits/stl_heap.h:
+
+forward_simulation.h:
+
+trace.h:
random.h:
@@ -441,8 +465,4 @@ random.h:
/usr/include/sys/types.h:
-trace.h:
-
-nucmodels.h:
-
../lib/getopt.h:
114 src/.deps/trace.Po
View
@@ -92,9 +92,35 @@ trace.o: trace.cpp trace.h tree.h /opt/local/include/gcc46/c++/string \
/opt/local/include/gcc46/c++//x86_64-apple-darwin10/bits/c++io.h \
/opt/local/include/gcc46/c++/bits/fstream.tcc \
/opt/local/include/gcc46/c++/iostream \
- /opt/local/include/gcc46/c++/limits gamma.h \
+ /opt/local/include/gcc46/c++/limits gamma.h motif.h \
+ /opt/local/include/gcc46/c++/bitset /opt/local/include/gcc46/c++/iomanip \
+ /opt/local/include/gcc46/c++/set \
+ /opt/local/include/gcc46/c++/bits/stl_tree.h \
+ /opt/local/include/gcc46/c++/bits/stl_set.h \
+ /opt/local/include/gcc46/c++/bits/stl_multiset.h \
+ /opt/local/include/gcc46/c++/memory \
+ /opt/local/include/gcc46/c++/bits/stl_tempbuf.h \
+ /opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h \
+ /opt/local/include/gcc46/c++/backward/auto_ptr.h /usr/include/assert.h \
+ evolve.h /usr/include/math.h /usr/include/architecture/i386/math.h \
/opt/local/include/gcc46/c++/sstream \
- /opt/local/include/gcc46/c++/bits/sstream.tcc
+ /opt/local/include/gcc46/c++/bits/sstream.tcc insert_freqs.h \
+ /opt/local/include/gcc46/c++/cstdlib model.h eigen.h inTree.h \
+ /opt/local/include/gcc46/c++/map \
+ /opt/local/include/gcc46/c++/bits/stl_map.h \
+ /opt/local/include/gcc46/c++/bits/stl_multimap.h \
+ /opt/local/include/gcc46/c++/cmath inClade.h twister.h seqGenOptions.h \
+ ../config.h propose_path.h stats.h \
+ /opt/local/include/gcc46/c++/algorithm \
+ /opt/local/include/gcc46/c++/utility \
+ /opt/local/include/gcc46/c++/bits/stl_relops.h \
+ /opt/local/include/gcc46/c++/bits/stl_algo.h \
+ /opt/local/include/gcc46/c++/bits/algorithmfwd.h \
+ /opt/local/include/gcc46/c++/bits/stl_heap.h treefile.h \
+ forward_simulation.h random.h \
+ /opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include/stdint.h \
+ /opt/local/lib/gcc46/gcc/x86_64-apple-darwin10/4.6.2/include-fixed/stdint.h \
+ /usr/include/sys/types.h
trace.h:
@@ -352,6 +378,90 @@ tree.h:
gamma.h:
+motif.h:
+
+/opt/local/include/gcc46/c++/bitset:
+
+/opt/local/include/gcc46/c++/iomanip:
+
+/opt/local/include/gcc46/c++/set:
+
+/opt/local/include/gcc46/c++/bits/stl_tree.h:
+
+/opt/local/include/gcc46/c++/bits/stl_set.h:
+
+/opt/local/include/gcc46/c++/bits/stl_multiset.h:
+
+/opt/local/include/gcc46/c++/memory:
+
+/opt/local/include/gcc46/c++/bits/stl_tempbuf.h:
+
+/opt/local/include/gcc46/c++/bits/stl_raw_storage_iter.h:
+
+/opt/local/include/gcc46/c++/backward/auto_ptr.h:
+
+/usr/include/assert.h:
+
+evolve.h:
+
+/usr/include/math.h:
+
+/usr/include/architecture/i386/math.h:
+
/opt/local/include/gcc46/c++/sstream:
/opt/local/include/gcc46/c++/bits/sstream.tcc:
+
+insert_freqs.h:
+
+/opt/local/include/gcc46/c++/cstdlib:
+
+model.h:
+
+eigen.h:
+
+inTree.h:
+
+/opt/local/include/gcc46/c++/map:
+
+/opt/local/include/gcc46/c++/bits/stl_map.h:
+
+/opt/local/include/gcc46/c++/bits/stl_multimap.h:
+
+/opt/local/include/gcc46/c++/cmath:
+
+inClade.h:
+
+twister.h:
+
+seqGenOptions.h:
+
+../config.h:
+
+propose_path.h:
+
+stats.h:
+
+/opt/local/include/gcc46/c++/algorithm:
+
+/opt/local/include/gcc46/c++/utility: