29 files changed, 1185 insertions, 0 deletions
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..dac0f89
--- a/dev/null
+++ b/AUTHORS
@@ -0,0 +1 @@
+Don Pellegrino, Drexel University, don@drexel.edu
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..a6d8603
--- a/dev/null
+++ b/Makefile.am
@@ -0,0 +1,2 @@
+ACLOCAL_AMFLAGS = -I ax
+SUBDIRS = src
diff --git a/README b/README
new file mode 100644
index 0000000..0c29887
--- a/dev/null
+++ b/README
@@ -0,0 +1,24 @@
+Visualization system to explore the data from exp004.
+======================
+CLUSTER.CIS.DREXEL.EDU
+======================
+Building on cluster.cis.drexel.edu requires explicitly adding a number
+of NCBI libraries and using the local install of the NCBI toolkit.
+Before running ./configure set the following:
+  export LDFLAGS=-L/usr/local/ncbi/lib
+  export CPPFLAGS=-I/usr/local/ncbi/include
+Before running a program that makes use of BLAST create a ~/.ncbirc
+file with the following contents.  This instruction is based on a
+message at
+http://osdir.com/ml/science.biology.informatics.bulletin/2006-02/msg00061.html
+  [NCBI]
+  data=/usr/local/ncbi/data
+  [BLAST]
+  BLASTMAT=/usr/local/ncbi/data
diff --git a/ax/acx_pthread.m4 b/ax/acx_pthread.m4
new file mode 100644
index 0000000..e4e91d3
--- a/dev/null
+++ b/ax/acx_pthread.m4
@@ -0,0 +1,242 @@
+dnl @synopsis ACX_PTHREAD([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
+dnl
+dnl @summary figure out how to build C programs using POSIX threads
+dnl
+dnl This macro figures out how to build C programs using POSIX threads.
+dnl It sets the PTHREAD_LIBS output variable to the threads library and
+dnl linker flags, and the PTHREAD_CFLAGS output variable to any special
+dnl C compiler flags that are needed. (The user can also force certain
+dnl compiler flags/libs to be tested by setting these environment
+dnl variables.)
+dnl
+dnl Also sets PTHREAD_CC to any special C compiler that is needed for
+dnl multi-threaded programs (defaults to the value of CC otherwise).
+dnl (This is necessary on AIX to use the special cc_r compiler alias.)
+dnl
+dnl NOTE: You are assumed to not only compile your program with these
+dnl flags, but also link it with them as well. e.g. you should link
+dnl with $PTHREAD_CC $CFLAGS $PTHREAD_CFLAGS $LDFLAGS ... $PTHREAD_LIBS
+dnl $LIBS
+dnl
+dnl If you are only building threads programs, you may wish to use
+dnl these variables in your default LIBS, CFLAGS, and CC:
+dnl
+dnl        LIBS="$PTHREAD_LIBS $LIBS"
+dnl        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+dnl        CC="$PTHREAD_CC"
+dnl
+dnl In addition, if the PTHREAD_CREATE_JOINABLE thread-attribute
+dnl constant has a nonstandard name, defines PTHREAD_CREATE_JOINABLE to
+dnl that name (e.g. PTHREAD_CREATE_UNDETACHED on AIX).
+dnl
+dnl ACTION-IF-FOUND is a list of shell commands to run if a threads
+dnl library is found, and ACTION-IF-NOT-FOUND is a list of commands to
+dnl run it if it is not found. If ACTION-IF-FOUND is not specified, the
+dnl default action will define HAVE_PTHREAD.
+dnl
+dnl Please let the authors know if this macro fails on any platform, or
+dnl if you have any other suggestions or comments. This macro was based
+dnl on work by SGJ on autoconf scripts for FFTW (www.fftw.org) (with
+dnl help from M. Frigo), as well as ac_pthread and hb_pthread macros
+dnl posted by Alejandro Forero Cuervo to the autoconf macro repository.
+dnl We are also grateful for the helpful feedback of numerous users.
+dnl
+dnl @category InstalledPackages
+dnl @author Steven G. Johnson <stevenj@alum.mit.edu>
+dnl @version 2006-05-29
+dnl @license GPLWithACException
+AC_DEFUN([ACX_PTHREAD], [
+AC_REQUIRE([AC_CANONICAL_HOST])
+AC_LANG_SAVE
+AC_LANG_C
+acx_pthread_ok=no
+# We used to check for pthread.h first, but this fails if pthread.h
+# requires special compiler flags (e.g. on True64 or Sequent).
+# It gets checked for in the link test anyway.
+# First of all, check if the user has set any of the PTHREAD_LIBS,
+# etcetera environment variables, and if threads linking works using
+# them:
+if test x"$PTHREAD_LIBS$PTHREAD_CFLAGS" != x; then
+        save_CFLAGS="$CFLAGS"
+        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+        save_LIBS="$LIBS"
+        LIBS="$PTHREAD_LIBS $LIBS"
+        AC_MSG_CHECKING([for pthread_join in LIBS=$PTHREAD_LIBS with CFLAGS=$PTHREAD_CFLAGS])
+        AC_TRY_LINK_FUNC(pthread_join, acx_pthread_ok=yes)
+        AC_MSG_RESULT($acx_pthread_ok)
+        if test x"$acx_pthread_ok" = xno; then
+                PTHREAD_LIBS=""
+                PTHREAD_CFLAGS=""
+        fi
+        LIBS="$save_LIBS"
+        CFLAGS="$save_CFLAGS"
+fi
+# We must check for the threads library under a number of different
+# names; the ordering is very important because some systems
+# (e.g. DEC) have both -lpthread and -lpthreads, where one of the
+# libraries is broken (non-POSIX).
+# Create a list of thread flags to try.  Items starting with a "-" are
+# C compiler flags, and other items are library names, except for "none"
+# which indicates that we try without any flags at all, and "pthread-config"
+# which is a program returning the flags for the Pth emulation library.
+acx_pthread_flags="pthreads none -Kthread -kthread lthread -pthread -pthreads -mthreads pthread --thread-safe -mt pthread-config"
+# The ordering *is* (sometimes) important.  Some notes on the
+# individual items follow:
+# pthreads: AIX (must check this before -lpthread)
+# none: in case threads are in libc; should be tried before -Kthread and
+#       other compiler flags to prevent continual compiler warnings
+# -Kthread: Sequent (threads in libc, but -Kthread needed for pthread.h)
+# -kthread: FreeBSD kernel threads (preferred to -pthread since SMP-able)
+# lthread: LinuxThreads port on FreeBSD (also preferred to -pthread)
+# -pthread: Linux/gcc (kernel threads), BSD/gcc (userland threads)
+# -pthreads: Solaris/gcc
+# -mthreads: Mingw32/gcc, Lynx/gcc
+# -mt: Sun Workshop C (may only link SunOS threads [-lthread], but it
+#      doesn't hurt to check since this sometimes defines pthreads too;
+#      also defines -D_REENTRANT)
+#      ... -mt is also the pthreads flag for HP/aCC
+# pthread: Linux, etcetera
+# --thread-safe: KAI C++
+# pthread-config: use pthread-config program (for GNU Pth library)
+case "${host_cpu}-${host_os}" in
+        *solaris*)
+        # On Solaris (at least, for some versions), libc contains stubbed
+        # (non-functional) versions of the pthreads routines, so link-based
+        # tests will erroneously succeed.  (We need to link with -pthreads/-mt/
+        # -lpthread.)  (The stubs are missing pthread_cleanup_push, or rather
+        # a function called by this macro, so we could check for that, but
+        # who knows whether they'll stub that too in a future libc.)  So,
+        # we'll just look for -pthreads and -lpthread first:
+        acx_pthread_flags="-pthreads pthread -mt -pthread $acx_pthread_flags"
+        ;;
+esac
+if test x"$acx_pthread_ok" = xno; then
+for flag in $acx_pthread_flags; do
+        case $flag in
+                none)
+                AC_MSG_CHECKING([whether pthreads work without any flags])
+                ;;
+                -*)
+                AC_MSG_CHECKING([whether pthreads work with $flag])
+                PTHREAD_CFLAGS="$flag"
+                ;;
+                pthread-config)
+                AC_CHECK_PROG(acx_pthread_config, pthread-config, yes, no)
+                if test x"$acx_pthread_config" = xno; then continue; fi
+                PTHREAD_CFLAGS="`pthread-config --cflags`"
+                PTHREAD_LIBS="`pthread-config --ldflags` `pthread-config --libs`"
+                ;;
+                *)
+                AC_MSG_CHECKING([for the pthreads library -l$flag])
+                PTHREAD_LIBS="-l$flag"
+                ;;
+        esac
+        save_LIBS="$LIBS"
+        save_CFLAGS="$CFLAGS"
+        LIBS="$PTHREAD_LIBS $LIBS"
+        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+        # Check for various functions.  We must include pthread.h,
+        # since some functions may be macros.  (On the Sequent, we
+        # need a special flag -Kthread to make this header compile.)
+        # We check for pthread_join because it is in -lpthread on IRIX
+        # while pthread_create is in libc.  We check for pthread_attr_init
+        # due to DEC craziness with -lpthreads.  We check for
+        # pthread_cleanup_push because it is one of the few pthread
+        # functions on Solaris that doesn't have a non-functional libc stub.
+        # We try pthread_create on general principles.
+        AC_TRY_LINK([#include <pthread.h>],
+                    [pthread_t th; pthread_join(th, 0);
+                     pthread_attr_init(0); pthread_cleanup_push(0, 0);
+                     pthread_create(0,0,0,0); pthread_cleanup_pop(0); ],
+                    [acx_pthread_ok=yes])
+        LIBS="$save_LIBS"
+        CFLAGS="$save_CFLAGS"
+        AC_MSG_RESULT($acx_pthread_ok)
+        if test "x$acx_pthread_ok" = xyes; then
+                break;
+        fi
+        PTHREAD_LIBS=""
+        PTHREAD_CFLAGS=""
+done
+fi
+# Various other checks:
+if test "x$acx_pthread_ok" = xyes; then
+        save_LIBS="$LIBS"
+        LIBS="$PTHREAD_LIBS $LIBS"
+        save_CFLAGS="$CFLAGS"
+        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+        # Detect AIX lossage: JOINABLE attribute is called UNDETACHED.
+        AC_MSG_CHECKING([for joinable pthread attribute])
+        attr_name=unknown
+        for attr in PTHREAD_CREATE_JOINABLE PTHREAD_CREATE_UNDETACHED; do
+            AC_TRY_LINK([#include <pthread.h>], [int attr=$attr; return attr;],
+                        [attr_name=$attr; break])
+        done
+        AC_MSG_RESULT($attr_name)
+        if test "$attr_name" != PTHREAD_CREATE_JOINABLE; then
+            AC_DEFINE_UNQUOTED(PTHREAD_CREATE_JOINABLE, $attr_name,
+                               [Define to necessary symbol if this constant
+                                uses a non-standard name on your system.])
+        fi
+        AC_MSG_CHECKING([if more special flags are required for pthreads])
+        flag=no
+        case "${host_cpu}-${host_os}" in
+            *-aix* | *-freebsd* | *-darwin*) flag="-D_THREAD_SAFE";;
+            *solaris* | *-osf* | *-hpux*) flag="-D_REENTRANT";;
+        esac
+        AC_MSG_RESULT(${flag})
+        if test "x$flag" != xno; then
+            PTHREAD_CFLAGS="$flag $PTHREAD_CFLAGS"
+        fi
+        LIBS="$save_LIBS"
+        CFLAGS="$save_CFLAGS"
+        # More AIX lossage: must compile with xlc_r or cc_r
+        if test x"$GCC" != xyes; then
+          AC_CHECK_PROGS(PTHREAD_CC, xlc_r cc_r, ${CC})
+        else
+          PTHREAD_CC=$CC
+        fi
+else
+        PTHREAD_CC="$CC"
+fi
+AC_SUBST(PTHREAD_LIBS)
+AC_SUBST(PTHREAD_CFLAGS)
+AC_SUBST(PTHREAD_CC)
+# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
+if test x"$acx_pthread_ok" = xyes; then
+        ifelse([$1],,AC_DEFINE(HAVE_PTHREAD,1,[Define if you have POSIX threads libraries and header files.]),[$1])
+        :
+else
+        acx_pthread_ok=no
+        $2
+fi
+AC_LANG_RESTORE
+])dnl ACX_PTHREAD
diff --git a/ax/ax_check_gl.m4 b/ax/ax_check_gl.m4
new file mode 100644
index 0000000..08305c1
--- a/dev/null
+++ b/ax/ax_check_gl.m4
@@ -0,0 +1,95 @@
+dnl @synopsis AX_CHECK_GL
+dnl
+dnl Check for an OpenGL implementation. If GL is found, the required
+dnl compiler and linker flags are included in the output variables
+dnl "GL_CFLAGS" and "GL_LIBS", respectively. This macro adds the
+dnl configure option "--with-apple-opengl-framework", which users can
+dnl use to indicate that Apple's OpenGL framework should be used on Mac
+dnl OS X. If Apple's OpenGL framework is used, the symbol
+dnl "HAVE_APPLE_OPENGL_FRAMEWORK" is defined. If no GL implementation
+dnl is found, "no_gl" is set to "yes".
+dnl
+dnl @category InstalledPackages
+dnl @author Braden McDaniel <braden@endoframe.com>
+dnl @version 2004-11-15
+dnl @license AllPermissive
+AC_DEFUN([AX_CHECK_GL],
+[AC_REQUIRE([AC_PATH_X])dnl
+AC_REQUIRE([ACX_PTHREAD])dnl
+#
+# There isn't a reliable way to know we should use the Apple OpenGL framework
+# without a configure option.  A Mac OS X user may have installed an
+# alternative GL implementation (e.g., Mesa), which may or may not depend on X.
+#
+AC_ARG_WITH([apple-opengl-framework],
+            [AC_HELP_STRING([--with-apple-opengl-framework],
+                            [use Apple OpenGL framework (Mac OS X only)])])
+if test "X$with_apple_opengl_framework" = "Xyes"; then
+  AC_DEFINE([HAVE_APPLE_OPENGL_FRAMEWORK], [1],
+            [Use the Apple OpenGL framework.])
+  GL_LIBS="-framework OpenGL"
+else
+  AC_LANG_PUSH(C)
+  AX_LANG_COMPILER_MS
+  if test X$ax_compiler_ms = Xno; then
+    GL_CFLAGS="${PTHREAD_CFLAGS}"
+    GL_LIBS="${PTHREAD_LIBS} -lm"
+  fi
+  #
+  # Use x_includes and x_libraries if they have been set (presumably by
+  # AC_PATH_X).
+  #
+  if test "X$no_x" != "Xyes"; then
+    if test -n "$x_includes"; then
+      GL_CFLAGS="-I${x_includes} ${GL_CFLAGS}"
+    fi
+    if test -n "$x_libraries"; then
+      GL_LIBS="-L${x_libraries} -lX11 ${GL_LIBS}"
+    fi
+  fi
+  AC_CHECK_HEADERS([windows.h])
+  AC_CACHE_CHECK([for OpenGL library], [ax_cv_check_gl_libgl],
+  [ax_cv_check_gl_libgl="no"
+  ax_save_CPPFLAGS="${CPPFLAGS}"
+  CPPFLAGS="${GL_CFLAGS} ${CPPFLAGS}"
+  ax_save_LIBS="${LIBS}"
+  LIBS=""
+  ax_check_libs="-lopengl32 -lGL"
+  for ax_lib in ${ax_check_libs}; do
+    if test X$ax_compiler_ms = Xyes; then
+      ax_try_lib=`echo $ax_lib | sed -e 's/^-l//' -e 's/$/.lib/'`
+    else
+      ax_try_lib="${ax_lib}"
+    fi
+    LIBS="${ax_try_lib} ${GL_LIBS} ${ax_save_LIBS}"
+    AC_LINK_IFELSE(
+    [AC_LANG_PROGRAM([[
+# if HAVE_WINDOWS_H && defined(_WIN32)
+#   include <windows.h>
+# endif
+# include <GL/gl.h>]],
+                     [[glBegin(0)]])],
+    [ax_cv_check_gl_libgl="${ax_try_lib}"; break])
+  done
+  LIBS=${ax_save_LIBS}
+  CPPFLAGS=${ax_save_CPPFLAGS}])
+  if test "X${ax_cv_check_gl_libgl}" = "Xno"; then
+    no_gl="yes"
+    GL_CFLAGS=""
+    GL_LIBS=""
+  else
+    GL_LIBS="${ax_cv_check_gl_libgl} ${GL_LIBS}"
+  fi
+  AC_LANG_POP(C)
+fi
+AC_SUBST([GL_CFLAGS])
+AC_SUBST([GL_LIBS])
+])dnl
diff --git a/ax/ax_check_glu.m4 b/ax/ax_check_glu.m4
new file mode 100644
index 0000000..29d30bd
--- a/dev/null
+++ b/ax/ax_check_glu.m4
@@ -0,0 +1,71 @@
+dnl @synopsis AX_CHECK_GLU
+dnl
+dnl Check for GLU. If GLU is found, the required preprocessor and
+dnl linker flags are included in the output variables "GLU_CFLAGS" and
+dnl "GLU_LIBS", respectively. This macro adds the configure option
+dnl "--with-apple-opengl-framework", which users can use to indicate
+dnl that Apple's OpenGL framework should be used on Mac OS X. If
+dnl Apple's OpenGL framework is used, the symbol
+dnl "HAVE_APPLE_OPENGL_FRAMEWORK" is defined. If no GLU implementation
+dnl is found, "no_glu" is set to "yes".
+dnl
+dnl @category InstalledPackages
+dnl @author Braden McDaniel <braden@endoframe.com>
+dnl @version 2004-11-15
+dnl @license AllPermissive
+AC_DEFUN([AX_CHECK_GLU],
+[AC_REQUIRE([AX_CHECK_GL])dnl
+AC_REQUIRE([AC_PROG_CXX])dnl
+GLU_CFLAGS="${GL_CFLAGS}"
+if test "X${with_apple_opengl_framework}" != "Xyes"; then
+  AC_CACHE_CHECK([for OpenGL Utility library], [ax_cv_check_glu_libglu],
+  [ax_cv_check_glu_libglu="no"
+  ax_save_CPPFLAGS="${CPPFLAGS}"
+  CPPFLAGS="${GL_CFLAGS} ${CPPFLAGS}"
+  ax_save_LIBS="${LIBS}"
+  LIBS=""
+  ax_check_libs="-lglu32 -lGLU"
+  for ax_lib in ${ax_check_libs}; do
+    if test X$ax_compiler_ms = Xyes; then
+      ax_try_lib=`echo $ax_lib | sed -e 's/^-l//' -e 's/$/.lib/'`
+    else
+      ax_try_lib="${ax_lib}"
+    fi
+    LIBS="${ax_try_lib} ${GL_LIBS} ${ax_save_LIBS}"
+    #
+    # libGLU typically links with libstdc++ on POSIX platforms. However,
+    # setting the language to C++ means that test program source is named
+    # "conftest.cc"; and Microsoft cl doesn't know what to do with such a
+    # file.
+    #
+    AC_LANG_PUSH([C++])
+    if test X$ax_compiler_ms = Xyes; then
+      AC_LANG_PUSH([C])
+    fi
+    AC_LINK_IFELSE(
+    [AC_LANG_PROGRAM([[
+# if HAVE_WINDOWS_H && defined(_WIN32)
+#   include <windows.h>
+# endif
+# include <GL/glu.h>]],
+                     [[gluBeginCurve(0)]])],
+    [ax_cv_check_glu_libglu="${ax_try_lib}"; break])
+    if test X$ax_compiler_ms = Xyes; then
+      AC_LANG_POP([C])
+    fi
+    AC_LANG_POP([C++])
+  done
+  LIBS=${ax_save_LIBS}
+  CPPFLAGS=${ax_save_CPPFLAGS}])
+  if test "X${ax_cv_check_glu_libglu}" = "Xno"; then
+    no_glu="yes"
+    GLU_CFLAGS=""
+    GLU_LIBS=""
+  else
+    GLU_LIBS="${ax_cv_check_glu_libglu} ${GL_LIBS}"
+  fi
+fi
+AC_SUBST([GLU_CFLAGS])
+AC_SUBST([GLU_LIBS])
+])
diff --git a/ax/ax_check_glut.m4 b/ax/ax_check_glut.m4
new file mode 100644
index 0000000..239769f
--- a/dev/null
+++ b/ax/ax_check_glut.m4
@@ -0,0 +1,78 @@
+dnl @synopsis AX_CHECK_GLUT
+dnl
+dnl Check for GLUT. If GLUT is found, the required compiler and linker
+dnl flags are included in the output variables "GLUT_CFLAGS" and
+dnl "GLUT_LIBS", respectively. This macro adds the configure option
+dnl "--with-apple-opengl-framework", which users can use to indicate
+dnl that Apple's OpenGL framework should be used on Mac OS X. If
+dnl Apple's OpenGL framework is used, the symbol
+dnl "HAVE_APPLE_OPENGL_FRAMEWORK" is defined. If GLUT is not found,
+dnl "no_glut" is set to "yes".
+dnl
+dnl @category InstalledPackages
+dnl @author Braden McDaniel <braden@endoframe.com>
+dnl @version 2004-11-15
+dnl @license AllPermissive
+AC_DEFUN([AX_CHECK_GLUT],
+[AC_REQUIRE([AX_CHECK_GLU])dnl
+AC_REQUIRE([AC_PATH_XTRA])dnl
+if test "X$with_apple_opengl_framework" = "Xyes"; then
+  GLUT_CFLAGS="${GLU_CFLAGS}"
+  GLUT_LIBS="-framework GLUT -lobjc ${GL_LIBS}"
+else
+  GLUT_CFLAGS=${GLU_CFLAGS}
+  GLUT_LIBS=${GLU_LIBS}
+  #
+  # If X is present, assume GLUT depends on it.
+  #
+  # if test "X${no_x}" != "Xyes"; then
+  #   GLUT_LIBS="${X_PRE_LIBS} -lXmu -lXi ${X_EXTRA_LIBS} ${GLUT_LIBS}"
+  # fi
+  AC_LANG_PUSH(C)
+  ax_save_CPPFLAGS="${CPPFLAGS}"
+  CPPFLAGS="${GLUT_CFLAGS} ${CPPFLAGS}"
+  AC_CACHE_CHECK([for GLUT library], [ax_cv_check_glut_libglut],
+  [ax_cv_check_glut_libglut="no"
+  ax_save_LIBS="${LIBS}"
+  LIBS=""
+  ax_check_libs="-lglut32 -lglut"
+  for ax_lib in ${ax_check_libs}; do
+    if test X$ax_compiler_ms = Xyes; then
+      ax_try_lib=`echo $ax_lib | sed -e 's/^-l//' -e 's/$/.lib/'`
+    else
+      ax_try_lib="${ax_lib}"
+    fi
+    LIBS="${ax_try_lib} ${GLUT_LIBS} ${ax_save_LIBS}"
+    AC_LINK_IFELSE(
+    [AC_LANG_PROGRAM([[
+# if HAVE_WINDOWS_H && defined(_WIN32)
+#   include <windows.h>
+# endif
+# include <GL/glut.h>]],
+                     [[glutMainLoop()]])],
+    [ax_cv_check_glut_libglut="${ax_try_lib}"; break])
+  done
+  LIBS=${ax_save_LIBS}
+  ])
+  CPPFLAGS="${ax_save_CPPFLAGS}"
+  AC_LANG_POP(C)
+  if test "X${ax_cv_check_glut_libglut}" = "Xno"; then
+    no_glut="yes"
+    GLUT_CFLAGS=""
+    GLUT_LIBS=""
+  else
+    GLUT_LIBS="${ax_cv_check_glut_libglut} ${GLUT_LIBS}"
+  fi
+fi
+AC_SUBST([GLUT_CFLAGS])
+AC_SUBST([GLUT_LIBS])
+])dnl
diff --git a/ax/ax_lang_compiler_ms.m4 b/ax/ax_lang_compiler_ms.m4
new file mode 100644
index 0000000..2b3d5a8
--- a/dev/null
+++ b/ax/ax_lang_compiler_ms.m4
@@ -0,0 +1,23 @@
+dnl @synopsis AX_LANG_COMPILER_MS
+dnl
+dnl Check whether the compiler for the current language is Microsoft.
+dnl
+dnl This macro is modeled after _AC_LANG_COMPILER_GNU in the GNU
+dnl Autoconf implementation.
+dnl
+dnl @category InstalledPackages
+dnl @author Braden McDaniel <braden@endoframe.com>
+dnl @version 2004-11-15
+dnl @license AllPermissive
+AC_DEFUN([AX_LANG_COMPILER_MS],
+[AC_CACHE_CHECK([whether we are using the Microsoft _AC_LANG compiler],
+                [ax_cv_[]_AC_LANG_ABBREV[]_compiler_ms],
+[AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[#ifndef _MSC_VER
+       choke me
+#endif
+]])],
+                   [ax_compiler_ms=yes],
+                   [ax_compiler_ms=no])
+ax_cv_[]_AC_LANG_ABBREV[]_compiler_ms=$ax_compiler_ms
+])])
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..a7924d3
--- a/dev/null
+++ b/configure.ac
@@ -0,0 +1,24 @@
+AC_INIT([exp005], [0.1], [don@drexel.edu])
+AM_INIT_AUTOMAKE([-Wall, -Werror, -Wno-portability])
+AC_PROG_CC
+AM_CONFIG_HEADER([config.h])
+AC_CONFIG_FILES([
+        Makefile
+        src/Makefile
+])
+# Check for OpenGL libraries GLUT, GLU and GL.  OpenGL is used for the
+# visualization rendering and interaction.
+AX_CHECK_GLUT
+# Check for the NCBI Toolkit libraries.
+AC_SEARCH_LIBS([log10],[m])
+AC_SEARCH_LIBS([NlmThreadsAvailable],[ncbi])
+AC_SEARCH_LIBS([SeqAlignNew],[ncbiobj])
+AC_SEARCH_LIBS([Blast_RedoOneMatch],[blastcompadj])
+AC_SEARCH_LIBS([BioseqBlastEngine],[ncbitool])
+# Check for the new curses library for terminal output.
+AC_SEARCH_LIBS([clrtoeol],[ncurses])
+AC_OUTPUT
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100644
index 0000000..bd0d702
--- a/dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,28 @@
+bin_PROGRAMS = exp004viz
+exp004viz_SOURCES = \
+        controller/exp004display.c \
+        controller/exp004mouse.c \
+        controller/exp004processhits.c \
+        controller/exp004reshape.c \
+        exp004viz.c \
+        model/exp004base.c \
+        util/check_error.c \
+        view/exp004geometry.c \
+        view/exp004view.c
+exp004viz_LDADD = ${GLUT_LIBS}
+noinst_HEADERS = \
+        controller/exp004display.h \
+        controller/exp004mouse.h \
+        controller/exp004processhits.h \
+        controller/exp004reshape.h \
+        model/exp004base.h \
+        model/exp004state.h \
+        util/check_error.h \
+        view/exp004geometry.h \
+        view/exp004state0.h \
+        view/exp004view.h
+AM_CFLAGS = -Wall -std=gnu99 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/include/ncbi
diff --git a/src/controller/exp004display.c b/src/controller/exp004display.c
new file mode 100644
index 0000000..e893ad6
--- a/dev/null
+++ b/src/controller/exp004display.c
@@ -0,0 +1,16 @@
+#include "exp004display.h"
+#include "../view/exp004geometry.h"
+#include <GL/glut.h>
+#include <stdio.h>
+#define WINHEIGHT 500
+void
+exp004display (void)
+{
+  glClear (GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+  exp004geometry (GL_RENDER);
+  glutSwapBuffers ();
+  return;
+}
diff --git a/src/controller/exp004display.h b/src/controller/exp004display.h
new file mode 100644
index 0000000..6a5f9f7
--- a/dev/null
+++ b/src/controller/exp004display.h
@@ -0,0 +1,6 @@
+#ifndef EXP004DISPLAY_H
+#define EXP004DISPLAY_H
+void exp004display (void);
+#endif // EXP004DISPLAY_H
diff --git a/src/controller/exp004mouse.c b/src/controller/exp004mouse.c
new file mode 100644
index 0000000..11117bf
--- a/dev/null
+++ b/src/controller/exp004mouse.c
@@ -0,0 +1,90 @@
+#include "exp004mouse.h"
+#include "exp004processhits.h"
+#include "../view/exp004geometry.h"
+#include "../view/exp004state0.h"
+#include "../util/check_error.h"
+#include <GL/glut.h>
+#include <stdio.h>
+#define SIZE 500
+#define N 3
+void
+exp004mouse (int button, int state, int x, int y)
+{
+  if (button == GLUT_LEFT_BUTTON && state == GLUT_DOWN)
+    {
+      /*
+       * "Specify the array to be used for the returned hit records
+       * with glSelectBuffer () [Redbook]."
+       */
+      GLuint select_buf[SIZE];
+      glSelectBuffer (SIZE, select_buf);
+      /*
+       * "Enter selection mode by specifying GL_SELECT with
+       * glRenderMode () [Redbook]."
+       */
+      glRenderMode (GL_SELECT);
+      /*
+       * "Initialize the name stack using glInitNames () and glPush
+       * Names () [Redbook]."
+       */
+      glInitNames ();
+      glPushName (0);
+      /*
+       * "Define the viewing volume you want to use for selection.
+       * Usually this is different from the viewing volume you
+       * originally used to draw the scene, so you probably want to
+       * save and then restore the current transformation state with
+       * glPushMatrix () and glPopMatrix () [Redbook]."
+       */
+      glMatrixMode (GL_PROJECTION);
+      glPushMatrix ();
+      glLoadIdentity ();
+      GLint viewport[4];
+      glGetIntegerv (GL_VIEWPORT, viewport);
+      gluPickMatrix ((GLdouble) x,
+                     (GLdouble) (viewport[3] - y),
+                     N,
+                     N,
+                     viewport);
+      gluOrtho2D(exp004state0.ortho.min_x,
+                 exp004state0.ortho.max_x,
+                 exp004state0.ortho.min_y,
+                 exp004state0.ortho.max_y);      
+      /*
+       * "Alternately issue primitive drawing commands and commands to
+       * manipulate the name stack so that each primitive of interest
+       * has appropriate names assigned [Redbook]."
+       */
+      exp004geometry (GL_SELECT);
+      glMatrixMode (GL_PROJECTION);      
+      glPopMatrix ();
+      glutSwapBuffers ();
+      /*
+       * "Exit selection mode and process the returned selection data
+       * (the hit records) [Redbook]."
+       */
+      GLint hits = glRenderMode (GL_RENDER);
+      check_error (__FILE__, __LINE__);
+      
+      /* "process hits from selection mode rendering [Angel,2008]." */
+      exp004processhits (hits, select_buf);
+      
+      /* "normal render [Angel,2008]." */      
+      glutPostRedisplay ();
+    }
+  return;
+}
diff --git a/src/controller/exp004mouse.h b/src/controller/exp004mouse.h
new file mode 100644
index 0000000..a6809be
--- a/dev/null
+++ b/src/controller/exp004mouse.h
@@ -0,0 +1,6 @@
+#ifndef EXP004MOUSE_H
+#define EXP004MOUSE_H
+void exp004mouse (int button, int state, int x, int y);
+#endif // EXP004MOUSE_H
diff --git a/src/controller/exp004processhits.c b/src/controller/exp004processhits.c
new file mode 100644
index 0000000..29fbbbc
--- a/dev/null
+++ b/src/controller/exp004processhits.c
@@ -0,0 +1,54 @@
+/* I seem to need this for glGenBuffers as per
+   http://www.gamedev.net/community/forums/topic.asp?topic_id=422358 */
+#define GL_GLEXT_PROTOTYPES
+#include "exp004processhits.h"
+#include "../view/exp004state0.h"
+#include <stdio.h>
+/*
+ * The implementation of this function is based on
+ * [Angel,2008,pp80-81].
+ */
+void
+exp004processhits (GLint hits, GLuint buffer[])
+{
+  /*
+   * A simple alias to make the code more readable.
+   */
+  EXP004STATE* S = &exp004state0;
+  printf ("Hits: %d\n", hits);
+  GLuint *hitlist = buffer;
+  
+  for (int i = 0; i < hits; i++)
+    {
+      hitlist += 3;
+      /*
+       * Report the hit to the terminal.
+       */
+      printf ("Hit %i: %s\n", i + 1, exp004state0.gi_data[*hitlist]);
+      /*
+       * Add the hits to the selection.
+       */
+      exp004state0.selection[*hitlist] = true;
+      exp004state0.base_colors_data[*hitlist][0] = SELECT_COLOR_R;
+      exp004state0.base_colors_data[*hitlist][1] = SELECT_COLOR_G;
+      exp004state0.base_colors_data[*hitlist][2] = SELECT_COLOR_B;
+      hitlist++;
+    }
+  glBindBuffer (GL_ARRAY_BUFFER, S->buffers[BASE_COLORS]);
+  glColorPointer (3, GL_FLOAT, 0, 0);
+  glBufferData (GL_ARRAY_BUFFER,
+                sizeof (S->base_colors_data), S->base_colors_data,
+                GL_STATIC_DRAW);
+  
+  printf ("\n");
+  return;
+}
diff --git a/src/controller/exp004processhits.h b/src/controller/exp004processhits.h
new file mode 100644
index 0000000..d61e9a7
--- a/dev/null
+++ b/src/controller/exp004processhits.h
@@ -0,0 +1,8 @@
+#ifndef EXP004PROCESSHITS_H
+#define EXP004PROCESSHITS_H
+#include <GL/glut.h>
+void exp004processhits (GLint hits, GLuint buffer[]);
+#endif // EXP004PROCESSHITS_H
diff --git a/src/controller/exp004reshape.c b/src/controller/exp004reshape.c
new file mode 100644
index 0000000..7aaff08
--- a/dev/null
+++ b/src/controller/exp004reshape.c
@@ -0,0 +1,55 @@
+#include "exp004reshape.h"
+#include "../view/exp004state0.h"
+#include <GL/glut.h>
+void
+exp004reshape (int w, int h)
+{
+  glMatrixMode (GL_PROJECTION);
+  glLoadIdentity ();
+  /*
+   * This scaling produces an odd effect when the coordinates are not
+   * centered at 0,0.  When 0,0 is the lower left rather than the
+   * center this reshape is a bit unnatural since the image is not
+   * centered in the middle of the window.
+   */
+  if (w <= h)
+    {      
+      exp004state0.ortho.min_x = 
+        exp004state0.ortho_min;
+      exp004state0.ortho.max_x = 
+        exp004state0.ortho_max;
+      exp004state0.ortho.min_y = 
+        exp004state0.ortho_min * (GLfloat) h / (GLfloat) w;
+      exp004state0.ortho.max_y = 
+        exp004state0.ortho_max * (GLfloat) h / (GLfloat) w;
+    }
+  else
+    {
+      exp004state0.ortho.min_x =
+        exp004state0.ortho_min * (GLfloat) w / (GLfloat) h;
+      exp004state0.ortho.max_x =
+        exp004state0.ortho_max * (GLfloat) w / (GLfloat) h;
+      exp004state0.ortho.min_y =
+        exp004state0.ortho_min;
+      exp004state0.ortho.max_y =
+        exp004state0.ortho_max;
+    }
+  gluOrtho2D(exp004state0.ortho.min_x,
+             exp004state0.ortho.max_x,
+             exp004state0.ortho.min_y,
+             exp004state0.ortho.max_y);
+  glMatrixMode (GL_MODELVIEW);
+  // Set the viewport equal to the size of the window.
+  glViewport (0, 0, (GLsizei) w, (GLsizei) h);
+  exp004state0.viewport.w = w;
+  exp004state0.viewport.h = h;
+  return;
+}
diff --git a/src/controller/exp004reshape.h b/src/controller/exp004reshape.h
new file mode 100644
index 0000000..3bb20a5
--- a/dev/null
+++ b/src/controller/exp004reshape.h
@@ -0,0 +1,6 @@
+#ifndef EXP004RESHAPE_H
+#define EXP004RESHAPE_H
+void exp004reshape (int w, int h);
+#endif // EXP004RESHAPE_H
diff --git a/src/exp004viz.c b/src/exp004viz.c
new file mode 100644
index 0000000..08d5953
--- a/dev/null
+++ b/src/exp004viz.c
@@ -0,0 +1,15 @@
+#include <GL/glut.h>
+#include "view/exp004view.h"
+int
+main (int argc, char **argv)
+{
+  glutInit (&argc, argv);
+  glutInitDisplayMode (GLUT_DOUBLE | GLUT_RGB | GLUT_DEPTH);
+  exp004view ();
+  glutMainLoop ();
+  return 0;
+}
diff --git a/src/model/exp004base.c b/src/model/exp004base.c
new file mode 100644
index 0000000..56a20e5
--- a/dev/null
+++ b/src/model/exp004base.c
@@ -0,0 +1,107 @@
+/* I seem to need this for glGenBuffers as per
+   http://www.gamedev.net/community/forums/topic.asp?topic_id=422358 */
+#define GL_GLEXT_PROTOTYPES
+#include "exp004base.h"
+#include "../view/exp004state0.h"
+#include <GL/glut.h>
+#include <stdio.h>
+#include <string.h>
+void
+exp004base (void)
+{
+  /*
+   * A simple alias to make the code more readable.
+   */
+  EXP004STATE* S = &exp004state0;
+  /* 
+   * This implementation can be improved by mapping the video memory
+   * directly rather than loading into system memory and then copying
+   * into video memory.
+  */
+  FILE* coords = 
+    fopen ("/home/don/exp004/test/run20090514/run20090514.coords", "r");
+  int i = 0;
+  /* 
+   * Initialize the bounding box of the points.
+   */
+  S->bb.min_x = 0.0;
+  S->bb.max_x = 0.0;
+  S->bb.min_y = 0.0;
+  S->bb.max_y = 0.0;
+  for (i = 0; i < ROWS; i++)
+    {
+      fscanf (coords, "%s %f %f\n",
+              S->gi_data[i],
+              &S->base_vertices_data[i][0],
+              &S->base_vertices_data[i][1]);
+      if (S->base_vertices_data[i][0] < S->bb.min_x)
+        S->bb.min_x = S->base_vertices_data[i][0];
+      if (S->base_vertices_data[i][0] > S->bb.max_x)
+        S->bb.max_x = S->base_vertices_data[i][0];
+      if (S->base_vertices_data[i][1] < S->bb.min_y)
+        S->bb.min_y = S->base_vertices_data[i][1];
+      if (S->base_vertices_data[i][1] > S->bb.max_y)
+        S->bb.max_y = S->base_vertices_data[i][1];
+      /*
+       * Deselected by default.
+       */
+      S->selection[i] = false;
+      S->base_colors_data[i][0] = DEFAULT_COLOR_R;
+      S->base_colors_data[i][1] = DEFAULT_COLOR_G;
+      S->base_colors_data[i][2] = DEFAULT_COLOR_B;
+    }
+  fclose (coords);
+  /*
+   * Find the largest axis and use it to setup the projection.  This
+   * is done to preserve the aspect ratio.  The aspect ratio should be
+   * preserved since relative distance is a meaningful indicator in
+   * the map.
+   */
+  // Min of min x or min y.
+  if (S->bb.min_x <= S->bb.min_y)
+    S->ortho_min = S->bb.min_x;
+  else
+    S->ortho_min = S->bb.min_y;
+  S->ortho_min--;
+  // Max of max x or max y.
+  if (S->bb.max_x >= S->bb.max_y)
+    S->ortho_max = S->bb.max_x;
+  else
+    S->ortho_max = S->bb.max_y;
+  S->ortho_max++;
+  // Invert the y coordinate to match up with the LGL Java viewer.
+  for (i = 0; i < ROWS; i++)
+    S->base_vertices_data[i][1] = 
+      S->ortho_max - S->base_vertices_data[i][1];
+  S->points = i;
+  glGenBuffers (2, S->buffers);
+  glBindBuffer (GL_ARRAY_BUFFER, S->buffers[BASE_VERTICES]);
+  glVertexPointer (2, GL_FLOAT, 0, 0);
+  glBufferData (GL_ARRAY_BUFFER, 
+                sizeof (S->base_vertices_data), S->base_vertices_data,
+                GL_STATIC_DRAW);
+  glBindBuffer (GL_ARRAY_BUFFER, S->buffers[BASE_COLORS]);
+  glColorPointer (3, GL_FLOAT, 0, 0);
+  glBufferData (GL_ARRAY_BUFFER,
+                sizeof (S->base_colors_data), S->base_colors_data,
+                GL_STATIC_DRAW);
+  return;
+}
diff --git a/src/model/exp004base.h b/src/model/exp004base.h
new file mode 100644
index 0000000..4f8492d
--- a/dev/null
+++ b/src/model/exp004base.h
@@ -0,0 +1,9 @@
+#ifndef EXP004BASE_H
+#define EXP004BASE_H
+/*
+ * Build the base layer of the map.
+ */
+void exp004base (void);
+#endif // EXP004BASE_H
diff --git a/src/model/exp004state.h b/src/model/exp004state.h
new file mode 100644
index 0000000..e45f679
--- a/dev/null
+++ b/src/model/exp004state.h
@@ -0,0 +1,101 @@
+#ifndef EXP004STATE_H
+#define EXP004STATE_H
+#include <stdbool.h>
+/*
+ * Buffer object identifiers.
+ */
+#define BASE_VERTICES 0
+#define BASE_COLORS 1
+/*
+ * Vertices in the graph.
+ */
+#define ROWS 83905
+#define DEFAULT_COLOR_R 0.2
+#define DEFAULT_COLOR_G 0.2
+#define DEFAULT_COLOR_B 0.2
+#define SELECT_COLOR_R 1.0
+#define SELECT_COLOR_G 1.0
+#define SELECT_COLOR_B 1.0
+/*
+ * Maintain state of the model.
+ */
+typedef struct
+{
+  /* 
+   * Track the bounding box of the points.
+   */
+  struct {
+    float min_x;
+    float max_x;
+    float min_y;
+    float max_y;
+  } bb;
+  /*
+   * Minimum coordinate for the orthographic projection. 
+   */
+  float ortho_min;
+  /*
+   * Maximum coordinate for the orthographic projection.
+   */
+  float ortho_max;
+  /*
+   * Orthographic coordinates after aspect preserving scaling.
+   */
+  struct {
+    float min_x;
+    float max_x;
+    float min_y;
+    float max_y;
+  } ortho;
+  /*
+   * Viewport size.
+   */
+  struct {
+    int w;
+    int h;
+  } viewport;
+  /*
+   * Points loaded.
+   */
+  int points;
+  /*
+   * Buffer objects.
+   */
+  unsigned int buffers[1];
+  /*
+   * GI Identifiers indexed by row.
+   */
+  char gi_data[ROWS][20];
+  /*
+   * 2D coordinates for each protein.
+   */
+  float base_vertices_data[ROWS][2];
+  /*
+   * RGB color for each protein.
+   */
+  float base_colors_data[ROWS][3];
+  /*
+   * Selection list.
+   */
+  bool selection[ROWS];
+} EXP004STATE;
+#endif // EXP004STATE_H
diff --git a/src/util/check_error.c b/src/util/check_error.c
new file mode 100644
index 0000000..dbe5b8f
--- a/dev/null
+++ b/src/util/check_error.c
@@ -0,0 +1,17 @@
+#include <GL/glut.h>
+#include <error.h>
+#include <errno.h>
+void
+check_error (const char *filename, unsigned int linenum)
+{
+  GLenum errCode = glGetError ();
+  if (errCode != GL_NO_ERROR)
+    {
+      const GLubyte *errString = gluErrorString (errCode);
+      error_at_line (-1, errno, filename, linenum,
+                     "OpenGL Error %s", errString);
+    }
+  return;
+}
diff --git a/src/util/check_error.h b/src/util/check_error.h
new file mode 100644
index 0000000..7aa6495
--- a/dev/null
+++ b/src/util/check_error.h
@@ -0,0 +1,9 @@
+#ifndef CHECK_ERROR_H
+#define CHECK_ERROR_H
+/*
+ * Based on example 14-1 in Shreiner p603.
+ */
+void check_error (const char *filename, unsigned int linenum);
+#endif // CHECK_ERROR_H
diff --git a/src/view/exp004geometry.c b/src/view/exp004geometry.c
new file mode 100644
index 0000000..9ff6475
--- a/dev/null
+++ b/src/view/exp004geometry.c
@@ -0,0 +1,32 @@
+/* I seem to need this for glGenBuffers as per
+   http://www.gamedev.net/community/forums/topic.asp?topic_id=422358 */
+#define GL_GLEXT_PROTOTYPES
+#include "exp004geometry.h"
+#include "exp004state0.h"
+#include <GL/glut.h>
+void
+exp004geometry (GLenum mode)
+{
+  glMatrixMode (GL_MODELVIEW);
+  glLoadIdentity ();
+  glPointSize (0.1);
+  glColor3f (0.2, 0.2, 0.2);
+  if (mode == GL_SELECT) 
+    {
+      for (int i = 0; i < ROWS; i++)
+        {
+          glLoadName (i);
+          glDrawArrays (GL_POINTS, i, 1);
+        }      
+    }
+  else
+    {
+      glDrawArrays (GL_POINTS, 0, ROWS);
+    }
+  
+  return;
+}
diff --git a/src/view/exp004geometry.h b/src/view/exp004geometry.h
new file mode 100644
index 0000000..582be48
--- a/dev/null
+++ b/src/view/exp004geometry.h
@@ -0,0 +1,8 @@
+#ifndef EXP004GEOMETRY_H
+#define EXP004GEOMETRY_H
+#include <GL/glut.h>
+void exp004geometry (GLenum mode);
+#endif // EXP004GEOMETRY_H
diff --git a/src/view/exp004state0.h b/src/view/exp004state0.h
new file mode 100644
index 0000000..2b60ce9
--- a/dev/null
+++ b/src/view/exp004state0.h
@@ -0,0 +1,8 @@
+#ifndef EXP004STATE0_H
+#define EXP004STATE0_H
+#include "../model/exp004state.h"
+EXP004STATE exp004state0;
+#endif // EXP004STATE0_H
diff --git a/src/view/exp004view.c b/src/view/exp004view.c
new file mode 100644
index 0000000..5e3b8ab
--- a/dev/null
+++ b/src/view/exp004view.c
@@ -0,0 +1,44 @@
+#include "../controller/exp004display.h"
+#include "../controller/exp004mouse.h"
+#include "../controller/exp004reshape.h"
+#include "../model/exp004base.h"
+#include "exp004view.h"
+#include <GL/glut.h>
+void
+exp004view (void)
+{
+  // GLUT Initialization
+  glutInitWindowSize (500, 500);
+  glutInitWindowPosition (100, 100);
+  glutCreateWindow ("Exp004");
+  // GL Initialization
+  glClearColor (0.0, 0.0, 0.0, 1.0);
+  glColor3f (1.0, 1.0, 1.0);
+  glEnable (GL_AUTO_NORMAL);
+  glEnable (GL_DEPTH_TEST);
+  glEnable (GL_MAP1_VERTEX_3);
+  glShadeModel (GL_SMOOTH);
+  /* Buffer objects to use. */
+  glEnableClientState (GL_COLOR_ARRAY);
+  glEnableClientState (GL_VERTEX_ARRAY);
+  
+  /* Enable Antialiasing as described in "Antialiasing"
+     [Shreiner,247]. */
+  glEnable (GL_LINE_SMOOTH);
+  glEnable (GL_BLEND);
+  glBlendFunc (GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
+  glHint (GL_LINE_SMOOTH_HINT, GL_NICEST);
+  // Initialize the model.
+  exp004base ();
+  // Callbacks (Controllers)
+  glutDisplayFunc (exp004display);
+  glutMouseFunc (exp004mouse);
+  glutReshapeFunc (exp004reshape);
+  return;
+}
diff --git a/src/view/exp004view.h b/src/view/exp004view.h
new file mode 100644
index 0000000..0086f53
--- a/dev/null
+++ b/src/view/exp004view.h
@@ -0,0 +1,6 @@
+#ifndef EXP004VIEW_H
+#define EXP004VIEW_H
+void exp004view (void);
+#endif // EXP004VIEW_H