Merge branch 'develop'

.travis.yml

@@ -0,0 +1,8 @@
+os: linux
+dist: trusty
+language: cpp
+install:
+  - curl -L --create-dirs -o ~/bin/yaggo https://github.com/gmarcais/yaggo/releases/download/v1.5.9/yaggo
+  - chmod a+rx ~/bin/yaggo
+  - export PATH=~/bin:$PATH
+script: autoreconf -fi && ./configure && make -j 2 && make check

Makefile.am

@@ -146,11 +146,13 @@ CLEANFILES += $(libs_scripts) $(all_scripts)
 script_inst_subst  = sed -e 's,[@]PERL[@],$(PERL),g' \
                        -e 's,[@]BIN_DIR[@],$(bindir),g' \
                        -e 's,[@]LIB_DIR[@],$(script_libdir),g' \
-	               -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g'
+	               -e 's,[@]LIBEXEC_DIR[@],$(pkglibexecdir),g' \
+		       -e 's,[@]GNUPLOT_EXE[@],$(GNUPLOT),g'
 script_local_subst = sed -e 's,[@]PERL[@],$(PERL),g' \
                        -e 's,[@]BIN_DIR[@],$(abs_builddir),g' \
                        -e 's,[@]LIB_DIR[@],$(abs_srcdir)/scripts,g' \
-	               -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g'
+	               -e 's,[@]LIBEXEC_DIR[@],$(abs_builddir),g' \
+                       -e 's,[@]GNUPLOT_EXE[@],$(GNUPLOT),g'
 
 .libs/%: scripts/%.pl
 	@mkdir -p $(dir $@) && $(script_inst_subst) < $< > $@

README.md

@@ -1,3 +1,7 @@
+Master | Develop
+-------|--------
+[![Build Status](https://travis-ci.org/mummer4/mummer.svg?branch=master)](https://travis-ci.org/mummer4/mummer) | [![Build Status](https://travis-ci.org/mummer4/mummer.svg?branch=develop)](https://travis-ci.org/mummer4/mummer)
+
 # mummer
 
 MUMmer is a versatil alignment tool for DNA and protein sequences. To install the software, download the [latest release](../../releases) and follow the [installation instructions](INSTALL.md). For instruction on how to use the software, consult the [manual](MANUAL.md).

configure.ac

@@ -33,6 +33,10 @@ AS_IF([test "x$enable_openmp" != "xno"],
 AC_ARG_VAR([YAGGO], [Yaggo switch parser generator])
 AS_IF([test "x$YAGGO" = "x"], [AC_PATH_PROG([YAGGO], [yaggo], [false])])
 
+# Check for gnuplot
+AC_ARG_VAR([GNUPLOT], [Gnuplot plotting program])
+AS_IF([test "x$GNUPLOT" = "x"], [AC_PATH_PROGS([GNUPLOT], [gnuplot gnuplot5 gnuplot4], [false])])
+
 # Check that type __int128 is supported and if the
 AC_ARG_WITH([int128],
             [AS_HELP_STRING([--with-int128], [enable int128])],

scripts/mummerplot.pl

@@ -21,8 +21,9 @@
 use strict;
 use IO::Socket;
 
-my $BIN_DIR = "@BIN_DIR@";
-my $LIB_DIR = "@LIB_DIR@";
+my $BIN_DIR     = "@BIN_DIR@";
+my $LIB_DIR     = "@LIB_DIR@";
+my $GNUPLOT_EXE = "@GNUPLOT_EXE@";
 
 
 #================================================================= Globals ====#
@@ -1151,7 +1152,7 @@ ($$)
         $P_KEY = "unset key";
         $P_FORMAT .= "\nset mouse format \"$TFORMAT\"";
         $P_FORMAT .= "\nset mouse mouseformat \"$MFORMAT\"";
-        $P_FORMAT .= "\nset mouse clipboardformat \"$MFORMAT\"";
+        $P_FORMAT .= "\nif(GPVAL_VERSION < 5) { set mouse clipboardformat \"$MFORMAT\" }";
     }
     else {
         $P_LS = "set linestyle";
@@ -1308,7 +1309,7 @@ ( )
         print STDERR "Rendering plot to screen\n";
     }
 
-    my $cmd = "gnuplot";
+    my $cmd = $GNUPLOT_EXE;
 
     #-- x11 specifics
     if ( $OPT_terminal eq $X11 ) {
@@ -1499,7 +1500,7 @@ ( )
     }
     elsif ( $OPT_gpstatus ) {
         print STDERR
-            "WARNING: Using outdated gnuplot, use v4.0 for best results\n";
+            "WARNING: Using outdated gnuplot, use v4 or later for best results\n";
 
         if ( $OPT_color ) {
             print STDERR

src/essaMEM/mummer.cpp

@@ -218,7 +218,7 @@ int main(int argc, char* argv[]) {
       case 22:
 #ifdef VERSION
         std::cout << VERSION << '\n';
-#elif
+#else
         std::cout << "<unknown version>\n";
 #endif
         exit(0);