Merge changes for 1.1 release

Makefile.am

@@ -33,7 +33,7 @@ if DX_COND_xml
 docdata += @DX_DOCDIR@/RNAblueprint.tag 
 dist_xmldoc_DATA = @DX_DOCDIR@/xml/*
 
-$(dist_htmldoc_DATA): doxygen-doc
+$(dist_xmldoc_DATA): doxygen-doc
 
 endif
 

README.md

@@ -23,10 +23,11 @@ Please cite the software as specified at the bottom of the page!
 
 ### Optional:
 
- * Boost Programm Options
- * SWIG for interfaces
- * Python for interface
- * Perl for interface
+ * Boost Programm Options (default: on)
+ * SWIG for interfaces (default: on)
+ * Python for interface (default: on)
+ * Perl for interface (default: on)
+ * ExtUtils::Embed module for perl interface (default: on)
  * Doxygen for documentation
  * LaTeX for PDF documentation
  * libGMP for multiprecision integers
@@ -44,6 +45,9 @@ make
 make install
 ```
 
+In case of a local installation, please do not forget to adopt your path variables such as
+`PATH`, `LD_LIBRARY_PATH`, `CPLUS_INCLUDE_PATH`, `PYTHONPATH`, `PERL5LIB`
+
 ### Most important configure options are:
 
     --prefix Specify an installation path prefix
@@ -57,14 +61,17 @@ TIP: You might want call `./configure --help` for all install options!
 
 ## Documentation
 
-Documentation is done using Doxygen. Call `make doxygen-doc` for a offline version in HTML and PDF.
+Library documentation is done using Doxygen. Call `make doxygen-doc` for a offline version in HTML and PDF.
 There is also a online version available here: [http://ribonets.github.io/RNAblueprint/](http://ribonets.github.io/RNAblueprint/)
+Documentation of the RNAblueprint program is provided by calling `RNAblueprint --help`.
 
 ## Testing
 
 Unit tests are available for many functions of the library. Please call `make check` to run these tests!
 
 ## How to cite
 
+Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker and Sven Findeiß. Submitted 2016. "Flexible and universal multiple target nucleic acid sequence design" Journal: Pages. doi: DOI.
+
 Publication for this software package is in progress.
 We will update this information as soon as a preprint is available online!

configure.ac

@@ -1,7 +1,7 @@
 # RNAblueprint: configure.ac
 
 # initial information about the project
-AC_INIT([RNAblueprint],[1.0],[s.hammer@univie.ac.at],[RNAblueprint],[http://www.tbi.univie.ac.at/~jango/])
+AC_INIT([RNAblueprint],[1.1],[s.hammer@univie.ac.at],[RNAblueprint],[http://www.tbi.univie.ac.at/~jango/])
 
 # automake initialisation (mandatory)
 AC_PREREQ([2.59])
@@ -15,6 +15,7 @@ AC_CONFIG_MACRO_DIR([m4])
 
 # init doxygen
 ##########################################################################
+DX_DOXYGEN_FEATURE(OFF)
 DX_HTML_FEATURE(ON)
 DX_CHM_FEATURE(OFF)
 DX_CHI_FEATURE(OFF)

lib/RNAblueprint.h

@@ -32,10 +32,11 @@
  * - C++ Standard Library
  * 
  * Optional:
- * - Boost Programm Options
- * - SWIG for interfaces
- * - Python for interface
- * - Perl for interface
+ * - Boost Programm Options (default: on)
+ * - SWIG for interfaces (default: on)
+ * - Python for interface (default: on)
+ * - Perl for interface (default: on)
+ * - ExtUtils::Embed module for perl interface (default: on)
  * - Doxygen for documentation
  * - LaTeX for PDF documentation
  * - libGMP for multiprecision integers
@@ -50,6 +51,9 @@
  * ./configure\n
  * make\n
  * make install\n
+ *
+ * In case of a local installation, please do not forget to adopt your path variables such as
+ * `PATH`, `LD_LIBRARY_PATH`, `CPLUS_INCLUDE_PATH`, `PYTHONPATH`, `PERL5LIB`
  * 
  * Most important configure options are:
  * - \-\-prefix           Specify an installation path prefix
@@ -75,6 +79,8 @@
  * 
  * \section cite_sec How to cite
  * 
+ * Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker and Sven Findeiß. Submitted 2016. "Flexible and universal multiple target nucleic acid sequence design" Journal: Pages. doi: DOI.
+ *
  * Publication for this software package is in progress.
  * We will update this information as soon as a preprint is available online!
  * 

src/main.cc

@@ -1,5 +1,6 @@
-/* RNAblueprint
- * A program for designing RNA molecules.
+/* This program reads RNA secondary structures in dot-bracket notation as well as
+ * sequence constraints in IUPAC code and fairly samples RNA sequences compatible
+ * to both inputs.
  *
  * @date 25.03.2013
  * @author Stefan Hammer <s.hammer@univie.ac.at>
@@ -199,8 +200,12 @@ boost::program_options::variables_map init_options(int ac, char* av[]) {
     // boost option parser
     // http://www.boost.org/doc/libs/1_53_0/doc/html/program_options/tutorial.html
     namespace po = boost::program_options;
+    po::options_description desc(     
+        "This program reads RNA secondary structures in dot-bracket notation as well as\n"
+        "sequence constraints in IUPAC code and fairly samples RNA sequences compatible\n"
+        "to both inputs");
     // Group of options that will be allowed only on command line
-    po::options_description generic("Generic options");
+    po::options_description generic("Generic Options");
     generic.add_options()
             ("help,h", "print help message")
             ("verbose,v", po::bool_switch()->default_value(false)->zero_tokens(), "be verbose")
@@ -231,7 +236,7 @@ boost::program_options::variables_map init_options(int ac, char* av[]) {
     p.add("in", 1).add("out", 2);
 
     po::options_description cmdline_options;
-    cmdline_options.add(generic).add(config);
+    cmdline_options.add(desc).add(generic).add(config);
 
     po::variables_map vm;
     po::store(po::command_line_parser(ac, av).options(cmdline_options).positional(p).run(), vm);

src/main.h

@@ -1,5 +1,6 @@
-/* This program reads secundary RNA structures in dot-bracket and
- * builds a graph for a latter ear-decomposition and bipartitness-check
+/* This program reads RNA secondary structures in dot-bracket notation as well as
+ * sequence constraints in IUPAC code and fairly samples RNA sequences compatible
+ * to both inputs.
  *
  * @date 25.03.2013
  * @author Stefan Hammer <s.hammer@univie.ac.at>