version 2.1.0

version 2.1.0

ChangeLog

@@ -1,4 +1,79 @@
 
+version 2.1.0
+
+171010 Martin Mann :
+ * README.md :
+   + explicit seed description
+ * AccessibilityVrna :
+   * fillByConstraints() :
+   * fillByRNAup() :
+   * callbackForStorage() :
+     * BUGFIX : only check for block-constraint for region ends (is allowed to
+       contain a blocked subregion)
+
+171009 Martin Mann :
+ * tests/*BasePair_test :
+   * explicit use of std::abs (should fix test error of github issue #91)
+   * BUGFIX: test values wrong (were derived from rounded values)
+     -> fixes github issue #91 (thanks to @sjannielefevre) 
+ * AccessibilityBasePair :
+   * constructor() :
+     + RT sanity check to avoid division by zero
+ * NussinovHandler :
+   + printMatrix() : utility function for debug to see matrix content
+   * getQ(), getQb(), getPbp(), getPu() :
+     * BUGFIX : boundary checks partially wrong
+     + explicit lower bound handling
+ + SeedHandlerMfe : former SeedHandler implementation for mfe-seed access
+ * SeedHandler : now abstract interface
+ * Predictor*Seed :
+   * constructor() :
+     * takes now directly a SeedHandler instance instead of a SeedConstraint
+ * CommandLineParsing :
+   + getSeedHandler() : provides the seed handler according to the user input
+   * getPredictor() :
+     * uses now getSeedHandler() to setup Predictor*Seed instances
+   + '--seedTQ' argument for explicit seed encodings
+ * SeedHandlerMfe() :
+   * constructor() : sanity check in debug mode 
+ + SeedHandlerExplicit() : seed handler for explicitly defined seed interactions
+   + checkSeedEncoding() : tests sanity of seed encoding
+   + SeedData() : data structure that parses and holds explicit seed information
+ * SeedConstraint :
+   + explicitSeeds + getter : explicit seed encodings to be used
+ + tests/SeedHandlerExplicit :
+   + test checkSeedEncoding()
+   + test SeedData() parsing
+
+171006 Martin Mann :
+ * AccessibilityVrna :
+   * fillByRNAup() :
+     * BUGFIX : have to check whether region is blocked not if constrained
+ * AccessibilityBasePair :
+ * AccessibilityFromStream :
+   + "not implemented" notification if accessibility constraints given
+
+171005 Martin Mann :
+ * configure.ac :
+   + disable-log-coloring : sets INTARNA_LOG_COLORING for console log coloring
+ * bin/IntaRNA :
+   * colored log output depends now on INTARNA_LOG_COLORING macro
+ * IntaRNA/AccessibilityVrna :
+   + callbackForStorage() : callback function to use new VRNA API
+   * fillByRNAplfold() : window-based PU computation via new VRNA API
+
+171004 Martin Mann :
+ * configure.ac :
+   * bump minimal ViennaRNA version to 2.4.1 (for constraint interface) 
+   * bump easylogging++ version to 9.95
+   + easylogging preprocessor macros to get new version compiled
+ + src/easylogging++.cc : source code of new easylogging++ version
+ + src/easylogging++.LICENCE.txt : licence information of easylogging++
+ + lib 'easylogging' since new version comes with source file
+ * tests : adaptation to new easylogging++ version and library
+ * bin/IntaRNA : 
+   * adaptation to new easylogging++ version and library
+
 version 2.0.5
 
 170926 Martin Mann :

README.md

@@ -71,6 +71,7 @@ The following topics are covered by this documentation:
   - [Prediction modes, their features and emulated tools](#predModes)
   - [Interaction restrictions](#interConstr)
   - [Seed constraints](#seed)
+  - [Explicit seed input](#seedExplicit)
   - [Output modes](#outmodes)
   - [Suboptimal RNA-RNA interaction prediction and output restrictions](#subopts)
   - [Energy parameters and temperature](#energy)
@@ -129,7 +130,7 @@ dependencies:
     - libboost_program_options
     - libboost_filesystem
     - libboost_system
-- [Vienna RNA package](http://www.tbi.univie.ac.at/RNA/) version >= 2.3.0
+- [Vienna RNA package](http://www.tbi.univie.ac.at/RNA/) version >= 2.4.1
 - if [cloning from github](#instgithub): GNU autotools (automake, autoconf, ..)
 
 Also used by IntaRNA, but already part of the source code distribution (and thus
@@ -295,6 +296,7 @@ to balance predication quality and runtime requirement. Furthermore, it is
 possible to define 
 [interaction restrictions](#interConstr),
 [seed constraints](#seed), 
+[explicit seed information](#seedExplicit), 
 [output modes](#outmodes),
 [suboptimal enumeration](#subopts), 
 [energy parameters, temperature](#energy),
@@ -374,6 +376,7 @@ of equal length *n*.
 | Time complexity (prediction only) | O(*n*^2) | O(*n*^4) | O(*n*^4) |
 | Space complexity | O(*n*^2) | O(*n*^2) | O(*n*^4) |
 | [Seed constraint](#seed) | x | x | x |
+| [Explicit seeds](#seedExplicit) | x | x | x |
 | No [seed constraint](#seed) | x | x | x |
 | Minimum free energy interaction | not guaranteed | x | x |
 | Overlapping [suboptimal interactions](#subopts) | x | x | x |
@@ -487,6 +490,34 @@ Seed constraint usage can be globally disabled using the `--noSeed` flag.
 
 
 
+<br /><br />
+<a name="seedExplicit" />
+## Explicit seed input
+
+Some experiments provide hints or explicit knowledge about the seed or
+even provide details about some intermolecular base pairs formed between two RNAs.
+This information can be incorporated into IntaRNA predictions by providing
+*explicit seed information*. To this end, the `--seedQT` parameter can be used.
+It takes a comma-separated list of seed string encodings in the format 
+`startTbpsT&startQbpsQ`, which is in the same format as the IntaRNA `hybridDB`
+output (see below), i.e. e.g. `4|||.|&7||.||` to encode a seed interaction like 
+the following 
+```bash
+target
+             4    8
+             |    |
+      5'-AAAC    C UGGUUUGG-3'
+             AC C C
+             || | |
+             UG G G
+      3'-GGUU  U   CCCACAAA-5'
+             |    |
+            11    7
+query
+```
+If several or alternative seeds are known, you can provide all as a 
+comma-separated list and IntaRNA will consider all interactions that cover at
+least one of them.
 
 
 <br /><br />

configure.ac

@@ -2,13 +2,13 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT( [IntaRNA], [2.0.5], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT( [IntaRNA], [2.1.0], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 
 # minimal required version of the boost library 
 BOOST_REQUIRED_VERSION=1.50.0
 # minimal required version of the Vienna RNA library
-VRNA_REQUIRED_VERSION=2.3.0
+VRNA_REQUIRED_VERSION=2.4.1
 
 
 AC_CANONICAL_HOST
@@ -175,8 +175,36 @@ AS_IF([test "x$HAVE_DOXYGEN" = "xyes"], [
 ])
 
 ###############################################################################
+# EASYLOGGING++
 ###############################################################################
 
+# enable easylogging++ performance tracking
+AM_CXXFLAGS="$AM_CXXFLAGS -DELPP_FEATURE_PERFORMANCE_TRACKING"
+# disable default log file creation
+AM_CXXFLAGS="$AM_CXXFLAGS -DELPP_NO_DEFAULT_LOG_FILE"
+
+#############################
+# COLORING SETUP
+#############################
+
+AC_MSG_CHECKING([whether to enable coloring of console log output])
+logColoring=yes
+AC_ARG_ENABLE([log-coloring],
+	[AS_HELP_STRING([--disable-log-coloring],
+	    [disable console log coloring (def=enabled)])],
+  	[logColoring="$enableval"])
+AC_MSG_RESULT([$logColoring])
+AS_IF([test x"$logColoring" = x"yes"], [
+	AC_DEFINE([INTARNA_LOG_COLORING], [1], [Enabling console log coloring])
+	AC_SUBST([INTARNA_LOG_COLORING],[1])
+], [
+	AC_DEFINE([INTARNA_LOG_COLORING], [0], [Disabling console log coloring])
+	AC_SUBST([INTARNA_LOG_COLORING],[0])
+])
+
+
+
+###############################################################################
 
 ###############################################################################
 # BOOST CHECK

src/IntaRNA/AccessibilityBasePair.cpp

@@ -15,14 +15,20 @@ AccessibilityBasePair::AccessibilityBasePair(const RnaSequence& seq,
       logPu(seq.size(), seq.size()),
       basePairEnergy(bpEnergy),
       RT(_RT),
-      basePairWeight(std::exp(-bpEnergy / _RT)),
+      basePairWeight( _RT == 0.0 ? 0.0 : std::exp(-bpEnergy / _RT) ),
       minLoopLength(minLoopLen)
 {
+	if (accConstr_ != NULL && !accConstr_->isEmpty()) {
+		INTARNA_NOT_IMPLEMENTED("AccessibilityBasePair: accessibility constraints not supported yet");
+	}
+	if (RT == 0.0) {
+		throw std::runtime_error("AccessibilityBasePair: RT == 0.0");
+	}
   const size_t N = seq.size();
   // create temporary matrices for ED computation
   NussinovHandler::E2dMatrix Q(N, N);
   NussinovHandler::E2dMatrix Qb(N, N);
-  NussinovHandler::P2dMatrix Ppb(N, N);
+  NussinovHandler::P2dMatrix Pbp(N, N);
   NussinovHandler::P2dMatrix Pu(N, N);
 
   logPu.resize(N, N);
@@ -32,14 +38,14 @@ AccessibilityBasePair::AccessibilityBasePair(const RnaSequence& seq,
     for (size_t j = i; j < N; ++j) {
       Q(i, j) = -1.0;
       Qb(i, j) = -1.0;
-      Ppb(i, j) = -1.0;
+      Pbp(i, j) = -1.0;
       Pu(i, j) = -1.0;
     }
   }
   // compute ED values
   for (size_t i = 0u; i < N; ++i) {
     for (size_t j = i; j < N; ++j) {
-      logPu(i, j) = -RT * std::log(NussinovHandler::getPu(i, j, seq, basePairWeight, minLoopLength, Q, Qb, Ppb, Pu));
+      logPu(i, j) = -RT * std::log(NussinovHandler::getPu(i, j, seq, basePairWeight, minLoopLength, Q, Qb, Pbp, Pu));
     }
   }
 }

src/IntaRNA/AccessibilityFromStream.cpp

@@ -21,6 +21,9 @@ AccessibilityFromStream(
 	, edValues()
 	, availMaxLength( Accessibility::getMaxLength() )
 {
+	if (accConstraint != NULL && !accConstraint->isEmpty()) {
+		INTARNA_NOT_IMPLEMENTED("AccessibilityFromStream: accessibility constraints not supported yet");
+	}
 	switch( inStreamType ) {
 
 	case Pu_RNAplfold_Text :