Adjust behavior of locarna and mlocarna for pairwise alignments

  -- do not use alifold in binaries when calculating base pairs
     for single sequences
  -- use noLP in mlocarna for calculating base pair probabilties
     /and/ the alignment
  -- increase output precision for probabilities in pp files
     (reducing rounding issues for the typical cutoff)

ChangeLog

@@ -1,6 +1,12 @@
 <<<<<<< HEAD
 === 2018
 
+2.0.0RC6
+	adjust behavior of locarna and mlocarna for pairwise alignments
+	-- do not use alifold in binaries when calculating base pairs for single sequences
+	-- use noLP in mlocarna for calculating base pair probabilties /and/ the alignment
+	-- increase output precision for probabilities in pp files
+	   (reducing rounding issues for the typical cutoff)
 
 2.0.0RC5 (2018-05-08)
 	Allow penalized in global alignment

configure.ac

@@ -2,7 +2,7 @@ dnl                                               -*- Autoconf -*-
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([LocARNA], [2.0.0RC5], [[email protected]], [locarna],
+AC_INIT([LocARNA], [2.0.0RC6], [[email protected]], [locarna],
         [http://www.bioinf.uni-freiburg.de/Software/LocARNA/])
 
 dnl special dir for aux config files

src/LocARNA/rna_data.cc

@@ -55,7 +55,7 @@ namespace LocARNA {
             // recompute all probabilities
             RnaEnsemble rna_ensemble(
                 pimpl_->sequence_, pfoldparams, false,
-                true); // use given parameters, no in loop, use alifold
+                pimpl_->sequence_.num_of_rows()>1); // use given parameters, no in loop, use alifold unless single seq
 
             // initialize from RnaEnsemble; note: method is virtual
             init_from_rna_ensemble(rna_ensemble, pfoldparams);
@@ -152,7 +152,7 @@ namespace LocARNA {
             // recompute all probabilities
             RnaEnsemble rna_ensemble(
                 sequence(), pfoldparams, true,
-                true); // use given parameters, in-loop, use alifold
+                pimpl_->sequence_.num_of_rows()>1); // use given parameters, in-loop, use alifold unless single seq
 
             // initialize
             init_from_rna_ensemble(rna_ensemble, pfoldparams);
@@ -1278,20 +1278,23 @@ namespace LocARNA {
      */
     std::string
     format_prob(double prob) {
+        size_t precision = 4;
+
         std::ostringstream outd;
-        outd.precision(3);
+        outd.precision(precision);
         outd << prob;
 
-        if (outd.str().length() <= 6) {
-            return outd.str();
-        }
+        std::string s = outd.str();
 
-        std::ostringstream outs;
-        outs.setf(std::ios::scientific, std::ios::floatfield);
-        outs.precision(2);
-        outs << prob;
+        if (outd.str().length() > precision+4) {
+            std::ostringstream outs;
+            outs.setf(std::ios::scientific, std::ios::floatfield);
+            outs.precision(precision-1);
+            outs << prob;
+
+            s = outs.str();
+        }
 
-        std::string s = outs.str();
         size_t pos = s.find("e-0");
         if (pos != std::string::npos) {
             s.replace(pos, 3, "e-");

src/LocARNA/rna_data_impl.hh

@@ -11,7 +11,6 @@
 
 namespace LocARNA {
 
-    class MultipleAlignment;
     class RnaEnsemble;
     class PFoldParams;
     //    template<class T> class SparseVector<T>;

src/Tests/mlocarna-threads.testresult

@@ -1,18 +1,18 @@
-CLUSTAL W --- LocARNA 2.0.0RC1
+CLUSTAL W --- LocARNA 2.0.0RC5
 
 
-X58295.1_1384-1453       UGGCGUCU-UCAUGAGGGAGGGGCCCAAAGCC----CUUGUGGGCGGACCUCCCCUGAGCCUGUCUGAGGGGCCA
-D25220.1_1493-1556       CU-UGCGU-UAAUGAGAACAGAAACGAAAACUAUAA-C-CU-AGGGGUUUCUGUUGGAU---GGUU-GGCAAC--
-AY060611.1_560-627       GU-GGCGC-UUAUGACGCAGUUGUCUUAAACUCGAA-CUCG-AGCGGGCAAUUGCUGAUUACGAUU-AACCAC--
-L24896.1_600-665         CC-GGCAC-UCAUGACGGUCUGCCUGAAAACCAGCC-CGCU-GGUGGGGCAGUCCCGAGGAC--CU-GGCGUG--
-AF096875.1_5504-5568     GU-GUG-C-GAAUGAUAACUACUGACGAAAGAGCUGUCUGC-UCAGUCUGUGGUUGGAU---GUAG-UCACAC--
-AF093774.1_5851-5916     GU-GUG-C-GGAUGAUAACUACUGACGAAAGAGUCAUCGACCUCAGUUAGUGGUUGGAU---GUAG-UCACAU--
-AE003628.2_106178-106240 UU-CAA-C-UUAUGAGGAUUAUUUCUUAAAGGCC--UCUGG-CUCGGAAAUAGUCUGAA---CCUU-AUUGUA--
-AC000078.2_21139-21077   GC-CAG-A-UGAUGACGACCUGGGUGGAAACCUACCCUGUG--GGCACCCAUGUCCGAG---CC-C-CCUGGC--
-AF241527.2_359-424       GC-CGC-U-UCAUGACAGGAAGGACUGAAA-UGUCUUAGACCUGUGGUCUUUCCUCGAU---GU-U-CCUGCGGC
-AF333036.1_2190-2249     CA-UGCGU-CCAUGAAGUCACUGGCC----UCAAGCCCAAGUGGUGGGCAGUGACAGA---------AGAGCUGC
-X57999.1_1526-1586       AUAUUUGU-UUAUGAUGGUCACAGUGUAAA-----GUUCAC--ACAGCUGUGACUUGAUU-UUUAA---AAAU--
-X12367.1_703-764         GU-UUU-U-CCAUGACGGUGUUUCCUCUAA-----AUUUAC-AUGGAGAAACACCUGAUU-UCCAG-AAAAAU--
-X13710.1_946-1008        UU-UUCAU-CUAUGAGGGUGUUUCCUCUAA-----ACCUACGAGGGAGGAACACCUGAUC-U-UAC-AGAAAA--
-AF322071.1_1577-1642     AUGUGGUCUUUAUGAAGGCAGGUGCAGAAACUAUGCACUAGUGG-UGUC--UGUCUGAU---GUUUGGCCAU---
-AC002327.1_156204-156268 --CUCAGCAGGAUGAUGAGAAGGGCUGAAAUGCUGC-CAAACCA-GGUCCUUUUCUGAU---GGUGGCUGGG---
+X58295.1_1384-1453       --UGGCGUCUUCAUGAGGGAGGGGCCCAAAGCC----CUUGUGGGCGGACCUCCCCUGAGCCUGUCUGAGGGGCCA
+AC000078.2_21139-21077   --GC-CAG-AUGAUGACGACCUGGGUGGAAACCUACCCUGUG--GGCACCCAUGUCCGA---GCCCCCU--GGC--
+AE003628.2_106178-106240 --UU-CAA-CUUAUGAGGAUUAUUUCUUAAA-GGCCUCUGGC--UCGGAAAUAGUCUGA---ACCUUAU--UGUA-
+AF241527.2_359-424       --GC-CGC-UUCAUGACAGGAAGGACUGAAA-UGUCUUAGACCUGUGGUCUUUCCUCGA---UGUUCCU--GCGGC
+AF096875.1_5504-5568     --GU-GUG-CGAAUGAUAACUACUGACGAAAGAGCUGUCUGC-UCAGUCUGUGGUUGGA---UG-UAGU--CACAC
+AF093774.1_5851-5916     --GU-GUG-CGGAUGAUAACUACUGACGAAAGAGUCAUCGACCUCAGUUAGUGGUUGGA---UG-UAGU--CACAU
+D25220.1_1493-1556       --CU-UGCGUUAAUGAGAACAGAAACGAAAACUAUAAC--CU-AGGGGUUUCUGUUGGA---U---GGUUGGCAAC
+AY060611.1_560-627       --GU-GGCGCUUAUGACGCAGUUGUCUUAAACUCGAAC-UCG-AGCGGGCAAUUGCUGA---UUACGAUUAACCAC
+L24896.1_600-665         --CC-GGCACUCAUGACGGUCUGCCUGAAAACCAGCCC-GCU-GGUGGGGCAGUCCCGA---GGAC--CUGGCGUG
+AF333036.1_2190-2249     --CA-UGCGUCCAUGAAGUCACUGGCC----UCAAGCCCAAGUGGUGGGCAGUGACAGA---AGA------GCUGC
+X12367.1_703-764         --GU-UUU-UCCAUGACGGUGUUUCCUCUAA-----AUUUAC-AUGGAGAAACACCUGA---UUUCCAG-AAAAAU
+X13710.1_946-1008        --UU-UUCAUCUAUGAGGGUGUUUCCUCUAA-----ACCUACGAGGGAGGAACACCUGA---UCU-UAC-AGAAAA
+X57999.1_1526-1586       --AUAUUUGUUUAUGAUGGUCACAGUGUAAA-----GUUCAC--ACAGCUGUGACUUGA---UUUUUAA---AAAU
+AF322071.1_1577-1642     AUGU-GGUCUUUAUGAAGGCAGGUGCAGAAACUAUGCA--CUAGU-GGUGUCUGUCUGA------UGUUUGGCCAU
+AC002327.1_156204-156268 --CU-CAGCAGGAUGAUGAGAAGGGCUGAAAUGCUGCC--AAACCAGGUCCUUUUCUGA------UGGUGGCUGGG

src/Utils/mlocarna

@@ -1076,7 +1076,8 @@ my %opts;
 ## some default values
 #
 
-$opts{'noLP'}=1;
+# handle noLP / LP later
+# $opts{'noLP'}=1;
 
 $opts{'skip-pp'}=0; ## =1 skips the computation of pair probabilities
                     ## for files that exist already
@@ -1274,15 +1275,16 @@ if (defined($opts{'evaluate'})) {
     exit 0;
 }
 
+# LP and noLP should never both be given on the command line
 if (defined($opts{'LP'}) && defined($opts{'noLP'})) {
-    printerr "Only one of the options --noLP and --LP can be defined at a time.\n";
-    pod2usage(1);
+    printerr "ERROR: The flags --noLP and --LP contradict each other.\n";
+    exit(-1);
 }
 
+# this makes noLP the default, unless LP is given
 if (defined($opts{'LP'})) {
     $opts{'noLP'}=0;
-}
-if (defined($opts{'noLP'})) {
+} else {
     $opts{'noLP'}=1;
 }
 
@@ -2903,6 +2905,10 @@ sub compute_dotplot_rnafold_pp {
 
     my @fold_cmd = ( "$bindir/locarna_rnafold_pp", "-p" => $opts{'min-prob'} );
 
+    if ($opts{'noLP'}) {
+        push @fold_cmd, "--noLP";
+    }
+
     if ($opts{'in-loop-robabilities'}) {
         push @fold_cmd, "--in-loop";
     }
@@ -2981,6 +2987,10 @@ sub compute_dotplot_rnafold {
     my @fold_cmd = ("$RNAfold", "-p2");
     push  @fold_cmd, @RNAfold_args;
 
+    if ($opts{'noLP'}) {
+        push @fold_cmd, '--noLP';
+    }
+
     my $seq_str = $seq->{seq}; ## the sequence string
 
     my $input = ">$tmpname\n$seq_str\n";
@@ -3022,6 +3032,10 @@ sub compute_dotplot_rnaplfold {
       "-L" => $opts{'plfold-span'},
       "-W" => $opts{'plfold-winsize'}, @RNAfold_args;
 
+    if ($opts{'noLP'}) {
+        push @fold_cmd, '--noLP';
+    }
+
     my $slen=length($seq_str);
     my $win = $slen;
     for (my $i=0; $i < @fold_cmd; $i++) {