Merge pull request #74 from jlab/codestyle

sjanssen2 · web-flow · commit 4236ed095dbc · 2024-07-10T21:22:29.000+02:00
adding auto tikz algebra to grammars + fixing whitespace to be compat…
diff --git a/Algebras/Pfunc/alg_pknot_pfunc.gap b/Algebras/Pfunc/alg_pknot_pfunc.gap
@@ -1,6 +1,6 @@
-//Eine Partition Function f�r Pseudoknoten so wie wir sie definieren (pknotsRG) kann garnicht richtig sein, denn
-// 1) verwenden wir ja absichtlich nur canonische / repr�sentative Pseudoknoten und nicht alle im Suchraum (potentiell m�ssten die Wahrscheinlichkeiten also untersch�tzt werden)
-// 2) die Dangles von au�en auf die beiden PK Stems werden nicht korrekt addiert. Um diese f�r MFE richtig berechnen zu k�nnen werden die Indizes der inneren Basenpaar-Partner mitgeschleppt um sp�ter den Dangle berechnen zu k�nnen. Bei Pfunc wird aber einfach die Summe �ber alle verschiedenen Indizes genommen und darauf dann nur EINE Art von Dangling berechnet!
+//Eine Partition Function fuer Pseudoknoten so wie wir sie definieren (pknotsRG) kann garnicht richtig sein, denn
+// 1) verwenden wir ja absichtlich nur canonische / repraesentative Pseudoknoten und nicht alle im Suchraum (potentiell muessten die Wahrscheinlichkeiten also unterschaetzt werden)
+// 2) die Dangles von aussen auf die beiden PK Stems werden nicht korrekt addiert. Um diese fuer MFE richtig berechnen zu koennen werden die Indizes der inneren Basenpaar-Partner mitgeschleppt um spaeter den Dangle berechnen zu koennen. Bei Pfunc wird aber einfach die Summe ueber alle verschiedenen Indizes genommen und darauf dann nur EINE Art von Dangling berechnet!
 // im Moment braucht das generierte Programm noch einen manuellen Schuppser: in X.hh muss folgendes an passender Stelle eingefuegt werden:
 //answer_pknot_pfunc operator+=(const answer_pknot_pfunc &other) const
 //{
diff --git a/Misc/Applications/pAliKiss/ali_pknot_stems.gap b/Misc/Applications/pAliKiss/ali_pknot_stems.gap
@@ -18,7 +18,7 @@ acgucgaaauaaaugccuugucugcuauauucgacgcgagcuuaauauuuggggcc
 .[[[[[[[......{{{{{{.........]]]]]]].............}}}}}}.
 */
 
-signature sig_stack(alphabet,answer) {
+signature sig_stack(alphabet, answer) {
 	answer sr(Subsequence, answer, Subsequence);
 	answer end(Subsequence);
 	choice [answer] h([answer]);
diff --git a/Misc/Applications/pKiss/pknot_stems.gap b/Misc/Applications/pKiss/pknot_stems.gap
@@ -13,7 +13,7 @@ acgucgaaauaaaugccuugucugcuauauucgacgcgagcuuaauauuuggggcc
 .[[[[[[[......{{{{{{.........]]]]]]].............}}}}}}.
 */
 
-signature sig_stack(alphabet,answer) {
+signature sig_stack(alphabet, answer) {
 	answer sr(Subsequence, answer, Subsequence);
 	answer end(Subsequence);
 	choice [answer] h([answer]);
diff --git a/Misc/Test-Suite/StefanStyle/generate_ambig_seqs.gap b/Misc/Test-Suite/StefanStyle/generate_ambig_seqs.gap
@@ -6,7 +6,8 @@
 
   In order to ensure that ViennaRNA -d1 and microstate and macrostate assign same energies, I here define a grammar generating RNA input sequences for amibiguous situations.
 */
-signature sig_genseq(alphabet,answer) {
+
+signature sig_genseq(alphabet, answer) {
   //answer mladldr(alphabet, answer, answer, answer, answer, alphabet);
   answer cadd_Amb_Amb(answer, answer);
   answer cadd_Amb_Nor(answer, alphabet, answer, alphabet);
diff --git a/Signatures/sig_cofold_foldrna.gap b/Signatures/sig_cofold_foldrna.gap
@@ -1,4 +1,4 @@
-signature sig_foldrna(alphabet,answer) {
+signature sig_foldrna(alphabet, answer) {
 	include "Signatures/Parts/sigpart_basic.gap"
 	include "Signatures/Parts/sigpart_cofold.gap"
 	
diff --git a/Signatures/sig_foldrna.gap b/Signatures/sig_foldrna.gap
@@ -1,4 +1,4 @@
-signature sig_foldrna(alphabet,answer) {
+signature sig_foldrna(alphabet, answer) {
 	include "Signatures/Parts/sigpart_basic.gap"
 	
 //microstate extensions:
diff --git a/Signatures/sig_outside_foldrna.gap b/Signatures/sig_outside_foldrna.gap
@@ -1,4 +1,4 @@
-signature sig_outside_foldrna(alphabet,answer) {
+signature sig_outside_foldrna(alphabet, answer) {
 	include "Signatures/Parts/sigpart_basic.gap"
 	
 //outside extensions:
diff --git a/ali_macrostate.gap b/ali_macrostate.gap
@@ -23,6 +23,7 @@ include "Algebras/Pfunc/alg_ali_pfunc_macrostate.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_mfe_macrostate.gap"
 
diff --git a/ali_microstate.gap b/ali_microstate.gap
@@ -25,6 +25,7 @@ include "Algebras/alg_ali_consensus.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_mfe.gap"
 
diff --git a/ali_nodangle.gap b/ali_nodangle.gap
@@ -24,6 +24,7 @@ include "Algebras/Pfunc/alg_ali_pfunc.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_mfe.gap"
 include "Grammars/gra_nodangle.gap"
diff --git a/ali_outside_microstate.gap b/ali_outside_microstate.gap
@@ -13,6 +13,7 @@ include "Algebras/DotBracket/alg_ali_outside_dotBracket.gap"
 
 algebra alg_ali_outside_count auto count;
 algebra alg_ali_outside_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_outside_mfe.gap"
 include "Algebras/Pfunc/alg_ali_outside_pfunc.gap"
diff --git a/ali_outside_nodangle.gap b/ali_outside_nodangle.gap
@@ -13,6 +13,7 @@ include "Algebras/DotBracket/alg_ali_outside_dotBracket.gap"
 
 algebra alg_ali_outside_count auto count;
 algebra alg_ali_outside_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_outside_mfe.gap"
 include "Algebras/Pfunc/alg_ali_outside_pfunc.gap"
diff --git a/ali_outside_overdangle.gap b/ali_outside_overdangle.gap
@@ -13,6 +13,7 @@ include "Algebras/DotBracket/alg_ali_outside_dotBracket.gap"
 
 algebra alg_ali_outside_count auto count;
 algebra alg_ali_outside_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_outside_mfe.gap"
 
diff --git a/ali_overdangle.gap b/ali_overdangle.gap
@@ -25,6 +25,7 @@ include "Algebras/Shapes/alg_ali_shapes.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_ali_mfe.gap"
 include "Algebras/MFE/alg_ali_puremfe.gap"
diff --git a/ali_pKiss.gap b/ali_pKiss.gap
@@ -28,6 +28,8 @@ include "Signatures/sig_pknot_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/DotBracket/alg_ali_pknot_dotBracket.gap"
 include "Algebras/MFE/alg_ali_pknot_mfe.gap"
 include "Algebras/Pfunc/alg_ali_pknot_pfunc.gap"
diff --git a/cofold_nodangle.gap b/cofold_nodangle.gap
@@ -23,6 +23,7 @@ include "Algebras/Shapes/alg_shapes_rope.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_cofold_mfe.gap"
 include "Algebras/alg_cofold.gap"
diff --git a/eval_ali_macrostate.gap b/eval_ali_macrostate.gap
@@ -14,6 +14,8 @@ include "Signatures/sig_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/MFE/alg_ali_mfe_macrostate.gap"
 include "Algebras/Shapes/alg_ali_shapes.gap"
 include "Algebras/DotBracket/alg_ali_dotBracket.gap"
diff --git a/eval_ali_microstate.gap b/eval_ali_microstate.gap
@@ -14,6 +14,8 @@ include "Signatures/sig_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/MFE/alg_ali_mfe.gap"
 include "Algebras/Shapes/alg_ali_shapes.gap"
 include "Algebras/DotBracket/alg_ali_dotBracket.gap"
diff --git a/eval_ali_nodangle.gap b/eval_ali_nodangle.gap
@@ -14,6 +14,8 @@ include "Signatures/sig_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/MFE/alg_ali_mfe.gap"
 include "Algebras/Shapes/alg_ali_shapes.gap"
 include "Algebras/DotBracket/alg_ali_dotBracket.gap"
diff --git a/eval_ali_overdangle.gap b/eval_ali_overdangle.gap
@@ -14,6 +14,8 @@ include "Signatures/sig_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/MFE/alg_ali_mfe.gap"
 include "Algebras/Shapes/alg_ali_shapes.gap"
 include "Algebras/DotBracket/alg_ali_dotBracket.gap"
diff --git a/eval_ali_pKiss.gap b/eval_ali_pKiss.gap
@@ -20,6 +20,8 @@ include "Signatures/sig_pknot_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/DotBracket/alg_ali_pknot_dotBracket.gap"
 include "Algebras/Shapes/alg_ali_pknot_shapes.gap"
 algebra alg_ali_pknot_dotBracket_id extends alg_ali_pknot_dotBracket {
diff --git a/eval_macrostate.gap b/eval_macrostate.gap
@@ -17,6 +17,7 @@ include "Algebras/Shapes/alg_shapes.gap"
 include "Algebras/DotBracket/alg_dotBracket.gap"
 algebra alg_count auto count ;
 algebra alg_enum auto enum ;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_macrostate.gap"
 
diff --git a/eval_microstate.gap b/eval_microstate.gap
@@ -18,6 +18,7 @@ algebra alg_dotBracket_id extends alg_dotBracket {
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_microstate.gap"
 
diff --git a/eval_nodangle.gap b/eval_nodangle.gap
@@ -12,6 +12,7 @@ include "Algebras/Shapes/alg_shapes.gap"
 include "Algebras/MFE/alg_mfe.gap"
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_nodangle.gap"
 
diff --git a/eval_overdangle.gap b/eval_overdangle.gap
@@ -11,6 +11,7 @@ include "Algebras/Shapes/alg_shapes.gap"
 include "Algebras/MFE/alg_mfe.gap"
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_overdangle.gap"
 
diff --git a/eval_pKiss.gap b/eval_pKiss.gap
@@ -17,6 +17,8 @@ include "Signatures/sig_pknot_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/DotBracket/alg_pknot_dotBracket.gap"
 include "Algebras/Shapes/alg_pknot_shapes.gap"
 algebra alg_pknot_dotBracket_id extends alg_pknot_dotBracket {
diff --git a/g5compatibilityCheck.gap b/g5compatibilityCheck.gap
@@ -1,6 +1,7 @@
 include "Signatures/sig_g5compatibilityCheck.gap"
 
 algebra alg_g5compatibilityCheck_count auto count;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_g5compatibilityCheck.gap"
 
diff --git a/knotInFrame.gap b/knotInFrame.gap
@@ -20,6 +20,8 @@ include "Signatures/sig_pknot_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/DotBracket/alg_pknot_dotBracket.gap"
 include "Algebras/MFE/alg_pknot_mfe.gap"
 include "Algebras/Pfunc/alg_pknot_pfunc.gap"
diff --git a/macrostate.gap b/macrostate.gap
@@ -26,9 +26,14 @@ include "Algebras/Probing/alg_probing_macrostate.gap" //an algebra for integrati
 
 algebra alg_count auto count ;
 algebra alg_enum auto enum ;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_macrostate.gap"
 
+/*
+example inputs: CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGACCA
+*/
+
 //start: instances used in the FoldingSpaces paper
 instance shape5pfx = gra_macrostate ((alg_shape5 * alg_pfunc) suchthat filterLowProbShapes);
 instance shape4pfx = gra_macrostate ((alg_shape4 * alg_pfunc) suchthat filterLowProbShapes);
diff --git a/macrostateCenter.gap b/macrostateCenter.gap
@@ -12,7 +12,7 @@ type shape_t = shape
 type base_t = extern
 type Rope = extern
 
-signature sig_foldrna(alphabet,answer) {
+signature sig_foldrna(alphabet, answer) {
 	answer sadd(Subsequence,answer);
 	answer cadd(answer,answer);
 	answer cadd_Pr(answer,answer);
@@ -706,9 +706,10 @@ algebra alg_HairpinCenter implements sig_foldrna(alphabet = char, answer = strin
 
 algebra alg_count auto count ;
 algebra alg_enum auto enum ;
+algebra alg_tikz auto tikz;
 
 include "Grammars/gra_macrostate_centers.gap"
 
 instance count = gra_macrostate_centers (alg_count);
 instance enum = gra_macrostate_centers (alg_enum);
-instance centerpfx = gra_macrostate_centers(alg_HairpinCenter * alg_pfunc_macrostate);
+instance centerpfx = gra_macrostate_centers(alg_HairpinCenter * alg_pfunc_macrostate);
diff --git a/microstate.gap b/microstate.gap
@@ -18,6 +18,7 @@ include "Algebras/Shapes/alg_shapes.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_mfe.gap"
 include "Algebras/MEA/alg_mea.gap"
@@ -32,6 +33,10 @@ algebra alg_mfe_id extends alg_mfe {
 
 include "Grammars/gra_microstate.gap"
 
+/*
+example inputs: CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGACCA
+*/
+
 //start: instances used in the FoldingSpaces paper
 instance shape5pfx = gra_microstate ((alg_shape5 * alg_pfunc) suchthat filterLowProbShapes);
 instance shape4pfx = gra_microstate ((alg_shape4 * alg_pfunc) suchthat filterLowProbShapes);
diff --git a/nodangle.gap b/nodangle.gap
@@ -18,6 +18,7 @@ include "Algebras/Shapes/alg_shapes.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_mfe.gap"
 include "Algebras/MEA/alg_mea.gap"
@@ -27,6 +28,10 @@ include "Algebras/MFE/alg_mfe_SHAPE.gap"
 
 include "Grammars/gra_nodangle.gap"
 
+/*
+example inputs: CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGACCA
+*/
+
 //start: instances used in the FoldingSpaces paper
 instance shape5pfx = gra_nodangle ((alg_shape5 * alg_pfunc) suchthat filterLowProbShapes);
 instance shape4pfx = gra_nodangle ((alg_shape4 * alg_pfunc) suchthat filterLowProbShapes);
diff --git a/outside_microstate.gap b/outside_microstate.gap
@@ -10,6 +10,7 @@ include "Algebras/DotBracket/alg_outside_dotBracket.gap"
 
 algebra alg_outside_count auto count;
 algebra alg_outside_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_outside_mfe.gap"
 include "Algebras/Pfunc/alg_outside_pfunc.gap"
diff --git a/outside_nodangle.gap b/outside_nodangle.gap
@@ -10,6 +10,7 @@ include "Algebras/DotBracket/alg_outside_dotBracket.gap"
 
 algebra alg_outside_count auto count;
 algebra alg_outside_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_outside_mfe.gap"
 include "Algebras/Pfunc/alg_outside_pfunc.gap"
diff --git a/outside_overdangle.gap b/outside_overdangle.gap
@@ -10,6 +10,7 @@ include "Algebras/DotBracket/alg_outside_dotBracket.gap"
 
 algebra alg_outside_count auto count;
 algebra alg_outside_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_outside_mfe.gap"
 include "Algebras/Pfunc/alg_outside_pfunc.gap"
diff --git a/overdangle.gap b/overdangle.gap
@@ -20,6 +20,7 @@ include "Algebras/Shapes/alg_hishapes.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/MFE/alg_mfe.gap"
 include "Algebras/MFE/alg_mfe_SHAPE.gap"
@@ -32,6 +33,10 @@ include "Algebras/Pfunc/alg_pfunc.gap"
 
 include "Grammars/gra_overdangle.gap"
 
+/*
+example inputs: CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGACCA
+*/
+
 //start: instances used in the FoldingSpaces paper
 instance shape5pfx = gra_overdangle ((alg_shape5 * alg_pfunc) suchthat filterLowProbShapes);
 instance shape4pfx = gra_overdangle ((alg_shape4 * alg_pfunc) suchthat filterLowProbShapes);
diff --git a/pKiss.gap b/pKiss.gap
@@ -25,6 +25,8 @@ include "Signatures/sig_pknot_foldrna.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
+
 include "Algebras/DotBracket/alg_pknot_dotBracket.gap"
 include "Algebras/MFE/alg_pknot_mfe.gap"
 include "Algebras/Pfunc/alg_pknot_pfunc.gap"
diff --git a/structure2shape.gap b/structure2shape.gap
@@ -3,7 +3,7 @@ import "Extensions/rnaoptions_defaults.hh"
 type shape_t = shape
 
 //copied from "Signatures/sig_foldrna.gap", replaced terminal data type with "alphabet" and removed function not necessary in a NoDangle style grammar
-signature sig_db2shape(alphabet,answer) {
+signature sig_db2shape(alphabet, answer) {
 	answer sadd(alphabet,answer); //add one unpaired base
 	answer cadd(answer,answer); //adds one component, which has dangling bases from both sides, next component has a dangling base from left
 	answer nil(Subsequence); //empty structure
@@ -22,6 +22,7 @@ signature sig_db2shape(alphabet,answer) {
 
 algebra alg_enum auto enum ;
 algebra alg_count auto count ;
+algebra alg_tikz auto tikz;
 
 //copied from "Algebras/Shapes/alg_shapes.gap", replaced terminal data type alphabet with "char" and removed function not necessary in a NoDangle style grammar
 algebra alg_shapeX implements sig_db2shape(alphabet = char, answer = shape_t) {
diff --git a/tdmGenerator.gap b/tdmGenerator.gap
@@ -9,6 +9,7 @@ include "Signatures/sig_tdm.gap"
 
 algebra alg_count auto count;
 algebra alg_enum auto enum;
+algebra alg_tikz auto tikz;
 
 include "Algebras/alg_tdm.gap" //provides 20 algebras to generate the B-GAP grammar code for a TDM: available grammars are nodangle, overdangle, microstate and macrostate. Available shape levels: 5 to 1. Naming: alg_tdm_GRAMMAR_LEVEL
 include "Grammars/gra_tdm.gap" //provides 6 grammars to parse a shape string of a specific level for an arbitraty grammar. Why 6 for 5 shape levels? Because grammars for level 4 and 3 are identical -1 and we need two special versions in level 1 for microstate and macrostate +2

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-signature sig_foldrna(alphabet,answer) {`
	`1`	`+signature sig_foldrna(alphabet, answer) {`
`2`	`2`	`include "Signatures/Parts/sigpart_basic.gap"`
`3`	`3`	`include "Signatures/Parts/sigpart_cofold.gap"`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-signature sig_outside_foldrna(alphabet,answer) {`
	`1`	`+signature sig_outside_foldrna(alphabet, answer) {`
`2`	`2`	`include "Signatures/Parts/sigpart_basic.gap"`
`3`	`3`
`4`	`4`	`//outside extensions:`