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Basepair probs #217

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Basepair probs #217

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Commits on Jun 22, 2019

  1. PredictionTrackerBasePairProb layout

    @Fulanko
    Fulanko committed Jun 22, 2019
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Commits on Jun 23, 2019

  1. added base-pair probability recursion

    @Fulanko
    Fulanko committed Jun 23, 2019
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Commits on Jun 29, 2019

  1. updated PredictionTrackerBasePairProb + added dot plot (probabilities… 

    … still incorrect)
    @Fulanko
    Fulanko committed Jun 29, 2019
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  2. fixed overallHybridizationZ

    @Fulanko
    Fulanko committed Jun 29, 2019
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Commits on Jul 1, 2019

  1. code cleanup

    @Fulanko
    Fulanko committed Jul 1, 2019
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  2. fixed probabilities of > 1

    @Fulanko
    Fulanko committed Jul 1, 2019
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Commits on Jul 14, 2019

  1. various fixes and cleanup in PredictionTrackerBasePairProb

    @Fulanko
    Fulanko committed Jul 14, 2019
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Commits on Jul 23, 2019

  1. added versions to postscript comment

    @Fulanko
    Fulanko committed Jul 23, 2019
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Commits on Aug 27, 2019

  1. added code for seedbased base-pair probs (Not working correctly)

    @Fulanko
    Fulanko committed Aug 27, 2019
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Commits on Sep 13, 2019

  1. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Sep 13, 2019
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  2. rebase fixes

    @Fulanko
    Fulanko committed Sep 13, 2019
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  3. fixed some missing changes

    @Fulanko
    Fulanko committed Sep 13, 2019
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  4. Merge branch 'dev' into basepair-probs 

    # Conflicts:
#	src/IntaRNA/PredictorMfeEnsSeedOnly.cpp
    @Fulanko
    Fulanko committed Sep 13, 2019
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Commits on Sep 14, 2019

  1. added test for Zall

    @Fulanko
    Fulanko committed Sep 14, 2019
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  2. refactored predictionTrackerBasePairProb

    @Fulanko
    Fulanko committed Sep 14, 2019
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  3. changed getZ -> getHybridZ + added default argument to reportZ

    @Fulanko
    Fulanko committed Sep 14, 2019
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Commits on Sep 15, 2019

  1. fixed basepairProb tracker bugs + added test

    @Fulanko
    Fulanko committed Sep 15, 2019
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  2. refactor

    @Fulanko
    Fulanko committed Sep 15, 2019
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Commits on Sep 17, 2019

  1. added script for basepair prob dot plots

    @Fulanko
    Fulanko committed Sep 17, 2019
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  2. fixed reversed sequence in dotplot

    @Fulanko
    Fulanko committed Sep 17, 2019
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Commits on Sep 18, 2019

  1. added python script to compute concentrations of homo/hetero dimers

    @Fulanko
    Fulanko committed Sep 18, 2019
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  2. input validation

    @Fulanko
    Fulanko committed Sep 18, 2019
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Commits on Sep 19, 2019

  1. outer loop changes

    @Fulanko
    Fulanko committed Sep 19, 2019
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  2. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Sep 19, 2019
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  3. renamed test + changed IntaRNA_precisionEpsilon

    @Fulanko
    Fulanko committed Sep 19, 2019
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  4. renamed test

    @Fulanko
    Fulanko committed Sep 19, 2019
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  5. changed dotplot template to inline string

    @Fulanko
    Fulanko committed Sep 19, 2019
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  6. intaRNAtube.py refactoring

    @Fulanko
    Fulanko committed Sep 19, 2019
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Commits on Sep 20, 2019

  1. added outline of intaRNA prediction to dotplot

    @Fulanko
    Fulanko committed Sep 20, 2019
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  2. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Sep 20, 2019
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  3. added tests for predictionTrackerBasePairProb

    @Fulanko
    Fulanko committed Sep 20, 2019
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  4. reverted bp prob loop restrictions

    @Fulanko
    Fulanko committed Sep 20, 2019
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Commits on Sep 22, 2019

  1. updated prediction Tracker + added tests

    @Fulanko
    Fulanko committed Sep 22, 2019
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  2. fixed bpPropTracker no seed

    @Fulanko
    Fulanko committed Sep 22, 2019
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Commits on Sep 23, 2019

  1. fixed some base pair prob tests

    @Fulanko
    Fulanko committed Sep 23, 2019
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  2. added leftIndex to bp tracker + fixed dotplot dashing

    @Fulanko
    Fulanko committed Sep 23, 2019
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  3. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Sep 23, 2019
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  4. refactored predictionTracker code for seed-based predictions

    @Fulanko
    Fulanko committed Sep 23, 2019
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Commits on Sep 24, 2019

  1. refactoring

    @Fulanko
    Fulanko committed Sep 24, 2019
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Commits on Sep 26, 2019

  1. added non-dotted line every 10th line in dotplot

    @Fulanko
    Fulanko committed Sep 26, 2019
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  2. reverted Zall changes

    @Fulanko
    Fulanko committed Sep 26, 2019
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Commits on Sep 28, 2019

  1. implemented left-index based prediction (performance improvement)

    @Fulanko
    Fulanko committed Sep 28, 2019
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Commits on Sep 29, 2019

  1. removed unneeded loops in bp prob computation + minor fixes for seed-… 

    …based computation
    @Fulanko
    Fulanko committed Sep 29, 2019
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Commits on Oct 2, 2019

  1. minor changes

    @martin-raden
    martin-raden committed Oct 2, 2019
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  2. simplify

    @martin-raden
    martin-raden committed Oct 2, 2019
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  3. cleanup + todos

    @martin-raden
    martin-raden committed Oct 2, 2019
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  4. comments

    @martin-raden
    martin-raden committed Oct 2, 2019
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  5. comments

    @martin-raden
    martin-raden committed Oct 2, 2019
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  6. comments

    @martin-raden
    martin-raden committed Oct 2, 2019
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  7. some refactoring

    @Fulanko
    Fulanko committed Oct 2, 2019
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Commits on Oct 4, 2019

  1. temporary fix for most seed-based probabilities

    @Fulanko
    Fulanko committed Oct 4, 2019
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  2. working seed-based tracker (needs some more testing)

    @Fulanko
    Fulanko committed Oct 4, 2019
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  3. fixed bp prob tests

    @Fulanko
    Fulanko committed Oct 4, 2019
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Commits on Oct 5, 2019

  1. some cleanup

    @Fulanko
    Fulanko committed Oct 5, 2019
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  2. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Oct 5, 2019
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  3. remove python script from this branch ...

    @Fulanko
    Fulanko committed Oct 5, 2019
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  4. added test with overlapping seeds

    @Fulanko
    Fulanko committed Oct 5, 2019
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  5. fixed grid spacing on large dotplots

    @Fulanko
    Fulanko committed Oct 5, 2019
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Commits on Oct 7, 2019

  1. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Oct 7, 2019
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  2. removed logs

    @Fulanko
    Fulanko committed Oct 7, 2019
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Commits on Oct 8, 2019

  1. bug spotted and todos added

    @martin-raden
    martin-raden committed Oct 8, 2019
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  2. fixed numerous bugs in PredictionTracker

    @Fulanko
    Fulanko committed Oct 8, 2019
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  3. fixed bug related to error in theory (all tests working now)

    @Fulanko
    Fulanko committed Oct 8, 2019
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Commits on Oct 9, 2019

  1. added test for buggy example + added outline to dotplots

    @Fulanko
    Fulanko committed Oct 9, 2019
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  2. joint brains

    @martin-raden
    martin-raden committed Oct 9, 2019
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  3. binary removed

    @martin-raden
    martin-raden committed Oct 9, 2019
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  4. fixed a number of typos & bugs

    @Fulanko
    Fulanko committed Oct 9, 2019
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Commits on Oct 10, 2019

  1. renamed some variables

    @Fulanko
    Fulanko committed Oct 10, 2019
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  2. removed test binary

    @Fulanko
    Fulanko committed Oct 10, 2019
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  3. changed Interaction::Basepair to struct (+ added ostream operator)

    @Fulanko
    Fulanko committed Oct 10, 2019
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  4. fixed << operators

    @Fulanko
    Fulanko committed Oct 10, 2019
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  5. fixed broken basepair < operator

    @Fulanko
    Fulanko committed Oct 10, 2019
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  6. fixed missing Z values + index

    @Fulanko
    Fulanko committed Oct 10, 2019
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  7. fix for noseed bp probs ...

    @Fulanko
    Fulanko committed Oct 10, 2019
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Commits on Oct 11, 2019

  1. kaputtgemacht.. :)

    @martin-raden
    martin-raden committed Oct 11, 2019
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Commits on Oct 13, 2019

  1. fix for tests

    @Fulanko
    Fulanko committed Oct 13, 2019
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  2. fixed noseed bp probabilities as dedicated method + made variables const

    @Fulanko
    Fulanko committed Oct 13, 2019
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Commits on Oct 14, 2019

  1. Zinit obsolete

    @martin-raden
    martin-raden authored Oct 14, 2019
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Commits on Oct 23, 2019

  1. add missing bracket

    @martin-raden
    martin-raden committed Oct 23, 2019
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Commits on Nov 10, 2019

  1. added automatic scaling of larger dotplots + added grayscale dots

    @Fulanko
    Fulanko committed Nov 10, 2019
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Commits on Nov 13, 2019

  1. removed relics from old attempts at seed-based bp probs

    @Fulanko
    Fulanko committed Nov 13, 2019
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Commits on Jan 11, 2020

  1. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Jan 11, 2020
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Commits on Jan 28, 2020

  1. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Jan 28, 2020
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  2. type fix in basePairProb test

    @Fulanko
    Fulanko committed Jan 28, 2020
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  3. added static fill_hybridZ method to PredictorMfeEns

    @Fulanko
    Fulanko committed Jan 28, 2020
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Commits on Feb 4, 2020

  1. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Feb 4, 2020
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  2. updated seed-constrain fillHybridZ_left + moved static methods to cor… 

    …rect class
    @Fulanko
    Fulanko committed Feb 4, 2020
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  3. minor fix

    @Fulanko
    Fulanko committed Feb 4, 2020
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Commits on Feb 5, 2020

  1. added access to hybridZ for predictionTracker

    @Fulanko
    Fulanko committed Feb 5, 2020
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Commits on Feb 9, 2020

  1. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Feb 9, 2020
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  2. added trackBPprob flag + hashed ZL partitions

    @Fulanko
    Fulanko committed Feb 9, 2020
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Commits on Feb 11, 2020

  1. seed-based prediction tracker cleanup + progress

    @Fulanko
    Fulanko committed Feb 11, 2020
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  2. getOverlappingSeed

    @Fulanko
    Fulanko committed Feb 11, 2020
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Commits on Feb 12, 2020

  1. twaks and todos

    @martin-raden
    martin-raden committed Feb 12, 2020
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Commits on Feb 16, 2020

  1. PredictionTrackerBPProb fixed ZNL:seed:ZNR case + added seedHandler.i… 

    …sSeedBasePair()
    @Fulanko
    Fulanko committed Feb 16, 2020
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Commits on Feb 17, 2020

  1. basepairProb tracker bug fixes

    @Fulanko
    Fulanko committed Feb 17, 2020
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Commits on Feb 18, 2020

  1. predictionTrackerBPprob

    @Fulanko
    Fulanko committed Feb 18, 2020
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Commits on Feb 19, 2020

  1. fixes...

    @martin-raden
    martin-raden committed Feb 19, 2020
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  2. input check

    @martin-raden
    martin-raden committed Feb 19, 2020
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  3. fix the fix

    @martin-raden
    martin-raden committed Feb 19, 2020
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  4. cleanup

    @Fulanko
    Fulanko committed Feb 19, 2020
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Commits on Feb 20, 2020

  1. bugfix

    @martin-raden
    martin-raden committed Feb 20, 2020
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Commits on Feb 25, 2020

  1. fixed bug in ZHR computation

    @Fulanko
    Fulanko committed Feb 25, 2020
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  2. new variant (has missing cases?)

    @Fulanko
    Fulanko committed Feb 25, 2020
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Commits on Feb 26, 2020

  1. added missing case

    @Fulanko
    Fulanko committed Feb 26, 2020
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Commits on Mar 3, 2020

  1. ZR memoization

    @Fulanko
    Fulanko committed Mar 3, 2020
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  2. Merge branch 'dev' into basepair-probs

    @Fulanko
    Fulanko committed Mar 3, 2020
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  3. added includeBoundaries bool to isSeedBP

    @Fulanko
    Fulanko committed Mar 3, 2020
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  4. updateToNextSeedWithK

    @Fulanko
    Fulanko committed Mar 3, 2020
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Commits on Mar 4, 2020

  1. seedhandler extension

    @martin-raden
    martin-raden committed Mar 4, 2020
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  2. added SVG dotplots with accessibility energies

    @Fulanko
    Fulanko committed Mar 4, 2020
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Commits on Mar 5, 2020

  1. improved SVG output

    @Fulanko
    Fulanko committed Mar 5, 2020
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Commits on Mar 10, 2020

  1. fixed MFE in svg output + moved back to inline css

    @Fulanko
    Fulanko committed Mar 10, 2020
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Commits on Mar 11, 2020

  1. bugfix

    @martin-raden
    martin-raden committed Mar 11, 2020
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  2. svg output fix + changes

    @Fulanko
    Fulanko committed Mar 11, 2020
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  3. Merge branch 'basepair-probs' of github.com:Fulanko/IntaRNA into base… 

    …pair-probs
    @Fulanko
    Fulanko committed Mar 11, 2020
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  4. fixed text positioning

    @Fulanko
    Fulanko committed Mar 11, 2020
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Commits on Mar 26, 2020

  1. box function return now std::string

    @martin-raden
    martin-raden committed Mar 26, 2020
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Commits on Nov 10, 2023

  1. fprintf() formatting corrected

    @martin-raden
    martin-raden committed Nov 10, 2023
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  2. basepairprob parameter docu extended

    @martin-raden
    martin-raden committed Nov 10, 2023
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