BioSeqDataLib issueshttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues2022-12-02T11:09:18+01:00https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/15std::path2022-12-02T11:09:18+01:00Dr. Carsten Kemenastd::pathSo far we were using boost path. But given the advances of the std library one should think about switching to std::path now.So far we were using boost path. But given the advances of the std library one should think about switching to std::path now.2.0https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/14Better Code testing2022-12-02T11:09:30+01:00Dr. Carsten KemenaBetter Code testingThe tested code coverage should reach 95%The tested code coverage should reach 95%2.0https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/12deprecated tree iterator2022-10-07T10:28:01+02:00Dr. Carsten Kemenadeprecated tree iteratorThe tree iterators are currently inherited from std::iterator. This is now deprecated and needs to be changedThe tree iterators are currently inherited from std::iterator. This is now deprecated and needs to be changed2.0https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/11Finish external interface2022-10-06T08:59:06+02:00Dr. Carsten KemenaFinish external interfaceMove remaining free external_interface functions to a classMove remaining free external_interface functions to a classversion 1.0Dr. Carsten KemenaDr. Carsten Kemenahttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/10Use of strategy pattern for SequenceSet2020-06-24T15:18:50+02:00Dr. Carsten KemenaUse of strategy pattern for SequenceSetImplement the strategy pattern for SequenceSet
- move all currently supported formats to the new designImplement the strategy pattern for SequenceSet
- move all currently supported formats to the new designversion 1.0Dr. Carsten KemenaDr. Carsten Kemenahttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/9Improve Input/Output2019-12-16T13:04:37+01:00Dr. Carsten KemenaImprove Input/OutputChange Algorithm Output/Input class:
- move from AlgorithmPack namespace to BioSeqDataLib
- check automatic close when destructor is called
- function to store and retrieve filenameChange Algorithm Output/Input class:
- move from AlgorithmPack namespace to BioSeqDataLib
- check automatic close when destructor is called
- function to store and retrieve filenameversion 1.0Dr. Carsten KemenaDr. Carsten Kemenahttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/7domain visulization2019-11-28T14:07:34+01:00Dr. Carsten Kemenadomain visulizationImplement a library, or use existing one to implement visualization of:
- domain arrangements
- domain alignments
- dotplots
Use the same kind of display for all programs (e.g. Rads, DoMosaics) as well as for standalone program as well w...Implement a library, or use existing one to implement visualization of:
- domain arrangements
- domain alignments
- dotplots
Use the same kind of display for all programs (e.g. Rads, DoMosaics) as well as for standalone program as well webservices
<!-- @KB:null -->https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/6add domain similarity matrix2017-04-26T15:36:33+02:00Dr. Carsten Kemenaadd domain similarity matrixImplement the domain similarity matrix into the domain world
Following features should be supported:
- this should support all interposcan domains
- read matrix from sparse file
- score(domain, domain) returns the value for the mat...Implement the domain similarity matrix into the domain world
Following features should be supported:
- this should support all interposcan domains
- read matrix from sparse file
- score(domain, domain) returns the value for the match of two domains
version 1.0Dr. Carsten KemenaDr. Carsten Kemenahttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/5nw with domains2017-04-26T15:36:33+02:00Dr. Carsten Kemenanw with domainsChange the gotoh and needleman wunsch algorithms to be able to handle domains as well. This will require as well to add the domain similarity matrix.Change the gotoh and needleman wunsch algorithms to be able to handle domains as well. This will require as well to add the domain similarity matrix.version 1.0https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/4DomainArrangementSet from sequences2017-10-10T14:37:47+02:00Dr. Carsten KemenaDomainArrangementSet from sequencesExtend the DomainArrangementSet class to automatically call pfam (or hmmscan) on sequence set to get domain arrangement.Extend the DomainArrangementSet class to automatically call pfam (or hmmscan) on sequence set to get domain arrangement.version 1.0https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/3Parsimony implementation2017-04-26T15:36:33+02:00Dr. Carsten KemenaParsimony implementationImplement wagner/fitsch and dollo parsimony
<!-- @KB:{"andon":"none"} -->Implement wagner/fitsch and dollo parsimony
<!-- @KB:{"andon":"none"} -->version 1.0Dr. Carsten KemenaDr. Carsten Kemenahttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/2clan handling2017-04-26T15:36:33+02:00Dr. Carsten Kemenaclan handlingHow should the clan handling be done? seems not to be very intuitive at the moment. How should the clan handling be done? seems not to be very intuitive at the moment. Dr. Carsten KemenaDr. Carsten Kemenahttps://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib/-/issues/1handling other domain databases than pfam2017-04-26T15:36:33+02:00Dr. Carsten Kemenahandling other domain databases than pfamCurrently only pfam can handadled. It would be good to add other major databases e.g. Superfamily. Unfortunately the information is quite different. What is the best way to handle it? One domain class handling all, template solution like...Currently only pfam can handadled. It would be good to add other major databases e.g. Superfamily. Unfortunately the information is quite different. What is the best way to handle it? One domain class handling all, template solution like for sequences, special class for each domain?
Dr. Carsten KemenaDr. Carsten Kemena