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Added clustalW 'realignment' (primitive)
[jalview.git] / src /
2005-05-30 jprocterAdded clustalW 'realignment' (primitive) tree | commitdiff
2005-05-30 jprocteradded default ClustalWS or MuscleWS to remove gaps. tree | commitdiff
2005-05-30 jprocterpropagated use of jalview.util.GapChars for gap removal. tree | commitdiff
2005-05-30 jproctermore robust parsing for DBset/DBname|id1|id2 type ids tree | commitdiff
2005-05-30 jproctermodified history for redundancy removal. tree | commitdiff
2005-05-30 jprocterfixed stacktrace potential for pairwise alignment action. tree | commitdiff
2005-05-30 jprocterModified output on stdout for similarity matrix. tree | commitdiff
2005-05-27 jprocterfixed brain interruption bug. tree | commitdiff
2005-05-27 amwaterhouseignores blank lines read in and write out tree | commitdiff
2005-05-27 jprocterright ordering for RedundancyPanel constructor tree | commitdiff
2005-05-27 jprocteradded proper state check for failedJob flag. tree | commitdiff
2005-05-27 jprocterAdded jobFail state tree | commitdiff
2005-05-27 jprocterbetter recognition of MSF files. tree | commitdiff
2005-05-27 amwaterhouseidentity changed tree | commitdiff
2005-05-27 amwaterhouseCut and paste menus added tree | commitdiff
2005-05-27 amwaterhouseCut and paste changes tree | commitdiff
2005-05-27 amwaterhouseC&P changes tree | commitdiff
2005-05-27 amwaterhouseCheck if colos are null tree | commitdiff
2005-05-27 amwaterhouseCut and paste changes tree | commitdiff
2005-05-27 amwaterhouseAdd cut and paste menus tree | commitdiff
2005-05-27 amwaterhouseCutAndPaste changed tree | commitdiff
2005-05-27 jprocterAdded nicer header formatting for MSFfile output. tree | commitdiff
2005-05-27 jprocterrecovered changes from v 1.84 tree | commitdiff
2005-05-27 amwaterhouseCheck if usrCol is null tree | commitdiff
2005-05-27 amwaterhouseNew cut and paste tree | commitdiff
2005-05-27 jprocterJpredfile now uses the PileUpfile io class. tree | commitdiff
2005-05-27 jprocterAddred GapChar string for convenient regex construction tree | commitdiff
2005-05-27 jprocterResponse to bug mantis?id=8187 - some quick hacks to... tree | commitdiff
2005-05-27 amwaterhouseRemove desc for conserve graph tree | commitdiff
2005-05-27 jprocterOld MSF Format writer now renamed. tree | commitdiff
2005-05-26 jprocterfixed use of PID rather than 'Comparison' Alignment... tree | commitdiff
2005-05-26 jprocterfairly pointless catch exception error information... tree | commitdiff
2005-05-26 jprocterfixed redundancy Undo and allowed it to work on UNALIGN... tree | commitdiff
2005-05-26 jprocterbug fix in jpred client. TreeViewer display state and... tree | commitdiff
2005-05-26 amwaterhousecheck for null residues tree | commitdiff
2005-05-26 amwaterhouseDOnt add Conservation graph to every residue tree | commitdiff
2005-05-26 amwaterhousetoString modified tree | commitdiff
2005-05-25 amwaterhousereset colours added tree | commitdiff
2005-05-25 amwaterhousemore clustalx bugs fixed tree | commitdiff
2005-05-25 amwaterhousegetHexString added tree | commitdiff
2005-05-25 amwaterhouseall can threshold tree | commitdiff
2005-05-25 amwaterhouseoutput to textbox tree | commitdiff
2005-05-25 amwaterhouselayout changes tree | commitdiff
2005-05-25 amwaterhousecapitals tree | commitdiff
2005-05-25 amwaterhouseformat changes tree | commitdiff
2005-05-25 amwaterhouseremove scrollpane tree | commitdiff
2005-05-25 amwaterhouseCapitalise tree | commitdiff
2005-05-25 amwaterhousec&p changed tree | commitdiff
2005-05-25 amwaterhouseuse getHexString in util tree | commitdiff
2005-05-25 amwaterhouseusercolours changed tree | commitdiff
2005-05-25 amwaterhouseoutput text to textbox tree | commitdiff
2005-05-25 amwaterhouseall colours can threshold tree | commitdiff
2005-05-25 amwaterhouseselectiongroup could be null tree | commitdiff
2005-05-25 amwaterhousesaves usercolours tree | commitdiff
2005-05-25 amwaterhouseformatforoutput never used tree | commitdiff
2005-05-25 amwaterhouseoutput values to textbox tree | commitdiff
2005-05-25 amwaterhousetoString method added tree | commitdiff
2005-05-25 amwaterhouseXML schema changes tree | commitdiff
2005-05-25 amwaterhouseusercolourscheme changed tree | commitdiff
2005-05-25 amwaterhouseformatting changes tree | commitdiff
2005-05-25 amwaterhouseall colours can threshold tree | commitdiff
2005-05-25 amwaterhouseusercolours changed tree | commitdiff
2005-05-25 amwaterhouseremove comment tree | commitdiff
2005-05-25 amwaterhousecan output details to textbox tree | commitdiff
2005-05-25 jprocteradded jalview.browser property so a linux user can... tree | commitdiff
2005-05-25 jprocterdoh - compile before commit! tree | commitdiff
2005-05-25 jproctertidied up system.out messages and moved many to stderr. tree | commitdiff
2005-05-25 jprocterImproved consistency between JPredWS and MsaWS tree | commitdiff
2005-05-25 jprocterbase class for web service clients. tree | commitdiff
2005-05-24 jproctertitle parameter for single sequence prediction. tree | commitdiff
2005-05-24 jprocterAdded more firePropertyChange calls - mainly for sequen... tree | commitdiff
2005-05-24 jprocterextended the UpdatePlaceholders to check for any new... tree | commitdiff
2005-05-24 jprocteradded PropertyChangeListeners for alignviewport.alignme... tree | commitdiff
2005-05-24 amwaterhouseremove . tree | commitdiff
2005-05-24 amwaterhouseURL getresource adds %20 for spaces. Use user.dir instead tree | commitdiff
2005-05-24 amwaterhousefilefilter might not be JalviewFileFilter tree | commitdiff
2005-05-24 amwaterhouseequalsIgnoreCase tree | commitdiff
2005-05-24 amwaterhousesetDefaultFileFormat tree | commitdiff
2005-05-24 amwaterhousereplace get with elementAt tree | commitdiff
2005-05-24 amwaterhousesetgraphics black tree | commitdiff
2005-05-24 amwaterhousesetgraphics black tree | commitdiff
2005-05-24 jprocterseveral ordering bug fixes. tree | commitdiff
2005-05-23 jprocterAdded PadGaps and made treeSortMenu dynamic (it gets... tree | commitdiff
2005-05-23 jprocteradded some assertions and rangechecks for insert/delete... tree | commitdiff
2005-05-23 jprocteradded getSequencesInOrder (part of refactor from AlignP... tree | commitdiff
2005-05-23 jproctereditMenuPadGaps and sortByTree/sort items tree | commitdiff
2005-05-23 jprocterfixed window title names for prediction on MSA or Sequence. tree | commitdiff
2005-05-23 amwaterhousecolour groups by text colour tree | commitdiff
2005-05-23 amwaterhousemake sure fonts are not null tree | commitdiff
2005-05-23 amwaterhouseremove separator tree | commitdiff
2005-05-23 amwaterhousenew savestate method tree | commitdiff
2005-05-23 jprocterUgly but improved recovery of sequence names, starts... tree | commitdiff
2005-05-23 jprocterbug fix for wierdness retrieving QUERY sequence index. tree | commitdiff
2005-05-23 amwaterhouseboxes, colour text, show text added to groups tree | commitdiff
2005-05-23 amwaterhousehistoryitem added tree | commitdiff
2005-05-22 jprocterinclude MsaWS ordering but not perfect (undo destroys... tree | commitdiff
2005-05-22 jprocterAdded alignment ordering option to 'Sort by' and implem... tree | commitdiff
2005-05-22 jprocterlater version of client-side WSDL2Java generated simple... tree | commitdiff
2005-05-20 jprocterSemiworking generic MSA client tree | commitdiff
2005-05-20 jprocteradded placeholder indicators and menu item tree | commitdiff
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