Changes.txt

2.7
* Changed header storage to allow for larger files
* Changed to updated installation package.

2.6.3
* Change the PhysioChemical properties display. Moved the Aromatic group to be between the Positive and 
  Negative groups.

2.6
* Fixed DDE abilities. 
* Added saving of backup files. 
* Several Fixes for corrupt files problem. 
* Added location number after sequence name. 
* Added reports showing shading locations. 
* Fixed bug in header for more than 256 sequences. 
* Fixed bug in header for more than 256 manual shadings or comments. 
* Changed composition report to not double count ambiguous codes. 
* Added feature for saving sequence orderings and sort by name. 
* Added a feature to rasmol scripts. 
* Added Report formating options. 
* Added PAIRWISE Alignment under Edit Menu. 
* Added Genbank file Import. 
* Fixed bug for file cannot be read after edited and saved. 
* Fixed up some translation problems. 
* Fixed bugs for crashing on larger files after edits. 
* Added Column Composition reports. 
* Fixed bug where editing a project created by edit/copy caused crashes. 
* Fixed Bug causes crash when trying to do file/save as a project that was created by importing

2.5
* Made spaces in sequence names a warning. 
* Fixed bug where loading user files after EMBL files fails. 
* Fixed bug in Enzyme Report where first cut 1 too short. 
* Changed caret handling a bit.
* Added Copy Consensus to clipboard as fasta file function.
* Changed toolbar copy button to copy as metafile.
* Changed replace to work on whole alignment if nothing selected.
* Added Saving of Manual Shading with show/hide config and button.
* Added Saving of Comments with show/hide config and button.
* Added Quick Find Function with MisMatches and Ins/Deletes.
* Added Ins/Del keys to Insert and Delete Gaps always.
* Added Right Mouse buttons does opposite of left mouse button in Arrangement modes.
* Fixed bug that hangs when export as Text/No Gaps.
* Changed user cannot enter spaces into data area.
* Added Display '~' as ' ' feature.
* Changed Fixed width parameter to be as high as 1000000.
* Removed 'Protected First Line' from Titling Facility.
* Fixed DNA complement to include ambiguities.
* Improved Slide Text routine so it does not unnecessarily grow alignment.
* Added Alignment Width Block Size option.
* Fixed possible crash when scoring/stats on few sequences.
* Added sequence description field.
* Added import IUPAC only funtion.
* Added Delete Data Columns function.
* Added Print Filename and Date with pagenumber.
* Fixed manual data input from crashing

2.4
* Fixed Group Properties function of Identity Tab.
* Fixed Error in Copy to New Project function.
* Added Summary View mode.
* Added copy as .RTF support.
* Fixed Bitmap copy function.
* Added Pict File support to summary view, fixed summary view bug.
* Changed fasta file max sequence name length from 20 to 50.
* Improved Import/Export routines to handle the clipboard and text files.
* Fixed scoring routines to handle lower case chars properly.
* Added LogOdds Display Mode: Reads and Display MEME files.
* Added LogOdds Calc and Write routine.
* Added LogOdds Report routine.
* Fixed possible bug in Search Display: Patterns at end of sequences.
* Removed built in PSDB support from 16-bit version to make space.
* Fixed a big causing crashes in Grab and Drag mode.
* Added Grab and Slide arrangement mode.
* Changed RTF Files to work better for background shading.
* Fixed DStat Plot save plot data for Percent Identity Plots.
* Fixed scorefile and scoring routines when encounter unusual characters.
* Fixed display bug when names shorter than sequence indicators.
* Added optional Carbonyl Oxygen display on backbone in rasmol script.

2.3
* Fixed Configuration Variables not being initialized properly.
* Added DNA Ambiguity code.
* Fixed input sequences detecting gap chars.
* Possible fix of input sequences duplicating data.
* Added DNA group set analysis display.
* Fixed Contrast mode to not include zero level scores.
* Fixed GeneDoc .msf header reader to be forward compatable.
* Fixed rebase file read for larger patterns.
* Added Rebase Search Filters.
* Added user configurable rebase shading overlap color.
* Added export of search list to rebase readable file.
* Added reporting of duplicate sequence names.
* Added Display/No Display of individual Physiochemical properties.
* Fixed bug ReBase patterns found twice if following a gap char.
* Added Rebase cut sites/fragment length/unique fragment/unique frags per group report.
* Added Plot of unique fragment lengths.
* Added Display of reports that can handle any size files.
* Added print function to reports.
* Added ability to print shading only.
* Added Identity Display Mode.
* Fixed Changing project type setting properties and score tables.
* Fixed change gap char for alignment code.
* Fixed RasMol script to not blank display when no sidechains selected.
* Added Shade backbone only and sidechain only to rasmol script.
* Added Sequence Start Position attribute.
* Added Ident All or Ident conserved styles to Ident Display Mode.
* Fixed Structure Shading changing when have both Non-Group and Groups structure info loaded.
* Added PDB Read routines for structure shading.


2.2
* Fixed 'Clear all Gap Columns' Function.
* Added AutoJustify of Max Name Length and Max Position Indicator Length.
* Added Max Name Length Displayed Field.
* Added User Configured Name/Sequence Block seperation string.
* Added User Configured Seq Loc Ind/Sequence Block seperation string.
* Added Phylip File Import function.
* Fixed program hanging when doing File/New, File/Import,
  and then a caret positioning function.
* Fixed program crashing when deleting all sequences.
* Added UnOfficial CrossHatch pattern support for background shading.
* Added ability to select Sequences to be exported.
* Changed the GeneDoc information section of the .MSF file.
  *** NOTE: This new header can NOT be read by previous versions of GeneDoc
* Added ProSite/ReBase Search Results mode.
* Added Auto-Load Search Lists with ProSite or ReBase files.
  List gets loaded with matches found in the ProSite or Rebase Files.
* Fixed the Copy to New Project function in many cases, most having
  to do with group information being copied.
* Changed Structure Sequence Matching rountine to work for both
  overlap and within cases.
* Added HTML output.
* Added RasMol coloring script output.
* Added Weights in Phylogenetic tree parsing.
* Fixed page up bug.
* Fixed Pict files sequence names not being group colored.
* Relaxed .MSF input routine, does not need spaces every 10 in data rows.
* Fixed import routines to get last char if no last CR/LF.
* Added RasMol SideChain display options to coloring script output.
* Changed Duplicate Sequence Names To Complain and Notify, but not abort.
* Changed Group Names in Group Sequence Dialog to be colored with
  group colors.
* Changed Fasta input to limit names to length of 20.
* Added conserved shading of substitution groups styles. 
* Fixed extra CR/LF being added to comments in file with each additional file save.

2.1
* Added Configurable Marker Line above Consensus Line to show column position.
* Added Configurable Gap Indicator For Consensus Line.
* Added Import and Export of additional file types: Phylip, PIR, Clustal ALN, Fasta.
* Added a function to clear Columns that are All gaps.
* Rewrote fasta import sequence routine.
* Fixed bug in filler block at end in Print in Landscape mode.
* Fixed bug where stat file tests of residue identity and score was case sensitive.
* Added residue display in upper, lower, or as_is case.
* Added sequence reverse and DNA compliment functions.
* Added (and fixed) manual input and clipboard paste of sequence data.
* A Bunch of Fixes to the DStat Display.
* Added C.D.F. plot of Statistics Scores for Alignment and Groups.
* Fixed Bug of DNA/RNA Project type being switched.
* Added Status Line Sequence Location Indicator.
* Added File Import Type Selection Dialog for import of *.*
* Added PhysioChemical Properties Group Shading Display(s).
* Added Sequence String Substitution Function.
* Added Sequence Duplicate Function.
* Added Sequence Block Copy of Data Function.
* Added Copy Sequence to Clipboard Function.
* Added PhysioChemical Shading Mode(s).
* Fixed Phylogenetic tree import function.
* Changed Phylogenetic tree name parsing slightly.
* Fixed a rescore phyogenetic tree score bug.
* Added Conserved Group With Cross Shading display.
* Updated and Fixed help file.

2.0.4:
* Fixed new Project wont reopen bug.
* changed .msf file open code to be much faster.
* fixed a global free invalid handle in import fasta bug.
* added support for up to 50 char sequence names.
* better detection and error message for duplicate sequence names.
* duplicate sequences skipped on file imports.
* User Defined structure shading now overrides built in structure shading when already defined.
* fixed handling of '!' in residue field in dssp files.

2.0.1: Fixed input fasta bug.

Version 2.0: What didn't change?