X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=e93bf300cc16ca1feff0c289bc40197e3f382dc1;hb=dc6f1dbbd2c3e951c94f969703d595ea22e33f73;hp=802621987ff310d6dc80e6b6c8f72895654932a3;hpb=a05186c1168e5e0a96a8825fe4c53d439079fdb3;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 8026219..e93bf30 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -3,74 +3,111 @@

Release History

- + - + + + + + + + 12/2/07 +
  • Annotation file format extended to allow Sequence_groups + to be defined +
  • Default opening of alignment overview panel can be specified in + preferences +
  • PDB residue numbering annotation added to associated sequences +
    • - + - + - + - + - + @@ -115,7 +152,7 @@
  • Righthand label on wrapped alignments shows correct value
    • - + - + - + - + - + - + - + - + @@ -222,7 +259,7 @@
  • Copy & Paste order of sequences maintains alignment order.
    • - + - +
    Release
    New Features
    Issues Resolved
    2.3
    + 8/5/07
      +
    • Jmol 11.0.2 integration
      • +
    • PDB views stored in Jalview XML files
      • +
    • Slide sequences
      • +
    • Edit sequence in place
      • +
    • EMBL CDS features
      • +
    • DAS Feature mapping
      • +
    • Feature ordering
      • +
    • Alignment Properties
      • +
    • Annotation Scores
      • +
    • Sort by scores
      • +
    • Feature/annotation editing in applet
      • +
    		 +
      +
    • Headless state operation in 2.2.1
      • +
    • Incorrect and unstable DNA pairwise alignment
      • +
    • Cut and paste of sequences with annotation
      • +
    • Feature group display state in XML
      • +
    • Feature ordering in XML
      • +
    • blc file iteration selection using filename # suffix
      • +
    • Stockholm alignment properties
      • +
    • Stockhom alignment secondary structure annotation
      • +
    • 2.2.1 applet had no feature transparency
      • +
    • Number pad keys can be used in cursor mode
      • +
    • Structure Viewer mirror image resolved
      • +
    +
    2.2.1
    - ?/ 2/07
    • Non standard characters can be read and displayed
    • Annotations/Features can be imported/exported to the applet via textbox
    • Applet allows editing of sequence/annotation/group name & description
    • Preference setting to display sequence name in italics -
    • Annotation file format extended to allow Sequence_groups to be defined
    • Applet crash under certain Linux OS with Java 1.6 installed
    • Annotation file export / import bugs fixed
    • PNG / EPS image output bugs fixed
    2.2
    27/11/06
      -
    • Multiple views on alignment -
    • Sequence feature editing -
    • "Reload" alignment -
    • "Save" to current filename -
    • Background dependent text colour -
    • Right align sequence ids -
    • User-defined lower case residue colours -
    • Format Menu -
    • Select Menu -
    • Menu item accelerator keys -
    • Control-V pastes to current alignment -
    • Cancel button for DAS Feature Fetching -
    • PCA and PDB Viewers zoom via mouse roller -
    • User-defined sub-tree colours and sub-tree selection +
    • Multiple views on alignment +
    • Sequence feature editing +
    • "Reload" alignment +
    • "Save" to current filename +
    • Background dependent text colour +
    • Right align sequence ids +
    • User-defined lower case residue colours +
    • Format Menu +
    • Select Menu +
    • Menu item accelerator keys +
    • Control-V pastes to current alignment +
    • Cancel button for DAS Feature Fetching +
    • PCA and PDB Viewers zoom via mouse roller +
    • User-defined sub-tree colours and sub-tree selection
    • 'New Window' button on the 'Output to Text box'
      -
    • New memory efficient Undo/Redo System -
    • Optimised symbol lookups and conservation/consensus calculations -
    • Region Conservation/Consensus recalculated after edits -
    • Fixed Remove Empty Columns Bug (empty columns at end of alignment) -
    • Slowed DAS Feature Fetching for increased robustness. -
    • Made angle brackets in ASCII feature descriptions display correctly -
    • Re-instated Zoom function for PCA -
    • Sequence descriptions conserved in web service analysis results -
    • Uniprot ID discoverer uses any word separated by ∣ -
    • WsDbFetch query/result association resolved -
    • Tree leaf to sequence mapping improved +
    • New memory efficient Undo/Redo System +
    • Optimised symbol lookups and conservation/consensus calculations +
    • Region Conservation/Consensus recalculated after edits +
    • Fixed Remove Empty Columns Bug (empty columns at end of alignment) +
    • Slowed DAS Feature Fetching for increased robustness. +
    • Made angle brackets in ASCII feature descriptions display correctly +
    • Re-instated Zoom function for PCA +
    • Sequence descriptions conserved in web service analysis results +
    • Uniprot ID discoverer uses any word separated by ∣ +
    • WsDbFetch query/result association resolved +
    • Tree leaf to sequence mapping improved
    • Smooth fonts switch moved to FontChooser dialog box.
    2.1.1
    12/9/06
    • Copy consensus sequence to clipboard
      -
    • Image output - rightmost residues are rendered if sequence id panel +
    • Image output - rightmost residues are rendered if sequence id panel has been resized
    • Image output - all offscreen group boundaries are rendered
      • -
    • Annotation files with sequence references - all elements in file are +
    • Annotation files with sequence references - all elements in file are relative to sequence position
    • Mac Applet users can use Alt key for group editing
    2.1
    22/8/06
      @@ -93,20 +130,20 @@
    • Annotation files with sequence references bug fixed
    2.08.1
    2/5/06
    • Change case of selected region from Popup menu
    • Choose to match case when searching
      • -
    • Middle mouse button and mouse movement can compress / expand the visible +
    • Middle mouse button and mouse movement can compress / expand the visible width and height of the alignment
    • Annotation Panel displays complete JNet results
    2.08b
    18/4/06
    		  
    2.08
    10/4/06
      @@ -130,11 +167,11 @@
    • Drag & Drop fixed on Linux
      • -
    • Jalview Archive file faster to load/save, sequence descriptions saved. +
    • Jalview Archive file faster to load/save, sequence descriptions saved.
    2.07
    12/12/05
      @@ -142,7 +179,7 @@
    • Sequence Feature retrieval and display enhanced
    • Choose to output sequence start-end after sequence name for file output
    • Sequence Fetcher WSDBFetch@EBI
      • -
    • Applet can read feature files, PDB files and can be used for HTML +
    • Applet can read feature files, PDB files and can be used for HTML form input
      @@ -151,7 +188,7 @@
    • File IO bugs
    2.06
    28/9/05
      @@ -163,7 +200,7 @@
    • Runs with -nodisplay from command line
    2.05b
    15/9/05
      @@ -177,7 +214,7 @@
    • Several GUI bugs resolved
    2.05
    30/8/05
      @@ -187,7 +224,7 @@
    • Several GUI bugs resolved
    2.04
    24/8/05
      @@ -198,7 +235,7 @@
    • Improved loading of Jalview files
    2.03
    18/8/05
      @@ -214,7 +251,7 @@
    • InstallAnywhere download for Sparc Solaris
    2.02
    18/7/05
    		  
    2.01
    12/7/05
      @@ -237,12 +274,12 @@
    • FileChooser sorts columns.
    • Can remove groups one by one.
    • Filechooser icons installed.
      • -
    • Finder ignores return character when searching. Return key will initiate +
    • Finder ignores return character when searching. Return key will initiate a search.
    2.0
    20/6/05