From: jprocter Date: Tue, 15 Jan 2008 14:05:29 +0000 (+0000) Subject: draft of 2.4 features in feature list X-Git-Tag: Release_2_4~152 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ae96518a241a9808dce180d926745aa7cdefc55f;p=jalview.git draft of 2.4 features in feature list --- diff --git a/help/html/releases.html b/help/html/releases.html index f70327e..a4c79c1 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,293 +1,529 @@ - -Release History - -

Release History

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Release
New Features
Issues Resolved
2.3
- 9/5/07
    -
  • 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
- 12/2/07
    -
  • 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 -
  • Default opening of alignment overview panel can be specified in - preferences -
  • PDB residue numbering annotation added to associated sequences -
    -
  • 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 -
  • '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 -
  • 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 - has been resized
  • -
  • Image output - all offscreen group boundaries are rendered
  • -
  • 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
    -
  • MAFFT Multiple Alignment in default Web Service list
  • -
  • DAS Feature fetching
  • -
  • Hide sequences and columns
  • -
  • Export Annotations and Features
  • -
  • GFF file reading / writing
  • -
  • Associate structures with sequences from local PDB files
  • -
  • Add sequences to exisiting alignment
  • -
  • Recently opened files / URL lists
  • -
  • Applet can launch the full application
  • -
  • Applet has transparency for features (Java 1.2 required)
  • -
  • Applet has user defined colours parameter
  • -
  • Applet can load sequences from parameter "sequencex"
  • -
    -
  • Redundancy Panel reinstalled in the Applet
  • -
  • Monospaced font - EPS / rescaling bug fixed
  • -
  • 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 - width and height of the alignment
  • -
    -
  • Annotation Panel displays complete JNet results
  • -
2.08b
- 18/4/06
 
    -
  • Java 1.5 bug - InternalMessageDialog fix for threads
  • -
  • Righthand label on wrapped alignments shows correct value
  • -
2.08
- 10/4/06
    -
  • Editing can be locked to the selection area
  • -
  • Keyboard editing
  • -
  • Create sequence features from searches
  • -
  • Precalculated annotations can be loaded onto alignments
  • -
  • Features file allows grouping of features
  • -
  • Annotation Colouring scheme added
  • -
  • Smooth fonts off by default - Faster rendering
  • -
  • Choose to toggle Autocalculate Consensus On/Off
  • -
    -
  • Drag & Drop fixed on Linux
  • -
  • Jalview Archive file faster to load/save, sequence descriptions saved. -
  • -
2.07
- 12/12/05
    -
  • PDB Structure Viewer enhanced
  • -
  • 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 - form input
  • -
    -
  • HTML output writes groups and features
  • -
  • Group editing is Control and mouse click
  • -
  • File IO bugs
  • -
2.06
- 28/9/05
    -
  • View annotations in wrapped mode
  • -
  • More options for PCA viewer
  • -
    -
  • GUI bugs resolved
  • -
  • Runs with -nodisplay from command line
  • -
2.05b
- 15/9/05
    -
  • Choose EPS export as lineart or text
  • -
  • Jar files are executable
  • -
  • Can read in Uracil - maps to unknown residue
  • -
    -
  • Known OutOfMemory errors give warning message
  • -
  • Overview window calculated more efficiently
  • -
  • Several GUI bugs resolved
  • -
2.05
- 30/8/05
    -
  • Edit and annotate in "Wrapped" view
  • -
    -
  • Several GUI bugs resolved
  • -
2.04
- 24/8/05
    -
  • Hold down mouse wheel & scroll to change font size
  • -
    -
  • Improved JPred client reliability
  • -
  • Improved loading of Jalview files
  • -
2.03
- 18/8/05
    -
  • Set Proxy server name and port in preferences
  • -
  • Multiple URL links from sequence ids
  • -
  • User Defined Colours can have a scheme name and added to Colour Menu
  • -
  • Choose to ignore gaps in consensus calculation
  • -
  • Unix users can set default web browser
  • -
  • Runs without GUI for batch processing
  • -
  • Dynamically generated Web Service Menus
  • -
    -
  • InstallAnywhere download for Sparc Solaris
  • -
2.02
- 18/7/05
 
    -
  • Copy & Paste order of sequences maintains alignment order.
  • -
2.01
- 12/7/05
    -
  • Use delete key for deleting selection.
  • -
  • Use Mouse wheel to scroll sequences.
  • -
  • Help file updated to describe how to add alignment annotations.
  • -
  • Version and build date written to build properties file.
  • -
  • InstallAnywhere installation will check for updates at launch of Jalview.
  • -
    -
  • Delete gaps bug fixed.
  • -
  • FileChooser sorts columns.
  • -
  • Can remove groups one by one.
  • -
  • Filechooser icons installed.
  • -
  • Finder ignores return character when searching. Return key will initiate - a search.
    -
  • -
2.0
- 20/6/05
    -
  • New codebase
  • -
 
-

 

- - + + +Release History + + +

Release History

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
Release
+
+
New Features
+
+
Issues Resolved
+
+
2.4
+ Feb/2008
+
+
    +
  • New VAMSAS capabilities in Jalview +
      +
    • treenode binding for VAMSAS tree exchange
    • +
    • local editing and update of sequences in VAMSAS alignments + (experimental)
    • +
    • Create new or select existing session to join
    • +
    • load and save of vamsas documents
    • +
    +
  • +
  • Retrieval of cross-referenced sequences from other databases +
  • +
  • export annotation rows as CSV for spreadsheet import
  • +
  • Jalview projects record alignment dataset associations, EMBL + products, and cDNA sequence mappings
  • +
  • Linked highlighting of codon and amino acid from translation + and protein products
  • +
  • JPred3 web service
  • +
  • Generalised database reference retrieval and validation to + all fetchable databases
  • +
  • Application command line +
      +
    • -tree parameter to open trees (introduced for passing from + applet)
    • +
    • -fetchfrom command line argument to specify nicknames of + DAS servers to query for alignment features
    • +
    • -dasserver command line argument to add new servers that + are also automatically queried for features
    • +
    • -groovy command line argument executes a given groovy + script after all input data has been loaded and parsed
    • +
    +
  • +
  • Trees passed as applet parameters can be passed to + application (when using "View in full application")
  • +
  • MemoryMonitor added as an option under Desktop's Tools menu +
  • +
  • allow reading of JPred concise files as a normal filetype
  • +
  • sort sequences by named annotation scores
  • +
  • Re-instated Full AMSA support and .amsa file association
  • +
  • Stockholm annotation parsing and alignment properties import +
  • +
  • Applet Parameters +
      +
    • feature group display control parameter
    • +
    • debug parameter
    • +
    +
  • +
  • Applet API methods +
      +
    • newView public method
    • +
    • Window (current view) specific get/set public methods
    • +
    • Feature display control methods
    • +
    +
  • +
+ New Jalview distribution features +
    +
  • RELEASE file gives build properties for the latest Jalview + release.
  • +
  • Java 1.1 Applet build made easier and donotobfuscate + property controls execution of obfuscator
  • +
  • Build target for generating source distribution
  • +
  • Debug flag for javacc
  • +
  • .jalview_properties file is documented (slightly) in + jalview.bin.Cache
  • +
+
+
    +
  • selected region output includes visible annotations (for + certain formats)
  • +
  • edit label/displaychar contains existing label/char for + editing
  • +
  • update PDBEntries when DBRefEntries change (vamsas)
  • +
  • shorter peptide product names from EMBL records
  • +
  • Newick string generator makes compact representations
  • +
  • bootstrap values parsed correctly for tree files with + comments
  • +
  • pathological filechooser bug avoided by not allowing + filenames containing a ':'
  • +
  • Fixed exception when parsing GFF files containing global + sequence features
  • +
  • Alignment datasets are finalized only when number of + references from alignment sequences goes to zero
  • +
  • Close of tree branch colour box without colour selection + causes cascading exceptions
  • +
  • occasional negative imgwidth exceptions
  • +
  • better reporting of non-fatal warnings to user when file + parsing fails.
  • +
  • Save works when Jalview project is default format
  • +
  • Uniprot canonical names introduced for both das and vamsas
  • +
  • Histidine should be midblue (not pink!) in Zappo
  • +
  • error messages passed up and output when data read fails
  • +
  • edit undo recovers previous dataset sequence when sequence + is edited
  • +
  • allow PDB files without pdb ID HEADER lines (like those + generated by MODELLER) to be read in properly
  • +
  • annotation consisting of sequence associated scores can be + read and written correctly to annotation file
  • +
  • Aligned cDNA translation to aligned peptide works correctly +
  • +
  • Fixed display of hidden sequence markers and non-italic font + for representatives in Applet
  • +
  • Applet Menus are always embedded in applet window on Macs.
  • +
  • Newly shown features appear at top of stack (in Applet)
  • +
  • Annotations added via parameter not drawn properly due to + null pointer exceptions
  • +
  • Secondary structure lines are drawn starting from first + column of alignment
  • +
+
+
2.3
+ 9/5/07
+
+
    +
  • 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
+ 12/2/07
+
+
    +
  • 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 +
  • Default opening of alignment overview panel can be specified + in preferences +
  • PDB residue numbering annotation added to associated + sequences +
+
+
    +
  • 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 +
  • '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 +
  • 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 has been resized
  • +
  • Image output - all offscreen group boundaries are rendered
  • +
  • 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
+
+
    +
  • MAFFT Multiple Alignment in default Web Service list
  • +
  • DAS Feature fetching
  • +
  • Hide sequences and columns
  • +
  • Export Annotations and Features
  • +
  • GFF file reading / writing
  • +
  • Associate structures with sequences from local PDB files
  • +
  • Add sequences to exisiting alignment
  • +
  • Recently opened files / URL lists
  • +
  • Applet can launch the full application
  • +
  • Applet has transparency for features (Java 1.2 required)
  • +
  • Applet has user defined colours parameter
  • +
  • Applet can load sequences from parameter "sequencex"
  • +
+
+
    +
  • Redundancy Panel reinstalled in the Applet
  • +
  • Monospaced font - EPS / rescaling bug fixed
  • +
  • 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 width and height of the alignment
  • +
+
+
    +
  • Annotation Panel displays complete JNet results
  • +
+
+
2.08b
+ 18/4/06
+
  +
    +
  • Java 1.5 bug - InternalMessageDialog fix for threads
  • +
  • Righthand label on wrapped alignments shows correct value
  • +
+
+
2.08
+ 10/4/06
+
+
    +
  • Editing can be locked to the selection area
  • +
  • Keyboard editing
  • +
  • Create sequence features from searches
  • +
  • Precalculated annotations can be loaded onto alignments
  • +
  • Features file allows grouping of features
  • +
  • Annotation Colouring scheme added
  • +
  • Smooth fonts off by default - Faster rendering
  • +
  • Choose to toggle Autocalculate Consensus On/Off
  • +
+
+
    +
  • Drag & Drop fixed on Linux
  • +
  • Jalview Archive file faster to load/save, sequence + descriptions saved.
  • +
+
+
2.07
+ 12/12/05
+
+
    +
  • PDB Structure Viewer enhanced
  • +
  • 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 form input
  • +
+
+
    +
  • HTML output writes groups and features
  • +
  • Group editing is Control and mouse click
  • +
  • File IO bugs
  • +
+
+
2.06
+ 28/9/05
+
+
    +
  • View annotations in wrapped mode
  • +
  • More options for PCA viewer
  • +
+
+
    +
  • GUI bugs resolved
  • +
  • Runs with -nodisplay from command line
  • +
+
+
2.05b
+ 15/9/05
+
+
    +
  • Choose EPS export as lineart or text
  • +
  • Jar files are executable
  • +
  • Can read in Uracil - maps to unknown residue
  • +
+
+
    +
  • Known OutOfMemory errors give warning message
  • +
  • Overview window calculated more efficiently
  • +
  • Several GUI bugs resolved
  • +
+
+
2.05
+ 30/8/05
+
+
    +
  • Edit and annotate in "Wrapped" view
  • +
+
+
    +
  • Several GUI bugs resolved
  • +
+
+
2.04
+ 24/8/05
+
+
    +
  • Hold down mouse wheel & scroll to change font size
  • +
+
+
    +
  • Improved JPred client reliability
  • +
  • Improved loading of Jalview files
  • +
+
+
2.03
+ 18/8/05
+
+
    +
  • Set Proxy server name and port in preferences
  • +
  • Multiple URL links from sequence ids
  • +
  • User Defined Colours can have a scheme name and added to + Colour Menu
  • +
  • Choose to ignore gaps in consensus calculation
  • +
  • Unix users can set default web browser
  • +
  • Runs without GUI for batch processing
  • +
  • Dynamically generated Web Service Menus
  • +
+
+
    +
  • InstallAnywhere download for Sparc Solaris
  • +
+
+
2.02
+ 18/7/05
+
  +
    +
  • Copy & Paste order of sequences maintains alignment + order.
  • +
+
+
2.01
+ 12/7/05
+
+
    +
  • Use delete key for deleting selection.
  • +
  • Use Mouse wheel to scroll sequences.
  • +
  • Help file updated to describe how to add alignment + annotations.
  • +
  • Version and build date written to build properties file.
  • +
  • InstallAnywhere installation will check for updates at + launch of Jalview.
  • +
+
+
    +
  • Delete gaps bug fixed.
  • +
  • FileChooser sorts columns.
  • +
  • Can remove groups one by one.
  • +
  • Filechooser icons installed.
  • +
  • Finder ignores return character when searching. Return key + will initiate a search.
    +
  • +
+
+
2.0
+ 20/6/05
+
+
    +
  • New codebase
  • +
+
 
+

 

+ +