X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=890f3438184681ca9ec2ededbc78328caa9fd98f;hb=b13f521553582ef2fbfd7815ae25e23284babdea;hp=e091da01b09297904b9662cc1219f78c70f04dd2;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index e091da0..890f343 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,45 +1,471 @@ + --> Release History

Release History

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-
Release
- 		-
New Features
- 		-
Issues Resolved
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+
+ Release +
+ 		+
+ New Features +
+ 		+
+ Issues Resolved +
+
+ 2.9
23/2/2015 +
General +
    +
Application +
    +
+ Applet +
    +
+ 		+ General +
    +
  • Make selection for columns now works on marked columns + rather than columns in rubber-band selection region.
    • +
+ Application +
    +
Deployment and Documentation +
    +
Application Known issues +
    +
Applet Known Issues +
    +
+
+ 2.8.2
3/12/2014 +
General +
    +
  • Updated Java code signing certificate donated by Certum.PL.
    • +
  • Features and annotation preserved when performing pairwise + alignment
    • +
  • RNA pseudoknot annotation can be + imported/exported/displayed
    • +
  • 'colour by annotation' can colour by RNA and + protein secondary structure
    • +
Application +
    +
  • Extract and display secondary structure for sequences with + 3D structures
    • +
  • Support for parsing RNAML
    • +
  • Annotations menu for layout +
      +
    • sort sequence annotation rows by alignment
      • +
    • place sequence annotation above/below alignment + annotation
      • +
    +
  • Output in Stockholm format
    • +
  • Internationalisation: improved Spanish (es) translation
    • +
  • Structure viewer preferences tab
    • +
  • Disorder and Secondary Structure annotation tracks shared + between alignments
    • +
  • UCSF Chimera launch and linked highlighting from Jalview
    • +
  • Show/hide all sequence associated annotation rows for all + or current selection
    • +
  • disorder and secondary structure predictions available as + dataset annotation
    • +
  • Per-sequence rna helices colouring
    • + + +
  • Sequence database accessions imported when fetching + alignments from Rfam
    • +
  • update VARNA version to 3.91
    • + +
  • New groovy scripts for exporting aligned positions, + conservation values, and calculating sum of pairs scores.
    • +
  • Command line argument to set default JABAWS server
    • +
  • include installation type in build properties and console + log output
    • +
  • Updated Jalview project format to preserve dataset annotation
    • +
+ Application +
    +
  • Distinguish alignment and sequence associated RNA + structure in structure->view->VARNA
    • +
  • Raise dialog box if user deletes all sequences in an + alignment
    • +
  • Pressing F1 results in documentation opening twice
    • +
  • Sequence feature tooltip is wrapped
    • +
  • Double click on sequence associated annotation selects + only first column
    • +
  • Redundancy removal doesn't result in unlinked leaves + shown in tree
    • +
  • Undos after several redundancy removals don't undo + properly
    • +
  • Hide sequence doesn't hide associated annotation
    • +
  • User defined colours dialog box too big to fit on screen + and buttons not visible
    • +
  • author list isn't updated if already written to jalview + properties
    • +
  • Popup menu won't open after retrieving sequence from + database
    • +
  • File open window for associate PDB doesn't open
    • +
  • Left-then-right click on a sequence id opens a browser + search window
    • +
  • Cannot open sequence feature shading/sort popup menu in + feature settings dialog
    • +
  • better tooltip placement for some areas of Jalview desktop
    • +
  • Allow addition of JABAWS Server which doesn't pass + validation
    • +
  • Web services parameters dialog box is too large to fit on + screen
    • +
  • Muscle nucleotide alignment preset obscured by tooltip
    • +
  • JABAWS preset submenus don't contain newly defined + user preset
    • +
  • MSA web services warns user if they were launched with + invalid input
    • +
  • Jalview cannot contact DAS Registy when running on Java 8
    • +
  • + + 'Superpose with' submenu not shown when new view created +
    • + +
Deployment and Documentation +
    +
  • 2G and 1G options in launchApp have no effect on memory + allocation
    • +
  • launchApp service doesn't automatically open + www.jalview.org/examples/exampleFile.jar if no file is given
    • +
  • + + InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is + available +
    • +
Application Known issues +
    +
  • + + corrupted or unreadable alignment display when scrolling alignment + to right +
    • +
  • + + retrieval fails but progress bar continues for DAS retrieval with + large number of ID +
    • +
  • + + flatfile output of visible region has incorrect sequence start/end +
    • +
  • + + rna structure consensus doesn't update when secondary + structure tracks are rearranged +
    • +
  • + + invalid rna structure positional highlighting does not highlight + position of invalid base pairs +
    • +
  • + + out of memory errors are not raised when saving jalview project + from alignment window file menu +
    • +
  • + + Switching to RNA Helices colouring doesn't propagate to + structures +
    • +
  • + + colour by RNA Helices not enabled when user created annotation + added to alignment +
    • +
  • + + Jalview icon not shown on dock in Mountain Lion/Webstart +
    • +
Applet Known Issues +
    +
  • + + JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies +
    • +
  • + + Jalview and Jmol example not compatible with IE9 +
    • + +
  • Sort by annotation score doesn't reverse order when + selected
    • +
+
+ 2.8.1
4/6/2014 +
+ + General +
    +
  • Internationalisation of user interface (usually called + i18n support) and translation for Spanish locale
    • +
  • Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G
    • +
  • Improved group creation/removal options in + alignment/sequence Popup menu
    • +
  • Sensible precision for symbol distribution percentages + shown in logo tooltip.
    • +
  • Annotation panel height set according to amount of + annotation when alignment first opened
    • +
Application +
    +
  • Interactive consensus RNA secondary structure prediction + VIENNA RNAAliFold JABA 2.1 service
    • +
  • Select columns containing particular features from Feature + Settings dialog
    • +
  • View all 'representative' PDB structures for selected + sequences
    • +
  • Update Jalview project format: +
      +
    • New file extension for Jalview projects '.jvp'
      • +
    • Preserve sequence and annotation dataset (to store + secondary structure annotation,etc)
      • +
    • Per group and alignment annotation and RNA helix + colouring
      • +
    +
    • +
  • New similarity measures for PCA and Tree calculation + (PAM250)
    • +
  • Experimental support for retrieval and viewing of flanking + regions for an alignment
    • +
+ 		+ Application +
    +
  • logo keeps spinning and status remains at queued or + running after job is cancelled
    • +
  • cannot export features from alignments imported from + Jalview/VAMSAS projects
    • +
  • Buggy slider for web service parameters that take float + values
    • +
  • Newly created RNA secondary structure line doesn't have + 'display all symbols' flag set
    • +
  • T-COFFEE alignment score shading scheme and other + annotation shading not saved in jalview project
    • +
  • Local file cannot be loaded in freshly downloaded Jalview
    • +
  • Jalview icon not shown on dock in Mountain Lion/Webstart
    • +
  • Load file from desktop file browser fails
    • +
  • Occasional NPE thrown when calculating large trees
    • +
  • Cannot reorder or slide sequences after dragging an + alignment onto desktop
    • +
  • Colour by annotation dialog throws NPE after using + 'extract scores' function
    • +
  • Loading/cut'n'pasting an empty file leads to a grey + alignment window
    • +
  • Disorder thresholds rendered incorrectly after performing + IUPred disorder prediction
    • +
  • Multiple group annotated consensus rows shown when + changing 'normalise logo' display setting
    • +
  • Find shows blank dialog after 'finished searching' if + nothing matches query
    • +
  • Null Pointer Exceptions raised when sorting by feature + with lots of groups +
    • +
  • Errors in Jmol console when structures in alignment don't + overlap +
    • +
  • Not all working JABAWS services are shown in Jalview's + menu
    • +
  • JAVAWS version of jalview fails to launch with 'invalid + literal/length code'
    • +
  • Annotation/RNA Helix colourschemes cannot be applied to + alignment with groups (actually fixed in 2.8.0b1)
    • +
  • RNA Helices and T-Coffee Scores available as default colourscheme
    • + +
Applet +
    +
  • Remove group option is shown even when selection is not a + group
    • +
  • Apply to all groups ticked but colourscheme changes don't + affect groups
    • +
  • Documented RNA Helices and T-Coffee Scores as valid colourscheme name
    • +
  • Annotation labels drawn on sequence IDs when Annotation panel is not displayed
    • +
  • Increased font size for dropdown menus on OSX and embedded windows
    • +
Other +
    +
  • Consensus sequence for alignments/groups with a single + sequence were not calculated
    • +
  • annotation files that contain only groups imported as + annotation and junk sequences
    • +
  • Fasta files with sequences containing '*' incorrectly + recognised as PFAM or BLC
    • +
  • conservation/PID slider apply all groups option doesn't + affect background (2.8.0b1) +
  • +
  • redundancy highlighting is erratic at 0% and 100%
    • +
  • Remove gapped columns fails for sequences with ragged + trailing gaps
    • +
  • AMSA annotation row with leading spaces is not registered + correctly on import
    • +
  • Jalview crashes when selecting PCA analysis for certain + alignments
    • +
  • Opening the colour by annotation dialog for an existing + annotation based 'use original colours' colourscheme loses + original colours setting
    • +
+
+ 2.8.0b1
30/1/2014 +
+ 		+
    +
  • Trusted certificates for JalviewLite applet and + Jalview Desktop application
    Certificate was donated by + Certum to the Jalview + open source project). +
    • +
  • Jalview SRS links replaced by Uniprot and EBI-search +
    • +
  • Output in Stockholm format
    • +
  • Allow import of data from gzipped files
    • +
  • Export/import group and sequence associated line + graph thresholds
    • +
  • Nucleotide substitution matrix that supports RNA and + ambiguity codes
    • +
  • Allow disorder predictions to be made on the current + selection (or visible selection) in the same way that JPred + works
    • +
  • Groovy scripting for headless jalview operation
    • +
Other improvements +
    +
  • Upgrade desktop installer to InstallAnywhere 2013
    • +
  • COMBINE statement uses current SEQUENCE_REF and + GROUP_REF scope to group annotation rows
    • +
  • Support '' style escaping of quotes in Newick + files
    • +
  • Group options for JABAWS service by command line name
    • +
  • Empty tooltip shown for JABA service options with a + link but no description
    • +
  • Select primary source when selecting authority in + database fetcher GUI
    • +
  • Add .mfa to FASTA file extensions recognised by + Jalview
    • +
  • Annotation label tooltip text wrap
    • +
+ 		+
    +
  • Slow scrolling when lots of annotation rows are + displayed
    • +
  • Lots of NPE (and slowness) after creating RNA + secondary structure annotation line
    • +
  • Sequence database accessions not imported when + fetching alignments from Rfam
    • +
  • Incorrect SHMR submission for sequences with + identical IDs
    • +
  • View all structures does not always superpose + structures
    • +
  • Option widgets in service parameters not updated to + reflect user or preset settings
    • +
  • Null pointer exceptions for some services without + presets or adjustable parameters
    • +
  • Discover PDB IDs entry in structure menu doesn't + discover PDB xRefs
    • +
  • Exception encountered while trying to retrieve + features with DAS
    • +
  • Lowest value in annotation row isn't coloured + when colour by annotation (per sequence) is coloured
    • +
  • Keyboard mode P jumps to start of gapped region when + residue follows a gap
    • +
  • Jalview appears to hang importing an alignment with + Wrap as default or after enabling Wrap
    • +
  • 'Right click to add annotations' message + shown in wrap mode when no annotations present
    • +
  • Disorder predictions fail with NPE if no automatic + annotation already exists on alignment
    • +
  • oninit javascript function should be called after + initialisation completes
    • +
  • Remove redundancy after disorder prediction corrupts + alignment window display
    • +
  • Example annotation file in documentation is invalid
    • +
  • Grouped line graph annotation rows are not exported + to annotation file
    • +
  • Multi-harmony analysis cannot be run when only two + groups created
    • +
  • Cannot create multiple groups of line graphs with + several 'combine' statements in annotation file
    • +
  • Pressing return several times causes Number Format + exceptions in keyboard mode
    • +
  • Multi-harmony (SHMMR) method doesn't submit + correct partitions for input data
    • +
  • Translation from DNA to Amino Acids fails
    • +
  • Jalview fail to load newick tree with quoted label
    • +
  • --headless flag isn't understood
    • +
  • ClassCastException when generating EPS in headless + mode
    • +
  • Adjusting sequence-associated shading threshold only + changes one row's threshold
    • +
  • Preferences and Feature settings panel panel + doesn't open
    • +
  • hide consensus histogram also hides conservation and + quality histograms
    • +
+
2.8
12/11/2012
Application -
  • Support for JABAWS 2.0 Services (AACon alignment +
    • Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega)
    • JABAWS server status indicator in Web Services preferences