X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=dac2c0b0c949d651bd7c3dbb780a7911693f35c0;hb=a0f5e2532e4114b22cb0203636e90d5ed3ba2d86;hp=184fa46d5ad8d446a5af80f9967aa30de7f40c5c;hpb=f0086cf54852e4f775d6502fe809dc998643a064;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index 184fa46..dac2c0b 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -70,8 +70,27 @@ li:before {
- 2.10.3
- 10/10/2017 + 2.10.3b1
23/1/2018 +
+ +
+ + +
+ + + + + +
+ 2.10.3
17/11/2017
@@ -89,21 +108,227 @@ li:before { Structure views don't get updated unless their colours have changed +
  • + All linked sequences are highlighted for + a structure mousover (Jmol) or selection (Chimera) +
    • +
  • + 'Cancel' button in progress bar for + JABAWS AACon, RNAAliFold and Disorder prediction jobs +
    • +
  • + Stop codons are excluded in CDS/Protein + view from Ensembl locus cross-references +
    • +
  • + Start/End limits are shown in Pairwise + Alignment report +
    • +
  • + Sequence fetcher's Free text 'autosearch' + feature can be disabled +
    • +
  • + Retrieve IDs tab added for UniProt and + PDB easier retrieval of sequences for lists of IDs +
    • +
  • + Short names for sequences retrieved from + Uniprot +
    • -
    • Example groovy script for generating a matrix of percent identity scores for current alignment.
    - + Scripting +
      +
    • Groovy interpreter updated to 2.4.12
      • +
    • Example groovy script for generating a matrix of + percent identity scores for current alignment.
      • +
    + Testing and Deployment +
      +
    • + Test to catch memory leaks in Jalview UI +
      • +
    +
    - + General
      -
    • Structures with whitespace chainCode cannot be viewed in Chimera
      • -
    • Protein annotation panel too high in CDS/Protein view -
      • -
    • Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs -
      • -
    • Slow EnsemblGenome ID lookup
      • -
    • Race condition when parsing sequence ID strings in parallel
      • +
    • + Pressing tab after updating the colour + threshold text field doesn't trigger an update to the + alignment view +
      • +
    • + Race condition when parsing sequence ID + strings in parallel +
      • +
    • + Overview windows are also closed when + alignment window is closed +
      • +
    • + Export of features doesn't always respect + group visibility +
      • +
    • + Jumping from column 1 to column 100,000 + takes a long time in Cursor mode +
    - + Desktop +
      +
    • + Structures with whitespace chainCode + cannot be viewed in Chimera +
      • +
    • + Protein annotation panel too high in + CDS/Protein view +
      • +
    • + Can't edit the query after the server + error warning icon is shown in Uniprot and PDB Free Text + Search Dialogs +
      • +
    • + Slow EnsemblGenome ID lookup +
      • +
    • + Revised Ensembl REST API CDNA query +
      • +
    • + Hidden column marker in last column not + rendered when switching back from Wrapped to normal view +
      • +
    • + Annotation display corrupted when + scrolling right in unwapped alignment view +
      • +
    • + Existing features on subsequence + incorrectly relocated when full sequence retrieved from + database +
      • +
    • + Last reported memory still shown when + Desktop->Show Memory is unticked (OSX only) +
      • +
    • + Amend Features dialog doesn't allow + features of same type and group to be selected for + amending +
      • +
    • + Jalview becomes sluggish in wide + alignments when hidden columns are present +
      • +
    • + Jalview freezes when loading and + displaying several structures +
      • +
    • + Black outlines left after resizing or + moving a window +
      • +
    • + Unable to minimise windows + within the Jalview desktop on OSX +
      • +
    • + Mouse wheel doesn't scroll vertically + when in wrapped alignment mode +
      • +
    • + Scale mark not shown when close to right + hand end of alignment +
      • +
    • + Pairwise alignment of selected regions of + each selected sequence do not have correct start/end + positions +
      • +
    • + Alignment ruler height set incorrectly + after canceling the Alignment Window's Font dialog +
      • +
    • + Show cross-references not enabled after + restoring project until a new view is created +
      • +
    • + Warning popup about use of SEQUENCE_ID in + URL links appears when only default EMBL-EBI link is + configured (since 2.10.2b2) +
      • +
    • + Overview redraws whole window when box + position is adjusted +
      • +
    • + Structure viewer doesn't map all chains + in a multi-chain structure when viewing alignment + involving more than one chain (since 2.10) +
      • +
    • + Double residue highlights in cursor mode + if new selection moves alignment window +
      • +
    • + Alignment vanishes when using + arrow key in cursor mode to pass hidden column marker +
      • +
    • + Ensembl Genomes example ID changed to one + that produces correctly annotated transcripts and products +
      • +
    • + Toggling a feature group after first time + doesn't update associated structure view +
      • +
    + Applet
    +
      +
    • + Concurrent modification exception when + closing alignment panel +
      • +
    + BioJSON
    +
      +
    • + BioJSON export does not preserve + non-positional features +
      • +
    + New Known Issues +
      +
    • + Delete/Cut selection doesn't relocate + sequence features correctly (for many previous versions of + Jalview) +
      • +
    • + Cursor mode unexpectedly scrolls when + using cursor in wrapped panel other than top +
      • +
    • + Select columns containing feature ignores + graduated colour threshold +
      • +
    • + Edit sequence operation doesn't + always preserve numbering and sequence features +
      • +
    + Known Java 9 Issues +
      +
    • + Groovy Console very slow to open and is + not responsive when entering characters (Webstart, Java + 9.01, OSX 10.10) +
      • +
    +
    @@ -1460,6 +1685,10 @@ li:before { after clicking on it to create new annotation for a column. +
  • + Null Pointer Exception raised when + pressing Add on an orphaned cut'n'paste window. +