X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=dac2c0b0c949d651bd7c3dbb780a7911693f35c0;hb=a0f5e2532e4114b22cb0203636e90d5ed3ba2d86;hp=b56442829556bfb5dc38f401cfce65f988575762;hpb=bbd978c6c697b2a4591d984e011198d7d4b5afc5;p=jalview.git diff --git a/help/html/releases.html b/help/html/releases.html index b564428..dac2c0b 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -70,6 +70,370 @@ li:before {
+ 2.10.3b1
23/1/2018 +
+ +
+ + +
+ + + + + +
+ 2.10.3
17/11/2017 +
+ +
+ +
    +
  • + Faster and more efficient management and + rendering of sequence features +
    • +
  • + More reliable Ensembl fetching with HTTP + 429 rate limit request hander +
    • +
  • + 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 +
    • +
+ 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 +
    +
  • + 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) +
    • +
+
+ + + +
+ 2.10.2b2
+ 2/10/2017 +
+ +
+ New features in Jalview Desktop +
    +
  • + Uniprot Sequence Fetcher now uses web API at uniprot.org +
    • +
  • HTTPS used for all connections to ebi.ac.uk +
    • +
+
+
+
+ + + +
+ 2.10.2b1
+ 7/9/2017 +
+ +
+ +
    +
  • + Show gaps in overview window by colouring + in grey (sequences used to be coloured grey, and gaps were + white) +
    • +
  • + Overview tab in Jalview Desktop + Preferences +
    • +
  • + Overview updates immediately on increase + in size and progress bar shown as higher resolution + overview is recalculated +
    • + +
+
+
+ +
    +
  • + Overview window redraws every hidden + column region row by row +
    • +
  • + duplicate protein sequences shown after + retrieving Ensembl crossrefs for sequences from Uniprot +
    • +
  • + Overview window throws NPE if show boxes + format setting is unticked +
    • +
  • + Groups are coloured wrongly in overview + if group has show boxes format setting unticked +
    • +
  • + Redraw problems when + autoscrolling whilst dragging current selection group to + include sequences and columns not currently displayed +
    • +
  • + Not all chains are mapped when multimeric + assemblies are imported via CIF file +
    • +
  • + Gap colour in custom colourscheme is not + displayed when threshold or conservation colouring is also + enabled. +
    • +
  • + JABAWS 2.2 services report wrong JABAWS + server version +
    • +
  • + Jalview continues to scroll after + dragging a selected region off the visible region of the + alignment +
    • +
  • + Cannot apply annotation based + colourscheme to all groups in a view +
    • +
  • + IDs don't line up with sequences + initially after font size change using the Font chooser or + middle-mouse zoom +
    • +
+
+ + + +
2.10.2
17/8/2017
@@ -122,10 +486,6 @@ li:before { with alignment and overview windows
  • - Linked scrolling of CDS/Protein views - via Overview or sequence motif search operations -
    • -
  • Scrolling of wrapped alignment views via overview
    • @@ -167,6 +527,10 @@ li:before { the application.
  • + Linked scrolling of CDS/Protein views + via Overview or sequence motif search operations +
    • +
  • Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent @@ -180,6 +544,10 @@ li:before { 3D Structure
    • +
    +
    2.10.1
    29/11/2016     @@ -1320,6 +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. +