What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=c260b5a960e861cffb0cc992ca0079664b7f10b0;hb=5ccaaa04373a6f6ae265c43c579adb58421efba0;hp=651292e0b5fa6c4ba15bda5a770cab93160a03b1;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 651292e..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,50 +1,71 @@ + What's new ? -

What's new ?

- -

Jalview Version 2.2

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Multiple views with different styles, colours, hidden regions for -one alignment

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Easily add, amend and delete sequence features

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"Reload" alignment from File or URL to revert to -original

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"Save" to current filename or "Save As" to -new filename

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New "New Window" button on the -"Output To Textbox" opens output window for quick 'sequence -editing'.

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Set different text colour for dark or light background

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Right align sequence ids

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Set colour of lower case residues in a user defined colour scheme -

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Menu Rearrangements: New Format for alignment -layout and Select for region selection.

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Menu item accelerator keys added

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Control-V pastes sequences to active window, Control-Shift-V -pastes to a new window.

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Raise/Minimise alignment and all associated windows from desktop -window's window menu

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Select and colour whole branches of a tree

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'New Window' button on the 'Output to Text box' alignment output -option to open a new alignment window after editing.

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Issues Resolved

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Optimisations for large alignments: faster multithreaded -calculations and Undo/Redo system.

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Remove empty columns - if empty columns exist at the end of the -alignment bug fixed.

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DAS feature fetching slowed down, doesn't overload DAS servers

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DAS feature fetching can be cancelled

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Correct display of > and < symbols for feature descriptions -without explicit <html> tags.

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Zoom working in PCA viewer

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Sequence Descriptions retained after running a web service

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See the Release History page for -details of all new features and resolved issues.

+

+ Jalview 2.11 - major and minor new features +

+

Jalview 2.11 introduces support for loading VCF files, and new + filters and shading models for sequence features. Under the hood, + we've addressed many bugs, and also made some important changes in + the way the Jalview desktop is installed and launched.

+

VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported + from a local VCF file.
The Jalview Launcher and Update System
+ Jalview's new installation model means you'll only need to + download and install Jalview once. After installation, Jalview + will automatically keep itself up to date. The launcher also sets + Jalview's memory automatically, so you'll never again have to + manually configure Java's memory settings.
We are grateful to + Install4J who provided us with a free license for their + installation system, and Jalview's over the air update system is + via Getdown.

+

+ The full list of bugs fixed in this release can be found in the 2.11 Release Notes. +

+

+ Jalview and Java 11, 13, and onwards +

+

Java 11 provides improved performance and better OS + integration, so we now recommend users select our Java 11 Jalview + distribution rather than the legacy Java 8 build.

+ Known Issues - update for 211 +

OSX: The 'Open File' dialog for Jalview's Groovy Console + appears with the title 'Save As', and attempting to select a file + to load yields a FileNotFound exception.
The workaround is to first + clear the 'Untitled' filename before selecting the file you wish + to load. +
OSX: Links don't open when clicked on or via the Sequence + or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items