problem with some features, windows 10

Dear Jalvew discussion group,
I installed the windows version but there are some problem with is, e.g if I go

Select View⇒ Feature settings
I don’t see any list of features

also, many windows appear with font sizes too small to be readable and I can change the font sizes in only a limited number of them.

Is it possible to install jalview in cygwin ?
if so, could I get some guidelines please ?

thnxalot
eugenia

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···

Maria Eugenia D’Amato
Professor

University of the Western Cape,
Department of Biotechnology,
Forensic DNA Lab.
Private Bag X17, 7535 Bellville.
Cape Town.
South Africa.

medamato@uwc.ac.za
Fax : + 27 21 959 3505
Te: +27 21 959 3372 / 2065

Hello Maria

*/Select View⇒Feature settings/*
I don't see any list of features

It may be that the sequences you are viewing do not have features available from the public databases. Also, if you loaded the sequences as a simple flat-file (e.g. fasta, clustalw, etc) then these formats don't provide features on sequences.

You can try to retreive features via the web service menu's 'Fetch DB References', which will use the sequence ID string to query ENA or Uniprot to retrieve annotation. We have a tutorial video on this topic: https://www.youtube.com/watch?v=nLINw__nfDg

also, many windows appear with font sizes too small to be readable and I can change the font sizes in only a limited number of them.

It sounds like you have a 4K/Hi DPI monitor or laptop display. The easiest route right now is to install the experimental Java 11 Jalview Application. You can download it at:
http://www.jalview.org/getdown/release/install4j/11/Jalview-2_11_1_0-windows-x64-java_11.exe

Is it possible to install jalview in cygwin ?
if so, could I get some guidelines please ?

The short answer is that we don't have a special cygwin installer for Jalview because cygwin uses windows native executables under the hood, so you can just execute the Jalview application's Jalview.exe directly from cygterm. However, the Jalview.exe is not a well behaved command line application so if you want to run Jalview as a command line program your best bet is to download the executable jar:
http://www.jalview.org/getdown/release/jalview-all-2.11.1.0-j1.8.jar
or the j11 version
http://www.jalview.org/getdown/release/jalview-all-2.11.1.0-j11.jar

You can then launch it from the terminal (assuming you have java on your path) via:

java -jar jalview-all-2.11.1.0-j11.jar

To see available arguments use '-h' !

Here's a stackoverflow solution on adding Java to your path:
https://stackoverflow.com/questions/28259282/run-and-compile-java-code-in-cygwin

Do let us know how you get on !
Jim.

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On 14/07/2020 17:42, Maria D'Amato wrote: