Could you tell me what java is Jalview being run with and what window manager you are using ?
Jim J. B. Procter Jalview/enfin Barton group -----Original Message----- From: "Fabian Glaser, Technion" <[email protected]> To: Jim Procter <[email protected]> Sent: Tue, 29 Nov 2011 6:06 Subject: Re: [Jalview-discuss] PCA custom coloring Dear Jim, Additionally, with the installation of the last version of Jalview on my Ubuntu 11.10, I get a "blured" alignment when I try to slide the windows and see different parts of the alignment. Is there any way to overcome this problem? Thanks, Fabian Fabian Glaser, PhD Bioinformatics Knowledge Unit The Lorry I. Lokey Interdisciplinary Center For Life Sciences and Engineering Technion, Haifa 32000, ISRAEL E-mail: [email protected] Tel: +972-4-8293701 Jim Procter said the following on 28/11/11 16:42: > Hello Fabian. > > On 28/11/2011 14:00, Fabian Glaser wrote: >> I am new to the list, so forgive me if this a repetitive topic. >> >> I would like to color the result of the PCA analysis but not by the >> clusters selected with a tree, I would like to color selected points >> on the PCA with specific colors. >> >> Is that possible with Jalview? > It is - but only just :) The graphical interface doesn't really have > any controls for doing this within the program. Something that we hope > to fix in a future release. > > The simplest way is to prepare an annotations file that creates a group > for each sequence in the alignment and assigns it a colour. The > annotation file has a tab-delimited structure, and its format is > described here: > http://www.jalview.org/help/html/features/annotationsFormat.html > > For example, to assign colours to three sequences 'FER1_MESCR', > 'FER1_SPIOL', 'FER1_MAIZE': > > JALVIEW_ANNOTATION > > SEQUENCE_GROUP\tFER1_MESCR\t0\t0\t-1\tFER1_MESCR > SEQUENCE_GROUP\tFER1_SPIOL\t0\t0\t-1\tFER1_SPIOL > SEQUENCE_GROUP\tFER1_MAIZE\t0\t0\t-1\tFER1_MAIZE > PROPERTIES\tFER1_MESCR\tidColour=red > PROPERTIES\tFER1_MAIZE\tidColour=blue > PROPERTIES\tFER1_SPIOL\tidColour=green > > Note - the '\t's need to be replaced with tab symbols! > > Jim. > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
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