From standley at protein.osaka-u.ac.jp Fri May 2 05:43:25 2008 From: standley at protein.osaka-u.ac.jp (Daron Standley) Date: Fri May 2 05:43:38 2008 Subject: [Jalview-discuss] coloring by annotation Message-ID: <3A75A582-0ADF-4AB9-9033-1FBF829D2235@protein.osaka-u.ac.jp> Hi- I am using Jalview to display pairwise alignments, with the residue similarity score defined by me and plotted as a bar graph using an external annotations file. From the menu, I can color the alignment by the residue similarity: color-> by annotation Is there an easy way to make this coloring appear by default so that the user doesn't have to use the pull-down menu? Also, I would like to ask the same question but in the cases where I use the "above threshold" option to color only high-scoring residue pairs. (I am curious about this since Jalview seems to figure out the threshold based on the distribution of scores.) Thanks in advance for your help. Best wishes, -Daron From jimp at compbio.dundee.ac.uk Fri May 2 09:41:31 2008 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Fri May 2 09:41:36 2008 Subject: [Jalview-discuss] coloring by annotation In-Reply-To: <3A75A582-0ADF-4AB9-9033-1FBF829D2235@protein.osaka-u.ac.jp> References: <3A75A582-0ADF-4AB9-9033-1FBF829D2235@protein.osaka-u.ac.jp> Message-ID: <20080502094131.78da88ea.jimp@compbio.dundee.ac.uk> Hello Daron. On Fri, 2 May 2008 13:43:25 +0900 Daron Standley wrote: > I am using Jalview to display pairwise alignments, with the residue > similarity score defined by me and plotted as a bar graph using an > external annotations file. > From the menu, I can color the alignment by the residue similarity: > > color-> by annotation > > Is there an easy way to make this coloring appear by default so that > the user doesn't have to use the pull-down menu? actually, there isn't, without some kind of modification to the source. This goes for both the thresholded and the shaded colouring style. The best solution would be to extend the jalview annotation file format to allow the the 'by annotation' colouring style to be specified for the alignment, or for a particular group, along with the additional parameters (threshold mode, min/max colouring, threshold value). > curious about this since Jalview seems to figure out the threshold > based on the distribution of scores.) I don't think that it does anything too clever, here! I'll have a think about the extensions to the annotations format and get back to you all on this. There are a few other things which can be added to the format, too (hidden column specification, view name/creation). cheers. Jim -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From erturkde at hotmail.com Tue May 6 21:01:07 2008 From: erturkde at hotmail.com (Deniz Erturk) Date: Tue May 6 21:01:11 2008 Subject: [Jalview-discuss] what does quality refer to in annotation of the alignment? Message-ID: Hi, Does anyone know what does "quality " exactly refer to in annotation of an alignment? Thanks, Denis _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20080506/fecbae66/attachment.htm From jimp at compbio.dundee.ac.uk Mon May 12 22:25:44 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon May 12 22:25:55 2008 Subject: [Jalview-discuss] what does quality refer to in annotation of the alignment? In-Reply-To: References: Message-ID: <4828B5D8.7040907@compbio.dundee.ac.uk> Hi Deniz, sorry - I left you hanging here (I guess I was hoping someone else might reply!). Deniz Erturk wrote: > Does anyone know what does "quality " exactly refer to in annotation of > an alignment? Its described in the online help (here: http://www.jalview.org/help/html/calculations/quality.html) - basically the height of the histogram at each alignment position reflects the cost of all residue substitutions observed in the column relative to the the sum of BLOSUM62 scores that would be obtained if the column were completely conserved. I don't have a precise reference to hand concerning this score, but its certainly not novel and is in essence a local multiple sequence alignment objective function. does that help ? Jim From standley at protein.osaka-u.ac.jp Tue May 13 10:06:37 2008 From: standley at protein.osaka-u.ac.jp (Daron Standley) Date: Tue May 13 10:06:44 2008 Subject: [Jalview-discuss] resizing alignment window Message-ID: <67FCAE06-98C8-4F3D-9165-B05B5703EDE6@protein.osaka-u.ac.jp> Hi- One of my colleagues asked me if, when the applet is used, and embedded= true, can the window where the alignment appears be resized? I think the answer is no, but I just wantedto be sure. Thanks, -Daron From jimp at compbio.dundee.ac.uk Tue May 13 10:50:12 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue May 13 10:50:47 2008 Subject: [Jalview-discuss] resizing alignment window In-Reply-To: <67FCAE06-98C8-4F3D-9165-B05B5703EDE6@protein.osaka-u.ac.jp> References: <67FCAE06-98C8-4F3D-9165-B05B5703EDE6@protein.osaka-u.ac.jp> Message-ID: <48296454.2020508@compbio.dundee.ac.uk> Hi Daron. Daron Standley wrote: > One of my colleagues asked me if, when the applet is used, and embedded= > true, can the window where the alignment appears be resized? > > I think the answer is no, but I just wantedto be sure. This is the case, as far as we are aware. I strong suspect it is possible to construct a page with a dynamically resizing canvas - but I'm not enough of a javascript expert to know how to do it (there are probably some resizing events which jalviewLite might need to handle for this to work, too). sorry! Jim -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From erturkde at hotmail.com Tue May 13 16:51:05 2008 From: erturkde at hotmail.com (Deniz Erturk) Date: Tue May 13 16:51:10 2008 Subject: [Jalview-discuss] what does quality refer to in annotation of the alignment? In-Reply-To: <4828B5D8.7040907@compbio.dundee.ac.uk> References: <4828B5D8.7040907@compbio.dundee.ac.uk> Message-ID: That helps, thanks Jim. Deniz > Date: Mon, 12 May 2008 22:25:44 +0100 > From: jimp@compbio.dundee.ac.uk > To: jalview-discuss@jalview.org > Subject: Re: [Jalview-discuss] what does quality refer to in annotation of the alignment? > > Hi Deniz, sorry - I left you hanging here (I guess I was hoping someone > else might reply!). > > Deniz Erturk wrote: > > Does anyone know what does "quality " exactly refer to in annotation of > > an alignment? > Its described in the online help (here: > http://www.jalview.org/help/html/calculations/quality.html) - basically > the height of the histogram at each alignment position reflects the cost > of all residue substitutions observed in the column relative to the the > sum of BLOSUM62 scores that would be obtained if the column were > completely conserved. I don't have a precise reference to hand > concerning this score, but its certainly not novel and is in essence a > local multiple sequence alignment objective function. > > does that help ? > Jim > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss _________________________________________________________________ Connect to the next generation of MSN Messenger? http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20080513/a63333c6/attachment.htm From jimp at compbio.dundee.ac.uk Thu May 15 12:42:33 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu May 15 12:42:51 2008 Subject: [Jalview-discuss] starting Jalview via webstart from your own website In-Reply-To: References: <482BEB38.7060101@compbio.dundee.ac.uk> Message-ID: <482C21A9.8080903@compbio.dundee.ac.uk> Hi again Marcelo. I've cc'ed this to the discussion list, just for the record. Marcelo bertalan wrote: > Thank you for your reply. no problem. > I have been using Javaws for artemis without any problem, but I still > have problems with Jalview. oh - ok... > I was wondering if is possible to use jalview.jnlp and ask to open my > files: yes. that's the preferred (and only reliable) way of doing that. > Like: > "... > > > http://www.someplace/~me/Alignment.aln > > > " that looks ok - but you need the -open parameter before the alignment filename. The example file will only be opened if there were no valid input files given on the command line *and* the user preferences indicate that the example should be opened on startup by default. My guess is that you haven't specified the argument correctly. There's a jalview jnlp generator servlet here: http://www.jalview.org/services/launchApp Try this URL: http://www.jalview.org/services/launchApp?open=http://www.jalview.org/examples/uniref50.fa&colour=C=yellow;%20R,K,H=FF5555;%20D,E=5555FF wget on this url returns a jnlp with the following args: .. -open http://www.jalview.org/examples/uniref50.fa -colour C=yellow; R,K,H=FF5555; D,E=5555FF .. > Can I open Jalview from your server opening files from my server (like I > do with artemis) or should I put Jalview in my server opening my files ? If you want, you could just use the www.jalview.org/services/launchApp service directly - by embedding the URL in pages served by your own site. We try to make sure the servlet is available continuously and it will always refer to the latest Jalview webstart install. As far as privacy goes we do occasionally analyse the logs there, but won't touch the data otherwise, since for us its nice to know that Jalview is being used on other people's sites. If your concerned about that, then feel free to host a jnlp or jnlp generator of your own! you should also check out the development URL for jalview - we are hoping to release version 2.4 sometime this year (actually sooner rather than later, but ... oh well). The development build is refreshed here: http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/ - here you can see the most up to date versions of the applet, application and source. I wouldn't recommend using the webstart build there for your website, though - since it is an automated build from CVS - and not guaranteed to be stable. best of luck - and please send us a URL for your site so we can make a link to it on the Jalview links page ! Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096.