From jimp at compbio.dundee.ac.uk Tue Sep 2 01:35:59 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Sep 2 01:36:36 2008 Subject: [Jalview-discuss] Jalview 2.4 Release Message-ID: <48BC8A6F.70509@compbio.dundee.ac.uk> Hello Jalviewers. On behalf of the Jalview team, I am pleased to inform you that after a rather prolonged testing period, Jalview 2.4 is now released. This release includes fixes for many minor bugs, and includes a variety of improvements, including new features for working with DAS sequence sources, EMBL coding regions, and also support for the VAMSAS interoperation framework (which is still experimental - see the built in help). The new release details are here : http://www.jalview.org/releaseHistory.html. The Jalview website has also been updated. The Applet API page has been extended with more API use examples, and we have added a version archive which includes details of the automated builds at http://www.jalview.org/versions.html Finally, we now ask that instead of emailing the help address at jalview.org, you forward all bugs and help requests to the discussion list - where they can be dealt with by the first person who knows the answer! Happy Jalviewing! Jim Procter. (for The Jalview Team) -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group www.jalview.org http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From bvroling at cmbi.ru.nl Wed Sep 3 15:55:54 2008 From: bvroling at cmbi.ru.nl (Bas Vroling) Date: Wed Sep 3 15:55:59 2008 Subject: [Jalview-discuss] links in multiple sequence alignment Message-ID: Hi, I've got a multiple sequence alignment with an annotation file. For some residues, I want to link to a another page on my site. However, when I put something like this in the annotations file: K136 ACM1_RAT -1 136 136 mutation I can right-click on those residues in the msa and the link menu appears, but when I click on it nothing happens... Regards, Bas From jimp at compbio.dundee.ac.uk Thu Sep 4 10:59:53 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Sep 4 11:00:48 2008 Subject: [Jalview-discuss] links in multiple sequence alignment In-Reply-To: References: Message-ID: <48BFB199.1070602@compbio.dundee.ac.uk> Hello Bas. Bas Vroling wrote: > I've got a multiple sequence alignment with an annotation file. For some > residues, I want to link to a another page on my site. > However, when I put something like this in the annotations file: > > K136 ACM1_RAT > -1 136 136 mutation > > > I can right-click on those residues in the msa and the link menu > appears, but when I click on it nothing happens... Can you check in your browser that the applet examples page works ? http://www.jalview.org/examples/applets.html Open the 'Displays a features file on the alignment' jalview appet, and try to open a link from the PFAM annotation. A problem that we have noticed recently is that popup-blockers (specifically, on windows vista) do not inform you when they block the 'showURL' call that an applet makes when it tries to open a URL in the browser. So check the popup-blocker settings for your site. 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 bvroling at cmbi.ru.nl Thu Sep 4 11:08:51 2008 From: bvroling at cmbi.ru.nl (Bas Vroling) Date: Thu Sep 4 11:09:15 2008 Subject: [Jalview-discuss] links in multiple sequence alignment In-Reply-To: <48BFB199.1070602@compbio.dundee.ac.uk> References: <48BFB199.1070602@compbio.dundee.ac.uk> Message-ID: <7F7651F7-5189-416E-8876-F4D6C26D6FC5@cmbi.ru.nl> Hi Jim, The applet version on the jalview site works great. Might it have something to do with the links being relative instead of absolute? Bas On 4 Sep, at 11:59, James Procter wrote: > Hello Bas. > > Bas Vroling wrote: >> I've got a multiple sequence alignment with an annotation file. For >> some >> residues, I want to link to a another page on my site. >> However, when I put something like this in the annotations file: >> >> K136 ACM1_RAT >> -1 136 136 mutation >> >> >> I can right-click on those residues in the msa and the link menu >> appears, but when I click on it nothing happens... > Can you check in your browser that the applet examples page works ? > > http://www.jalview.org/examples/applets.html > > Open the 'Displays a features file on the alignment' jalview appet, > and > try to open a link from the PFAM annotation. > > A problem that we have noticed recently is that popup-blockers > (specifically, on windows vista) do not inform you when they block the > 'showURL' call that an applet makes when it tries to open a URL in the > browser. So check the popup-blocker settings for your site. > > 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. > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss From jimp at compbio.dundee.ac.uk Thu Sep 4 14:01:15 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu Sep 4 14:01:28 2008 Subject: [Jalview-discuss] links in multiple sequence alignment In-Reply-To: <7F7651F7-5189-416E-8876-F4D6C26D6FC5@cmbi.ru.nl> References: <48BFB199.1070602@compbio.dundee.ac.uk> <7F7651F7-5189-416E-8876-F4D6C26D6FC5@cmbi.ru.nl> Message-ID: <48BFDC1B.7040103@compbio.dundee.ac.uk> Bas Vroling wrote: > Hi Jim, > > The applet version on the jalview site works great. Might it have > something to do with the links being relative instead of absolute? ah. maybe. yes! >>> K136 ACM1_RAT >>> -1 136 136 mutation Have you tried opening the console window ? there should be an 'open url: ...' message output when jalview tries to open the URL. When I tried using a bare href string like the one above, it failed with a 'malformedURLException'. So - the applet does not try to append the codebase to the URL before it opens it. I've put a TODO and a quick check for this in the jalview applet code, and this should propagate to the latest CVS release build shortly. However, it will need testing. 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 bvroling at cmbi.ru.nl Thu Sep 4 14:09:33 2008 From: bvroling at cmbi.ru.nl (Bas Vroling) Date: Thu Sep 4 14:10:01 2008 Subject: [Jalview-discuss] links in multiple sequence alignment In-Reply-To: <48BFDC1B.7040103@compbio.dundee.ac.uk> References: <48BFB199.1070602@compbio.dundee.ac.uk> <7F7651F7-5189-416E-8876-F4D6C26D6FC5@cmbi.ru.nl> <48BFDC1B.7040103@compbio.dundee.ac.uk> Message-ID: Wow, thanks for the quick response. I got the error too, so I'll try to checkout the cvs release and start testing :) Regards, Bas On 4 Sep, at 15:01, James Procter wrote: > Bas Vroling wrote: >> Hi Jim, >> >> The applet version on the jalview site works great. Might it have >> something to do with the links being relative instead of absolute? > ah. maybe. yes! >>>> K136 ACM1_RAT >>>> -1 136 136 mutation > Have you tried opening the console window ? there should be an 'open > url: ...' message output when jalview tries to open the URL. > > When I tried using a bare href string like the one above, it failed > with > a 'malformedURLException'. So - the applet does not try to append the > codebase to the URL before it opens it. I've put a TODO and a quick > check for this in the jalview applet code, and this should propagate > to > the latest CVS release build shortly. However, it will need testing. > > 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 Sebastien.Moretti at unil.ch Mon Sep 8 10:58:07 2008 From: Sebastien.Moretti at unil.ch (Sebastien MORETTI) Date: Mon Sep 8 10:58:03 2008 Subject: [Jalview-discuss] linkUrl and regexp Message-ID: <48C4F72F.7030806@unil.ch> Hi, With JalView 2.4, we try to extract an identifier from gene description to make an external link. Does it work with sequence description ? If it does, how to extract this kind of pattern: GENEID=ENSPTRG00000030533 TAXID=9598 I have tried this syntax, but nothing appends. $SEQUENCE_ID=/GENEID=(\w+) /=$ Thanks -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 From jimp at compbio.dundee.ac.uk Mon Sep 8 11:35:49 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon Sep 8 11:36:08 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C4F455.3030800@unil.ch> References: <48C4F455.3030800@unil.ch> Message-ID: <48C50005.9020407@compbio.dundee.ac.uk> G'day Sebastien. Sebastien MORETTI wrote: > With JalView 2.4, we try to extract an identifier from gene description > to make an external link. > > Does it work with sequence description ? no it doesn't, I'm afraid. When I put the regex feature in, I tried to keep the behaviour similar to 2.3 to avoid 'unexpected' additional URLs being generated. If the URL generation is extended so it operates on the description line then static URL links result in the whole description line being substituted for $SEQUENCE_ID$ - so a sequence header like >FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor generates two SRS links - one for FER1_SPIOL and the other for "Ferredoxin-1, chloroplast precursor". I didn't want to clutter the existing URL link menu too much, so I didn't include this additional URL generation step, but the implementation is trivial (and I'll leave it in the development code, but commented out). Does anyone else have an opinion on whether this behaviour should be included by default ? > If it does, how to extract this kind of pattern: > GENEID=ENSPTRG00000030533 TAXID=9598 > > I have tried this syntax, but nothing appends. > $SEQUENCE_ID=/GENEID=(\w+) /=$ The easiest way to do generate these links without changing the existing URL link behaviour would be to create a features file with URL links embedded in the description line - these will be shown in the link menu when the user right clicks on the sequence ID. Jim From Sebastien.Moretti at unil.ch Mon Sep 8 12:54:21 2008 From: Sebastien.Moretti at unil.ch (Sebastien MORETTI) Date: Mon Sep 8 12:54:13 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C50005.9020407@compbio.dundee.ac.uk> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> Message-ID: <48C5126D.9080305@unil.ch> > G'day Sebastien. Hi Jim, >> With JalView 2.4, we try to extract an identifier from gene description >> to make an external link. >> >> Does it work with sequence description ? > no it doesn't, I'm afraid. When I put the regex feature in, I tried to > keep the behaviour similar to 2.3 to avoid 'unexpected' additional URLs > being generated. > > If the URL generation is extended so it operates on the description line > then static URL links result in the whole description line being > substituted for $SEQUENCE_ID$ - so a sequence header like > >> FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor > > generates two SRS links - one for FER1_SPIOL and the other for > "Ferredoxin-1, chloroplast precursor". > > I didn't want to clutter the existing URL link menu too much, so I > didn't include this additional URL generation step, but the > implementation is trivial (and I'll leave it in the development code, > but commented out). Does anyone else have an opinion on whether this > behaviour should be included by default ? > >> If it does, how to extract this kind of pattern: >> GENEID=ENSPTRG00000030533 TAXID=9598 >> >> I have tried this syntax, but nothing appends. >> $SEQUENCE_ID=/GENEID=(\w+) /=$ > > The easiest way to do generate these links without changing the existing > URL link behaviour would be to create a features file with URL links > embedded in the description line - these will be shown in the link menu > when the user right clicks on the sequence ID. I think I will try this. Should I use this kind of syntax: http://... seq_ID With URL as description, a tab, sequence identifier ? Or is there a featureType keyword to change URL description to link to add ? Thanks > Jim > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss S?bastien -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ From jimp at compbio.dundee.ac.uk Mon Sep 8 13:29:52 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon Sep 8 13:30:09 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C5126D.9080305@unil.ch> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> Message-ID: <48C51AC0.7020401@compbio.dundee.ac.uk> Sebastien MORETTI wrote: >> The easiest way to do generate these links without changing the existing >> URL link behaviour would be to create a features file with URL links >> embedded in the description line - these will be shown in the link menu >> when the user right clicks on the sequence ID. > > I think I will try this. > Should I use this kind of syntax: > http://... seq_ID > > With URL as description, a tab, sequence identifier ? not quite... Here's an example from http://www.jalview.org/examples/exampleFeatures.txt : Fer2 Status: True Positive Pfam 8_8 FER_CAPAA -1 8 83 Pfam Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath Specify start and end as -1 in order to add a non-positional feature Jalview will recognise the anchors embedded in the description and parse them as URL links where the link text is used for the menu name. I see that this process is not described in the features file documentation ( http://www.jalview.org/help/html/features/featuresFormat.html ) - that'll have to be fixed ! Jim ps. With regard to 'magic FeatureTypes' - Jalview does not do anything intelligent with feature types, currently (with the exception of the disulphide_bond type), which is a big limitation. It is easy to imagine that features like 'DBRef' or 'Reference' might be translated into database accession links and citation lists, and may actually be implemented in the future. From sebastien.moretti at unil.ch Tue Sep 9 08:01:40 2008 From: sebastien.moretti at unil.ch (Sebastien MORETTI) Date: Tue Sep 9 08:02:04 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C51AC0.7020401@compbio.dundee.ac.uk> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> Message-ID: <48C61F54.6040602@unil.ch> >>> The easiest way to do generate these links without changing the existing >>> URL link behaviour would be to create a features file with URL links >>> embedded in the description line - these will be shown in the link menu >>> when the user right clicks on the sequence ID. >> I think I will try this. >> Should I use this kind of syntax: >> http://... seq_ID >> >> With URL as description, a tab, sequence identifier ? > not quite... > > Here's an example from http://www.jalview.org/examples/exampleFeatures.txt : > > Fer2 Status: True Positive href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam > 8_8 FER_CAPAA -1 8 83 Pfam > Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 93 Cath > > Specify start and end as -1 in order to add a non-positional feature > Jalview will recognise the anchors embedded in the description and parse > them as URL links where the link text is used for the menu name. > > I see that this process is not described in the features file > documentation ( > http://www.jalview.org/help/html/features/featuresFormat.html ) - > that'll have to be fixed ! > > Jim > > ps. With regard to 'magic FeatureTypes' - Jalview does not do anything > intelligent with feature types, currently (with the exception of the > disulphide_bond type), which is a big limitation. It is easy to imagine > that features like 'DBRef' or 'Reference' might be translated into > database accession links and citation lists, and may actually be > implemented in the future. I have tried this syntax but it fails with an error in the java console: Sequence not found: ensembl ENPL_HUMAN -1 -1 -1 DBRef Feature lines look like this: ensembl ENPL_HUMAN -1 -1 -1 DBRef ensembl HSP90B1_PANTR -1 -1 -1 DBRef And sequence headers look like this: >ENPL_HUMAN ID=ENST00000299767.4 GENEID=ENSG00000166598 >HSP90B1_PANTR ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372 So, it seems the features cannot be allocated to the proper sequences. What should be the right sequence name in this case ? Thanks -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ From sebastien.moretti at unil.ch Tue Sep 9 10:24:35 2008 From: sebastien.moretti at unil.ch (Sebastien MORETTI) Date: Tue Sep 9 10:24:27 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C61F54.6040602@unil.ch> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> Message-ID: <48C640D3.6040304@unil.ch> Sebastien MORETTI a ?crit : >>>> The easiest way to do generate these links without changing the >>>> existing >>>> URL link behaviour would be to create a features file with URL links >>>> embedded in the description line - these will be shown in the link menu >>>> when the user right clicks on the sequence ID. >>> I think I will try this. >>> Should I use this kind of syntax: >>> http://... seq_ID >>> >>> With URL as description, a tab, sequence identifier ? >> not quite... >> >> Here's an example from >> http://www.jalview.org/examples/exampleFeatures.txt : >> >> Fer2 Status: True Positive > href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam >> 8_8 FER_CAPAA -1 8 83 Pfam >> Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 >> 93 Cath >> >> Specify start and end as -1 in order to add a non-positional feature >> Jalview will recognise the anchors embedded in the description and parse >> them as URL links where the link text is used for the menu name. >> >> I see that this process is not described in the features file >> documentation ( >> http://www.jalview.org/help/html/features/featuresFormat.html ) - >> that'll have to be fixed ! >> >> Jim >> >> ps. With regard to 'magic FeatureTypes' - Jalview does not do anything >> intelligent with feature types, currently (with the exception of the >> disulphide_bond type), which is a big limitation. It is easy to imagine >> that features like 'DBRef' or 'Reference' might be translated into >> database accession links and citation lists, and may actually be >> implemented in the future. > > I have tried this syntax but it fails with an error in the java console: > Sequence not found: href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl > ENPL_HUMAN -1 -1 -1 DBRef > > Feature lines look like this: > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl > ENPL_HUMAN -1 -1 -1 DBRef > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl > HSP90B1_PANTR -1 -1 -1 DBRef > > > And sequence headers look like this: > >ENPL_HUMAN ID=ENST00000299767.4 GENEID=ENSG00000166598 > >HSP90B1_PANTR ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372 > > So, it seems the features cannot be allocated to the proper sequences. > What should be the right sequence name in this case ? > > Thanks "Sequence not found" message came from a forgotten tab. It is resolved now, sorry. But I do not have links yet. Now, feature file looks like this: ensembl red ensembl ENPL_HUMAN -1 -1 -1 ensembl ensembl HSP90B1_PANTR -1 -1 -1 ensembl ... And sequence headers look like this: >ENPL_HUMAN ID=ENST00000299767.4 GENEID=ENSG00000166598 >HSP90B1_PANTR ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372 I have nothing but SRS link in the links menu. -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ From sebastien.moretti at unil.ch Tue Sep 9 11:43:38 2008 From: sebastien.moretti at unil.ch (Sebastien MORETTI) Date: Tue Sep 9 11:43:30 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C640D3.6040304@unil.ch> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> <48C640D3.6040304@unil.ch> Message-ID: <48C6535A.9020905@unil.ch> Sebastien MORETTI a ?crit : > Sebastien MORETTI a ?crit : >>>>> The easiest way to do generate these links without changing the >>>>> existing >>>>> URL link behaviour would be to create a features file with URL links >>>>> embedded in the description line - these will be shown in the link >>>>> menu >>>>> when the user right clicks on the sequence ID. >>>> I think I will try this. >>>> Should I use this kind of syntax: >>>> http://... seq_ID >>>> >>>> With URL as description, a tab, sequence identifier ? >>> not quite... >>> >>> Here's an example from >>> http://www.jalview.org/examples/exampleFeatures.txt : >>> >>> Fer2 Status: True Positive >> href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam >>> 8_8 FER_CAPAA -1 8 83 Pfam >>> Ferredoxin_fold Status: True Positive FER_CAPAA -1 3 >>> 93 Cath >>> >>> Specify start and end as -1 in order to add a non-positional feature >>> Jalview will recognise the anchors embedded in the description and parse >>> them as URL links where the link text is used for the menu name. >>> >>> I see that this process is not described in the features file >>> documentation ( >>> http://www.jalview.org/help/html/features/featuresFormat.html ) - >>> that'll have to be fixed ! >>> >>> Jim >>> >>> ps. With regard to 'magic FeatureTypes' - Jalview does not do anything >>> intelligent with feature types, currently (with the exception of the >>> disulphide_bond type), which is a big limitation. It is easy to imagine >>> that features like 'DBRef' or 'Reference' might be translated into >>> database accession links and citation lists, and may actually be >>> implemented in the future. >> >> I have tried this syntax but it fails with an error in the java console: >> Sequence not found: > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl >> ENPL_HUMAN -1 -1 -1 DBRef >> >> Feature lines look like this: >> > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl >> ENPL_HUMAN -1 -1 -1 DBRef >> > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl >> HSP90B1_PANTR -1 -1 -1 DBRef >> >> >> And sequence headers look like this: >> >ENPL_HUMAN ID=ENST00000299767.4 GENEID=ENSG00000166598 >> >HSP90B1_PANTR ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372 >> >> So, it seems the features cannot be allocated to the proper sequences. >> What should be the right sequence name in this case ? >> >> Thanks > > "Sequence not found" message came from a forgotten tab. It is resolved > now, sorry. > > But I do not have links yet. > > Now, feature file looks like this: > ensembl red > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl > ENPL_HUMAN -1 -1 -1 ensembl > href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl > HSP90B1_PANTR -1 -1 -1 ensembl > ... > > And sequence headers look like this: > >ENPL_HUMAN ID=ENST00000299767.4 GENEID=ENSG00000166598 > >HSP90B1_PANTR ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372 > > > > I have nothing but SRS link in the links menu. Another point ! With reel start and end positions, links appear on sequences but not in link menu of the sequence name. And href MUST have URL between double quotes because it does not work with simple quotes. So now, how to have links in link menu of the sequence name ? And / or how to get links on sequences without changing amino acid colours with the feature colour ? Best regards S?bastien -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 From jimp at compbio.dundee.ac.uk Tue Sep 9 12:22:26 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Sep 9 12:22:49 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C640D3.6040304@unil.ch> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> <48C640D3.6040304@unil.ch> Message-ID: <48C65C72.7070206@compbio.dundee.ac.uk> Hello Sebastien. congratulations - you have uncovered more bugs in Jalview! As a result, this is a lengthy reply... (but not as long as the three emails you have already sent today - thanks for your patience) Sebastien MORETTI wrote: > "Sequence not found" message came from a forgotten tab. It is resolved > now, sorry. ah. OK. That error is usually raised when the parser cannot find enough tab-separated fields from the feature file line (it's not a very informative error message, I'm afraid..). > But I do not have links yet. ahem - yes. about that. Providing your feature file parses (ie it has tab characters separating each field), then the problems are as follows: 1. As you have noticed, the html parser in jalview is _very_ basic. It expects XML attributes to be quoted with double quotes ('"') not a single quote (''') (also, please bear in mind that single quoted attributes is non-standard XML and will not validate). This means you should have a feature file with lines like: ensembl ENPL_HUMAN -1 0 0 DBRef Note I have used '0' in the start/end fields. This is because I was in error in my previous reply: 2. Non-positional features are specified by putting a '0' in both the start and end (not a '-1' as I said previously - sorry). Finally... the real problem: 3. Link display for non-positional features appears to be broken... So even if you got the features to be listed in the sequence ID tooltip, no links would be generated from the URL links embedded in the sequence features. This successfully scuppers my original suggestion of using non-positional sequence features to append URLs......... however... I have checked in a bug fix for #3. Both the applet and application now generate URL links from links embedded in non-positional features. Furthermore, the applet now displays non-positional features within the tooltip. can you try it out ? (http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest) Jim. ps. As an alternative, I have also re-instated the 'generate URL from sequence description' code too, but made it so that only URLs which contain regexes are used to process the description. This is still not ideal, but more appropriate than simply making a URL substitution using the whole description string. -- ------------------------------------------------------------------- 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 jimp at compbio.dundee.ac.uk Tue Sep 9 12:34:44 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Sep 9 12:34:59 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp (non positional features bugfix/feature) In-Reply-To: <48C65C72.7070206@compbio.dundee.ac.uk> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> <48C640D3.6040304@unil.ch> <48C65C72.7070206@compbio.dundee.ac.uk> Message-ID: <48C65F54.2080101@compbio.dundee.ac.uk> > This successfully scuppers my original suggestion of using > non-positional sequence features to append URLs......... however... I > have checked in a bug fix for #3. Both the applet and application now > generate URL links from links embedded in non-positional features. > Furthermore, the applet now displays non-positional features within the > tooltip. > > can you try it out ? > (http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest) as an addendum - this feature allows access to many more URLs extracted from the database references and retrieved via DAS (use the 'fetch DB references' function from webservices menu). This includes direct links to uniprot, taxonomy links (although the Uniprot NEWT taxonomy URLs that are retrieved appear not to be properly at the moment), and links to DOI's for publications. 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 sebastien.moretti at unil.ch Tue Sep 9 13:38:42 2008 From: sebastien.moretti at unil.ch (Sebastien MORETTI) Date: Tue Sep 9 13:38:34 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C65C72.7070206@compbio.dundee.ac.uk> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> <48C640D3.6040304@unil.ch> <48C65C72.7070206@compbio.dundee.ac.uk> Message-ID: <48C66E52.4010607@unil.ch> James Procter a ?crit : > Hello Sebastien. > > congratulations - you have uncovered more bugs in Jalview! As a result, > this is a lengthy reply... (but not as long as the three emails you have > already sent today - thanks for your patience) > > Sebastien MORETTI wrote: > >> "Sequence not found" message came from a forgotten tab. It is resolved >> now, sorry. > ah. OK. That error is usually raised when the parser cannot find enough > tab-separated fields from the feature file line (it's not a very > informative error message, I'm afraid..). > >> But I do not have links yet. > ahem - yes. about that. > > Providing your feature file parses (ie it has tab characters separating > each field), then the problems are as follows: > > 1. As you have noticed, the html parser in jalview is _very_ basic. It > expects XML attributes to be quoted with double quotes ('"') not a > single quote (''') (also, please bear in mind that single quoted > attributes is non-standard XML and will not validate). > > This means you should have a feature file with lines like: > > href="http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598">ensembl > ENPL_HUMAN -1 0 0 DBRef > > Note I have used '0' in the start/end fields. This is because I was in > error in my previous reply: > > 2. Non-positional features are specified by putting a '0' in both the > start and end (not a '-1' as I said previously - sorry). > > Finally... the real problem: > > 3. Link display for non-positional features appears to be broken... > So even if you got the features to be listed in the sequence ID tooltip, > no links would be generated from the URL links embedded in the sequence > features. > > > This successfully scuppers my original suggestion of using > non-positional sequence features to append URLs......... however... I > have checked in a bug fix for #3. Both the applet and application now > generate URL links from links embedded in non-positional features. > Furthermore, the applet now displays non-positional features within the > tooltip. > > can you try it out ? > (http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest) > Jim. > > ps. As an alternative, I have also re-instated the 'generate URL from > sequence description' code too, but made it so that only URLs which > contain regexes are used to process the description. This is still not > ideal, but more appropriate than simply making a URL substitution using > the whole description string. Many thanks ! Both strategies work, non-positional features within the tooltip & with linkURL. I have kept linkLabel_1/linkUrl_1 only because I think it is easier for users and I have no feature file to create. Maybe you have to specify in the documentation that regexp in $SEQUENCE_ID have to be back-slash protected following computer languages used to make applet parameters. Thanks again. p.s.: We will send you something for Christmas ;-) -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ From jimp at compbio.dundee.ac.uk Tue Sep 9 15:19:19 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Sep 9 15:19:31 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C66E52.4010607@unil.ch> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> <48C640D3.6040304@unil.ch> <48C65C72.7070206@compbio.dundee.ac.uk> <48C66E52.4010607@unil.ch> Message-ID: <48C685E7.5030400@compbio.dundee.ac.uk> Sebastien MORETTI wrote: > Many thanks ! > Both strategies work, non-positional features within the tooltip & with > linkURL. great! > > I have kept linkLabel_1/linkUrl_1 only because I think it is easier for > users and I have no feature file to create. Understandable, and I agree. Non-positional links now serve almost the same purpose, but they do have the advantage of offloading the additional sequence metadata into another file, rather than stuffing it all into the description line. > > value="http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=\$SEQUENCE_ID=/GENEID=(\\w+) > TAXID/=\$" /> > > Maybe you have to specify in the documentation that regexp in > $SEQUENCE_ID have to be back-slash protected following computer > languages used to make applet parameters. Normally, this is not necessary. Are you talking about when the applet tag is generated within a Perl CGI script ? (then all $ within double quoted strings must be escaped) If you escape the '$' and set the debug flag (param name="debug" value="true") then jalviewLite raises an error because it cannot parse the value of the linkURL_2 as a valid sequence ID regex link (in this case it is because the /=$ cannot be found). > p.s.: We will send you something for Christmas ;-) > I'll look forward to it! thanks for your patience, again... Jim From sebastien.moretti at unil.ch Tue Sep 9 15:32:36 2008 From: sebastien.moretti at unil.ch (Sebastien MORETTI) Date: Tue Sep 9 15:32:26 2008 Subject: [Jalview-discuss] Re: linkUrl and regexp In-Reply-To: <48C685E7.5030400@compbio.dundee.ac.uk> References: <48C4F455.3030800@unil.ch> <48C50005.9020407@compbio.dundee.ac.uk> <48C5126D.9080305@unil.ch> <48C51AC0.7020401@compbio.dundee.ac.uk> <48C61F54.6040602@unil.ch> <48C640D3.6040304@unil.ch> <48C65C72.7070206@compbio.dundee.ac.uk> <48C66E52.4010607@unil.ch> <48C685E7.5030400@compbio.dundee.ac.uk> Message-ID: <48C68904.6080900@unil.ch> >> Many thanks ! >> Both strategies work, non-positional features within the tooltip & with >> linkURL. > great! >> I have kept linkLabel_1/linkUrl_1 only because I think it is easier for >> users and I have no feature file to create. > Understandable, and I agree. Non-positional links now serve almost the > same purpose, but they do have the advantage of offloading the > additional sequence metadata into another file, rather than stuffing it > all into the description line. > >> >> > value="http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=\$SEQUENCE_ID=/GENEID=(\\w+) >> TAXID/=\$" /> >> >> Maybe you have to specify in the documentation that regexp in >> $SEQUENCE_ID have to be back-slash protected following computer >> languages used to make applet parameters. > Normally, this is not necessary. Are you talking about when the applet > tag is generated within a Perl CGI script ? (then all $ within double > quoted strings must be escaped) Yes, the applet tags are generated within a Perl CGI script. It should be the same for applet tags generated by Java code. > If you escape the '$' and set the debug flag (param name="debug" > value="true") then jalviewLite raises an error because it cannot parse > the value of the linkURL_2 as a valid sequence ID regex link (in this > case it is because the /=$ cannot be found). Thus, I have escaped $ surrounding SEQUENCE_ID and every backslashed metacharacter in the regexp like \w \$SEQUENCE_ID=/GENEID=(\\w+) TAXID/=\$ This should not to be done for single quoted strings. >> p.s.: We will send you something for Christmas ;-) >> > I'll look forward to it! > > thanks for your patience, again... > Jim Thanks again and again S?bastien -- S?bastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ From avilella at gmail.com Tue Sep 16 11:34:56 2008 From: avilella at gmail.com (Albert Vilella) Date: Tue Sep 16 11:34:59 2008 Subject: [Jalview-discuss] Representing Exon boundaries Message-ID: <358f4d650809160334x63388a35ve7a9879ce8d4fa2c@mail.gmail.com> Hi, Is there any formal way to represent exon boundaries in a protein alignment in Jalview? Cheers, Albert. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20080916/b401e02d/attachment.htm From jimp at compbio.dundee.ac.uk Tue Sep 16 11:51:43 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Sep 16 11:52:00 2008 Subject: [Jalview-discuss] Representing Exon boundaries In-Reply-To: <358f4d650809160334x63388a35ve7a9879ce8d4fa2c@mail.gmail.com> References: <358f4d650809160334x63388a35ve7a9879ce8d4fa2c@mail.gmail.com> Message-ID: <48CF8FBF.80508@compbio.dundee.ac.uk> Hello Albert. Albert Vilella wrote: > Is there any formal way to represent exon boundaries in a protein > alignment in Jalview? Actually, no. There is support for this kind of annotation internally, but it is currently only used for the linked highlighting of DNA and protein views, and mapping features and annotation. I have also noticed cases in the literature where exon boundaries have been added to an alignment as vertical bars, and at the time realised that it would be useful to do this. I guess it would be possible to mock up the annotation by creating a group on the sequence for each exon region on the peptide product - but this is pretty painful to do by hand, and would be alignment annotation - rather than sequence annotation, so would be broken as soon as the alignment was edited. This will be a good addition to the jalview feature list - no guarantees about when it is done .. of course.. but perhaps sometime soon (unless there are any volunteers!). thanks. 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 arve at csc.kth.se Tue Sep 16 16:57:44 2008 From: arve at csc.kth.se (Lars Arvestad) Date: Tue Sep 16 16:58:00 2008 Subject: [Jalview-discuss] Representing Exon boundaries In-Reply-To: <48CF8FBF.80508@compbio.dundee.ac.uk> References: <358f4d650809160334x63388a35ve7a9879ce8d4fa2c@mail.gmail.com> <48CF8FBF.80508@compbio.dundee.ac.uk> Message-ID: <48CFD778.7010801@csc.kth.se> Hi, I am glad this topic comes up because it is something I have done more or less by hand in a couple of cases, and it is inconvenient. However, I just want to point out that exon boundaries can occur within codons, so it is not straightforward to represent it on the amino acid level. In fact, it is not obvious how to visualize it. Lars, a happy Jalview user James Procter wrote: > Hello Albert. > > Albert Vilella wrote: > >> Is there any formal way to represent exon boundaries in a protein >> alignment in Jalview? >> > Actually, no. There is support for this kind of annotation internally, > but it is currently only used for the linked highlighting of DNA and > protein views, and mapping features and annotation. > > I have also noticed cases in the literature where exon boundaries have > been added to an alignment as vertical bars, and at the time realised > that it would be useful to do this. I guess it would be possible to mock > up the annotation by creating a group on the sequence for each exon > region on the peptide product - but this is pretty painful to do by > hand, and would be alignment annotation - rather than sequence > annotation, so would be broken as soon as the alignment was edited. > > This will be a good addition to the jalview feature list - no guarantees > about when it is done .. of course.. but perhaps sometime soon (unless > there are any volunteers!). > > thanks. > Jim > > -- Stockholm Bioinformatics Center and School of Computer Science and Communication http://www.csc.kth.se/~arve From jimp at compbio.dundee.ac.uk Tue Sep 16 17:23:39 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Sep 16 17:23:58 2008 Subject: [Jalview-discuss] Representing Exon boundaries In-Reply-To: <48CFD778.7010801@csc.kth.se> References: <358f4d650809160334x63388a35ve7a9879ce8d4fa2c@mail.gmail.com> <48CF8FBF.80508@compbio.dundee.ac.uk> <48CFD778.7010801@csc.kth.se> Message-ID: <48CFDD8B.1000700@compbio.dundee.ac.uk> Hi Lars.. Lars Arvestad wrote: > I am glad this topic comes up because it is something I have done more > or less by hand in a couple of cases, and it is inconvenient. > > However, I just want to point out that exon boundaries can occur within > codons, so it is not straightforward to represent it on the amino acid > level. In fact, it is not obvious how to visualize it. Very good point. I suspect there are one or two different conventions, in fact. With regards to handling the underlying data, within the VAMSAS datamodel we explicitly built in the concept of annotation being either at a discrete position (i.e. base or residue) in a coordinate system, or after it, in order to properly reflect inclusive or exclusive boundaries. I think it might be possible to utilise the same trick for proteins. Codon boundaries are at a residue, or after it. Anything more would have to be a subtype. Of course, the original issue stands - jalview won't render exon boundaries after a residue. It could, however, be 'hacked' in as a special feature representation: 'disulphide' feature type rendering is done this way.. ( as a hack - but in principle, the rendering model could re-implemented as something more generic that is driven by some ontology/look up table of feature types and styles). One could almost imagine positioning a bar either mid-left, mid-right, or at the right of the residue symbol. j. -- ------------------------------------------------------------------- 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 standley at protein.osaka-u.ac.jp Wed Sep 24 02:02:53 2008 From: standley at protein.osaka-u.ac.jp (Daron Standley) Date: Wed Sep 24 02:03:08 2008 Subject: [Jalview-discuss] secondary structure annotation Message-ID: <31F38BF7-1F0F-4FBF-BB1D-6DDF7D2198FF@protein.osaka-u.ac.jp> Hi- I am getting strange results for my secondary structure in a pairwise alignment using the jalview applet: http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/ SS32349/3bknmodA_PDP_A_1jgcC_SCOP_A_applet.html The secondary structure is supposed to correspond to the first sequence, which is passed to the applet as What is strange is that there is a helix where there are no 3bknmodA residues (e.g., in the N-terminal gap). The secondary structure assignment is specified in an annotations file with the 3bknmodA sequence provided as the reference: JALVIEW_ANNOTATION SEQUENCE_REF 3bknmodA BAR_GRAPH Score 0.06| 3.33| 1.68|-3.97|-1.44| 5.15| 0.97|-3.17|-3.01| 6.67|-3.19| 0.22| 5.66|-2.99|-3.08|-1.60|-4.00|-1.35| 4.88| 9.29| 0.86| 6.61|-1.60|-2.18| 0.11|-1.57|-1.47|-2.34|-3.20|-2.28| 0.09|-1.60|-1.56| 5.89|-1.59|-2.96|-3.17| 1.69| 2.06|-3.85| 0.03| 6.65|-1.44|-3.19| 9.99|-1.51|-3.94|-0.64| 3.32| 3.31|-0.65| 2.48| 1.83| 0.85| 0.00|-2.13|-4.00|-1.59| 0.86|-4.00| 0.91| 1.06|-2.37|-0.70| 5.19|-3.97|-0.77| 0.86|-2.31| 0.03|-3.96|-3.98| 0.01| 8.89| 6.64|-0.76| 1.61|-3.17| 0.17|-1.51|-3.96|-4.00|-2.40|-3.56| 6.82| 0.14|-1.56| 5.34| 0.94|-0.58|-3.01| 8.57|-1.53| 4.76|-0.64|-2.53|-1.47|-2.39|-1.50|-2.27| 0.22|-3.11|-2.37| 8.56|-1.51| 0.18|-3.10| 2.97| 2.12|-1.59| 1.55|-3.10|-1.57| 2.37|-3.20| 0.27| 7.74| 6.53|-0.77|-1.42| 9.90|-3.19|-3.98|-0.80|-4.00| 0.01| 1.75|-2.18|-4.79| 0.27|-1.50| 8.03| 7.46| 2.78|-3.20|-1.56| 8.82|-2.40| 0.00|-0.80|-0.80|0|0|0|0|0| 0|0|0|0|0| NO_GRAPH Secondary Structure H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| H|H|H|H|H|H|H|||H|H|H|H|H|||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| H|||||||||||||||||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| H|H|H|H|||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| H||H|H|H|H|H|H|H|H|||||||| I thought I had all of this secondary structure stuff sorted out, but obviously not. Can someone tell me what I am doing wrong? Best wishes, Daron -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20080924/f4674ccd/attachment.htm From jimp at compbio.dundee.ac.uk Wed Sep 24 09:09:45 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed Sep 24 09:10:16 2008 Subject: [Jalview-discuss] secondary structure annotation In-Reply-To: <31F38BF7-1F0F-4FBF-BB1D-6DDF7D2198FF@protein.osaka-u.ac.jp> References: <31F38BF7-1F0F-4FBF-BB1D-6DDF7D2198FF@protein.osaka-u.ac.jp> Message-ID: <48D9F5C9.2060006@compbio.dundee.ac.uk> Hello Daron. Daron Standley wrote: > I thought I had all of this secondary structure stuff sorted out, but > obviously not. Can someone tell me what I am doing wrong? It looks like a bug to me. The score annotation is correctly associated with the sequence, but the secondary structure annotation is not (you can see this when you edit the alignment, or when you output the annotation to a text box). I'll have a look at the jalview.io.AnnotationFile parser and see what its up to. You can work around this by adding another SEQUENCE_REF entry before the secondary structure row : JALVIEW_ANNOTATION SEQUENCE_REF 3bknmodA BAR_GRAPH Score 0.06| 3.33| 1.68|-3.97|-1.44| 5.15| 0.97|-3.17|-3.01| 6.67|-3.19| 0.22| 5.66|-2.99|-3.08|-1.60|-4.00|-1.35| 4.88| 9.29| 0.86| 6.61|-1.60|-2.18| 0.11|-1.57|-1.47|-2.34|-3.20|-2.28| 0.09|-1.60|-1.56| 5.89|-1.59|-2.96|-3.17| 1.69| 2.06|-3.85| 0.03| 6.65|-1.44|-3.19| 9.99|-1.51|-3.94|-0.64| 3.32| 3.31|-0.65| 2.48| 1.83| 0.85| 0.00|-2.13|-4.00|-1.59| 0.86|-4.00| 0.91| 1.06|-2.37|-0.70| 5.19|-3.97|-0.77| 0.86|-2.31| 0.03|-3.96|-3.98| 0.01| 8.89| 6.64|-0.76| 1.61|-3.17| 0.17|-1.51|-3.96|-4.00|-2.40|-3.56| 6.82| 0.14|-1.56| 5.34| 0.94|-0.58|-3.01| 8.57|-1.53| 4.76|-0.64|-2.53|-1.47|-2.39|-1.50|-2.27| 0.22|-3.11|-2.37| 8.56|-1.51| 0.18|-3.10| 2.97| 2.12|-1.59| 1.55|-3.10|-1.57| 2.37|-3.20| 0.27| 7.74| 6.53|-0.77|-1.42| 9.90|-3.19|-3.98|-0.80|-4.00| 0.01| 1.75|-2.18|-4.79| 0.27|-1.50| 8.03| 7.46| 2.78|-3.20|-1.56| 8.82|-2.40| 0.00|-0.80|-0.80|0|0|0|0|0|0|0|0|0|0| SEQUENCE_REF 3bknmodA NO_GRAPH Secondary Structure H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||H|H|H|H|H|||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||||||||||||||||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H||H|H|H|H|H|H|H|H|||||||| perseverence always wins out in the end ! 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 jonas at cloud8.se Tue Sep 30 14:02:26 2008 From: jonas at cloud8.se (Jonas T Larsson) Date: Tue Sep 30 14:01:04 2008 Subject: [Jalview-discuss] How to rename a project? Message-ID: <20080930130226.GA720@df.lth.se> Is there any way to rename .jar projects? And with name here, I mean the title of the window. I Would like to rename if from "Cut and paste input" or the original filename (including path) that the sequences came from. Is this possible? / Jonas