From ian.donaldson at mshri.on.ca Thu Sep 2 15:19:44 2004 From: ian.donaldson at mshri.on.ca (Ian Donaldson) Date: Thu Sep 2 15:22:57 2004 Subject: [Biojava-l] SeqHound release v3.0 now available Message-ID: <490D0AFAF3D2D3119F6C00508B6FDF150690F78F@ex.mshri.on.ca> Dear BioJava SeqHound v3.0 is available for download now from http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html BioJava users may be interested in using SeqHound to retrieve sequence and structure records using the remote Java API. SeqHound has the advantage that it allows unrestricted, fast access to data supported by redundant servers and a FastCGI. SeqHound also offers access to many other data types including GO annotation, precomputed RPS-BLAST and precomputed protein BLAST results. We are interested in identifying developers who are already using SeqHound. If you are, please sign up for the seqhound.usergroup email list at http://lists.blueprint.org/mailman/listinfo/seqhound.usergroup. Feedback and discussions on future development are welcome at this list. We are also interested in incorporating SeqHound functionality into the BioJava tree. We would like feedback to this list on those functionalities that developers would find most useful as part of BioJava so we can direct development. A complete list of API functions is available at http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html. Best regards, Ian Ian Donaldson, Ph.D. Manager of Bioinformatics Software Development The Blueprint Initiative - North America 522 University Ave. Toronto, Ontario, Canada M5G 1W7 http://blueprint.org ian.donaldson@blueprint.org About SeqHound SeqHound is a freely available bioinformatics database warehouse resource. Over 300 Gigabytes of data is collected, integrated and updated from around the world on a nightly basis. Sources include the National Center for Biotechnology Information and the Gene Ontology Consortium. Programmers have unrestricted access to up-to-date data via a remote Application Programming Interface (API) written in Perl, Java, C and C++. Over 150 function calls allow access to the complete collection of GenBank, RefSeq and SwissProt sequences, 3-D structures, precomputed protein neighbours, redundancies and conserved domain analyses. Users may also access collected sequence annotations including taxonomy, Gene Ontology assignments and PubMed links. All functions are fully documented and tested on a daily basis. The Blueprint SeqHound server is supported by a redundant architecture (failover load-balancers, failover servers and, failover SANs) for complete fault protection against component failure and to ensure rapid response time. SeqHound encourages unrestricted 24x7 calls to its servers, to allow programmers rapid, uninterrupted, access to biological data on a global basis. SeqHound services over 700,000 hits per day. All SeqHound code is freely distributed under the GNU Public License. Find SeqHound at www.blueprint.org. From halting at comcast.net Mon Sep 6 16:40:48 2004 From: halting at comcast.net (Joe Davison) Date: Mon Sep 6 16:41:05 2004 Subject: [Biojava-l] Getting Started In-Reply-To: References: Message-ID: <09076B8A-0045-11D9-BDFC-0003933F40D6@comcast.net> I'm trying to get started with BioJava. I've been looking at BioJava in Anger and it seems like a great resource. However, the "How do I get and install BioJava" section leaves a little to be desired. I'd already found the page it links to, and perhaps it's what needs updating. The problem is particularly acute for those not around other users where one can ask a question. There's no real "here's what you need first" info there comparable to the "You will also need" section. The link to the Download area leads to confusion, in that there are 6 or 7 directories full of multiple versions of probably wonderful things, but somehow I doubt I really need to download the whole mess to get started. Perhaps somewhere there could be a short Readme.txt that says "If you're just getting started, start with these files: .... Then check out the tutorials." or some such. Thanks. joe davison From mark.schreiber at group.novartis.com Mon Sep 6 20:49:21 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Mon Sep 6 20:49:37 2004 Subject: [Biojava-l] Getting Started Message-ID: Hello - Apologies for the out of dateness of the information. You have basically 3 options. 1) get biojava1.4 pre1 release (the most recent official release from the download site) 2) get a nightly snapshot from http://www.derkholm.net/autobuild/ (reccomended) 3) get biojava-live from CVS (probably not best for beginners) You need the following on your class path: biojava.jar (version number depends on release or date of snapshot) bytecode-0.92.jar commons-cli.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar At this point your done and dusted and should be able to run some demos from BioJava in Anger. You probably also want the docs and the source but you don't need them to run anything. Hope this helps... Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 Joe Davison Sent by: biojava-l-bounces@portal.open-bio.org 09/07/2004 04:40 AM To: biojava-l@portal.open-bio.org cc: Subject: [Biojava-l] Getting Started I'm trying to get started with BioJava. I've been looking at BioJava in Anger and it seems like a great resource. However, the "How do I get and install BioJava" section leaves a little to be desired. I'd already found the page it links to, and perhaps it's what needs updating. The problem is particularly acute for those not around other users where one can ask a question. There's no real "here's what you need first" info there comparable to the "You will also need" section. The link to the Download area leads to confusion, in that there are 6 or 7 directories full of multiple versions of probably wonderful things, but somehow I doubt I really need to download the whole mess to get started. Perhaps somewhere there could be a short Readme.txt that says "If you're just getting started, start with these files: .... Then check out the tutorials." or some such. Thanks. joe davison _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From matthew_pocock at yahoo.co.uk Wed Sep 15 11:30:38 2004 From: matthew_pocock at yahoo.co.uk (Matthew Pocock) Date: Wed Sep 15 11:30:44 2004 Subject: [Biojava-l] too much spam Message-ID: <4148601E.2090205@yahoo.co.uk> Hi, I've got realy fed up with spam. Would anybody object if we got all mail from non-subscribers to be checked by a person before being allowed through? It adds slightly to the accessibility, but at the moment we get so much spam that I think it's worth it. Matthew From ah3 at sanger.ac.uk Wed Sep 15 17:20:10 2004 From: ah3 at sanger.ac.uk (Ashwin Hajarnavis) Date: Wed Sep 15 17:20:05 2004 Subject: [Biojava-l] Unexpected IllegalSymbolException Message-ID: I have the code below, where dinucs is a Symbol[] containing symbols from a DNA x DNA alphabet. ... System.out.println("only see this when there's an N"); System.out.println(seq.getAlphabet().getName()); int r = rand.nextInt(16); Edit e = new Edit(i,seq.getAlphabet(), dinucs[r]); seq.edit(e); index[i] = r; ... The code returns [untrusted21:~/Java_src/ah3/apps] ashwin% java PAjHMMA --model ~/Projects/jHMM/C.elegans_PolyA.D --file ~/Projects/jHMM/TESTING/N.dna >Y119D3B.4 only see this when there's an N (DNA x DNA) Exception in thread "main" org.biojava.bio.symbol.IllegalSymbolException: Symbol (guanine cytosine) not found in alphabet (DNA x DNA) at org.biojava.bio.symbol.AbstractAlphabet.validate(AbstractAlphabet.java:278) at org.biojava.bio.symbol.SimpleSymbolList.(SimpleSymbolList.java:140) at org.biojava.bio.symbol.Edit.(Edit.java:66) at ah3.DP.SequenceUtils.Dnumerify(SequenceUtils.java:90) at PAjHMMA.main(PAjHMMA.java:55) I am confused by this, as the symbol stated in the exception DOES appear to be part of the DNA x DNA alphabet. Any ideas? Thanks Ashwin --- Ashwin Hajarnavis, Informatics Research Group, Sanger Institute, Cambridgeshire, CB10 1SA +44 (0) 1223 494820 ah3@sanger.ac.uk From mark.schreiber at group.novartis.com Wed Sep 15 20:47:48 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Sep 15 20:47:47 2004 Subject: [Biojava-l] too much spam Message-ID: I'd vote for that. The signal to noise ratio is very low! Matthew Pocock Sent by: biojava-l-bounces@portal.open-bio.org 09/15/2004 11:30 PM To: "biojava-l@biojava.org" cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] too much spam Hi, I've got realy fed up with spam. Would anybody object if we got all mail from non-subscribers to be checked by a person before being allowed through? It adds slightly to the accessibility, but at the moment we get so much spam that I think it's worth it. Matthew _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l From max_dipl at web.de Fri Sep 17 02:21:56 2004 From: max_dipl at web.de (Maximilian Haussler) Date: Fri Sep 17 08:51:54 2004 Subject: [Biojava-l] viewsequence is unchangeable? Message-ID: <414A8284.5010509@web.de> Hi everyone, why is ViewSequence an implementation of the Unchangeable interface? Isn't a view (among others) meant for adding features to an otherwise unchangeable sequence? I have a class derived from the view, but I don't get it to notify the GUI when changes occur, as I don't find the getChangeSupport() in ViewSequence... [Well, simply adding standard java change support instead of this overly complicated biojava system would also do the trick... :-) ] Thanks Max From mark.schreiber at group.novartis.com Wed Sep 22 04:54:11 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Sep 22 04:54:03 2004 Subject: [Biojava-l] Base Calling Message-ID: Hi - Does anyone know of a base calling program or library that is truely open source? (eg not phred). Thanks, Mark From kalle.naslund at genpat.uu.se Mon Sep 27 08:46:33 2004 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Mon Sep 27 08:46:37 2004 Subject: [Biojava-l] viewsequence is unchangeable? In-Reply-To: <414C6413.9060804@web.de> References: <414A8284.5010509@web.de> <414AF0FD.2000909@genpat.uu.se> <414C6413.9060804@web.de> Message-ID: <41580BA9.8030903@genpat.uu.se> Maximilian Haussler wrote: > Thanks for your extensive reply. I did exactly that, but (hack hack) > did not use changeable but standard java change support. Anyways, it's > no use. > I'm using a sequence panel, but something that has to redraw sometimes > when there are new features. It is a sequence panel with many > different tracks (lines) and when there is a new feature added, > sometimes a new line has to be added. BJ design isn't made for this, > of course, so I cannot re-build the multilinerenderers each time a > change is made (to expensive) and I cannot call revalidate of the > sequencepanel either, as it will not add new lines by itself. > Oh geez, so i simply do a repaint of my sequencepanel anytime I'm > finished doing some modification. This is a nuisance but it works. > > I have no good design for my problem... I would perhaps need a > sequencepanel with dynamically updating lines, but I don't know how to > write that... or where to build upon, as it would not be an extension > of sequencepanel, but rather something new... > > Thanks nevertheless! > Max > As i dont fully understand what it is you are trying to do, im not sure these suggestions are helpfull, anyway. Im assuming that you have a MultilineRenderer setup, where each line renders a certain feature type. I dont know of the type of Feature data you connect to your Sequences, but i would assume that most changes to the Features, will not completely remove a certain Feature type from the Sequence, or add a new type. Most will just change the count of the different Feature types. So there is no need to rebuild the MultilineRenderer unless you remove or add a new type of Feature to the Sequence. You could implement this by a ChangeListener setup, that listens for changes on the Sequence, and takes appropriate action, if a new type is added, or the last of a certain type is removed, and if so, rebuild the MultiLineRenderer. Also, if most of your changes do not occur one and one, but in sets, you could do some uggly hacking, and just emit one ChangeEvent for the whole set of changes, and not one Event for each. This has the potential to be pretty uggly i guess but if you know what you are doing, it might be used to speed up your app, as a last measure. mvh Kalle > Kalle N?slund wrote: > >> Maximilian Haussler wrote: >> >>> Hi everyone, >>> >>> why is ViewSequence an implementation of the Unchangeable interface? >>> Isn't a view (among others) meant for adding features to an >>> otherwise unchangeable sequence? >> >> >> >> Exactly what a view is for, is a question you can argue a lot about i >> guess =). But, just from reading the javadocs of the class, it seems >> this one, is to be used to add data "on top" of another sequence. One >> example would indeed be to use it to add Features to an otherwise >> Unchangeable Sequence. >> >>> I have a class derived from the view, but I don't get it to notify >>> the GUI when changes occur, as I don't find the getChangeSupport() >>> in ViewSequence... >> >> >> >> ViewSequence extends Unchangeable, this is a minimal implementation >> of the Changeable Interface, that basicly just refuses any changes. >> The getChangeSupport() method belongs to the AbstractChangeable >> class. Most classes extend AbstractChangeable, so that is why you are >> used to always having getchangeSupport() around. >> >> As ViewSequence will never change, it will never emit any change >> events, and that is what the SWING gui widgets listen for, as a >> trigger to redraw, just as you say. >> >> I think that the correct way to fix this problem, is to have >> ViewSequence to emit change events, i guess alter it to extend >> AbstractChangeable, and then listen for Changes to the underlying >> sequence, and take appropriate action when change events are caught, >> aswell as emitting ChangeEvents when Features are added to the view >> itself. >> >>> [Well, simply adding standard java change support instead of this >>> overly complicated biojava system would also do the trick... :-) ] >> >> >> >> The biojava Changeability thingy, isnt realy that much more complex, >> atleast not from the view of the programmer, that just wants to make >> his class implement Changeable , and the added complexity has its >> uses. I wont claim that the current BJ way is the greatest way >> though =) >> >> So, my suggestion would be to make your own ViewSequene class, that >> does listen for changes on the underlying Sequence, aswell as emiting >> changes. You would start by taking the ViewSequence class, make it >> extend AbstractChangeable instead of Unchanging, then add a >> ChangeListener to the underlying Sequence, and hammer togheter some >> code that does the right thing[tm] when the listener notices the >> underlying sequence have changed ( most likely, check if the change >> affects the features in the view, if so, take some action) and then >> have a change forwarder that also forwards the changes. >> >> Im not sure i have the time at hand, or the mental capability right >> now, to fix this for you, but if you try something like this, and get >> into problems, feel free to mail the ml again, and i will try to help >> as much as i can. >> >> mvh Kalle N?slund >> >>> Thanks >>> Max >>> >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l@biojava.org >>> http://biojava.org/mailman/listinfo/biojava-l >> >> >> >> >> > > From kalle.naslund at genpat.uu.se Fri Sep 17 10:14:38 2004 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Sun Oct 3 21:50:34 2004 Subject: [Biojava-l] viewsequence is unchangeable? In-Reply-To: <414A8284.5010509@web.de> References: <414A8284.5010509@web.de> Message-ID: <414AF0FD.2000909@genpat.uu.se> Maximilian Haussler wrote: > Hi everyone, > > why is ViewSequence an implementation of the Unchangeable interface? > Isn't a view (among others) meant for adding features to an otherwise > unchangeable sequence? Exactly what a view is for, is a question you can argue a lot about i guess =). But, just from reading the javadocs of the class, it seems this one, is to be used to add data "on top" of another sequence. One example would indeed be to use it to add Features to an otherwise Unchangeable Sequence. > I have a class derived from the view, but I don't get it to notify the > GUI when changes occur, as I don't find the getChangeSupport() in > ViewSequence... ViewSequence extends Unchangeable, this is a minimal implementation of the Changeable Interface, that basicly just refuses any changes. The getChangeSupport() method belongs to the AbstractChangeable class. Most classes extend AbstractChangeable, so that is why you are used to always having getchangeSupport() around. As ViewSequence will never change, it will never emit any change events, and that is what the SWING gui widgets listen for, as a trigger to redraw, just as you say. I think that the correct way to fix this problem, is to have ViewSequence to emit change events, i guess alter it to extend AbstractChangeable, and then listen for Changes to the underlying sequence, and take appropriate action when change events are caught, aswell as emitting ChangeEvents when Features are added to the view itself. > [Well, simply adding standard java change support instead of this > overly complicated biojava system would also do the trick... :-) ] The biojava Changeability thingy, isnt realy that much more complex, atleast not from the view of the programmer, that just wants to make his class implement Changeable , and the added complexity has its uses. I wont claim that the current BJ way is the greatest way though =) So, my suggestion would be to make your own ViewSequene class, that does listen for changes on the underlying Sequence, aswell as emiting changes. You would start by taking the ViewSequence class, make it extend AbstractChangeable instead of Unchanging, then add a ChangeListener to the underlying Sequence, and hammer togheter some code that does the right thing[tm] when the listener notices the underlying sequence have changed ( most likely, check if the change affects the features in the view, if so, take some action) and then have a change forwarder that also forwards the changes. Im not sure i have the time at hand, or the mental capability right now, to fix this for you, but if you try something like this, and get into problems, feel free to mail the ml again, and i will try to help as much as i can. mvh Kalle N?slund > Thanks > Max > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l From kalle.naslund at genpat.uu.se Mon Sep 20 11:52:05 2004 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Sun Oct 3 21:50:35 2004 Subject: [Biojava-l] viewsequence is unchangeable? In-Reply-To: <414C6413.9060804@web.de> References: <414A8284.5010509@web.de> <414AF0FD.2000909@genpat.uu.se> <414C6413.9060804@web.de> Message-ID: <414EFCA5.9060305@genpat.uu.se> Maximilian Haussler wrote: > Thanks for your extensive reply. I did exactly that, but (hack hack) > did not use changeable but standard java change support. Anyways, it's > no use. > I'm using a sequence panel, but something that has to redraw sometimes > when there are new features. It is a sequence panel with many > different tracks (lines) and when there is a new feature added, > sometimes a new line has to be added. BJ design isn't made for this, > of course, so I cannot re-build the multilinerenderers each time a > change is made (to expensive) and I cannot call revalidate of the > sequencepanel either, as it will not add new lines by itself. > Oh geez, so i simply do a repaint of my sequencepanel anytime I'm > finished doing some modification. This is a nuisance but it works. > > I have no good design for my problem... I would perhaps need a > sequencepanel with dynamically updating lines, but I don't know how to > write that... or where to build upon, as it would not be an extension > of sequencepanel, but rather something new... > > Thanks nevertheless! > Max > As i dont fully understand what it is you are trying to do, im not sure these suggestions are helpfull, anyway. Im assuming that you have a MultilineRenderer setup, where each line renders a certain feature type. I dont know of the type of Feature data you connect to your Sequences, but i would assume that most changes to the Features, will not completely remove a certain Feature type from the Sequence, or add a new type. Most will just change the count of the different Feature types. So there is no need to rebuild the MultilineRenderer unless you remove or add a new type of Feature to the Sequence. You could implement this by a ChangeListener setup, that listens for changes on the Sequence, and takes appropriate action, if a new type is added, or the last of a certain type is removed, and if so, rebuild the MultiLineRenderer. Also, if most of your changes do not occur one and one, but in sets, you could do some uggly hacking, and just emit one ChangeEvent for the whole set of changes, and not one Event for each. This has the potential to be pretty uggly i guess but if you know what you are doing, it might be used to speed up your app, as a last measure. mvh Kalle > Kalle N?slund wrote: > >> Maximilian Haussler wrote: >> >>> Hi everyone, >>> >>> why is ViewSequence an implementation of the Unchangeable interface? >>> Isn't a view (among others) meant for adding features to an >>> otherwise unchangeable sequence? >> >> >> >> Exactly what a view is for, is a question you can argue a lot about i >> guess =). But, just from reading the javadocs of the class, it seems >> this one, is to be used to add data "on top" of another sequence. One >> example would indeed be to use it to add Features to an otherwise >> Unchangeable Sequence. >> >>> I have a class derived from the view, but I don't get it to notify >>> the GUI when changes occur, as I don't find the getChangeSupport() >>> in ViewSequence... >> >> >> >> ViewSequence extends Unchangeable, this is a minimal implementation >> of the Changeable Interface, that basicly just refuses any changes. >> The getChangeSupport() method belongs to the AbstractChangeable >> class. Most classes extend AbstractChangeable, so that is why you are >> used to always having getchangeSupport() around. >> >> As ViewSequence will never change, it will never emit any change >> events, and that is what the SWING gui widgets listen for, as a >> trigger to redraw, just as you say. >> >> I think that the correct way to fix this problem, is to have >> ViewSequence to emit change events, i guess alter it to extend >> AbstractChangeable, and then listen for Changes to the underlying >> sequence, and take appropriate action when change events are caught, >> aswell as emitting ChangeEvents when Features are added to the view >> itself. >> >>> [Well, simply adding standard java change support instead of this >>> overly complicated biojava system would also do the trick... :-) ] >> >> >> >> The biojava Changeability thingy, isnt realy that much more complex, >> atleast not from the view of the programmer, that just wants to make >> his class implement Changeable , and the added complexity has its >> uses. I wont claim that the current BJ way is the greatest way >> though =) >> >> So, my suggestion would be to make your own ViewSequene class, that >> does listen for changes on the underlying Sequence, aswell as emiting >> changes. You would start by taking the ViewSequence class, make it >> extend AbstractChangeable instead of Unchanging, then add a >> ChangeListener to the underlying Sequence, and hammer togheter some >> code that does the right thing[tm] when the listener notices the >> underlying sequence have changed ( most likely, check if the change >> affects the features in the view, if so, take some action) and then >> have a change forwarder that also forwards the changes. >> >> Im not sure i have the time at hand, or the mental capability right >> now, to fix this for you, but if you try something like this, and get >> into problems, feel free to mail the ml again, and i will try to help >> as much as i can. >> >> mvh Kalle N?slund >> >>> Thanks >>> Max >>> >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l@biojava.org >>> http://biojava.org/mailman/listinfo/biojava-l >> >> >> >> >> > > From moontigresschiko at hotmail.com Sun Sep 19 04:21:31 2004 From: moontigresschiko at hotmail.com (MoonTigress Chiko) Date: Sun Oct 3 21:50:58 2004 Subject: [Biojava-l] Questions about simple alignment Message-ID: Hi everyone, I'm quite new to biojava and to the mailinglist so I'm not sure if my question has been answered before, although I did look into the older mailinglist entries and found nothing... Anyway, I'm writing a little java programn to align two protein sequences, using the pam250 matrix. So there is my first question, is the pam250 matrix already loaded in biojava? (like with the needleman algoritm, which has its own class) I looked al over the API en cookbook and wherever on google, but I couldn't find any information on this. If not, how can I make the simple alignment use the pam250 matrix? My second question is how to make penalty's in the alignment. Like a origination penalty (of 8) and a length penalty (of 2). It seemed impossible to scan the entry string (given in a textfield) for the existance of an '-' and then add the penalty's so that's not an option. How can I do it otherwise? TIA! Chiko. _________________________________________________________________ Nieuw: Hotmail Medium, Large, Extra Large en Extra Extra Large http://join.msn.com/?pgmarket=nl-nl&page=hotmail/es2 From rahul at genebrew.com Sun Sep 19 15:40:03 2004 From: rahul at genebrew.com (Rahul Karnik) Date: Sun Oct 3 21:50:59 2004 Subject: [Biojava-l] Per-sequence information from PairwiseAlignment Message-ID: <414DE093.9000402@genebrew.com> Hello, [I am a new user of BioJava, so please forgive any obvious errors I may make.] I was trying to modify the PairwiseAlignment demo to show the traditional output of alignment programs, i.e. the aligned sequences alongside one another. It seems this information is available from: StatePath result = aligner.viterbi(seqs, ScoreType.PROBABILITY); I was able to get result.symbolListForLabel(StatePath.SEQUENCE) and display the symbols, but these seem to have both sequences in each symbol (of class SimpleAtomicSymbol). I could parse out each sequence from the combined SymbolList, but I was wondering if there is a better way to achieve this. Thanks, Rahul From mark.schreiber at group.novartis.com Sun Sep 19 21:03:43 2004 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Sun Oct 3 21:50:59 2004 Subject: [Biojava-l] viewsequence is unchangeable? Message-ID: Very good question! Maybe the idea was to make views on views. Seems a bit odd though. Does anyone know what the ideal solution here is? The Change support in biojava does derive from the standard java system but offers some more flexibility about pre and post condition changes and vetos. On the whole it may be overkill but could be useful for large systems. - Mark Maximilian Haussler Sent by: biojava-l-bounces@portal.open-bio.org 09/17/2004 02:21 PM To: biojava-l@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] viewsequence is unchangeable? Hi everyone, why is ViewSequence an implementation of the Unchangeable interface? Isn't a view (among others) meant for adding features to an otherwise unchangeable sequence? I have a class derived from the view, but I don't get it to notify the GUI when changes occur, as I don't find the getChangeSupport() in ViewSequence... [Well, simply adding standard java change support instead of this overly complicated biojava system would also do the trick... :-) ] Thanks Max _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l