From matthew.pocock at ncl.ac.uk Tue Nov 1 08:48:49 2005 From: matthew.pocock at ncl.ac.uk (Matthew Pocock) Date: Tue Nov 1 16:17:08 2005 Subject: [Biojava-dev] gaps and holes In-Reply-To: <436762B2.1070008@genpat.uu.se> References: <200510261220.40776.matthew.pocock@ncl.ac.uk> <436762B2.1070008@genpat.uu.se> Message-ID: <200511011348.50003.matthew.pocock@ncl.ac.uk> On Tuesday 01 November 2005 12:42, Kalle N?slund wrote: > Well, atleast it sounds complex and neat =) Jokes aside, i can > understand the need for > two types of gap symbols, so i agree that we should keep them. Hehe. It's a pita that it's needed, but I think it /realy/ is. > I will try to read your mail, and the javadocs a few more times, until i > think i understand > how the symbol magic works, and i will then try to figure out where in > the serialization > stuff goes b0rk. OK. I think the main magic would be to serialize things out as - or ~, and if you have a leading/trailing ~ then it may be reasonable to use {} rather than [] where as internal - is almost certainly meant to be []. Unfortunately, I think we may have lossy serialization here :( Would we need to pass some sort of 'how far through' hint to serialization? that feels sucky. > So far it seems that if i take a small DNA SymbolList, > write it to disk > and then read it. It no longer has the same symbols in it. So im fairly > sure this realy is > a serialization issue. Yup. It would be key to find out exactly which gaps where written out and which where loaded in. > > /kalle Matthew From kalle.naslund at genpat.uu.se Tue Nov 1 07:50:24 2005 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Tue Nov 1 16:50:18 2005 Subject: [Biojava-dev] Potential Enhancements, Defect In-Reply-To: References: Message-ID: <43676490.4090308@genpat.uu.se> Michael McCormick wrote: > Greetings, > > Ruihan Wang and I are developing an application that uses biojava in > a J2EE environment. We have made a few changes and would like to add > them to the biojava code. All of the changes except for one class > involve serialization issues. Here is a brief summary. > > Please let me know if you are interested in adding these changes and > how they should be submitted. > > Thanks. > Mike > > Michael McCormick > Systems Analyst > Fred Hutchinson Cancer Research Center > > > /org/biojava/bio/search/SeqSimilaritySearchHit should be Serializable > /org/biojava/bio/search/SeqSimilaritySearchResult should be Serializable > /org/biojava/bio/search/SeqSimilaritySearchSubHit should be Serializable > /org/biojava/bio/seq/FeatureHolder should be Serializable > /org/biojava/bio/seq/db/SequenceDB should be Serializable > /org/biojava/bio/symbol/Symbol should be Serializable > /org/biojava/bio/symbol/SymbolList should be Serializable > > / Hi! Some of the Interfaces you are talking about are realy Core interfaces, such as SymbolList. It is used in many different ways all trough biojava. Some implementations cant realy be serialized in a good way. For example the BioSQL classes that are just proxies for the data inside the RDBM. So if you were to take this type of SymbolList object, serialize it to disk, and load it back later, the RDBM might have changend, and you have a very wierd situation. Similar situations exist for FeatureHolder and SequenceDB and so on. Many of the actual implementations of FeatureHolder, SequenceDB and SymbolList and so on implement Serializable though. So as long as you just use those, you can serialize FeatureHolders, SequenceDBs just fine. /kalle From kalle.naslund at genpat.uu.se Tue Nov 1 07:42:26 2005 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Tue Nov 1 17:20:28 2005 Subject: [Biojava-dev] gaps and holes In-Reply-To: <200510261220.40776.matthew.pocock@ncl.ac.uk> References: <200510261220.40776.matthew.pocock@ncl.ac.uk> Message-ID: <436762B2.1070008@genpat.uu.se> Matthew Pocock wrote: >I hope this has made part of the rationalle for structured gaps more clear. I >agree that it is a bit strange, but if you want a consistent structure for >representing symbols as sets and for representing alignments, it prety much >drops out as The One True Way. We can split hairs about exactly when ~ and - >get uses, but they are different things, and if you confuse the two then >inside things like DP recursions, Very Bad Things happen which require >boundary conditions and nasty hacks to correct. Perhaps we need to use a >GapSymbol interface or have isGap on Symbol or something to make life easier. >It's a pitty the Java type system plays so badly with sets. Pitty ML isn't >generally accepted as being a useable language :-( > > > Well, atleast it sounds complex and neat =) Jokes aside, i can understand the need for two types of gap symbols, so i agree that we should keep them. I will try to read your mail, and the javadocs a few more times, until i think i understand how the symbol magic works, and i will then try to figure out where in the serialization stuff goes b0rk. So far it seems that if i take a small DNA SymbolList, write it to disk and then read it. It no longer has the same symbols in it. So im fairly sure this realy is a serialization issue. /kalle >Matthew >_______________________________________________ >biojava-dev mailing list >biojava-dev@biojava.org >http://biojava.org/mailman/listinfo/biojava-dev > > From kalle.naslund at genpat.uu.se Wed Nov 2 10:01:01 2005 From: kalle.naslund at genpat.uu.se (=?ISO-8859-1?Q?Kalle_N=E4slund?=) Date: Wed Nov 2 09:59:50 2005 Subject: [Biojava-dev] gaps and holes In-Reply-To: <200511011348.50003.matthew.pocock@ncl.ac.uk> References: <200510261220.40776.matthew.pocock@ncl.ac.uk> <436762B2.1070008@genpat.uu.se> <200511011348.50003.matthew.pocock@ncl.ac.uk> Message-ID: <4368D4AD.8070006@genpat.uu.se> >>I will try to read your mail, and the javadocs a few more times, until i >>think i understand >>how the symbol magic works, and i will then try to figure out where in >>the serialization >>stuff goes b0rk. >> >> > >OK. I think the main magic would be to serialize things out as - or ~, and if >you have a leading/trailing ~ then it may be reasonable to use {} rather than >[] where as internal - is almost certainly meant to be []. Unfortunately, I >think we may have lossy serialization here :( Would we need to pass some sort >of 'how far through' hint to serialization? that feels sucky. > > > The approach i was thinking of was to keep it as it is now. That is that SimpleSymbolList contains the symbols that was created with, or added later on, so there its up to the user to actualy handle - or ~ as the/she sees fit. This seem to have worked ok up to now. The GappedSymbolList on the other hand, handles gaps separately from the other symbols. So here it alread uses ~ and - appropriately i think, and the serialization isnt an issue as the gap symbols are never serialized. This is as it is now in BJ, and from what i understood, the HMM code uses GappedSymbolLists so it gets the needed ~ and -, and is happy. And people doing simple sequence manipulation only get - and are happy. Is this ok ? or am i missing something obvious ? From mark.schreiber at novartis.com Thu Nov 3 22:24:08 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Nov 3 22:29:47 2005 Subject: [Biojava-dev] gaps and holes Message-ID: >> So far it seems that if i take a small DNA SymbolList, >> write it to disk >> and then read it. It no longer has the same symbols in it. So im fairly >> sure this realy is >> a serialization issue. > >Yup. It would be key to find out exactly which gaps where written out and >which where loaded in. The serialization code seems to get confused during serialization of the basis gap symbol and ends up converting it to an n {a,c,g,t} rather than {}. Not entirely sure why, there is a very confusing if-else-then-but-except-onlyOnAMonday type loop in there. - Mark From mark.schreiber at novartis.com Thu Nov 3 22:40:18 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Nov 3 22:39:08 2005 Subject: [Biojava-dev] Potential Enhancements, Defect Message-ID: I agree with this. If you place implements Serializable on an interface you put a pretty heavy burden on the implementor. The next best place is on the Abstract class (although this forces every thing that inherits from it to be serializable). The very safest place would be on a final class. Other options include making serialization factories that do their best to clone all the information in a (for example) SequenceDB without needing to make the SequenceDB serializable. The factory could produce a SerializableSequenceDB that implements SequenceDB and Serializable. - Mark Kalle N?slund Sent by: biojava-dev-bounces@portal.open-bio.org 11/01/2005 08:50 PM To: Michael McCormick cc: biojava-dev@biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-dev] Potential Enhancements, Defect Michael McCormick wrote: > Greetings, > > Ruihan Wang and I are developing an application that uses biojava in > a J2EE environment. We have made a few changes and would like to add > them to the biojava code. All of the changes except for one class > involve serialization issues. Here is a brief summary. > > Please let me know if you are interested in adding these changes and > how they should be submitted. > > Thanks. > Mike > > Michael McCormick > Systems Analyst > Fred Hutchinson Cancer Research Center > > > /org/biojava/bio/search/SeqSimilaritySearchHit should be Serializable > /org/biojava/bio/search/SeqSimilaritySearchResult should be Serializable > /org/biojava/bio/search/SeqSimilaritySearchSubHit should be Serializable > /org/biojava/bio/seq/FeatureHolder should be Serializable > /org/biojava/bio/seq/db/SequenceDB should be Serializable > /org/biojava/bio/symbol/Symbol should be Serializable > /org/biojava/bio/symbol/SymbolList should be Serializable > > / Hi! Some of the Interfaces you are talking about are realy Core interfaces, such as SymbolList. It is used in many different ways all trough biojava. Some implementations cant realy be serialized in a good way. For example the BioSQL classes that are just proxies for the data inside the RDBM. So if you were to take this type of SymbolList object, serialize it to disk, and load it back later, the RDBM might have changend, and you have a very wierd situation. Similar situations exist for FeatureHolder and SequenceDB and so on. Many of the actual implementations of FeatureHolder, SequenceDB and SymbolList and so on implement Serializable though. So as long as you just use those, you can serialize FeatureHolders, SequenceDBs just fine. /kalle _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at novartis.com Thu Nov 3 22:34:54 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Thu Nov 3 22:40:11 2005 Subject: [Biojava-dev] Potential Enhancements, Defect Message-ID: Hello - Good to know that someone is giving biojava a good work out in J2EE! There are several possibilities to commit the code. 1) I could arrange for a cvs account for you. 2) Send me the files and I will commit them. 3) For the classes that only require "implements Serializable" I can do this. 4) Send me CVS patch files. It would also be really great if you could provide simple JUnit tests that proove the serialization regenerates objects that are .equals() and == where appropriate. eg Singletons and Fly weight objects must be == on deserialization. Also if you are going to use the new biojavax I don't think we have marked anything as serializable yet. - Mark Mark Schreiber Research Investigator (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 Michael McCormick Sent by: biojava-dev-bounces@portal.open-bio.org 10/29/2005 12:48 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Potential Enhancements, Defect Greetings, Ruihan Wang and I are developing an application that uses biojava in a J2EE environment. We have made a few changes and would like to add them to the biojava code. All of the changes except for one class involve serialization issues. Here is a brief summary. Please let me know if you are interested in adding these changes and how they should be submitted. Thanks. Mike Michael McCormick Systems Analyst Fred Hutchinson Cancer Research Center /org/biojava/bio/search/SeqSimilaritySearchHit should be Serializable /org/biojava/bio/search/SeqSimilaritySearchResult should be Serializable /org/biojava/bio/search/SeqSimilaritySearchSubHit should be Serializable /org/biojava/bio/seq/FeatureHolder should be Serializable /org/biojava/bio/seq/db/SequenceDB should be Serializable /org/biojava/bio/symbol/Symbol should be Serializable /org/biojava/bio/symbol/SymbolList should be Serializable /org/biojava/bio/symbol/SimpleAtomicSymbol and /org/biojava/bio/symbol/SimpleBasisSymbol do not serialize correctly, however the mailing list provided a work around by commenting out the defective code. org/biojava/bio/program/abi/ABIFChromatogram.java has a few issues. 1. Should be Serializable. 2. We experienced file handle count resource exceptions since File access was not being closed! This still needs future refactoring since the new close does not occur within a finally block. 3. Modify class to use readFully(). In our environment, this change allowed us to parse chromats at least 10 times faster. diff for org/biojava/bio/program/abi/ABIFChromatogram.java 27,28d26 < import java.io.RandomAccessFile; < import java.io.Serializable; 57c55 < public class ABIFChromatogram extends AbstractChromatogram implements Serializable { --- > public class ABIFChromatogram extends AbstractChromatogram { 141d138 < 151a149 > 153d150 < ((RandomAccessFile)getDataAccess()).close(); 164a162 > 166,171c164,166 < byte[] shortArray = new byte[2 * count]; < getDataAccess().readFully(shortArray); < int i = 0; < for (int s = 0; s < shortArray.length; s += 2) { < trace[i] = ((short)((shortArray[s] << 8) | (shortArray[s + 1] & 0xff))) & 0xffff; < max = Math.max(trace[i++], max); --- > for (int i = 0 ; i < count ; i++) { > trace[i] = getDataAccess().readShort() & 0xffff; > max = Math.max(trace[i], max); 175,178c170,171 < byte[] byteArray = new byte[count]; < getDataAccess().readFully(byteArray); < for (int i = 0; i < byteArray.length; i++) { < trace[i] = byteArray[i] & 0xff; --- > for (int i = 0 ; i < count ; i++) { > trace[i] = getDataAccess().readByte() & 0xff; 185c178 < --- > 212,216c205,206 < byte[] shortArray = new byte[2 * count]; < getDataAccess().readFully(shortArray); < IntegerAlphabet integerAlphabet = IntegerAlphabet.getInstance(); < for (int s = 0; s < shortArray.length; s += 2) { < offsets.add(integerAlphabet.getSymbol(((short) ((shortArray[s] << 8) | (shortArray[s + 1] & 0xff))) & 0xffff)); --- > for (int i = 0 ; i < offsetsPtr.numberOfElements ; i++) { > offsets.add(IntegerAlphabet.getInstance ().getSymbol(getDataAccess().readShort() & 0xffff)); 220,224c210,211 < byte[] byteArray = new byte[count]; < getDataAccess().readFully(byteArray); < IntegerAlphabet integerAlphabet = IntegerAlphabet.getInstance(); < for (int i = 0 ; i < byteArray.length; i++) { < offsets.add(integerAlphabet.getSymbol(byteArray [i] & 0xff)); --- > for (int i = 0 ; i < offsetsPtr.numberOfElements ; i++) { > offsets.add(IntegerAlphabet.getInstance ().getSymbol(getDataAccess().readByte() & 0xff)); 234,237c221,224 < byte[] byteArray = new byte[(int) basesPtr.numberOfElements]; < getDataAccess().readFully(byteArray); < for (int i = 0; i < byteArray.length; i++) { < dna.add(ABIFParser.decodeDNAToken((char) byteArray[i])); --- > char token; > for (int i = 0 ; i < basesPtr.numberOfElements ; i+ +) { > token = (char) getDataAccess().readByte(); > dna.add(ABIFParser.decodeDNAToken(token)); _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From russ at kepler-eng.com Tue Nov 8 12:11:25 2005 From: russ at kepler-eng.com (Russ Kepler) Date: Tue Nov 8 12:36:04 2005 Subject: [Biojava-dev] GUI object manipulation Message-ID: <200511081011.25965.russ@kepler-eng.com> All, I'm a recent user of the BioJava code, this in support of a project doing some specialized trace viewing/editing and sequence assembly. I'm hoping to use the BioJava library in support for much of this and am still acquiring an understanding of the classes and their interfaces. Since the project is going to have a lot of GUI I thought that I'd start by digging into the GUI code in org.biojava.bio.gui One thing I'm going to need is the ability to display a cursor on trace and sequence data. This is fairly easily handled on an individual object basis but it's not uncommon to have a set of objects who all want to display the same cursor position (consider a trace with the symbols and a ruler underneath) so it seems that the MultiLineRenderer is a natural place for the collective code to go. Before I dive in and muck things up does anyone have any suggestions? This area of the code is somewhat difficult and fairly unburdened with comments (plus I'd hate to introduce myself by screwing something up). In the spirit of introducing myself: I'm a long time software developer (long time meaning I remember punching paper tape and cards) with quite a bit of experience in Java, having started using Java about 1.1. I've lived mostly in the 'fat client' side of Java, starting with AWT and happily moving to Swing when it became available. I've done bioinformatics for a little longer than Java, but a lot of the work was more in the vein of pushing bytes in databases and doing sample management (think LIMS) than cool algorithm work. -- Russ Kepler 8600 La Sala del Centro Albuquerque NM 87111 office: 505 296 4783 cell: 505 301 4796 From mark.schreiber at novartis.com Tue Nov 8 20:12:32 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Tue Nov 8 20:11:17 2005 Subject: [Biojava-dev] GUI object manipulation Message-ID: I agree that the MultilineRenderer would probably be the place to put a ticker. Alternatively you could make a ticker that draws itself on top of any component and have them all listen to the same event source so they all move at the same time. GUI code seems to benefit greatly from extension and rewrites of the paintComponent(Graphics g) method. So your best bet would probably be extending MultilineRenderer and overiding the paintComponent(Graphics g) to do something like: public void paintComponent(Graphics g){ super.paintComponent(g); //paint the base stuff //code here to paint the ticker on top of the base stuff. } - Mark Russ Kepler Sent by: biojava-dev-bounces@portal.open-bio.org 11/09/2005 01:11 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] GUI object manipulation All, I'm a recent user of the BioJava code, this in support of a project doing some specialized trace viewing/editing and sequence assembly. I'm hoping to use the BioJava library in support for much of this and am still acquiring an understanding of the classes and their interfaces. Since the project is going to have a lot of GUI I thought that I'd start by digging into the GUI code in org.biojava.bio.gui One thing I'm going to need is the ability to display a cursor on trace and sequence data. This is fairly easily handled on an individual object basis but it's not uncommon to have a set of objects who all want to display the same cursor position (consider a trace with the symbols and a ruler underneath) so it seems that the MultiLineRenderer is a natural place for the collective code to go. Before I dive in and muck things up does anyone have any suggestions? This area of the code is somewhat difficult and fairly unburdened with comments (plus I'd hate to introduce myself by screwing something up). In the spirit of introducing myself: I'm a long time software developer (long time meaning I remember punching paper tape and cards) with quite a bit of experience in Java, having started using Java about 1.1. I've lived mostly in the 'fat client' side of Java, starting with AWT and happily moving to Swing when it became available. I've done bioinformatics for a little longer than Java, but a lot of the work was more in the vein of pushing bytes in databases and doing sample management (think LIMS) than cool algorithm work. -- Russ Kepler 8600 La Sala del Centro Albuquerque NM 87111 office: 505 296 4783 cell: 505 301 4796 _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From ap3 at sanger.ac.uk Wed Nov 9 04:44:39 2005 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed Nov 9 05:04:49 2005 Subject: [Biojava-dev] GUI object manipulation In-Reply-To: <200511081011.25965.russ@kepler-eng.com> References: <200511081011.25965.russ@kepler-eng.com> Message-ID: Hi Russ, > One thing I'm going to need is the ability to display a cursor on > trace and > sequence data. This is fairly easily handled on an individual object > basis > but it's not uncommon to have a set of objects who all want to display > the > same cursor position (consider a trace with the symbols and a ruler > underneath) For drawing a cursor over some other objects you also might want to have a look at JLayeredPane http://java.sun.com/docs/books/tutorial/uiswing/components/ layeredpane.html Cheers, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 From matthew.pocock at ncl.ac.uk Fri Nov 18 06:49:36 2005 From: matthew.pocock at ncl.ac.uk (Matthew Pocock) Date: Fri Nov 18 06:55:40 2005 Subject: [Biojava-dev] biojava workshop Message-ID: <200511181149.37238.matthew.pocock@ncl.ac.uk> Hi, We are going to apply to one of the research councils for some BioJava funding. There are now some grants available for supporting tools that support research. The plan would be to apply for: Funding for a workshop: Bring together people who use and develop BioJava (and other Bio* projects, if relevant) to discuss: * what they use BioJava for * the things it is good for * any things that could be improved This will result in a jointly authored BioJava paper discussing what we have learned and where we are going next. Funding for full-time biojava developers: We would be looking for two people. One post would concentrate on the core coding, and one to work on documentation, the biojava-in-anger and useful example applications. Depending on what came out of the workshop, the thrust of the developer time may well go into adding support for post-genomics, metabolomics and the rest. It would be realy helpful if people could let me know if you are interested in any of this. In particular, letters of support for BioJava would be awesome. Let me know if you woud like to attend the workshop, or have strong views about the future direction of biojava. Thanks, Matthew Pocock West Suite, 8th Floor Claremont Tower School of Computing Science University of Newcastle upon Tyne NE1 7RU, United Kingdom From hollandr at gis.a-star.edu.sg Tue Nov 22 23:59:35 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Wed Nov 23 00:10:19 2005 Subject: [Biojava-dev] RE: [Biojava-l] install Biojava Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D5602656F1C@BIONIC.biopolis.one-north.com> This is a general Java problem, not a BioJava one. There is no such concept of "installing" a Java library, just the process of adding it to your classpath whenever you need it. However... It sounds like you are logging out of your shell between each execution, hence it works for your first javac that is run in the same shell as the export command but not when you start another shell and run javac again without doing the export first. The classpath is only valid within your current shell session. If you want it to persist across all shell sessions, you have to add it to your user profile that is run when you start a shell, or to the system profile that is run for everyone when they start a shell. Or, write a wrapper script for javac that sets the classpath each time before calling the real javac. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biojava-l-bounces@portal.open-bio.org > [mailto:biojava-l-bounces@portal.open-bio.org] On Behalf Of > Te-yuan Chyou > Sent: Wednesday, November 23, 2005 12:38 PM > To: biojava-dev@biojava.org > Cc: biojava-l@biojava.org > Subject: [Biojava-l] install Biojava > > > Hi: > > I'm trying to install Biojava onto MacOS following informations in the > "Getting Started" section of the Biojava website, by putting > the following > jar files: > > biojava.jar > commons-cli.jar > commons-collections-2.1.jar > commons-dbcp-1.1.jar > commons-pool-1.1.jar > bytecode-0.92.jar > > into the directory > > Macintosh HD/System/Library/Java/Extensions > > Then, while trying to compile the demo code "TestEmbl.java" I get 15 > errors and looks like the computer cannot find the packages > in Biojava. > > At that time I didn't set the CLASSPATH because the website > says "It is > also possible to "install" JAR files onto your system by > copying them...". > > Then I put all the jar files in the directory: > /Users/davidchyou/Desktop/david/ > Then set the CLASSPATH by typing: > > export > CLASSPATH=/Users/davidchyou/Desktop/david/biojava.jar:/Users/d > avidchyou/Desktop/commons-cli.jar:/Users/davidchyou/Desktop/da > vid/commons-collections-2.1.jar:/Users/davidchyou/Desktop/davi > d/commons-dbcp-1.1.jar:/Users/davidchyou/Desktop/david/commons > -pool-1.1.jar: > > in a single line, and the command works. BUT after that when > I compile the > demos again, the computer still produces the same set of > error messages > (package not exist). > > Could anyone tell me what else I missed out? A step-by-step > istallation > guide may be helpful also. > > Thanks > > Te-yuan (David) Chyou > > I attached the error messages I get below: > > ou003153:~ davidchyou$ javac > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:5: package > org.biojava.bio > does not exist > import org.biojava.bio.*; > ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:6: package > org.biojava.bio.symbol does not exist > import org.biojava.bio.symbol.*; > ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:7: package > org.biojava.bio.seq does not exist > import org.biojava.bio.seq.*; > ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:8: package > org.biojava.bio.seq.io does not exist > import org.biojava.bio.seq.io.*; > ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot > resolve symbol > symbol ?: class SequenceFormat > location: class seq.TestEmbl > ?? ? ?SequenceFormat eFormat = new EmblLikeFormat(); > ?? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot > resolve symbol > symbol ?: class EmblLikeFormat > location: class seq.TestEmbl > ?? ? ?SequenceFormat eFormat = new EmblLikeFormat(); > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot > resolve symbol > symbol ?: class SequenceBuilderFactory > location: class seq.TestEmbl > ?? ? ?SequenceBuilderFactory sFact = new > EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); > ?? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: package > EmblProcessor > does not exist > ?? ? ?SequenceBuilderFactory sFact = new > EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot > resolve symbol > symbol ?: variable SimpleSequenceBuilder > location: class seq.TestEmbl > ?? ? ?SequenceBuilderFactory sFact = new > EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot > resolve symbol > symbol ?: class Alphabet > location: class seq.TestEmbl > ?? ? ?Alphabet alpha = DNATools.getDNA(); > ?? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot > resolve symbol > symbol ?: variable DNATools > location: class seq.TestEmbl > ?? ? ?Alphabet alpha = DNATools.getDNA(); > ?? ? ? ? ? ? ? ? ? ? ? ^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:23: cannot > resolve symbol > symbol ?: class SymbolTokenization > location: class seq.TestEmbl > ?? ? ?SymbolTokenization rParser = alpha.getTokenization("token"); > ?? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:24: cannot > resolve symbol > symbol ?: class SequenceIterator > location: class seq.TestEmbl > ?? ? ?SequenceIterator seqI = > ?? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:25: cannot > resolve symbol > symbol ?: class StreamReader > location: class seq.TestEmbl > ?? ? ? ?new StreamReader(eReader, eFormat, rParser, sFact); > ?? ? ? ? ? ?^ > Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:28: cannot > resolve symbol > symbol ?: class Sequence > location: class seq.TestEmbl > ?? ? ? ?Sequence seq = seqI.nextSequence(); > ?? ? ? ?^ > 15 errors > ou003153:~ davidchyou$ > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > From m.zblewski at fh-wolfenbuettel.de Tue Nov 15 09:36:46 2005 From: m.zblewski at fh-wolfenbuettel.de (Markus Josef Zblewski) Date: Mon Nov 28 21:07:00 2005 Subject: [Biojava-dev] Biojava in German Message-ID: <2fe0a2c3e0.2c3e02fe0a@fh-wolfenbuettel.de> Hello People, has anybody information about BioJava in German? Or good code examples ? thank you for help m.zblewski From chyte374 at student.otago.ac.nz Tue Nov 22 03:03:22 2005 From: chyte374 at student.otago.ac.nz (Te-yuan Chyou) Date: Mon Nov 28 21:07:00 2005 Subject: [Biojava-dev] installing Biojava Message-ID: <1132646602.4382d0ca54a41@www.studentmail.otago.ac.nz> Hi: I'm trying to install Biojava onto MacOS following informations in the "Getting Started" section of the Biojava website, by putting the following jar files: biojava.jar commons-cli.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar bytecode-0.92.jar into the directory Macintosh HD/System/Library/Java/Extensions Then, while trying to compile the demo code "TestEmbl.java" I get 15 errors and looks like the computer cannot find the packages in Biojava. I didn't set the CLASSPATH because the website says "It is also possible to "install" JAR files onto your system by copying them...". Could anyone tell me what else I missed out? A step-by-step istallation guide may be helpful also. Thanks Te-yuan (David) Chyou I attached the error messages I get below: ou003153:~ davidchyou$ javac Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:5: package org.biojava.bio does not exist import org.biojava.bio.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:6: package org.biojava.bio.symbol does not exist import org.biojava.bio.symbol.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:7: package org.biojava.bio.seq does not exist import org.biojava.bio.seq.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:8: package org.biojava.bio.seq.io does not exist import org.biojava.bio.seq.io.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol symbol : class SequenceFormat location: class seq.TestEmbl SequenceFormat eFormat = new EmblLikeFormat(); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol symbol : class EmblLikeFormat location: class seq.TestEmbl SequenceFormat eFormat = new EmblLikeFormat(); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol symbol : class SequenceBuilderFactory location: class seq.TestEmbl SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: package EmblProcessor does not exist SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol symbol : variable SimpleSequenceBuilder location: class seq.TestEmbl SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol symbol : class Alphabet location: class seq.TestEmbl Alphabet alpha = DNATools.getDNA(); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol symbol : variable DNATools location: class seq.TestEmbl Alphabet alpha = DNATools.getDNA(); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:23: cannot resolve symbol symbol : class SymbolTokenization location: class seq.TestEmbl SymbolTokenization rParser = alpha.getTokenization("token"); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:24: cannot resolve symbol symbol : class SequenceIterator location: class seq.TestEmbl SequenceIterator seqI = ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:25: cannot resolve symbol symbol : class StreamReader location: class seq.TestEmbl new StreamReader(eReader, eFormat, rParser, sFact); ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:28: cannot resolve symbol symbol : class Sequence location: class seq.TestEmbl Sequence seq = seqI.nextSequence(); ^ 15 errors ou003153:~ davidchyou$ From mmccormi at fhcrc.org Tue Nov 8 13:12:44 2005 From: mmccormi at fhcrc.org (Michael McCormick) Date: Mon Nov 28 21:07:01 2005 Subject: [Biojava-dev] Potential Enhancements, Defect In-Reply-To: References: Message-ID: <9A20DF81-9D90-4385-8D23-82BD3660F1BE@fhcrc.org> Hi, Unfortunately, I don't have time to provide a standalone JUnit for these changes since our JUnits are more focused on our surrounding business logic. However, they have been used for about 3 months now without problems. As you suggested below, I am enclosing an updated copy of org/biojava/bio/program/abi/ABIFChromatogram.java. The changes close the opened file resource and speed up ABI chromat reading. The only other changes that we recommended involve Serialization. Thanks. Mike Michael McCormick Systems Analyst Fred Hutchinson Cancer Research Center -------------- next part -------------- A non-text attachment was scrubbed... Name: ABIFChromatogram.java Type: application/octet-stream Size: 11058 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biojava-dev/attachments/20051108/eb6b9cf1/ABIFChromatogram-0001.obj -------------- next part -------------- On Nov 3, 2005, at 7:34 PM, mark.schreiber@novartis.com wrote: Hello - Good to know that someone is giving biojava a good work out in J2EE! There are several possibilities to commit the code. 1) I could arrange for a cvs account for you. 2) Send me the files and I will commit them. 3) For the classes that only require "implements Serializable" I can do this. 4) Send me CVS patch files. It would also be really great if you could provide simple JUnit tests that proove the serialization regenerates objects that are .equals() and == where appropriate. eg Singletons and Fly weight objects must be == on deserialization. Also if you are going to use the new biojavax I don't think we have marked anything as serializable yet. - Mark Mark Schreiber Research Investigator (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 Michael McCormick Sent by: biojava-dev-bounces@portal.open-bio.org 10/29/2005 12:48 AM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Potential Enhancements, Defect Greetings, Ruihan Wang and I are developing an application that uses biojava in a J2EE environment. We have made a few changes and would like to add them to the biojava code. All of the changes except for one class involve serialization issues. Here is a brief summary. Please let me know if you are interested in adding these changes and how they should be submitted. Thanks. Mike Michael McCormick Systems Analyst Fred Hutchinson Cancer Research Center /org/biojava/bio/search/SeqSimilaritySearchHit should be Serializable /org/biojava/bio/search/SeqSimilaritySearchResult should be Serializable /org/biojava/bio/search/SeqSimilaritySearchSubHit should be Serializable /org/biojava/bio/seq/FeatureHolder should be Serializable /org/biojava/bio/seq/db/SequenceDB should be Serializable /org/biojava/bio/symbol/Symbol should be Serializable /org/biojava/bio/symbol/SymbolList should be Serializable /org/biojava/bio/symbol/SimpleAtomicSymbol and /org/biojava/bio/symbol/SimpleBasisSymbol do not serialize correctly, however the mailing list provided a work around by commenting out the defective code. org/biojava/bio/program/abi/ABIFChromatogram.java has a few issues. 1. Should be Serializable. 2. We experienced file handle count resource exceptions since File access was not being closed! This still needs future refactoring since the new close does not occur within a finally block. 3. Modify class to use readFully(). In our environment, this change allowed us to parse chromats at least 10 times faster. diff for org/biojava/bio/program/abi/ABIFChromatogram.java 27,28d26 < import java.io.RandomAccessFile; < import java.io.Serializable; 57c55 < public class ABIFChromatogram extends AbstractChromatogram implements Serializable { --- > public class ABIFChromatogram extends AbstractChromatogram { > 141d138 < 151a149 > > 153d150 < ((RandomAccessFile)getDataAccess()).close(); 164a162 > > 166,171c164,166 < byte[] shortArray = new byte[2 * count]; < getDataAccess().readFully(shortArray); < int i = 0; < for (int s = 0; s < shortArray.length; s += 2) { < trace[i] = ((short)((shortArray[s] << 8) | (shortArray[s + 1] & 0xff))) & 0xffff; < max = Math.max(trace[i++], max); --- > for (int i = 0 ; i < count ; i++) { > trace[i] = getDataAccess().readShort() & 0xffff; > max = Math.max(trace[i], max); > 175,178c170,171 < byte[] byteArray = new byte[count]; < getDataAccess().readFully(byteArray); < for (int i = 0; i < byteArray.length; i++) { < trace[i] = byteArray[i] & 0xff; --- > for (int i = 0 ; i < count ; i++) { > trace[i] = getDataAccess().readByte() & 0xff; > 185c178 < --- > > 212,216c205,206 < byte[] shortArray = new byte[2 * count]; < getDataAccess().readFully(shortArray); < IntegerAlphabet integerAlphabet = IntegerAlphabet.getInstance(); < for (int s = 0; s < shortArray.length; s += 2) { < offsets.add(integerAlphabet.getSymbol(((short) ((shortArray[s] << 8) | (shortArray[s + 1] & 0xff))) & 0xffff)); --- > for (int i = 0 ; i < offsetsPtr.numberOfElements ; > i++) { > offsets.add(IntegerAlphabet.getInstance > ().getSymbol(getDataAccess().readShort() & 0xffff)); 220,224c210,211 < byte[] byteArray = new byte[count]; < getDataAccess().readFully(byteArray); < IntegerAlphabet integerAlphabet = IntegerAlphabet.getInstance(); < for (int i = 0 ; i < byteArray.length; i++) { < offsets.add(integerAlphabet.getSymbol(byteArray [i] & 0xff)); --- > for (int i = 0 ; i < offsetsPtr.numberOfElements ; > i++) { > offsets.add(IntegerAlphabet.getInstance > ().getSymbol(getDataAccess().readByte() & 0xff)); 234,237c221,224 < byte[] byteArray = new byte[(int) basesPtr.numberOfElements]; < getDataAccess().readFully(byteArray); < for (int i = 0; i < byteArray.length; i++) { < dna.add(ABIFParser.decodeDNAToken((char) byteArray[i])); --- > char token; > for (int i = 0 ; i < basesPtr.numberOfElements ; i+ > +) { > token = (char) getDataAccess().readByte(); > dna.add(ABIFParser.decodeDNAToken(token)); > _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From chyte374 at student.otago.ac.nz Tue Nov 22 23:37:51 2005 From: chyte374 at student.otago.ac.nz (Te-yuan Chyou) Date: Mon Nov 28 21:07:02 2005 Subject: [Biojava-dev] install Biojava Message-ID: <1132720671.4383f21f4dd66@www.studentmail.otago.ac.nz> Hi: I'm trying to install Biojava onto MacOS following informations in the "Getting Started" section of the Biojava website, by putting the following jar files: biojava.jar commons-cli.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar bytecode-0.92.jar into the directory Macintosh HD/System/Library/Java/Extensions Then, while trying to compile the demo code "TestEmbl.java" I get 15 errors and looks like the computer cannot find the packages in Biojava. At that time I didn't set the CLASSPATH because the website says "It is also possible to "install" JAR files onto your system by copying them...". Then I put all the jar files in the directory: /Users/davidchyou/Desktop/david/ Then set the CLASSPATH by typing: export CLASSPATH=/Users/davidchyou/Desktop/david/biojava.jar:/Users/davidchyou/Desktop/commons-cli.jar:/Users/davidchyou/Desktop/david/commons-collections-2.1.jar:/Users/davidchyou/Desktop/david/commons-dbcp-1.1.jar:/Users/davidchyou/Desktop/david/commons-pool-1.1.jar: in a single line, and the command works. BUT after that when I compile the demos again, the computer still produces the same set of error messages (package not exist). Could anyone tell me what else I missed out? A step-by-step istallation guide may be helpful also. Thanks Te-yuan (David) Chyou I attached the error messages I get below: ou003153:~ davidchyou$ javac Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:5: package org.biojava.bio does not exist import org.biojava.bio.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:6: package org.biojava.bio.symbol does not exist import org.biojava.bio.symbol.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:7: package org.biojava.bio.seq does not exist import org.biojava.bio.seq.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:8: package org.biojava.bio.seq.io does not exist import org.biojava.bio.seq.io.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol symbol ?: class SequenceFormat location: class seq.TestEmbl ?? ? ?SequenceFormat eFormat = new EmblLikeFormat(); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol symbol ?: class EmblLikeFormat location: class seq.TestEmbl ?? ? ?SequenceFormat eFormat = new EmblLikeFormat(); ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol symbol ?: class SequenceBuilderFactory location: class seq.TestEmbl ?? ? ?SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: package EmblProcessor does not exist ?? ? ?SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol symbol ?: variable SimpleSequenceBuilder location: class seq.TestEmbl ?? ? ?SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol symbol ?: class Alphabet location: class seq.TestEmbl ?? ? ?Alphabet alpha = DNATools.getDNA(); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol symbol ?: variable DNATools location: class seq.TestEmbl ?? ? ?Alphabet alpha = DNATools.getDNA(); ?? ? ? ? ? ? ? ? ? ? ? ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:23: cannot resolve symbol symbol ?: class SymbolTokenization location: class seq.TestEmbl ?? ? ?SymbolTokenization rParser = alpha.getTokenization("token"); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:24: cannot resolve symbol symbol ?: class SequenceIterator location: class seq.TestEmbl ?? ? ?SequenceIterator seqI = ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:25: cannot resolve symbol symbol ?: class StreamReader location: class seq.TestEmbl ?? ? ? ?new StreamReader(eReader, eFormat, rParser, sFact); ?? ? ? ? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:28: cannot resolve symbol symbol ?: class Sequence location: class seq.TestEmbl ?? ? ? ?Sequence seq = seqI.nextSequence(); ?? ? ? ?^ 15 errors ou003153:~ davidchyou$ From mark.schreiber at novartis.com Mon Nov 28 21:28:07 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Nov 28 21:33:13 2005 Subject: [Biojava-dev] Biojava in German Message-ID: There is an article in german written by a biojava developer. Follow the link under "Recent Updates" in the biojava home page. Not sure about german code examples but there are lots of other examples at http://www.biojava.org/docs/bj_in_anger/index.htm with English, French, Chinese and Japanese translations (for some examples). Anyone want ot make a german translation? - Mark Markus Josef Zblewski Sent by: biojava-dev-bounces@portal.open-bio.org 11/15/2005 10:36 PM To: biojava-dev@biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] Biojava in German Hello People, has anybody information about BioJava in German? Or good code examples ? thank you for help m.zblewski _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From mark.schreiber at novartis.com Mon Nov 28 21:32:59 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Mon Nov 28 21:37:32 2005 Subject: [Biojava-dev] install Biojava Message-ID: I think this came up a week ago. Is this a repost of the same problem or is it the flakey mail server sending old messages again? - Mark Te-yuan Chyou Sent by: biojava-dev-bounces@portal.open-bio.org 11/23/2005 12:37 PM To: biojava-dev@biojava.org cc: biojava-l@biojava.org, (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-dev] install Biojava Hi: I'm trying to install Biojava onto MacOS following informations in the "Getting Started" section of the Biojava website, by putting the following jar files: biojava.jar commons-cli.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar bytecode-0.92.jar into the directory Macintosh HD/System/Library/Java/Extensions Then, while trying to compile the demo code "TestEmbl.java" I get 15 errors and looks like the computer cannot find the packages in Biojava. At that time I didn't set the CLASSPATH because the website says "It is also possible to "install" JAR files onto your system by copying them...". Then I put all the jar files in the directory: /Users/davidchyou/Desktop/david/ Then set the CLASSPATH by typing: export CLASSPATH=/Users/davidchyou/Desktop/david/biojava.jar:/Users/davidchyou/Desktop/commons-cli.jar:/Users/davidchyou/Desktop/david/commons-collections-2.1.jar:/Users/davidchyou/Desktop/david/commons-dbcp-1.1.jar:/Users/davidchyou/Desktop/david/commons-pool-1.1.jar: in a single line, and the command works. BUT after that when I compile the demos again, the computer still produces the same set of error messages (package not exist). Could anyone tell me what else I missed out? A step-by-step istallation guide may be helpful also. Thanks Te-yuan (David) Chyou I attached the error messages I get below: ou003153:~ davidchyou$ javac Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:5: package org.biojava.bio does not exist import org.biojava.bio.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:6: package org.biojava.bio.symbol does not exist import org.biojava.bio.symbol.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:7: package org.biojava.bio.seq does not exist import org.biojava.bio.seq.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:8: package org.biojava.bio.seq.io does not exist import org.biojava.bio.seq.io.*; ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol symbol ?: class SequenceFormat location: class seq.TestEmbl ?? ? ?SequenceFormat eFormat = new EmblLikeFormat(); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol symbol ?: class EmblLikeFormat location: class seq.TestEmbl ?? ? ?SequenceFormat eFormat = new EmblLikeFormat(); ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol symbol ?: class SequenceBuilderFactory location: class seq.TestEmbl ?? ? ?SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: package EmblProcessor does not exist ?? ? ?SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol symbol ?: variable SimpleSequenceBuilder location: class seq.TestEmbl ?? ? ?SequenceBuilderFactory sFact = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY); ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol symbol ?: class Alphabet location: class seq.TestEmbl ?? ? ?Alphabet alpha = DNATools.getDNA(); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol symbol ?: variable DNATools location: class seq.TestEmbl ?? ? ?Alphabet alpha = DNATools.getDNA(); ?? ? ? ? ? ? ? ? ? ? ? ^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:23: cannot resolve symbol symbol ?: class SymbolTokenization location: class seq.TestEmbl ?? ? ?SymbolTokenization rParser = alpha.getTokenization("token"); ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:24: cannot resolve symbol symbol ?: class SequenceIterator location: class seq.TestEmbl ?? ? ?SequenceIterator seqI = ?? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:25: cannot resolve symbol symbol ?: class StreamReader location: class seq.TestEmbl ?? ? ? ?new StreamReader(eReader, eFormat, rParser, sFact); ?? ? ? ? ? ?^ Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:28: cannot resolve symbol symbol ?: class Sequence location: class seq.TestEmbl ?? ? ? ?Sequence seq = seqI.nextSequence(); ?? ? ? ?^ 15 errors ou003153:~ davidchyou$ _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From Martin.Szugat at GMX.net Tue Nov 29 09:55:47 2005 From: Martin.Szugat at GMX.net (Martin Szugat) Date: Tue Nov 29 09:54:27 2005 Subject: [Biojava-dev] Biojava in German Message-ID: <200511291454.jATEsE8U009405@portal.open-bio.org> There is a German article about BioJava (published in the German Java magazine): http://www.biojava.org/presentations/JM_2.05_20-23.pdf Viele Gr??e nach Wolfenb?ttel Martin > -----Urspr?ngliche Nachricht----- > Von: biojava-dev-bounces@portal.open-bio.org > [mailto:biojava-dev-bounces@portal.open-bio.org] Im Auftrag > von Markus Josef Zblewski > Gesendet: Dienstag, 15. November 2005 15:37 > An: biojava-dev@biojava.org > Betreff: [Biojava-dev] Biojava in German > > Hello People, > > has anybody information about BioJava in German? > > Or good code examples ? > > thank you for help > > m.zblewski > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > >