[Biojava-l] error with the proteomics package in the new release
Robert Stones
r.stones at csl.gov.uk
Fri Jun 20 16:38:02 EDT 2003
Why do I get error with the proteomics package in the new release
BioJava 1.3 which was not present in the pre-release version:
symbol : method setProtese (org.biojava.bio.proteomics.Protease)
location: class org.biojava.bio.proteomics.Digest
bioJavaDigest.setProtese(Protease.getProteaseByName(Protease.TRY
PSIN));
biojava-l-request at biojava.org wrote:
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> Today's Topics:
>
> 1. RE: Announcing BioJava 1.30 (Schreiber, Mark)
> 2. Using ChromatogramGraphic (Rhett Sutphin)
> 3. Online Marketing (Caroline)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 18 Jun 2003 07:08:11 +1200
> From: "Schreiber, Mark" <mark.schreiber at agresearch.co.nz>
> Subject: RE: [Biojava-l] Announcing BioJava 1.30
> To: "Thomas Down" <thomas at derkholm.net>, <biojava-l at biojava.org>
> Message-ID:
> <AF026AF0FF4B054590228FD1F1DE5165011BA55E at inbox.agresearch.co.nz>
> Content-Type: text/plain; charset="utf-8"
>
> Great news Thomas.
>
> For those going to ISMB in Brisbane I will bre presenting a short talk on the biojava 1,3 release at the BOSC sattelite conference.
>
> - Mark
>
> -----Original Message-----
> From: Thomas Down [mailto:thomas at derkholm.net]
> Sent: Mon 16/06/2003 1:26 a.m.
> To: biojava-l at biojava.org
> Cc:
> Subject: [Biojava-l] Announcing BioJava 1.30
>
>
>
> Hi...
>
> After a long series of pre-releases (and many bug fixes), I've
> just finished building BioJava 1.30. Source, binaries, and
> javadocs can all be found at:
>
> http://www.biojava.org/download/
>
> As with the pre-releases, separate binaries are available for
> java platform releases 1.3 and 1.4. The 1.4 releases include
> some extra features which depend on jdk1.4 extensions such
> as the java.nio package.
>
> Highlights of this release include:
>
> - Packed storage of sequence data in memory
>
> - Better support for the OBDA database access standards
>
> - Improvements to the parsers for output from tools like
> blast and fasta.
>
> - Many enhancements to the FeatureFilter system.
>
> Please check out the javadocs for information on these and
> other new features.
>
> I'd also like to take this opportunity to recomment the
> excellent BioJava in Anger website, which is now hosted
> on biojava.org:
>
> http://www.biojava.org/docs/bj_in_anger/index.htm
>
> Thanks to everyone who has made this release possible:
>
> Aroul Ramadass
> Brian Gilman
> Brian King
> Cambridge Antibody Technology (CAT)
> David Allen
> David H. Klatte, Ph.D.
> David Huen
> David Waring
> Ewan Birney
> Francois Pepin
> Gerald Loeffler
> Greg Cox
> Hanning Ni
> Jason Stajich
> Kalle Naslund
> Keith James
> Kim Rutherford
> Lachlan Coin
> Laurent Jourdren
> Leen Ammeraal
> Lei Lai
> Mark Schreiber
> Martin Senger
> Matthew Pocock
> Mayo Foundation
> Michael Heuer
> Michael Jones
> Moses Hohman
> Nimesh Singh
> Paul Seed
> Rhett Sutphin
> Robin Emig
> Ron Kuhn
> Russell Smithies
> Samiul Hasan
> Thad Welch
> Thomas Down
>
> I hope you all find it useful,
>
> Thomas.
> _______________________________________________
> Biojava-l mailing list - Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>
>
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> ------------------------------
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> Message: 2
> Date: Tue, 17 Jun 2003 16:41:41 -0500
> From: Rhett Sutphin <rhett-sutphin at uiowa.edu>
> Subject: [Biojava-l] Using ChromatogramGraphic
> To: biojava-l at biojava.org
> Cc: Simon Foote <simon.foote at nrc-cnrc.gc.ca>,
> mark.schreiber at agresearch.co.nz
> Message-ID: <7B46483C-A10C-11D7-B6E1-000393D44542 at uiowa.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> A couple of folks have asked for examples of the features of the
> Chromatogram support that we recently contributed to BioJava. This
> message will provide some info on using ChromatogramGraphic, the
> Java2D-based class for rendering chromatograms.
>
> First, there's Chromatogram Viewer, which is a simple Java Web Start
> application for, well, viewing chromatograms. I don't have permission
> to release the source (yet), but you can use it for free. (I
> anticipate that I will be able to release the source for at least the
> swing components that are directly involved in viewing the chromatogram
> in the not-to-distant future.) You can run it from:
> http://pdb.eng.uiowa.edu/~rsutphin/public-webstart/chromatogram-
> viewer.jnlp . You'll need a 1.3+ series JRE and Java Web Start 1.0 or
> later. Note that Sun's JRE version 1.4+ come with Java Web Start, as
> do all JREs on OS X 10.1+.
>
> In addition to looking at the chromatogram, Chromatogram Viewer allows
> you to save all or part of the chromatogram as a PNG image and to copy
> all or part of the sequence to the system clipboard. The checkboxes &
> sliders in the panel on the right of the interface allow for twiddling
> many of output options available in ChromatogramGraphic. (Note that
> the "Fixed Base Width" option reflects functionality not incorporated
> into the 1.30 released version of ChromatogramGraphic. I just
> committed it to CVS today.)
>
> But probably more useful for developers is the attached source code.
> It is a command-line demo program that reads in a chromatogram and
> outputs an image. It uses the Image I/O API (new in JDK 1.4), and is
> capable of writing in any format Image I/O supports. (By default, this
> is just PNG and JPEG, but there are more available:
> http://java.sun.com/products/java-media/jai/ ).
>
> -------------- next part --------------
> /*
> * BioJava development code
> *
> * This code may be freely distributed and modified under the
> * terms of the GNU Lesser General Public Licence. This should
> * be distributed with the code. If you do not have a copy,
> * see:
> *
> * http://www.gnu.org/copyleft/lesser.html
> *
> * Copyright for this code is held jointly by the individual
> * authors. These should be listed in @author doc comments.
> *
> * For more information on the BioJava project and its aims,
> * or to join the biojava-l mailing list, visit the home page
> * at:
> *
> * http://www.biojava.org/
> *
> */
>
> package chromatogram;
>
> import java.awt.image.BufferedImage;
> import java.awt.Color;
> import java.awt.Graphics2D;
> import java.awt.Rectangle;
> import java.awt.RenderingHints;
> import java.io.IOException;
> import java.io.File;
> import java.io.FileNotFoundException;
> import java.util.Iterator;
> import javax.imageio.ImageIO;
> import javax.imageio.ImageWriter;
> import javax.imageio.stream.FileImageOutputStream;
> import org.biojava.bio.chromatogram.Chromatogram;
> import org.biojava.bio.chromatogram.ChromatogramFactory;
> import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
> import org.biojava.bio.chromatogram.graphic.ChromatogramGraphic;
>
> /**
> * A command-line utility for dumping a chromatogram to an image using
> * <code>javax.imageio</code>. Demos {@link ChromatogramFactory} and
> * {@link ChromatogramGraphic}. Run it with no parameters to get help with
> * command line options. Requires JDK 1.4.
> */
> public class Chromat2Image {
> private static final int OUT_HEIGHT = 240;
> private static final float OUT_HORIZ_SCALE = 2.0f;
>
> private static final String USAGE =
> "USAGE:\n"
> + "Chromat2Image chromat-file output-image-file\n"
> + " chromat-file\n"
> + " - The chromatogram file from which to create the image\n"
> + " output-image-file\n"
> + " - The name of the file to which the chromatogram image\n"
> + " will be written. The format will be determined from\n"
> + " the extension, which must be png or jpg (unless there\n"
> + " are additional image writers on the classpath). PNG\n"
> + " is highly recommended over JPEG due to the discrete-\n"
> + " tone nature of chromatogram images.\n";
>
> public static void main(String[] args) {
> if (args.length != 2) {
> System.err.println("Invalid args.\n");
> System.err.println(USAGE);
> System.exit(1);
> }
>
> /* create Chromatogram object */
>
> File infile = new File(args[0]);
> if (!infile.canRead()) {
> System.err.println("Can't read " + infile);
> System.exit(1);
> }
>
> Chromatogram c = null;
> try {
> c = ChromatogramFactory.create(infile);
> } catch (UnsupportedChromatogramFormatException ucfe) {
> System.err.println("Unsupported chromatogram format (" + ucfe.getMessage());
> System.exit(1);
> } catch (IOException ioe) {
> System.err.println("Problem reading from " + infile + " (" + ioe.getMessage() + ")");
> System.exit(1);
> }
>
> /* find appropriate ImageWriter */
>
> String outExt = null;
> int lastdot = args[1].lastIndexOf('.');
> if (lastdot >= 0) {
> outExt = args[1].substring(lastdot+1);
> }
>
> if (outExt == null || outExt.length() == 0) {
> System.err.println("No extension on output file, so will use PNG format");
> outExt = "png";
> }
>
> Iterator writers = ImageIO.getImageWritersBySuffix(outExt);
> if (!writers.hasNext()) {
> System.err.println("No image writer found for suffix '" + outExt + "'");
> System.exit(1);
> }
> ImageWriter iw = (ImageWriter) writers.next();
>
> /* build output stream */
>
> File outfile = new File(args[1]);
> FileImageOutputStream out = null;
> try {
> out = new FileImageOutputStream(outfile);
> } catch (FileNotFoundException fnfe) {
> System.err.println("Can't write to " + outfile + " (" + fnfe.getMessage() + ")");
> System.exit(1);
> } catch (IOException ioe) {
> System.err.println("Problem writing to " + outfile + " (" + ioe.getMessage() + ")");
> System.exit(1);
> }
>
> /* create ChromatogramGraphic */
>
> ChromatogramGraphic gfx = new ChromatogramGraphic(c);
> gfx.setHeight(OUT_HEIGHT);
> gfx.setHorizontalScale(OUT_HORIZ_SCALE);
> // set some options that affect the output
> // turn off filled-in "callboxes"
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER, Boolean.FALSE);
> // this option controls whether each trace/callbox/etc is scaled/positioned
> // individually, or whether the scaling is done on all shapes at the level
> // of the graphics context
> // enabling this option is recommended for higher-quality output
> gfx.setOption(ChromatogramGraphic.Option.USE_PER_SHAPE_TRANSFORM, Boolean.TRUE);
>
> /* create output image */
>
> BufferedImage bi = new BufferedImage(
> gfx.getWidth(),
> gfx.getHeight(),
> BufferedImage.TYPE_INT_RGB);
> Graphics2D g2 = bi.createGraphics();
> g2.setBackground(Color.white);
> g2.clearRect(0, 0, bi.getWidth(), bi.getHeight());
> if (g2.getClip() == null) {
> g2.setClip(new Rectangle(0, 0, bi.getWidth(), bi.getHeight()));
> }
>
> /* draw chromatogram into image */
>
> // turn on AA for nicer output
> g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
> // the main event
> gfx.drawTo(g2);
> // work-around an OS X bug where sometimes the last Shape drawn
> // doesn't show up in the output
> g2.draw(new java.awt.Rectangle(-10, -10, 5, 5));
>
> /* write image out */
>
> iw.setOutput(out);
> try {
> iw.write(bi);
> out.close();
> } catch (IOException ioe) {
> System.err.println("Problem writing to " + outfile + " (" + ioe.getMessage() + ")");
> System.exit(1);
> }
>
> System.exit(0);
> }
> }
> -------------- next part --------------
>
> The chromatogram-specific parts are:
>
> /* create Chromatogram object */
>
> [...]
>
> Chromatogram c = null;
> try {
> c = ChromatogramFactory.create(infile);
> } catch (UnsupportedChromatogramFormatException ucfe) {
> System.err.println("Unsupported chromatogram format (" +
> ucfe.getMessage());
> System.exit(1);
> } catch (IOException ioe) {
> System.err.println("Problem reading from " + infile + " ("
> + ioe.getMessage() + ")");
> System.exit(1);
> }
>
> This chunk uses ChromatogramFactory to create a Chromatogram object
> from a File. Note that we don't have to know the format of the file
> (ABI and SCF are supported).
>
> /* create ChromatogramGraphic */
>
> ChromatogramGraphic gfx = new ChromatogramGraphic(c);
> gfx.setHeight(OUT_HEIGHT);
> gfx.setHorizontalScale(OUT_HORIZ_SCALE);
> // set some options that affect the output
> // turn off filled-in "callboxes"
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_A,
> Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_C,
> Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_G,
> Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_T,
> Boolean.FALSE);
> gfx.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER,
> Boolean.FALSE);
> // this option controls whether each trace/callbox/etc is
> scaled/positioned
> // individually, or whether the scaling is done on all shapes
> at the level
> // of the graphics context
> // enabling this option is recommended for higher-quality output
>
> gfx.setOption(ChromatogramGraphic.Option.USE_PER_SHAPE_TRANSFORM,
> Boolean.TRUE);
>
> This chunk creates the ChromatogramGraphic object which will be used to
> draw c, and sets several options that affect the output. The javadoc
> for org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option is
> a detailed list of the available options, the expected parameter types,
> and the default values.
>
> /* draw chromatogram into image */
> gfx.drawTo(g2);
>
> This line actually does the drawing. In this case, the Graphics2D
> object g2 was retrieved from a BufferedImage, but it just as easily
> could have been the Graphics2D instance you get as a parameter to
> paintComponent in a JComponent.
>
> So that's the basics. Please ask if you have any questions.
>
> Rhett
>
> --
> Rhett Sutphin
> Research Assistant (Software)
> Coordinated Laboratory for Computational Genomics
> and the Center for Macular Degeneration
> University of Iowa - Iowa City - Iowa - 52246
> mailto:rhett-sutphin at uiowa.edu
>
> ------------------------------
>
> Message: 3
> Date: Wed, 18 Jun 2003 17:18:56 +0800
> From: "Caroline" <Booster at ywzc.net>
> Subject: [Biojava-l] Online Marketing
> To: <biojava-l at biojava.org>
> Message-ID: <200306180919.h5I9JY3Z012283 at pw600a.bioperl.org>
> Content-Type: text/plain; charset="ISO-8859-1"
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