[Biojava-dev] Suggestions for the BioJava project
Richard HOLLAND
hollandr at gis.a-star.edu.sg
Tue Aug 16 21:13:47 EDT 2005
Thanks for that, it looks very interesting. About a month too late but ah well.... :) :)
Yeah I know the code we have written is a bit messy, I have a very bad habit of writing code that works first and looks good later. Mark and I will go through tidying up a bit and adding JavaDocs over the next few weeks.
Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: Michael Heuer [mailto:heuermh at shell3.shore.net] On
> Behalf Of Michael Heuer
> Sent: Wednesday, August 17, 2005 3:01 AM
> To: mark.schreiber at novartis.com
> Cc: Len Trigg; Andreas Dräger; Richard HOLLAND;
> biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] Suggestions for the BioJava project
>
>
> Hello Mark, Richard
>
> This is very cool. I took a quick look and noticed a few consistency
> problems and several different styles of javadoc comments, but nothing
> major. I'll wait until development slows down a bit before submitting
> any style-related patches.
>
> Unfortunately it's a little bit late, now that you already
> have something
> that works, but I committed a source code generation library and shell
> interface to the biojava subversion repository, at
>
> > http://www.derkholm.net/svn/repos/biojava-expr/trunk/codegen/
> > http://www.derkholm.net/svn/repos/biojava-expr/trunk/codegen-shell/
>
> to save myself a lot of typing, particularly in javadoc comments.
>
>
> You do a little of this
>
> $ java -jar codegen-shell.jar
>
> % InterfaceDescription foo = new InterfaceDescription("Foo");
> % foo.attribute(..., Cardinality.ZeroToOne);
> % foo.associate(..., Cardinality.OneToMany);
>
> % ClassDescription simpleFoo = new ClassDescription("SimpleFoo");
> % simpleFoo.realizes(foo);
>
> % generateSource(foo);
> % generateSource(simpleFoo, Style.RichlyMutable);
>
>
> and you get something like
>
> (sorry if the formatting doesn't work out)
>
> --- Foo.java
>
> import java.util.Set;
> import java.util.List;
> import java.util.SortedSet;
>
> /**
> * foo
> *
> * @author codegen
> * @version $Revision$ $Date$
> */
> public interface Foo
> {
>
> /**
> * Return the foo id for this foo.
> * The foo id will not be null.
> *
> * @return the foo id for this foo
> */
> Long getFooId();
>
> /**
> * Return the name for this foo.
> * The name may be null.
> *
> * @return the name for this foo
> */
> String getName();
>
> /**
> * Return an unmodifiable set of synonyms
> * for this foo. The returned set may be
> * empty but will not be null.
> *
> * @return an unmodifiable set of synonyms
> * for this foo
> */
> Set<String> getSynonyms();
>
> /**
> * Return an unmodifiable list of positions
> * for this foo. The returned list will
> * not be null and will contain at least one position.
> *
> * @return an unmodifiable list of positions
> * for this foo
> */
> List<Integer> getPositions();
>
> /**
> * Return the optional bar for this foo.
> * The optional bar may be null.
> *
> * @return the optional bar for this foo
> */
> Bar getOptionalBar();
>
> /**
> * Return the required bar for this foo.
> * The required bar will not be null.
> *
> * @return the required bar for this foo
> */
> Bar getRequiredBar();
>
> /**
> * Return an unmodifiable list of additional bars
> * for this foo. The returned list may be
> * empty but will not be null.
> *
> * @return an unmodifiable list of additional bars
> * for this foo
> */
> List<Bar> getAdditionalBars();
>
> /**
> * Return an unmodifiable sorted set of other bars
> * for this foo. The returned sorted set will
> * not be null and will contain at least one other bar.
> *
> * @return an unmodifiable sorted set of other bars
> * for this foo
> */
> SortedSet<Bar> getOtherBars();
> }
>
> --- SimpleFoo.java:
>
> import java.util.Set;
> import java.util.HashSet;
> import java.util.Collections;
> import java.util.List;
> import java.util.ArrayList;
> import java.util.SortedSet;
> import java.util.TreeSet;
>
> /**
> * simple foo.
> *
> * @author codegen
> * @version $Revision$ $Date$
> */
> public class SimpleFoo
> implements Foo
> {
> /** The foo id for this simple foo. */
> private Long fooId;
>
> /** The name for this simple foo. */
> private String name;
>
> /** The set of synonyms for this simple foo. */
> private final Set<String> synonyms;
>
> /** The list of positions for this simple foo. */
> private final List<Integer> positions;
>
> /** The optional bar for this simple foo. */
> private Bar optionalBar;
>
> /** The required bar for this simple foo. */
> private Bar requiredBar;
>
> /** The list of additional bars for this simple foo. */
> private final List<Bar> additionalBars;
>
> /** The sorted set of other bars for this simple foo. */
> private final SortedSet<Bar> otherBars;
>
>
> /**
> * Create a new simple foo from the specified required parameters.
> *
> * <p>The specified list of positions must contain at
> least one position.
> * The positions in <code>positions</code> are copied defensively
> * into this class.</p>
> *
> * <p>The specified sorted set of other bars must contain
> at least one other bar.
> * The other bars in <code>otherBars</code> are copied defensively
> * into this class.</p>
> *
> * @param fooId foo id for this simple foo, must not be null
> * @param positions list of integers, must not be null and must
> * contain at least one integer
> * @param requiredBar required bar for this simple foo,
> must not be null
> * @param otherBars sorted set of bars, must not be null and must
> * contain at least one bar
> *
> * @throws IllegalArgumentException if
> <code>positions.size() < 1</code>
> *
> * @throws IllegalArgumentException if
> <code>otherBars.size() < 1</code>
> */
> public SimpleFoo(
> final Long fooId,
> final List<Integer> positions,
> final Bar requiredBar,
> final SortedSet<Bar> otherBars)
> {
> if (fooId == null)
> {
> throw new IllegalArgumentException("fooId must
> not be null");
> }
> if (positions == null)
> {
> throw new IllegalArgumentException("positions
> must not be null");
> }
> if (positions.size() < 1)
> {
> throw new IllegalArgumentException("positions
> must contain at least one position");
> }
> if (requiredBar == null)
> {
> throw new IllegalArgumentException("requiredBar
> must not be null");
> }
> if (otherBars == null)
> {
> throw new IllegalArgumentException("otherBars
> must not be null");
> }
> if (otherBars.size() < 1)
> {
> throw new IllegalArgumentException("otherBars
> must contain at least one other bar");
> }
>
> setFooId(fooId);
> setName(null);
> this.synonyms = new HashSet<String>();
> this.positions = new ArrayList<Integer>(positions));
> setOptionalBar(null);
> setRequiredBar(requiredBar);
> this.additionalBars = new ArrayList<Bar>();
> this.otherBars = new TreeSet<Bar>(otherBars);
> }
>
> /**
> * Create a new simple foo from the specified parameters.
> *
> * <p>The synonyms in <code>synonyms</code> are copied defensively
> * into this class.</p>
> *
> * <p>The specified list of positions must contain at
> least one position.
> * The positions in <code>positions</code> are copied defensively
> * into this class.</p>
> *
> * <p>The additional bars in <code>additionalBars</code>
> are copied defensively
> * into this class.</p>
> *
> * <p>The specified sorted set of other bars must contain
> at least one other bar.
> * The other bars in <code>otherBars</code> are copied defensively
> * into this class.</p>
> *
> * @param fooId foo id for this simple foo, must not be null
> * @param name name for this simple foo
> * @param synonyms set of synonyms, must not be null
> * @param positions list of integers, must not be null and must
> * contain at least one integer
> * @param optionalBar optional bar for this simple foo
> * @param requiredBar required bar for this simple foo,
> must not be null
> * @param additionalBars list of additional bars, must not be null
> * @param otherBars sorted set of bars, must not be null and must
> * contain at least one bar
> *
> * @throws IllegalArgumentException if
> <code>positions.size() < 1</code>
> *
> * @throws IllegalArgumentException if
> <code>otherBars.size() < 1</code>
> */
> public SimpleFoo(
> final Long fooId,
> final String name,
> final Set<String> synonyms,
> final List<Integer> positions,
> final Bar optionalBar,
> final Bar requiredBar,
> final List<Bar> additionalBars,
> final SortedSet<Bar> otherBars)
> {
> if (fooId == null)
> {
> throw new IllegalArgumentException("fooId must
> not be null");
> }
> if (synonyms == null)
> {
> throw new IllegalArgumentException("synonyms must
> not be null");
> }
> if (positions == null)
> {
> throw new IllegalArgumentException("positions
> must not be null");
> }
> if (positions.size() < 1)
> {
> throw new IllegalArgumentException("positions
> must contain at least one position");
> }
> if (requiredBar == null)
> {
> throw new IllegalArgumentException("requiredBar
> must not be null");
> }
> if (additionalBars == null)
> {
> throw new
> IllegalArgumentException("additionalBars must not be null");
> }
> if (otherBars == null)
> {
> throw new IllegalArgumentException("otherBars
> must not be null");
> }
> if (otherBars.size() < 1)
> {
> throw new IllegalArgumentException("otherBars
> must contain at least one other bar");
> }
>
> setFooId(fooId);
> setName(name);
> this.synonyms = new HashSet<String>(synonyms);
> this.positions = new ArrayList<Integer>(positions);
> setOptionalBar(optionalBar);
> setRequiredBar(requiredBar);
> this.additionalBars = new ArrayList<Bar>(additionalBars);
> this.otherBars = new TreeSet<Bar>(otherBars);
> }
>
>
> /**
> * Return the foo id for this simple foo.
> * The foo id will not be null.
> *
> * @return the foo id for this simple foo
> */
> public final Long getFooId()
> {
> return fooId;
> }
>
> /**
> * Set the foo id for this simple foo to <code>fooId</code>.
> *
> * @param fooId foo id for this simple foo, must not be null
> */
> public final void setFooId(final Long fooId)
> {
> if (fooId == null)
> {
> throw new IllegalArgumentException("fooId must
> not be null");
> }
>
> this.fooId = fooId;
> }
>
> /**
> * Return the name for this simple foo.
> * The name may be null.
> *
> * @return the name for this simple foo
> */
> public final String getName()
> {
> return name;
> }
>
> /**
> * Set the name for this simple foo to <code>name</code>.
> *
> * @param name name for this simple foo
> */
> public final void setName(final String name)
> {
> this.name = name;
> }
>
> /**
> * Return an unmodifiable set of synonyms
> * for this simple foo. The returned set may be
> * empty but will not be null.
> *
> * @return an unmodifiable set of synonyms
> * for this simple foo
> */
> public final Set<String> getSynonyms()
> {
> return Collections.unmodifiableSet(synonyms);
> }
>
> /**
> * Add the specified synonym to the set of
> * synonyms for this simple foo. An exception
> * may be thrown if the underlying set prevents
> * <code>synonym</code> from being added.
> *
> * @param synonym synonym to add
> */
> public final void addSynonym(final String synonym)
> {
> synonyms.add(synonym);
> }
>
> /**
> * Add all of the synonyms in the specified collection of synonyms
> * to the set of synonyms for this simple foo.
> * An exception may be thrown if the underlying
> * set prevents any of the synonyms in
> * <code>synonyms</code> from being added.
> *
> * @param synonyms collection of synonyms to add
> */
> public final void addAllSynonyms(final Collection<?
> extends String> synonyms)
> {
> this.synonyms.addAll(synonyms);
> }
>
> /**
> * Remove the specified synonym from the set of
> * synonyms for this simple foo. An exception
> * may be thrown if the underlying set prevents
> * <code>synonym</code> from being removed.
> *
> * @param synonym synonym to remove
> */
> public final void removeSynonym(final String synonym)
> {
> synonyms.remove(synonym);
> }
>
> /**
> * Remove all of the synonyms in the set of
> * synonyms for this simple foo that are also contained in the
> * specified collection of synonyms. An exception
> * may be thrown if the underlying set prevents any
> * of the synonyms in <code>synonyms</code> from being removed.
> *
> * @param synonyms collection of synonyms to remove
> */
> public final void removeAllSynonyms(final Collection<?
> extends String> synonyms)
> {
> this.synonyms.removeAll(synonyms);
> }
>
> /**
> * Retain only the synonyms in the set of
> * synonyms for this simple foo that are contained in the
> specified
> * collection of synonyms. An exception may be thrown
> * if the underlying set prevents any of the synonyms
> * not in <code>synonyms</code> from being removed.
> *
> * @param synonyms collection of synonyms to retain
> */
> public final void retainAllSynonyms(final Collection<?
> extends String> synonyms)
> {
> this.synonyms.retainAll(synonyms);
> }
>
> /**
> * Remove all of the synonyms in the set of
> * synonyms for this simple foo. An exception may
> * be thrown if the underlying set prevents any of the
> * synonyms from being removed.
> */
> public final void clearSynonyms()
> {
> synonyms.clear();
> }
>
> /**
> * Return an unmodifiable list of positions
> * for this simple foo. The returned list will
> * not be null and will contain at least one position.
> *
> * @return an unmodifiable list of positions
> * for this simple foo
> */
> public final List<Integer> getPositions()
> {
> return Collections.unmodifiableList(positions);
> }
>
> /**
> * Add the specified position to the list of
> * positions for this simple foo. An exception
> * may be thrown if the underlying list prevents
> * <code>position</code> from being added.
> *
> * @param position position to add
> */
> public final void addPosition(final Integer position)
> {
> positions.add(position);
> }
>
> /**
> * Add all of the positions in the specified collection
> of positions
> * to the list of positions for this simple foo.
> * An exception may be thrown if the underlying
> * list prevents any of the positions in
> * <code>positions</code> from being added.
> *
> * @param positions collection of positions to add
> */
> public final void addAllPositions(final Collection<?
> extends Integer> positions)
> {
> this.positions.addAll(positions);
> }
>
> /**
> * Remove the specified position from the list of
> * positions for this simple foo. An exception
> * may be thrown if the underlying list prevents
> * <code>position</code> from being removed.
> *
> * @param position position to remove
> */
> public final void removePosition(final Integer position)
> {
> positions.remove(position);
> }
>
> /**
> * Remove all of the positions in the list of
> * positions for this simple foo that are also contained in the
> * specified collection of positions. An exception
> * may be thrown if the underlying list prevents any
> * of the positions in <code>positions</code> from being removed.
> *
> * @param positions collection of positions to remove
> */
> public final void removeAllPositions(final Collection<?
> extends Integer> positions)
> {
> this.positions.removeAll(positions);
> }
>
> /**
> * Retain only the positions in the list of
> * positions for this simple foo that are contained in
> the specified
> * collection of positions. An exception may be thrown
> * if the underlying list prevents any of the positions
> * not in <code>positions</code> from being removed.
> *
> * @param positions collection of positions to retain
> */
> public final void retainAllPositions(final Collection<?
> extends Integer> positions)
> {
> this.positions.retainAll(positions);
> }
>
> /**
> * Remove all of the positions in the list of
> * positions for this simple foo. An exception may
> * be thrown if the underlying list prevents any of the
> * positions from being removed.
> */
> public final void clearPositions()
> {
> positions.clear();
> }
>
> /**
> * Return the optional bar for this simple foo.
> * The optional bar may be null.
> *
> * @return the optional bar for this simple foo
> */
> public final Bar getOptionalBar()
> {
> return optionalBar;
> }
>
> /**
> * Set the optional bar for this simple foo to
> <code>optionalBar</code>.
> *
> * @param optionalBar optional bar for this simple foo
> */
> public final void setOptionalBar(final Bar optionalBar)
> {
> this.optionalBar = optionalBar;
> }
>
> /**
> * Return the required bar for this simple foo.
> * The required bar will not be null.
> *
> * @return the required bar for this simple foo
> */
> public final Bar getRequiredBar()
> {
> return requiredBar;
> }
>
> /**
> * Set the required bar for this simple foo to
> <code>requiredBar</code>.
> *
> * @param requiredBar required bar for this simple foo,
> must not be null
> */
> public final void setRequiredBar(final Bar requiredBar)
> {
> if (requiredBar == null)
> {
> throw new IllegalArgumentException("requiredBar
> must not be null");
> }
>
> this.requiredBar = requiredBar;
> }
>
> /**
> * Return an unmodifiable list of additional bars
> * for this simple foo. The returned list may be
> * empty but will not be null.
> *
> * @return an unmodifiable list of additional bars
> * for this simple foo
> */
> public final List<Bar> getAdditionalBars()
> {
> return Collections.unmodifiableList(additionalBars);
> }
>
> /**
> * Add the specified additional bar to the list of
> * additional bars for this simple foo. An exception
> * may be thrown if the underlying list prevents
> * <code>additionalBar</code> from being added.
> *
> * @param additionalBar additional bar to add
> */
> public final void addAdditionalBar(final Bar additionalBar)
> {
> additionalBars.add(additionalBar);
> }
>
> /**
> * Add all of the additional bars in the specified
> collection of additional bars
> * to the list of additional bars for this simple foo.
> * An exception may be thrown if the underlying
> * list prevents any of the additional bars in
> * <code>additionalBars</code> from being added.
> *
> * @param additionalBars collection of additional bars to add
> */
> public final void addAllAdditionalBars(final Collection<?
> extends Bar> additionalBars)
> {
> this.additionalBars.addAll(additionalBars);
> }
>
> /**
> * Remove the specified additional bar from the list of
> * additional bars for this simple foo. An exception
> * may be thrown if the underlying list prevents
> * <code>additionalBar</code> from being removed.
> *
> * @param additionalBar additional bar to remove
> */
> public final void removeAdditionalBar(final Bar additionalBar)
> {
> additionalBars.remove(additionalBar);
> }
>
> /**
> * Remove all of the additional bars in the list of
> * additional bars for this simple foo that are also
> contained in the
> * specified collection of additional bars. An exception
> * may be thrown if the underlying list prevents any
> * of the additional bars in <code>additionalBars</code>
> from being removed.
> *
> * @param additionalBars collection of additional bars to remove
> */
> public final void removeAllAdditionalBars(final
> Collection<? extends Bar> additionalBars)
> {
> this.additionalBars.removeAll(additionalBars);
> }
>
> /**
> * Retain only the additional bars in the list of
> * additional bars for this simple foo that are contained
> in the specified
> * collection of additional bars. An exception may be thrown
> * if the underlying list prevents any of the additional bars
> * not in <code>additionalBars</code> from being removed.
> *
> * @param additionalBars collection of additional bars to retain
> */
> public final void retainAllAdditionalBars(final
> Collection<? extends Bar> additionalBars)
> {
> this.additionalBars.retainAll(additionalBars);
> }
>
> /**
> * Remove all of the additional bars in the list of
> * additional bars for this simple foo. An exception may
> * be thrown if the underlying list prevents any of the
> * additional bars from being removed.
> */
> public final void clearAdditionalBars()
> {
> additionalBars.clear();
> }
>
> /**
> * Return an unmodifiable sorted set of other bars
> * for this simple foo. The returned sorted set will
> * not be null and will contain at least one other bar.
> *
> * @return an unmodifiable sorted set of other bars
> * for this simple foo
> */
> public final SortedSet<Bar> getOtherBars()
> {
> return Collections.unmodifiableSortedSet(otherBars);
> }
>
> /**
> * Add the specified other bar to the sorted set of
> * other bars for this simple foo. An exception
> * may be thrown if the underlying sorted set prevents
> * <code>otherBar</code> from being added.
> *
> * @param otherBar other bar to add
> */
> public final void addOtherBar(final Bar otherBar)
> {
> otherBars.add(otherBar);
> }
>
> /**
> * Add all of the other bars in the specified collection
> of other bars
> * to the sorted set of other bars for this simple foo.
> * An exception may be thrown if the underlying
> * sorted set prevents any of the other bars in
> * <code>otherBars</code> from being added.
> *
> * @param otherBars collection of other bars to add
> */
> public final void addAllOtherBars(final Collection<?
> extends Bar> otherBars)
> {
> this.otherBars.addAll(otherBars);
> }
>
> /**
> * Remove the specified other bar from the sorted set of
> * other bars for this simple foo. An exception
> * may be thrown if the underlying sorted set prevents
> * <code>otherBar</code> from being removed.
> *
> * @param otherBar other bar to remove
> */
> public final void removeOtherBar(final Bar otherBar)
> {
> otherBars.remove(otherBar);
> }
>
> /**
> * Remove all of the other bars in the sorted set of
> * other bars for this simple foo that are also contained in the
> * specified collection of other bars. An exception
> * may be thrown if the underlying sorted set prevents any
> * of the other bars in <code>otherBars</code> from being removed.
> *
> * @param otherBars collection of other bars to remove
> */
> public final void removeAllOtherBars(final Collection<?
> extends Bar> otherBars)
> {
> this.otherBars.removeAll(otherBars);
> }
>
> /**
> * Retain only the other bars in the sorted set of
> * other bars for this simple foo that are contained in
> the specified
> * collection of other bars. An exception may be thrown
> * if the underlying sorted set prevents any of the other bars
> * not in <code>otherBars</code> from being removed.
> *
> * @param otherBars collection of other bars to retain
> */
> public final void retainAllOtherBars(final Collection<?
> extends Bar> otherBars)
> {
> this.otherBars.retainAll(otherBars);
> }
>
> /**
> * Remove all of the other bars in the sorted set of
> * other bars for this simple foo. An exception may
> * be thrown if the underlying sorted set prevents any of the
> * other bars from being removed.
> */
> public final void clearOtherBars()
> {
> otherBars.clear();
> }
>
> /** @see Object */
> public final boolean equals(final Object o)
> {
> if (o == this)
> {
> return true;
> }
> if (!(o instanceof SimpleFoo))
> {
> return false;
> }
>
> SimpleFoo simpleFoo = (SimpleFoo) o;
>
> return (true
> && (fooId.equals(simpleFoo.getFooId()))
> && ((name == null) ? (simpleFoo.getName() ==
> null) : name.equals(simpleFoo.getName()))
> && (synonyms.equals(simpleFoo.getSynonyms()))
> && (positions.equals(simpleFoo.getPositions()))
> && ((optionalBar == null) ?
> (simpleFoo.getOptionalBar() == null) :
> optionalBar.equals(simpleFoo.getOptionalBar()))
> && (requiredBar.equals(simpleFoo.getRequiredBar()))
> && (additionalBars.equals(simpleFoo.getAdditionalBars()))
> && (otherBars.equals(simpleFoo.getOtherBars()))
> );
> }
>
> /** @see Object */
> public final int hashCode()
> {
> int result = 17;
> result = 37 * result + ((fooId == null) ? 0 :
> fooId.hashCode());
> result = 37 * result + ((name == null) ? 0 : name.hashCode());
> result = 37 * result + synonyms.hashCode();
> result = 37 * result + positions.hashCode();
> result = 37 * result + ((optionalBar == null) ? 0 :
> optionalBar.hashCode());
> result = 37 * result + ((requiredBar == null) ? 0 :
> requiredBar.hashCode());
> result = 37 * result + additionalBars.hashCode();
> result = 37 * result + otherBars.hashCode();
> return result;
> }
> }
>
> ---
>
> Whew, now that's a lot of typing saved.
>
> michael
>
>
> On Mon, 15 Aug 2005 mark.schreiber at novartis.com wrote:
>
> > It's probably premature to announce this but Richard
> Holland and I have
> > been working on a new object model that will pesist very
> easily to BioSQL.
> > It extends the core interfaces and miraculously doesn't
> break anything so
> > you can still use the core stuff or you can use the new
> models if you want
> > to.
> >
> > For example we have the RichSequence interface which closely follows
> > biosql but also extends Sequence, so anywhere you can use
> Sequence you can
> > happily use a RichSequence (or just a plain old Sequence).
> The really cool
> > stuff is the work Richard has done with Hibernate. The
> whole of BioSQL can
> > now be happily transported back and forth to biojava via
> hibernate. It's
> > amazingly painless and seems to avoid many of the problems
> of our old SQL
> > system. The model is also decoupled from hibernate
> completely so you can
> > use the objects for your normal biojava stuff without ever having a
> > database for persistence.
> >
> > We also have a NCBITaxon class to handle all the issues
> Andreas brought
> > up.
> >
> > The whole thing is available from CVS under the
> org.biojavax.bio package.
> > We chose the name biojavax to be analogous to the
> relationship between
> > java and javax. The javax packages are extensions to the
> core java. They
> > improve it, they sometimes deprecate it, they use it, but they don't
> > replace it. The same is true for biojavax. It is not a
> replacement. It is
> > an extension that gives better functionality but still gets a lot of
> > milage out of biojava. Importantly, they are not seperate
> packages. There
> > is also a genetic algorithm framework under org.biojavax.ga
> but that's an
> > entirely different story : )
> >
> > The biojavax packages should be considered highly unstable
> at the moment
> > as we are still working out the kinks. More later.
> >
> > - Mark
> >
> > 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
> >
> >
> >
> >
> >
> > Len Trigg <len at reeltwo.com>
> > Sent by: biojava-dev-bounces at portal.open-bio.org
> > 08/15/2005 06:22 AM
> >
> >
> > To: Andreas Dräger
> <andreas.draeger at clever-telefonieren.de>
> > cc: biojava-dev at biojava.org, (bcc: Mark
> Schreiber/GP/Novartis)
> > Subject: Re: [Biojava-dev] Suggestions for
> the BioJava project
> >
> >
> >
> > Andreas Dräger wrote:
> > > I am and currently working with BioSQL and BioJava.
> Trying to insert
> > > the NCBI taxon hierachy and also different kinds of
> biosequences into
> > > the database I got to know that there are still some open
> problems in
> > > BioJava. Since I wrote some classes anyway, I would like
> to contribute
> > > them to the community.
> >
> > Good stuff. The work that I did with the TaxonSQL classes was based
> > on the fairly simple requirements of the project I was working on,
> > which is why you found the current implementation a bit limited. (I
> > don't have projects involving BioJava at the moment, so haven't been
> > doing much other than following the mailing list.)
> >
> >
> > > I modified the functions to put and retrieve taxa into
> the database so
> > > that they consider that the names Map could sometimes
> point to a Set of
> > > names instead of normal name Strings.
> > > In addition I considered the other information that can
> be inserted in
> > > the database like genetic code and so on.
> >
> > Excellent improvements.
> >
> >
> > > However, there are some methods in TaxonSQL.java that are
> defined to be
> > > private. If they were protected, an extension of this
> class could call
> > them.
> > > But because they're private, I had to copy and paste them.
> >
> > That class isn't really designed for extension, since it's plugged
> > directly into calls from BioSQLSequenceAnnotation and
> BioSQLSequenceDB
> > (you presumably had to change these to point to your MySQLTaxon) and
> > there's no need for multiple implementations. I'd say that your
> > changes should instead be folded directly as improvements
> to TaxonSQL
> > itself so that everyone gets the improvements out of the box.
> >
> >
> > Cheers,
> > Len.
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-dev
> >
> >
> >
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-dev
> >
>
>
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