Core 1.0.0 1.0.1 delta

These are detailed notes on changes made between bioperl-release-1-0-0 and bioperl-release-1-0-1.

Bio::Align::AlignI

Merge doc changes to branch

Bio::Align::DNAStatistics

Objects for calculated DNA and pairwise statistics for AlignI objects

Bio::Align::PairwiseStatistics

Objects for calculated DNA and pairwise statistics for AlignI objects

Bio::Align::StatisticsI

Very initial interface definition for doing distance calculations

Objects for calculated DNA and pairwise statistics for AlignI objects

Bio::AlignIO

Update doc for link to simplealign

Update doc for link to simplealign

Bio::AlignIO::bl2seq

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::clustalw

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::emboss

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::fasta

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::mase

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::mega

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::msf

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::nexus

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::pfam

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::phylip

Added sub idlength to enable using phylip which accepts id names that are greater in length than the default 10

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::prodom

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::psi

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::selex

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::AlignIO::stockholm

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Annotation::Collection

Documentation update including a synopsis

Added a synopsis

Bio::AnnotationCollectionI

Added more documentation

Bio::Biblio

Merged changes from trunk to branch

Bio::Biblio::BiblioBase

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Cluster::UniGene

Initial commit of UniGene modules

Inherit from Bio::Factory::SequenceStreamI interface and utilize sequence_factory method for creating sequence objects (may be overkill)

Changed module to parse multiple chromosome lines after NCBI UniGene format was altered.

Multiple defined chromosome function removed

Bio::Cluster::UniGeneI

Initial commit of UniGene modules

Changed module to parse multiple chromosome lines after NCBI UniGene format was altered.

Bio::Cluster::dbSNP

Not finished - classes for dbSNP parsing

Bio::ClusterIO

Created ClusterIO.pm from UniGene.pm, moved it to top level directory and made code changes as appropriate

Change to runtime load

Improve dynamic module loading procedure

Bio::ClusterIO::UniGeneIO

Initial commit of UniGene modules

Removed UniGeneIO.pm having converted it to ClusterIO.pm

Bio::ClusterIO::dbsnp

Not finished - classes for dbSNP parsing

Bio::ClusterIO::unigene

Moved unigene.pm up a level into the ClusterIO dir

Changed next_unigene to next_cluster to override ClusterIO.pm

Quote to keep my emacs happy

Changed module to parse multiple chromosome lines after NCBI UniGene format was altered.

Bio::DB::Biblio::soap

Notion of the HTTP proxy added

HTTP proxy code migrated from HEAD

Bio::DB::BiblioI

Remove old reference to abstract_Death

Bio::DB::Fasta

Fixed RootI warnings in Bio::DB::Fasta

Fixed RootI inclusion errors when calling get_Seq_by_id(). added new regression tests

Bio::DB::Flat::OBDAIndex

Get_Seq_by_secondary returns array of Bio::Seq

Bio::DB::GFF

Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module

Replaced a croak with a throw

Bio::DB::GFF::Feature now implements location() interface; replaced a croak() with a throw in Bio::DB::GFF

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Added experimental support for a Genbank/EMBL proxy. If a landmark isn't in the local Bio::DB::GFF database, it will treat the landmark as an accession number, use biofetch to fetch the accession entry from EMBL, parse it, and place it in the local Bio::DB::GFF database. There is currently support for the feature table, the DNA, secondary accession numbers and the description line. Other fields are tossed 'cause I don't care.

Made aggregation type matching case insensitive

Bio::DB::GFF::Adaptor::biofetch

Added experimental support for a Genbank/EMBL proxy. If a landmark isn't in the local Bio::DB::GFF database, it will treat the landmark as an accession number, use biofetch to fetch the accession entry from EMBL, parse it, and place it in the local Bio::DB::GFF database. There is currently support for the feature table, the DNA, secondary accession numbers and the description line. Other fields are tossed 'cause I don't care.

Bio::DB::GFF::Adaptor::dbi

Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

Bio::DB::GFF::Adaptor::dbi::caching_handle

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

Bio::DB::GFF::Adaptor::dbi::mysql

Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Allow get_feature_by_name() to accept wildcards

Allow get_feature_by_name() to accept wildcards

Bio::DB::GFF::Adaptor::memory

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Bio::DB::GFF::Adaptor::memory_iterator

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Bio::DB::GFF::Aggregator

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Bio::DB::GFF::Aggregator::alignment

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Bio::DB::GFF::Aggregator::wormbase_gene

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Bio::DB::GFF::Feature

Bio::DB::GFF::Feature now implements location() interface

Bio::DB::GFF::Feature now implements location() interface; replaced a croak() with a throw in Bio::DB::GFF

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects.

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Removed a duplicated score() definition.

Removed a duplicated score() definition.

Added heterogeneous_segments glyph and removed wormbase_transcript glyph

Bio::DB::GFF::RelSegment

As it happens, the RangeI methods weren't really working for relative segments. This is now fixed.

Fixed overlaps() to work correctly with reverse-strand features when using relative addressing

Bio::DB::GFF::Segment

Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature

Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature

Now inherits from SeqI and can be directly written out with Bio::SeqIO

Bio::DB::WebDBSeqI

Verbosity is pushed into instantiated classes

Pass verbose state to instantiated classes

Bio::Das::FeatureTypeI

Added Bio::Das::FeatureTypeI

Bio::Das::SegmentI

Finished the Bio::DasI and Bio::Das::SegmentI interface definitions.

Added Bio::Das::FeatureTypeI

Bio::DasI

Was inheriting from Bio::Root (doesn't exist). now inherits from Bio::Root::Root. Should be Bio::Root::RootI? Well, it seems to be working.

Should inherit from Bio::Root::RootI, does not need Carp

Should inherit from Bio::Root::RootI, does not need Carp

Finished the Bio::DasI and Bio::Das::SegmentI interface definitions.

Added Bio::Das::FeatureTypeI

Bio::DasSegmentI

Finished the Bio::DasI and Bio::Das::SegmentI interface definitions.

Bio::Factory::MapFactoryI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Factory::Pise

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Factory::SeqAnalysisParserFactory

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Factory::SeqAnalysisParserFactoryI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Factory::SequenceBuilderI

New interface to handle generic sequence building

Modules renamed to be more GoF happy

Bio::Factory::SequenceFactoryI

Modules renamed to be more GoF happy

Update doc and method name from new_sequence to create_sequence to comply with design pattern standard

Bio::Factory::SequenceStreamI

Added new interface describin what SeqIO is

Bio::Factory::TreeFactoryI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Graphics

Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module

Bumped up version number for Bio::Graphics to 1.03.

Bumped up version number for Bio::Graphics to 1.03.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Bumped up version number of Graphics.pm to 1.05

Bio::Graphics::Feature

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature

Added seq_id() method to Bio::DB::GFF::Segment and Bio::Graphics::Feature

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects.

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.

Work around uninitialized variable warnings

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Audit of the glyphs. Fixed some minor bugs.

Bio::Graphics::FeatureFile

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

Moved changes from bioperl-live into release

Bio::DB::GFF::Feature now implements location() interface

Bio::DB::GFF::Feature now implements location() interface; replaced a croak() with a throw in Bio::DB::GFF

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Modification to filehandle close() handling to accomodate perl 5.00503 backward compatibility

Aesthetic improvements to split-location features

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.

Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.

Work around uninitialized variable warnings

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Bio::Graphics::Glyph

Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Added an extra argument to the callback so that the callback can get at the glyph; restored dashed line for groups even when the right side of first feature is greater than the left side of second feature

Moved changes from bioperl-live into release

Fixed Glyph and Glyph::transcript2 so that the components always are drawn after the connectors. This cleans up some of the alignment glyphs in which the components overlap each other

Aesthetic improvements to split-location features

Fixed a bug that nuked connectors when both flanking parts are off screen.

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Bio::Graphics::Glyph::Factory

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Added an extra argument to the callback so that the callback can get at the glyph; restored dashed line for groups even when the right side of first feature is greater than the left side of second feature

Moved changes from bioperl-live into release

When I refactored the transcript and segments glyphs, I forgot to move the Bio::Location::Simple requiremejnt to where it belonged

Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.

Bio::Graphics::Glyph::anchored_arrow

Fixed anchored arrow off-by-one error

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Bio::Graphics::Glyph::arrow

Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.

Fixed tick mark code in arrow.pm so that ticks dont disappear when looking at reversed feature in absolute coordinate system

Reordered test of relative coordinate testing for efficiency.

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Fixed a new bug in the relative tickmarks in arrow.pm introduced when I fixed the old bug

Bio::Graphics::Glyph::crossbox

Audit of the glyphs. Fixed some minor bugs.

Bio::Graphics::Glyph::diamond

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects.

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Bio::Graphics::Glyph::ex

Audit of the glyphs. Fixed some minor bugs.

Bio::Graphics::Glyph::generic

Audit of the glyphs. Fixed some minor bugs.

Bio::Graphics::Glyph::graded_segments

Added heterogeneous_segments glyph and removed wormbase_transcript glyph

Bio::Graphics::Glyph::group

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Bio::Graphics::Glyph::heterogeneous_segments

Added heterogeneous_segments glyph and removed wormbase_transcript glyph

Bio::Graphics::Glyph::primers

Audit of the glyphs. Fixed some minor bugs.

Bio::Graphics::Glyph::ruler_arrow

Audit of the glyphs. Fixed some minor bugs.

Bio::Graphics::Glyph::segmented_keyglyph

Moved changes from bioperl-live into release

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Aesthetic improvements to split-location features

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Bio::Graphics::Glyph::segments

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

When I refactored the transcript and segments glyphs, I forgot to move the Bio::Location::Simple requiremejnt to where it belonged

Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.

Changed the tick mark code in arrow.pm to handle minus strand features differently. This might fix a bug -- or might introduce one.

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Bio::Graphics::Glyph::track

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Bio::Graphics::Glyph::transcript

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Moved changes from bioperl-live into release

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Aesthetic improvements to split-location features

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

When I refactored the transcript and segments glyphs, I forgot to move the Bio::Location::Simple requiremejnt to where it belonged

Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Bio::Graphics::Glyph::transcript2

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

Moved changes from bioperl-live into release

- Make the Bio::Graphics::Feature objects more-or-less compatible with Bio::LocationI. Still some work to do here. - Minor bugfixes to support Generic Genome browser version 1.37 - The diamond glyph now will now morph to show a rectangle for non-point objects. - Brought Bio::DB::GFF up to date with bioperl-live (regression tests still run)

Fixed Glyph and Glyph::transcript2 so that the components always are drawn after the connectors. This cleans up some of the alignment glyphs in which the components overlap each other

Fixed irregularity involving features with no internal structure

Aesthetic improvements to split-location features

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs.

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Moved "use Bio::Location::Simple" from Glyph::transcript to Glyph::segments. transcript now inherits from segments.

Minor fixes to Bio::Graphics. Silenced various uninitialized variable warnings, and fixed the arrow glyph so that the reversal of coordinate labels only occurs when relative coordinate addressing is requested.

Bio::Graphics::Glyph::wormbase_transcript

Added heterogeneous_segments glyph and removed wormbase_transcript glyph

Bio::Graphics::Panel

Multiple small fixes to graphics module; allow wildcard ID searches in Bio::DB::GFF module

Simplified Bio::Graphics internals for stability and generality

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Added an extra argument to the callback so that the callback can get at the glyph; restored dashed line for groups even when the right side of first feature is greater than the left side of second feature

Moved changes from bioperl-live into release

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway.

Added a "compound" flag to Bio::DB::GFF::Feature to indicate that it is expected to contain subparts (but not not actually). This allows for more efficient handling of semantic zooming in genome browser because at low mags, we no longer need to fetch all the parts that won't be drawn anyway. Modified Bio::Graphics::Glyph::segments and descendents to take advantage of this optimization.

Bio::Index::GenBank

Doc fix -- seq->layout no longer exists

Doc fix -- seq->layout no longer exists

Bio::LiveSeq::SeqI

Explicitly include Bio::PrimarySeqI interface

Bio::Location::Simple

Warning should not print if we've already specified minus strand

Bio::LocationI

Documentation fix

Add docs - convert to throw_not_implemented not _abstractDeath

Bio::Map::MapI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Map::PositionI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Map::SimpleMap

Issue #1154 fixed

Issue #1154 fixed

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::MapIO

Documentation fix

Merged changes from trunk to branch

Bio::MapIO::mapmaker

Remove abstract reference

Remove abstractDeath --branch

Bio::PrimarySeq

Protect against calling length on empty string

Update doc to describe circular feature

Optimize PrimarySeq _guess_alphabet to be more efficient using tr// to count rather than editing the sequence string

Bio::Root::Exception

Fixes bg #1146 as suggested by Martin. Steve, there are not tests for Bio::Root::Exception!

Fixes bg #1146 as suggested by Martin. Steve, there are not tests for Bio::Root::Exception!

Modified _reformat_stacktrace() to get the top-most file:linenum data (name of the script)

Migrating fixe 1.13 to branch-1-0-0

Bio::Root::RootI

Remove abstractDeath

Remove abstractDeath from branch

Moved code from HEAD: replaced _abstractDeath() by throw_not_implemented() fixes Issue #1155

Only print warnings when BIOPERLDEBUG env variable is set

No warnings for RootI on _cleanup_object either unless ->verbose or BIOPERLDEBUG defined

Bio::Search::HSP::BlastHSP

Some changes to have Blast* and Generic* play nicer

Bio::Search::HSP::GenericHSP

Update docs to clearly state that frame is GFF not BLAST

Added caveat in docs about how frame works and removed warning when HSP gaps param is unspecified

Doc fix

Bio::Search::HSP::HSPI

Fix doc to say pvalue not p

Use pvalue instead of p in docs -- merge from trunk

Bio::Search::Hit::BlastHit

Implementing accession() as required by HitI. Addresses Issue #1139

Migrating fix 1.10 to branch-1-0-0.

Bio::Search::Hit::GenericHit

Migrated some of SteveC's psiblast specific methods into the interfaces

Some changes to have Blast* and Generic* play nicer

Allow a Hit to have a bit score which is typically the best bit score of the contained HSPs

Bio::Search::Hit::HitI

Migrated some of SteveC's psiblast specific methods into the interfaces

Doc fixes

Allow a Hit to have a bit score which is typically the best bit score of the contained HSPs

Bio::Search::Processor

Processor module is not part of branch

Bio::Search::Result::BlastResult

Some changes to have Blast* and Generic* play nicer

Bio::Search::Result::GenericResult

Migrated some of SteveC's psiblast specific methods into the interfaces

Some changes to have Blast* and Generic* play nicer

Doc fixes

Bio::Search::Result::ResultI

Migrated some of SteveC's psiblast specific methods into the interfaces

Some changes to have Blast* and Generic* play nicer

Doc fixes

Bio::SearchIO::Writer::HSPTableWriter

Fixed method name (psiblast_round -> iteration). Fixes the 'all zeros' bug with default table.

Migrating fix 1.6.2.1 to the trunk.

Enable some debugging when -verbose => 1 and tracked down problems with different API from Interface

Bio::SearchIO::Writer::HTMLResultWriter

Added BLAST/FASTA reference generator and more detailed statistics/parameter value, also allow linkout to be set to empty to omit linking out

Handle cases when parser didn't pull in values (BlastHSP)

Bio::SearchIO::Writer::HitTableWriter

Fixed method name (psiblast_round -> iteration). Fixes the 'all zeros' bug with default table.

Migrating fix 1.6.2.1 to the trunk.

Enable some debugging when -verbose => 1 and tracked down problems with different API from Interface

Bio::SearchIO::Writer::ResultTableWriter

More debugging in ResultTableWriter

Enable some debugging when -verbose => 1 and tracked down problems with different API from Interface

Bio::SearchIO::blast

Fixed bug reported by Bill Morgart with wublast output - missing 'Sum P(D)' handler

Branch fix of bug reported by Bill Morgart with wublast output - missing 'Sum P(D)' handler

Handle wu-blast P values and desc-lines that have line wrappings

Handle parsing wu-blast reports where frame is listed on same line as the score

Merge blast parsing fixes for wu-blast from trunk to branch

Handle NOTE or WARNING lines in WU-BLAST reports, what a just, excellent, report format....

Save whole line as version not just first \S+

Support extracting more parameters and statistics from wu-blast reports

Merged changes from trunk to branch

Split out accession and description from query name

Split the query_name and description into 2 fields

Bio::SearchIO::fasta

Fixed bug that would have parser lose place when HSP is at the end of hit seq and the flanking region of the query is displayed on a line by itsself

Migrated bug fix to branch that deals with trailing query/hit seq when HSP is at the end of one seq

Added fix for fasta33 which doesn't produce percent gapped

Changes to parse fasta33 reports properly

Bio::Seq

Handle object init of features and annotation object - this allows for delayed object instantiation in Bio::SeqIO

Update version number for release

Some doc updates propigated in

Version number for release

Bio::Seq::PrimaryQual

Modules renamed to be more GoF happy

Some minor changes in primary qual and a change in the way that contig keys are treated in consed.

Prettier, less chatty code - better logic for setting qual() data

Remove debug stmt which will cause uninit val wrns when @args is empty

Drop alphabet(), it is not proper to be part of the API

Merged changes for Issue #1202 and cleanup of primaryseq/qual methods

Handle empty strs,undefs, and zeros identically

Handle empty strs,undefs, and zeros identically

Bio::Seq::SeqBuilder

Implement interface to handle generic sequence building

Modules renamed to be more GoF happy

Bio::Seq::SeqFactory

Modules renamed to be more GoF happy

Bio::Seq::SeqWithQuality

Modules renamed to be more GoF happy

Drop alphabet(), it is not proper to be part of the API

Merged changes for Issue #1202 and cleanup of primaryseq/qual methods

Bio::SeqAnalysisParserI

Remove abstractDeath for throw_not_implemented

Remove abstractDeath for throw_not_implemented

Bio::SeqFeature::Collection

New collection object to allow for efficient sub querying of features that fall within a range

Bio::SeqFeature::Computation

More tests for computation object for Issue #1165

Merged computation bugs from trunk to branch

Bio::SeqFeature::Gene::ExonI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::SeqFeature::Gene::GeneStructureI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::SeqFeature::Gene::NC_Feature

Renamed utr to UTR, fixed Issue #1181

Merged changes to branch wrt the renamed UTR class (wasn't completely done right before release, this is not an API chg) and fixed Issue #1181

Bio::SeqFeature::Gene::Promoter

Some more documentation

Bio::SeqFeature::Gene::Transcript

Renamed utr to UTR, fixed Issue #1181

Merged changes to branch wrt the renamed UTR class (wasn't completely done right before release, this is not an API chg) and fixed Issue #1181

Some more documentation

Bio::SeqFeature::Gene::TranscriptI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::SeqFeature::Gene::UTR

Renamed utr to UTR, fixed Issue #1181

Merged changes to branch wrt the renamed UTR class (wasn't completely done right before release, this is not an API chg) and fixed Issue #1181

Enforce that primary tag with be uniform (this all may change soon anyways...)

Bio::SeqI

Don't need Carp anymore

Some doc updates propigated in

Bio::SeqIO

Migrate to using new Factory object for sequence building

Inherit from Bio::Factory::SequenceStreamI

Bio::SeqIO::FTHelper

Migrate to using new Factory object for sequence building

Bio::SeqIO::ace

Migrate to using new Factory object for sequence building

Bio::SeqIO::bsml

Noted that the XML::DOM::Parser object was becoming undef before DESTROY was called, so put a test in DESTROY to see if that object exists before trying to call dispose() on it.

Merged changes from trunk to branch

Migrate to using new Factory object for sequence building

Bio::SeqIO::embl

Migrate to using new Factory object for sequence building

Small correct to set desc

Don't assume that a SeqI object has a primary_seq object underneath

Bio::SeqIO::fasta

Migrate to using new Factory object for sequence building

Slight optimization with fasta reading

Use the object method not the hash key

Bio::SeqIO::fastq

Migrate to using new Factory object for sequence building

Bio::SeqIO::game

Migrate to using new Factory object for sequence building

Updated DTDs, added an empty field yto PREFIX_MAP to keep undef warnings out of XML::Writer call, and explicitly set strand in feature creation

Skip cases when score is undefined

Merge GAME parsing and writing changes to trunk

Explicitly use STDOUT if fh is not defined rather than sending in an undef - this should prevent problems with autoflush on STDOUT

Remove sequence_builder reference cause it just isn't going to work easily with game right now - and use STDOUT as fh explicitly when no fh set for the object to help with autoflushing problems seen when running in a CGI

Bio::SeqIO::game::featureHandler

Updated DTDs, added an empty field yto PREFIX_MAP to keep undef warnings out of XML::Writer call, and explicitly set strand in feature creation

Merge GAME parsing and writing changes to trunk

Bio::SeqIO::game::seqHandler

Migrate to using new Factory object for sequence building

Bio::SeqIO::gcg

Migrate to using new Factory object for sequence building

Bio::SeqIO::genbank

Migrate to using new Factory object for sequence building

Forgot leading slash in specified params PID and DATE

Issue #1062

Merge Issue #1062 from branch to trunk

Bio::SeqIO::largefasta

Migrate to using new Factory object for sequence building

Bio::SeqIO::phd

Migrate to using new Factory object for sequence building

Bio::SeqIO::pir

Migrate to using new Factory object for sequence building

Bio::SeqIO::qual

Migrate to using new Factory object for sequence building

Fixed Issue #1108 on branch - doc fix and return a 1 on successful writing

Fixed Issue #1108 on trunk - doc fix and return 1 on successful writing.

Fix for Issue #1202

Merged changes for Issue #1202 and cleanup of primaryseq/qual methods

Bio::SeqIO::raw

Migrate to using new Factory object for sequence building

Bio::SeqIO::scf

Migrate to using new Factory object for sequence building

Bio::SeqIO::swiss

Migrate to using new Factory object for sequence building

Bio::SimpleAlign

Simple align has overall percent id method

Doc fixes

Fixes Issue #1205

Fixes Issue #1205

Added contributor names

Bio::Structure::Entry

Make seqres() work when entry contains chains Bug reported by Yan-Yuan Tseng <ytseng3@uic.edu>

Make seqres() work when entry contains chains Bug reported by Yan-Yuan Tseng <ytseng3@uic.edu>

Make seqres() work on more then first chain

Make seqres() work with more then one chain

Make seqres work with default chain (bug reported by ytseng3@uic.edu)

Make seqres work with default chain (bug reported by ytseng3@uic.edu)

Bio::Structure::StructureI

Fixed package statement. Added 'use Bio::Root::RootI'.

Migrating fix 1.2 to the 1.0 branch.

Bio::Symbol::AlphabetI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Symbol::SymbolI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Tools::Alignment::Consed

Some minor changes in primary qual and a change in the way that contig keys are treated in consed.

Updated to use a pure-perl implementation and no grep

Merged consed no-use-grep changes to trunk

Bio::Tools::BPlite

Added eof bugfix

Protect the EOF call in the event we're talking to an IO::String which apparently doesn't implement all of IO::Handle...

Bio::Tools::GFF

Simplify parsing loop for extra textfields

Bio::Tools::Gel

Protect against log of 0 callsmore flexible cmd line arguments parsed in

Merged changes from trunk to branch

Bio::Tools::HMMER::Results

Fixed Issue #1172

Fixed Issue #1172 (main trunk)

Fixed Issue #1178 to use the Root::IO destructor

Fixed Issue #1178 to use the Root::IO destructor

Bio::Tools::RestrictionEnzyme

Added debuggin capability and better seq object validataion

Merged changes from trunk to branch

Bio::Tools::Run::EMBOSSApplication

Cleanup before each run of an application

Merged changes from trunk to branch

Handle some weird boundary cases

Bio::Tools::Run::PiseApplication

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Tools::Run::PiseJob

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Tools::Run::PiseJobParser

Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page

Bio::Tools::Run::RemoteBlast

SYNOPSIS needed -readmethod argument

Bio::Tools::Run::RepeatMasker

Alpha Wrapper for RepeatMasker

Bio::Tools::SeqWords

Fixed bugs in synopsis reported by Will Hsiao

Fixed bugs in synopsis reported by Will Hsiao

Bio::Tree::NodeI

Handle empty branch lengths (a common occurance) by not whining so much

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::Tree::TreeI

Remove abstract death in favor of throw_not_implemented()

Remove abstract death in favor of throw_not_implemented() - on branch

Bio::TreeIO::newick

Added test for non-branch length tree files

Merged changes from trunk to branch

Bio::Variation::AAChange

Cleaning constructors

Cleaning constructors

Bio::Variation::AAReverseMutate

Cleaning constructors

Cleaning constructors

Bio::Variation::Allele

Cleaning constructors

Cleaning constructors

Added frequency() and count() methods to be used by Bio::Variation::SNP

Bio::Variation::DNAMutation

Cleaning constructors

Cleaning constructors

Bio::Variation::RNAChange

Cleaning constructors

Cleaning constructors

Bio::Variation::SNP

Not finished - classes for dbSNP parsing

Bio::Variation::SeqDiff

Cleaning constructors

Cleaning constructors

Added Eckhard Lehmann's code for calculating the mutated DNA sequence from the original using DNAMutations

FAQ

Minor updates

Merged changes from trunk to branch

Added some new contributor questions to the FAQ

Added mention of fuzzpro and fuzznuc

Added question/answer on BPLite's frame-change

Added answer to question about how to parse Sequence data from a $string.

Generated from doc/faq/faq.xml

Added mention of Pise

Prettier...

Merged changes from trunk to 1.0 release branch.

Makefile.PL

Missing extra slashes

Added missing section

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

Update version required for GD

Modified the transcript glyphs so that they will draw the gene correctly even when zoomed into an intron and no exon is showing. Removed the "wormbase_gene" aggregator, since it is specific to WormBase needs. Fixed the SearchIO.t regression test to report the correct number of tests being performed. Under 5.6.1 it misreported the number of tests, causing spurious failed tests.

Version number for release

biodesign.pod

Added mention of Bio::Root example scripts, some L<>s

Merged changes from trunk to branch

bioperl.pod

Added mention of flanks.pl revcom_dir.pl entropy.pl cat.pl ds.pl loocv_cat.pl info.pl loocv_ds.pl loocv_info.pl loocv_t.pl loocv_t_cc.pl loocv_u.pl loocv_u_rank.pl relation.pl relrand t_test.pl u_test.pl test-genscan.pl test1.pl test2.pl test3.pl test4.pl vector.pl destroy.pl error.pl filehandle.pl read.pl utilities.pl use_registry.pl scripts.

Merged changes from trunk to branch

Added mention of gb2features.pl, Damien's script

Added mention of the examples/pise scripts

bptutorial.pl

Changes for doc references

Soap -> SOAP

Changed Sigcleave section

Minor fixes to bptutorial code, need to do more...

Added more eval{ require } statements

Added mention of Parse-RecDescent, a dependency

Fixed run_remoteblast example, needed -readmethod argument

Removed list of recommended CPAN modules, maintaining these equivalent lists in bptutorial and in INSTALL is not wise

examples/biblio.pl

Notion of the HTTP proxy added

HTTP proxy code migrated from HEAD

models/bioperl.dia

Minor changes to the dia diagram -- I think

scripts/Bio-DB-GFF/bulk_load_gff.pl

Bulk_load_gff.pl will no longer become inoperative if interrupted during load

scripts/Bio-DB-GFF/load_gff.pl

FNOTE=>fnote table

scripts/render_sequence.pl

Teeny doc fix

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required); merged in simplifications of Bio::Graphics modules that will make the module more general

Altered BioDBGFF test sequence so that all questions are issued during Makefile.PL; if user answers no defaults to in-memory version of Bio::DB::GFF (no database required)

scripts/seq_length.pl

Simple script for displaying length and # residues in a db file