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POD fixes

svn path=/bioperl-gui/trunk/; revision=769
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heikkil committed Jun 3, 2003
1 parent 2c7d6fa commit cbf1619c3c903f2a00eb39764c3f1674c70e83f1
Showing with 43 additions and 39 deletions.
  1. +2 −2 Bio/Tk/GO_Annotation.pm
  2. +3 −3 Bio/Tk/GO_Browser.pm
  3. +6 −6 Bio/Tk/HitDisplay.pm
  4. +31 −27 Bio/Tk/SeqCanvas.pm
  5. +1 −1 Bio/Tk/SeqCanvasFeature.pm
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@@ -235,7 +235,7 @@ sub GO_id {
Comments: gets/sets the GO term (eg. apoptosis)
=cut
-
+
=head3 addEvidence
Usage: $GO_Annotation->addEvidence($code, [\@refs]);
@@ -344,5 +344,5 @@ sub gff2_attributes {
=cut
sub DESTROY {}
-
+
1;
View
@@ -9,15 +9,15 @@ Bio::Tk::GO_Browser.pm - Browser of the GO ontology
require GO::AppHandle; # you must have the GO perl_api from BDGP
# contact Chris Mungall for details
# (cjm@fruitfly.bdgp.berkeley.edu)
-
+
&begin;
MainLoop;
-
+
sub begin {
my $mw = MainWindow->new;
my $frame = $mw->Frame->pack;
my $GO = GO_Browser->new($frame);
-
+
my $Annotation;
# note that Button-1 events must be bound with <<...>>, not <...>
View
@@ -41,7 +41,7 @@ within it. The non-standard options for B<HitDisplay> are:
=over
-=item B<-hitdata> => \@hitdata
+=item B<-hitdata> =E<gt> \@hitdata
The structure of each element of this list is quite complex. They are
normally generated from object(s) representing Blast or Fasta hits e.g.
@@ -91,22 +91,22 @@ again.
The callback is a code reference which, if defined, will be bound to a
left mouse button click on the subject id in the canvas window.
-=item B<-hitcolours> => \%colourhash
+=item B<-hitcolours> =E<gt> \%colourhash
The hits or HSPs will be colour-coded according to percentage identity
-according to the key->value pairs in the colourhash. The default
+according to the key-E<gt>value pairs in the colourhash. The default
values are:
{ 90 => 'red',
80 => 'orange',
60 => 'gold',
40 => 'yellow' }
-This indicates that hits where the query is >= 90% identical to the
-subject will be red, >= 80% will be orange etc. The hash supplied to
+This indicates that hits where the query is E<gt>= 90% identical to the
+subject will be red, E<gt>= 80% will be orange etc. The hash supplied to
B<-hitcolours> will override the defaults.
-=item B<-interval> => integer >= 10
+=item B<-interval> =E<gt> integer E<gt>= 10
This defines the vertical spacing between hit lines on the canvas. The
minimum (and default) value is 10.
View
@@ -17,14 +17,14 @@ Bio::Tk::SeqCanvas.pm - (v3.0) Graphical display of SeqI objects
sub Begin {
# set up the Tk Windows
-
+
my $MW = MainWindow->new (-title => "Map Of BioSeq Object");
my $Frame = $MW->Frame()->pack(-side => 'top');
my $lblSysMess = $MW->Label()->pack(-side => 'bottom', -fill => 'both');
# create a BioSeq object
# (note: the test file used below is in the /t/ folder)
-
+
my $SIO = Bio::SeqIO->new(-file=> 'testseq.gb', -format => 'genbank');
my $SeqObj = $SIO->next_seq();
@@ -201,15 +201,15 @@ GeneMarkHMM" not just "GeneMarkHMM")
=head1 CODE EXAMPLES: Adding/Binding Features
- SeqCanvas is a dynamic map, allowing features to be added or removed
- after the object has been created. In addition, events occurring
- on this canvas can be externally bound and assigned to subroutines
- to allow the canvas to feed information out to an external program
- for further processing.
+SeqCanvas is a dynamic map, allowing features to be added or removed
+after the object has been created. In addition, events occurring on
+this canvas can be externally bound and assigned to subroutines to
+allow the canvas to feed information out to an external program for
+further processing.
+
+Some code examples are below; these can be added into the Begin()
+subroutine in the synopsis to see how they work:
- Some code examples are below; these can be added into the Begin()
- subroutine in the synopsis to see how they work:
-
# MAPPING SIMPLE GENERIC FEATURES
#________________________________
# make six arbitrary features and map them
@@ -690,7 +690,7 @@ sub AUTOLOAD {
$SeqObj,
-orientation => ['horizontal'|'vertical']
[, label => $tag])
-
+
Function : create a map from the Feature object provided
Returns : Handle to the Map object
Args :
@@ -2704,6 +2704,7 @@ sub getFeaturesWithTag {
=cut
+
sub clearSelections {
my $self = shift;
$self->DraftCanvas->delete('selection_box'); # we delete all reference to selected stuff on both maps
@@ -2980,18 +2981,19 @@ sub is_finished_feature {
=head1 EVENTS
-The SeqCanvas both internally responds to mouse events, and sets "tags" on the mapped feature in response to mouse events
-such that the user can "trap" these events in the top-level windowing system and evaluate which mapped feature the user was
-manupulating.
+The SeqCanvas both internally responds to mouse events, and sets
+"tags" on the mapped feature in response to mouse events such that the
+user can "trap" these events in the top-level windowing system and
+evaluate which mapped feature the user was manupulating.
=head2 Mouse-Click
-Clicking or shift-Clicking the left mouse button
-over a mapped feature causes the feature(s) to become "selected".
-A selected object is displayed on the screen with a black box surrounding
-the object, and the object becomes tagged with a testable tag "selected"
-(use the getSelectedFeatures or getSelectedIDs to retrieve additional information
-about this object)
+Clicking or shift-Clicking the left mouse button over a mapped feature
+causes the feature(s) to become "selected". A selected object is
+displayed on the screen with a black box surrounding the object, and
+the object becomes tagged with a testable tag "selected" (use the
+getSelectedFeatures or getSelectedIDs to retrieve additional
+information about this object)
=head2 Mouse-Double-Click
@@ -3001,16 +3003,18 @@ other features become unselected.
=head2 Mouse-Click and Drag
-Used to select multiple objects. Any object touched by the bounding box will be included in the selection.
+Used to select multiple objects. Any object touched by the bounding
+box will be included in the selection.
=head2 Mouse-Over
-As the mouse pointer enters the mapped widget, the tag "Mouse_over" is added to this object. information about this
-object could be retrieved by, for example, calling the getIDsWithTag(["Mouse_over"])
-method. This tag is removed when the mouse pointer leaves the mapped-feature
-space. Bind the <Movement> event in the top-level windowing
-system to track the mouse movements if you wish to monitor the Mouse-Over
-widget events.
+As the mouse pointer enters the mapped widget, the tag "Mouse_over" is
+added to this object. information about this object could be retrieved
+by, for example, calling the getIDsWithTag(["Mouse_over"])
+method. This tag is removed when the mouse pointer leaves the
+mapped-feature space. Bind the B<Movement> event in the top-level
+windowing system to track the mouse movements if you wish to monitor
+the Mouse-Over widget events.
=cut
@@ -28,7 +28,7 @@ the BioPerl feature itself, as well as the offset, and colour.
In addition, SeqCanvasFeature has the ability to rip itself apart into its constituent
transcripts and exons (if present). Thus there are only two types of SCF's: 'Gene', and
-'Generic'. "generic" features are alawys called by a simple ->_draw. "Gene" features
+'Generic'. "generic" features are alawys called by a simple -E<gt>_draw. "Gene" features
are pulled apart with sub-features created on-the-fly in this module, and then mapped onto
both the finished and draft canvas.

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