AcePerl
view release on metacpan or search on metacpan
Ace/Browser/SearchSubs.pm view on Meta::CPAN
sub AceSearchOffset {
my $offset = param('offset') || 0;
$offset += param('scroll') if param('scroll');
$offset;
}
=item AceSearchTable([{hash}],$title,@contents)
Given a title and the HTML contents, this formats the search into a
table and gives it the background and foreground colors used elsewhere
for searches. The formatted search is then printed.
The HTML contents are usually a fill-out form. For convenience, you
can provide the contents in multiple parts (lines or elements) and
they will be concatenated together.
If the first argument is a hashref, then its contents will be passed
to start_form() to override the form arguments.
=cut
Ace/Graphics/Glyph.pm view on Meta::CPAN
=over 4
=item $fgcolor = $glyph->fgcolor
=item $bgcolor = $glyph->bgcolor
=item $fontcolor = $glyph->fontcolor
=item $fillcolor = $glyph->fillcolor
These methods return the configured foreground, background, font and
fill colors for the glyph in the form of a GD::Image color index.
=item $width = $glyph->width
Return the maximum width allowed for the glyph. Most glyphs will be
smaller than this.
=item $font = $glyph->font
Return the font for the glyph.
Ace/Graphics/GlyphFactory.pm view on Meta::CPAN
sub option {
my $self = shift;
my $option_name = shift;
my $o = $self->{options} or return;
my $d = $o->{$option_name};
$o->{$option_name} = shift if @_;
$d;
}
# set the foreground and background colors
# expressed as GD color indices
sub _fgcolor {
my $self = shift;
my $c = $self->option('color',@_) || $self->option('fgcolor',@_) || $self->option('outlinecolor',@_);
$self->translate($c);
}
sub fgcolor {
my $self = shift;
my $linewidth = $self->option('linewidth');
Ace/Graphics/GlyphFactory.pm view on Meta::CPAN
=item $scale = $factory->scale([$scale])
Get or set the scale, in pixels/bp, for the glyph. This is
ordinarily set by the Ace::Graphics::Track object just prior to
rendering, and called by each glyphs' map_pt() method when performing
the rendering.
=item $color = $factory->bgcolor([$color])
Get or set the background color for the glyphs.
=item $color = $factory->fillcolor([$color])
Get or set the fill color for the glyphs.
=item $font = $factory->font([$font])
Get or set the font to use for rendering the glyph.
=item $color = $factory->fontcolor
Ace/Graphics/Panel.pm view on Meta::CPAN
-key Show this track in the undef
key
Colors can be expressed in either of two ways: as symbolic names such
as "cyan" and as HTML-style #RRGGBB triples. The symbolic names are
the 140 colors defined in the Netscape/Internet Explorer color cube,
and can be retrieved using the Ace::Graphics::Panel->color_names()
method.
The background color is used for the background color of the track
itself. The foreground color controls the color of lines and strings.
The interior color is used for filled objects such as boxes.
The -label argument controls whether or not the ID of the feature
should be printed next to the feature. It is accepted by most, but
not all of the glyphs.
The -bump argument controls what happens when glyphs collide. By
default, they will simply overlap (value 0). A -bump value of +1 will
cause overlapping glyphs to bump downwards until there is room for
Ace/Graphics/Track.pm view on Meta::CPAN
return $factory->glyph($feature);
}
# draw glyphs onto a GD object at the indicated position
sub draw {
my $self = shift;
my ($gd,$left,$top) = @_;
$top += 0; $left += 0;
my $glyphs = $self->layout;
# draw background
my $bgcolor = $self->factory->bgcolor;
# $gd->filledRectangle($left,$top,$left+$self->width,$top+$self->height,$bgcolor);
if (my $label = $self->factory->option('track_label')) {
my $font = $self->factory->font;
my $y = $top + ($self->height-$font->height)/2;
my $x = $left - length($label) * $font->width;
$gd->string($font,$x,$y,$label,$self->factory->fontcolor);
}
$_->draw($gd,$left,$top) foreach @$glyphs;
README.ACEBROWSER view on Meta::CPAN
RPC-based gifaceserver.
$USERNAME = '';
$PASSWORD = '';
For password-protected ACEDB databases, these variables contain the
username and password.
$STYLESHEET = "$DOCROOT/stylesheets/aceperl.css";
This is the cascading stylesheet used to set the background color,
font, table colors, and so forth. You probably don't need to change
this, but you might want to modify the stylesheet itself.
@PICTURES = ($IMAGES => "$HTML_PATH/images");
This array indicates the location of the "images" subdirectory. The
first element of the array is the location of the directory as a URL,
and the second element is the location of the directory as a physical
path on the file system. This array is ignored when running under
modperl/Apache::Registry; modperl uses $IMAGES to look up the
acebrowser/cgi-bin/generic/pic view on Meta::CPAN
<VAR>name</VAR> and <VAR>class,</VAR> where
"name" and "class" correspond to the name and class of the
Ace object of interest.
END
;
}
my $style = Style();
$style->{'code'} =<<END;
BODY {
background-color: #FFFFFF;
}
END
;
PrintTop($obj,undef,$obj ? "Graphic display of: $obj" : "Graphic display",
'-Bgcolor' => '#FFFFFF', # important to have a white bg for the gifs
'-Style' => $style,
-Script => JSCRIPT
);
acebrowser/cgi-bin/generic/pic view on Meta::CPAN
AceNotFound() unless $obj;
display_object($obj,$click);
PrintBottom();
sub print_prompt {
print
start_form(-name=>'question'),
table(
TR (th('Name'),td(textfield(-name=>'name')),
th('Class'),td(textfield(-name=>'class',-size=>15,-onChange=>'document.question.submit()')),
td(submit({-style=>'background: white',-name=>'Change'}))),
),
end_form;
}
sub display_object {
my ($obj,$click) = @_;
my $class = param('class');
my $name = $obj->name;
if (DISABLED) {
acebrowser/cgi-bin/generic/tree view on Meta::CPAN
AceNotFound() unless $obj;
display_object($obj);
PrintBottom();
sub print_prompt {
print
start_form(-name=>'question'),
table(
TR (th('Name'),td(textfield(-name=>'name')),
th('Class'),td(textfield(-name=>'class',-size=>15,-onChange=>'document.question.submit()')),
td(submit({-style=>'background: white',-name=>'Change'}))),
),
end_form;
}
sub display_object {
my $obj = shift;
my $name = $obj->name;
my $class = $obj->class;
my ($n,$c) = (escape($name),escape($class));
my $myimage = ($class =~ /^Picture/ ? $obj->Pick_me_to_call->right->right : 'No_Image') ;
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
A:visited { text-decoration: none;
color: #AA0088;
}
A:hover { text-decoration: underline;
}
A.banner { color : #FFFFFF;
font-size : small;
text-decoration : none;
}
A.bblue { color: #FFFFFF;
background-color: #9999FF;
font-size : small;
text-align: center;
}
A.bred { color: #FFFFFF;
background-color: #FF6666;
font-size : small;
text-align: center;
}
BODY { background-color: white;
font-family: sans-serif;
}
H1 { color: #3366FF;
font-family: sans-serif;
}
H2 { color: #3366FF;
font-family: sans-serif;
}
H3 { color: #3366FF;
font-family: sans-serif;
}
H4 { color: #3366FF;
font-family: sans-serif;
}
INPUT { background-color: white; }
OL { font-family: sans-serif; }
UL { font-family: sans-serif; }
LI { font-family: sans-serif;
list-style: url(/images/reddot.jpg) outside;
}
DL { font-family: sans-serif; }
DT { font-family: sans-serif; }
DD { font-family: sans-serif; }
LI.new { font-family: sans-serif;
list-style: url(/icons/new.gif) outside;
}
P { font-family: sans-serif; }
PRE.peptide { font-size: small; }
PRE.dna { font-size: small;
font-family: monospace;
}
SELECT { background-color: white; }
TABLE { padding: 0;
spacing: 2;
width: 100%;
}
TD { font-family: sans-serif; }
TH { font-family: sans-serif;
padding: 0;
}
.abstract { background-color: #FFEEEE; }
.acetree { font-size: 10pt; }
.banner { font-size: x-large;
align: center;
background-color: blue;
color: yellow;
padding: 3px 200px;
}
.data { font-size: small; }
.databody { background-color: #CCFFFF; }
.databodysmall { background-color: #EEFFFF; }
.datatitle { background-color: #93CBF4; }
.description { font-style: italic; }
.error { color: red; }
.exon { background-color: #00FFFF;
color: #000000;
}
.exonalt { background-color: #EEEE99;
color: #000000;
}
.exonm { /* font-weight: bold; */
background-color: #00FFFF;
color: #000000;
}
.flankm { background-color: #FFFFFF;
color: #888888;
}
.match { background-color: #FFFF77;
color: #FF00;
}
.gene { font-style: italic; }
.highlight { background-color: #f5deb3; }
.intron { background-color: #FFFFFF;
color: #000000;
}
.intronm { background-color: #FFFFFF;
color: #000000;
}
.mism { color: #000000;
background-color: #FF9999;
}
.note { color: red; }
.phenotype { font-style: italic;
margin-left: 2em;
}
.pre { font-family: monospace; }
.resultsbody { background-color: #CCFFFF; }
.resultsbodyalt { background-color: #EEFFFF; }
.resultstitle { background-color: #93cbf4; }
.search { font-size: small; }
.searchbody { background-color: #FFFFCC; }
.searchbodyalt { background-color: #CCFFFF; }
.searchtitle { background-color: #FFFF99; }
.searchbanner { background-color: #93cbf4;
color: white;
font-style: bold;
}
.small { font-size: small; }
.smalldescription { font-style: italic;
font-size: small;
}
.technicalinfo { background-color: #FFFFFF; }
.toggle { color: #3366FF; }
.tRNAs { background-color: white;
color: black;
curatedexon: slateblue;
fontcolor: slateblue;
bump: -1;
height: 3;
}
.transcriptf { background-color: white;
color: black;
curatedexon: slateblue;
fontcolor: slateblue;
bump: -1;
height: 10;
}
.transcriptr { background-color: white;
curatedexon: dodgerblue;
fontcolor: dodgerblue;
color: black;
bump: +1;
height: 10;
}
.BLAT { background-color: greenyellow;
color: black;
bump: +1;
height: 4;
connectgroups: 1;
connector: black;
key: 'ESTs\ aligned\ by\ BLAT';
}
.EST_GENOME { background-color: limegreen;
color: black;
bump: +1;
height: 4;
stranded: 1;
connectgroups: 1;
connector: black;
key: 'ESTs\ aligned\ by\ EST_GENOME';
}
.RNAi { background-color: goldenrod;
color: black;
height: 4;
bump: +1;
key: 'RNAi\ experiments';
}
.Worm-Transcriptome-Project-Genes { background-color: yellow;
color: black;
height: 4;
bump: +1;
key: 'Worm\ Transcriptome\ Project\ genes';
}
.Oligos { background-color: violet;
color: black;
connect: 1;
connect_color: cyan;
connector: violet;
bump: -1;
key: 'oligos';
}
.PolyA-sites { background-color: violet;
color: blue;
bump: -1;
key: 'polyA sites';
}
.Primers { background-color: violet;
color: black;
connect: 1;
connector: violet;
connect_color: gray;
bump: -1;
key: 'oligos';
}
.HMMer { background-color: red;
color: black;
connect: 1;
height: 4;
connector: black;
label: 1;
bump: -1;
key: 'motifs';
}
.Briggsae { background-color: tomato;
color: black;
height: 4;
bump: +1;
key: 'C.\ briggsae\ similarity';
}
.Prosite { background-color: bisque;
color: black;
height: 4;
bump: +1;
key: 'prosite';
}
.Misc_feature { background-color: bisque;
color: black;
height: 4;
bump: +1;
key: 'Miscellaneous';
}
.Clone { color: black;
height: 7;
bump: +1;
key: 'YACs\ &\ Cosmids';
}
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
height: 6;
color: wheat;
}
Sequence.default {
glyph: GENERIC;
das: 1;
label: 1;
bump: +1;
height: 6;
color: black;
background-color: gray;
}
ALLELE.default {
glyph: ANCHORED_ARROW;
das: 1;
label: 1;
bump: +1;
height: 3;
color: black;
background-color: tomato;
}
translation.default {
glyph: GENERIC;
das: 1;
height: 5;
bump: +1;
point: 2;
color: blue;
}
translated.default {
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
height: 6;
color: cyan;
}
Predicted_gene.default {
glyph: TRANSCRIPT;
das: 1;
label: 1;
bump: +1;
height: 10;
color: dodgerblue;
background-color: dodgerblue;
}
transcription.default {
glyph: TRANSCRIPT;
das: 1;
label: 1;
bump: +1;
height: 10;
color: black;
background-color: wheat;
}
transcription.transcript {
glyph: TRANSCRIPT;
das: 1;
label: 1;
bump: +1;
height: 10;
background-color: dodgerblue;
color: black;
linewidth: 1;
}
transcription.curated {
glyph: TRANSCRIPT;
das: 1;
label: 1;
height: 10;
color: black;
background-color: wheat;
}
transcription.exon {
glyph: GENERIC;
das: 1;
label: 1;
height: 10;
background-color: dodgerblue;
color: dodgerblue;
linewidth: 1;
}
transcription.intron {
glyph: CONNECTOR;
das: 1;
label: 1;
height: 10;
color: blue;
}
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
fontsize: 8;
string: r;
color: purple;
}
structural.oligo {
glyph: GENERIC;
das: 1;
bump: +1;
height: 3;
color: #669900;
background-color: white;
}
structural.SNP {
glyph: TRIANGLE;
point: 1;
das: 1;
label: 1;
height: 2;
color: green;
}
Homol_data.default {
glyph: SEGMENTS;
das: 1;
bump: +1;
label: 1;
height: 3;
color: black;
background-color: red;
}
Homol_data.NN {
glyph: TOOMANY;
das: 1;
label: 1;
height: 50;
color: #666666;
linewidth: 1;
}
Homol_data.NP {
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
height: 50;
color: #666666;
linewidth: 1;
}
similarity.default {
glyph: SEGMENTS;
das: 1;
label: 1;
bump: +1;
height: 5;
background-color: limegreen;
color: black;
}
similarity.BLAT_EST_GENOME {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: greenyellow;
fillcolor: red;
}
similarity.BLASTN {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: lawngreen;
}
similarity.BLASTN_EST_briggsae {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: thistle;
}
similarity.BLASTN_EST_elegans {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: springgreen;
}
similarity.BLASTN_TC1 {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: lime;
}
similarity.BLASTN_briggsae_cosmid {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: orchid;
}
similarity.BLASTN_eleg_brig {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: limegreen;
}
similarity.BLASTN_elegans_cosmid {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: darkgreen;
}
similarity.BLASTX {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: red;
}
similarity.BLASTX_wormpep {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: darkred;
}
similarity.BLASTP {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: yellow;
}
similarity.TBLASTN {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: cyan;
}
similarity.TBLASTX {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: royalblue;
}
similarity.TBLASTX_briggsae {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: violet;
}
similarity.TBLASTX_EST_elegans {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: dodgerblue;
}
similarity.TBLASTX_EST {
glyph: SEGMENTS;
das: 1;
bump: +1;
height: 5;
background-color: darkgray;
color: dodgerblue;
}
repeat.default {
glyph: GENERIC;
das: 1;
bump: +1;
height: 3;
background-color: #ffe4c4;
color: #8b7d6b;
}
repeat.microsatellite {
glyph: GENERIC;
das: 1;
label: 1;
height: 50;
color: #6699cc;
}
repeat.inverted_repeat {
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
height: 5;
color: #6699cc;
}
experimental.default {
glyph: GENERIC;
das: 1;
label: 1;
bump: +1;
height: 5;
color: black;
background-color: #b8860b;
}
experimental.cDNA_for_RNAi {
glyph: SPAN;
das: 1;
label: 1;
bump: +1;
height: 4;
color: black;
background-color: limegreen;
}
experimental.knockout {
glyph: TRIANGLE;
point: 1;
das: 1;
label: 1;
color: red;
}
experimental.expression_tag {
glyph: GENERIC;
acebrowser/htdocs/stylesheets/aceperl.css view on Meta::CPAN
glyph: TRIANGLE;
das: 1;
color: yellow;
}
experimental.RNAi {
glyph: GENERIC;
das: 1;
label: 1;
bump: +1;
height: 4;
background-color: goldenrod;
color: black;
}
experimental.transgenic {
glyph: GENERIC;
das: 1;
label: 1;
color: blue;
}
experimental.mutant {
glyph: GENERIC;
das: 1;
label: 1;
color: violet;
}
partial_gene.default {
glyph: GENERIC;
das: 1;
label: 1;
background-color: yellow;
color: orange;
height: 5;
bump: +1;
}
acebrowser/htdocs/stylesheets/elegans.css view on Meta::CPAN
HTML,BODY {
background-color: #EEEEE0
}
H1,H2,H3,H4,I,EM,B,LI,UL,OL,DD,DT,ADDRESS,DL,A,STRONG,BLOCKQUOTE,P {
font-family: sans-serif;
background-color: transparent;
}
TABLE {
font-family: sans-serif;
}
TR,TD.search {
font-size: 10pt;
}
.acetree {
font-size: 10pt;
}
P.caption {
font-size: 10pt;
}
P.note {
font-size: 10pt;
}
INPUT {
font-family: sans-serif;
background-color: #EEEEE0
}
SELECT {
font-family: sans-serif;
background-color: #EEEEE0
}
H1 {
font-size: 18pt;
color: red;
}
H2 {
font-size: 18pt;
}
H3 {
font-size: 14pt;
}
TH {
font-family: sans-serif;
padding: 0;
}
TD {
font-family: sans-serif;
padding: 0;
}
.highlight {
background-color: #f5deb3;
}
.small {
font-size: 10pt;
}
TH.small {
font-family: sans-serif;
font-size: 12pt;
padding: 0;
}
TD.small {
font-family: sans-serif;
font-size: 12pt;
padding: 0;
}
.banner {
font-family: sans-serif;
font-size: 18pt;
align: center;
background-color: blue;
color: yellow;
padding-top: 3px;
padding-bottom: 3px;
padding-left: 100px;
padding-right: 100px;
}
.gene {
font-style: italic
}
.error {
color: red;
}
.note {
font-size: 10pt;
}
Blockquote.abstract {
font-size: 10pt;
background-color: rgb(255,248,220);
}
.description {
color: black;
font-style: italic;
}
.smalldescription {
color: black;
font-style: italic;
font-size: 10pt;
}
acebrowser/htdocs/stylesheets/moviedb.css view on Meta::CPAN
HTML,BODY {
background-color: #EEEEE0
}
H1,H2,H3,H4,I,EM,B,LI,UL,OL,DD,DT,ADDRESS,DL,A,STRONG,BLOCKQUOTE,P {
font-family: sans-serif;
background-color: transparent;
}
TABLE {
font-family: sans-serif;
}
TABLE.search {
border-top: 0px;
padding-top: 0px;
margin-top: 0px;
}
.acetree {
font-size: 10pt;
}
P.caption {
font-size: 10pt;
}
INPUT {
font-family: sans-serif;
background-color: #EEEEE0
}
SELECT {
font-family: sans-serif;
background-color: #EEEEE0
}
H1 {
font-size: 18pt;
color: red;
}
H2 {
font-size: 18pt;
}
H3 {
font-size: 14pt;
}
TH {
font-family: sans-serif;
padding: 0;
}
TD {
font-family: sans-serif;
padding: 0;
}
.highlight {
background-color: #f5deb3;
}
.small {
font-size: 10pt;
}
TH.small {
font-family: sans-serif;
font-size: 12pt;
padding: 0;
}
TD.small {
font-family: sans-serif;
font-size: 12pt;
padding: 0;
}
.banner {
font-family: sans-serif;
font-size: 18pt;
align: center;
background-color: blue;
color: yellow;
padding-top: 3px;
padding-bottom: 3px;
padding-left: 100px;
padding-right: 100px;
}
.gene {
font-style: italic
}
.error {
color: red;
}
.note {
font-size: 10pt;
}
Blockquote.abstract {
font-size: 10pt;
background-color: rgb(255,248,220);
}
.description {
color: black;
}
TD.small {
font-size: 10pt;
}
TD.search {
font-size: 10pt;
}
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