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Bio::SAGE::Comparison 1.00
Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. more>>
Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries.
SYNOPSIS
use Bio::SAGE::Comparison;
$sage = Bio::SAGE::Comparison->new();
This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE) libraries.
BACKGROUND
Serial analysis of gene expression (SAGE) is a molecular technique for generating a near-global snapshot of a cell population’s transcriptome. Briefly, the technique extracts short sequences at defined positions of transcribed mRNA. These short sequences are then paired to form ditags. The ditags are concatamerized to form long sequences that are then cloned. The cloned DNA is then sequenced. Bioinformatic techniques are then employed to determine the original short tag sequences, and to derive their progenitor mRNA. The number of times a particular tag is observed can be used to quantitate the amount of a particular transcript. The original technique was described by Velculescu et al. (1995) and utilized an ~14bp sequence tag. A modified protocol was introduced by Saha et al. (2002) that produced ~21bp tags.
PURPOSE
This module facilitates the comparison of SAGE libraries. Specifically:
1. Calculations for determining the statistical
significance of expression differences.
2. Dynamically convert longer-tag libraries to
a shorter type for comparison (e.g. comparing
a LongSAGE vs. a regular SAGE library).
Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module.
Statistical significance in library comparisons is calculated using the method described by Audic and Claverie (1997). Code was generated by directly porting the authors original C source.
<<lessSYNOPSIS
use Bio::SAGE::Comparison;
$sage = Bio::SAGE::Comparison->new();
This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE) libraries.
BACKGROUND
Serial analysis of gene expression (SAGE) is a molecular technique for generating a near-global snapshot of a cell population’s transcriptome. Briefly, the technique extracts short sequences at defined positions of transcribed mRNA. These short sequences are then paired to form ditags. The ditags are concatamerized to form long sequences that are then cloned. The cloned DNA is then sequenced. Bioinformatic techniques are then employed to determine the original short tag sequences, and to derive their progenitor mRNA. The number of times a particular tag is observed can be used to quantitate the amount of a particular transcript. The original technique was described by Velculescu et al. (1995) and utilized an ~14bp sequence tag. A modified protocol was introduced by Saha et al. (2002) that produced ~21bp tags.
PURPOSE
This module facilitates the comparison of SAGE libraries. Specifically:
1. Calculations for determining the statistical
significance of expression differences.
2. Dynamically convert longer-tag libraries to
a shorter type for comparison (e.g. comparing
a LongSAGE vs. a regular SAGE library).
Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module.
Statistical significance in library comparisons is calculated using the method described by Audic and Claverie (1997). Code was generated by directly porting the authors original C source.
Download (0.008MB)
Added: 2007-07-14 License: Perl Artistic License Price:
832 downloads
Kernel Configuration Comparison 0.2
Kernel Configuration Comparison (kccmp) provides a GUI for comparing two Linux kernel .config files. more>>
Kernel Configuration Comparison (kccmp) provides a GUI for comparing two Linux kernel ".config" files.
It shows configuration variables with different values in a tabular format. It also shows configuration variables found in only one of the input configuration files.
Building:
kccmp by default requires Qt 3.x. However, by changing one line in kccmp.pro you can build against Qt 4.x. Note that the Qt 4.x build requilres libboost_regex as well.
The standard build is as easy as:
example:
% qmake
% make
Usage
% kccmp /path/to/first/.config path/to/second/.config
example:
% kccmp /usr/src/linux/.config /usr/src/linux/.config.old
Enhancements:
- This release was ported to Qt 3.x.
- The requirement for libboost_regex was removed.
- Building with either Qt 4.x or Qt 3.x is now supported.
<<lessIt shows configuration variables with different values in a tabular format. It also shows configuration variables found in only one of the input configuration files.
Building:
kccmp by default requires Qt 3.x. However, by changing one line in kccmp.pro you can build against Qt 4.x. Note that the Qt 4.x build requilres libboost_regex as well.
The standard build is as easy as:
example:
% qmake
% make
Usage
% kccmp /path/to/first/.config path/to/second/.config
example:
% kccmp /usr/src/linux/.config /usr/src/linux/.config.old
Enhancements:
- This release was ported to Qt 3.x.
- The requirement for libboost_regex was removed.
- Building with either Qt 4.x or Qt 3.x is now supported.
Download (0.012MB)
Added: 2005-10-03 License: GPL (GNU General Public License) Price:
1482 downloads
Apache XML Graphics Commons 1.1
Apache XML Graphics Commons project is a library that consists of several reusable components. more>>
Apache XML Graphics Commons project is a library that consists of several reusable components used by Apache Batik and Apache FOP.
Many of these components can easily be used separately outside the domains of SVG and XSL-FO. You will find components such as a PDF library, an RTF library, Graphics2D implementations that let you generate PDF & PostScript files, and much more.
Apache XML Graphics Commons has only just begun. Its in the process of being populated with components coming from Apache Batik and Apache FOP. Stay tuned for exciting treasures made available.
In the Wiki, we have a plan for building Apache XML Graphics Commons. The plan provides an idea of what you can expect to find here when were finished migrating components.
Main features:
- Image codecs for PNG and TIFF
- Bitmap image writer abstraction with implementation for the above codecs and for the Image I/O API.
- Java2D helper classes
- Graphics2D implementation that produces PostScript and EPS
- Helper classes for PostScript code production
- XMP metadata framework
- Various I/O classes, encoders and decoders for various formats
Enhancements:
- The ImageWriter abstraction now supports the writing of multi-page formats like TIFF.
- This uses the Image I/O API. A default implementation was provided for AbstractGraphics2D.drawText(ACI, float, float) so that PSGraphics2D supports painting of text using the AttributedCharacterIterator.
- Various fixes and improvements were made in the ImageWriter abstraction.
- A problem where the generation of the PostScript setdash command was assuming that only integer values can be used was fixed.
<<lessMany of these components can easily be used separately outside the domains of SVG and XSL-FO. You will find components such as a PDF library, an RTF library, Graphics2D implementations that let you generate PDF & PostScript files, and much more.
Apache XML Graphics Commons has only just begun. Its in the process of being populated with components coming from Apache Batik and Apache FOP. Stay tuned for exciting treasures made available.
In the Wiki, we have a plan for building Apache XML Graphics Commons. The plan provides an idea of what you can expect to find here when were finished migrating components.
Main features:
- Image codecs for PNG and TIFF
- Bitmap image writer abstraction with implementation for the above codecs and for the Image I/O API.
- Java2D helper classes
- Graphics2D implementation that produces PostScript and EPS
- Helper classes for PostScript code production
- XMP metadata framework
- Various I/O classes, encoders and decoders for various formats
Enhancements:
- The ImageWriter abstraction now supports the writing of multi-page formats like TIFF.
- This uses the Image I/O API. A default implementation was provided for AbstractGraphics2D.drawText(ACI, float, float) so that PSGraphics2D supports painting of text using the AttributedCharacterIterator.
- Various fixes and improvements were made in the ImageWriter abstraction.
- A problem where the generation of the PostScript setdash command was assuming that only integer values can be used was fixed.
Download (MB)
Added: 2006-12-27 License: The Apache License 2.0 Price:
1035 downloads
GD Graphics Library 2.0.35
Gd is a graphics library. more>>
Gd is a graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills, and write out the result as a PNG or JPEG file. This is particularly useful in World Wide Web applications, where PNG and JPEG are two of the formats accepted for inline images by most browsers.
In gd 1.0, it stood for "gif draw." After the Unisys patent on the LZW compression used in GIF came to light and GIF support was dropped, it did not officially stand for anything, but lets just say "graphics draw" and leave it at that. (GIF support is back, thanks to the expiration of the patent, but gd can draw much more than GIFs.)
This is a quick install guide:
1. Type ./configure
2. Type make install
<<lessIn gd 1.0, it stood for "gif draw." After the Unisys patent on the LZW compression used in GIF came to light and GIF support was dropped, it did not officially stand for anything, but lets just say "graphics draw" and leave it at that. (GIF support is back, thanks to the expiration of the patent, but gd can draw much more than GIFs.)
This is a quick install guide:
1. Type ./configure
2. Type make install
Download (1.2MB)
Added: 2007-06-22 License: GPL (GNU General Public License) Price:
860 downloads
Graphics Muse Tools 3.0.0B2
Graphics Muse Tools are plug-ins for use with the GIMP. more>>
The Graphics Muse Tools are a collection of plug-ins and scripts for use with GIMP. The package now includes a set of C plugins (GFXArrows, GFXCards, GFXTrans, GFXLayers, GFXMerge, and GFXShapes) and a set of Perl scripts (GFXDodge, GFXGallery, GFXLayerSave, and GFXLayerOffsets).
<<less Download (1.4MB)
Added: 2005-05-03 License: Free To Use But Restricted Price:
1640 downloads
PHP Greeting card class 1.1
PHP Greeting card class can be used to compose and send greeting cards by email. more>>
PHP Greeting card class can be used to compose and send greeting cards by email.
PHP Greeting card class can compose and send an email message with a greeting either in text, in HTML with an image, or in HTML with Flash content.
The HTML version of the card may include a greeting picture.
<<lessPHP Greeting card class can compose and send an email message with a greeting either in text, in HTML with an image, or in HTML with Flash content.
The HTML version of the card may include a greeting picture.
Download (0.95MB)
Added: 2006-12-21 License: GPL (GNU General Public License) Price:
1043 downloads
fid-graphics 0.2
fid-graphics is a simple toolkit for the Frigand Imperial Desktop. more>>
fid-graphics project is a simple toolkit for the Frigand Imperial Desktop.
It is probably the easiest toolkit to write a display engine for, but it does not support any widgets.
Enhancements:
- src/Desktop/Fid/Window.lhs (displayWaitRedisplay): New function.
- (requestRedisplay): Tidy up.
- src/Desktop/Fid/Main.lhs (data WinCapLine): New type.
- (data WindowType): Use it.
- (&&*, ||*, isnt, haveEnvVar, haveOpt): Deleted.
- (lookupFeature, lookupProtocol, lookupKeywords): New functions.
- (windowTypes): Use WindowCapLine.
- (forkProcess): Unused; deleted.
- (data FidOpt): Unused; deleted.
- (fidMain): Dont consider forking.
- Only call getOpt to sort out verbose options.
- src/Desktop/Fid/Control.lhs (PrimKey): New type.
- (instance Eq PrimKey, instance Ord PrimKey)
- (instance Show PrimKey, instance Arbitrary PrimKey): Instances for t.
- (data Key): Use it.
- (charKey, control, keyToChar): Do the right thing with PrimKey.
- (symbolKey): New function.
- (instance Arbitrary Key): Use instance Arbitrary PrimKey.
- (instance Arbitrary Char): New Instance.
<<lessIt is probably the easiest toolkit to write a display engine for, but it does not support any widgets.
Enhancements:
- src/Desktop/Fid/Window.lhs (displayWaitRedisplay): New function.
- (requestRedisplay): Tidy up.
- src/Desktop/Fid/Main.lhs (data WinCapLine): New type.
- (data WindowType): Use it.
- (&&*, ||*, isnt, haveEnvVar, haveOpt): Deleted.
- (lookupFeature, lookupProtocol, lookupKeywords): New functions.
- (windowTypes): Use WindowCapLine.
- (forkProcess): Unused; deleted.
- (data FidOpt): Unused; deleted.
- (fidMain): Dont consider forking.
- Only call getOpt to sort out verbose options.
- src/Desktop/Fid/Control.lhs (PrimKey): New type.
- (instance Eq PrimKey, instance Ord PrimKey)
- (instance Show PrimKey, instance Arbitrary PrimKey): Instances for t.
- (data Key): Use it.
- (charKey, control, keyToChar): Do the right thing with PrimKey.
- (symbolKey): New function.
- (instance Arbitrary Key): Use instance Arbitrary PrimKey.
- (instance Arbitrary Char): New Instance.
Download (0.078MB)
Added: 2006-10-02 License: Academic Free License (AFL) Price:
1122 downloads
Graphics::ColorUtils 0.17
Graphics::ColorUtils Perl module is an easy-to-use color space conversions and more. more>>
Graphics::ColorUtils Perl module is an easy-to-use color space conversions and more.
SYNOPSIS
use Graphics::ColorUtils;
( $y, $i, $q ) = rgb2yiq( $r, $g, $b );
( $r, $g, $b ) = yiq2rgb( $y, $i, $q );
$hex_string = yiq2rgb( $y, $i, $q );
( $c, $m, $y ) = rgb2cmy( $r, $g, $b );
( $r, $g, $b ) = cmy2rgb( $c, $m, $y );
$hex_string = cmy2rgb( $c, $m, $y );
( $h, $l, $s ) = rgb2hls( $r, $g, $b );
( $r, $g, $b ) = hls2rgb( $h, $l, $s );
$hex_string = hls2rgb( $h, $l, $s );
( $h, $s, $v ) = rgb2hsv( $r, $g, $b );
( $r, $g, $b ) = hsv2rgb( $h, $s, $v );
$hex_string = hsv2rgb( $h, $s, $v );
# -----
use Graphics::ColorUtils qw( :gradients );
( $r, $g, $b ) = grad2rgb( $name, $f ); # where 0.0 colorAllocate( hsv2rgb( 270, 0.5, 0.3 ) );.)
Features:
Color Space Conversions
Color space conversions, in particular between the "intuitive" color spaces HSV (Hue/Saturation/Value) and HLS (Hue/Lightness/Saturation) to and from RGB (Red/Green/Blue).
Color Lookup
Color lookup by name for three standard sets of colors: WWW/CSS, SVG, and X11.
Color Gradients
Management of color gradients, which can be indexed by a floating point number in the range 0..1. (Mostly intended for false-color data visualization.)
<<lessSYNOPSIS
use Graphics::ColorUtils;
( $y, $i, $q ) = rgb2yiq( $r, $g, $b );
( $r, $g, $b ) = yiq2rgb( $y, $i, $q );
$hex_string = yiq2rgb( $y, $i, $q );
( $c, $m, $y ) = rgb2cmy( $r, $g, $b );
( $r, $g, $b ) = cmy2rgb( $c, $m, $y );
$hex_string = cmy2rgb( $c, $m, $y );
( $h, $l, $s ) = rgb2hls( $r, $g, $b );
( $r, $g, $b ) = hls2rgb( $h, $l, $s );
$hex_string = hls2rgb( $h, $l, $s );
( $h, $s, $v ) = rgb2hsv( $r, $g, $b );
( $r, $g, $b ) = hsv2rgb( $h, $s, $v );
$hex_string = hsv2rgb( $h, $s, $v );
# -----
use Graphics::ColorUtils qw( :gradients );
( $r, $g, $b ) = grad2rgb( $name, $f ); # where 0.0 colorAllocate( hsv2rgb( 270, 0.5, 0.3 ) );.)
Features:
Color Space Conversions
Color space conversions, in particular between the "intuitive" color spaces HSV (Hue/Saturation/Value) and HLS (Hue/Lightness/Saturation) to and from RGB (Red/Green/Blue).
Color Lookup
Color lookup by name for three standard sets of colors: WWW/CSS, SVG, and X11.
Color Gradients
Management of color gradients, which can be indexed by a floating point number in the range 0..1. (Mostly intended for false-color data visualization.)
Download (0.021MB)
Added: 2007-07-03 License: Perl Artistic License Price:
843 downloads
Graphics::Simple 0.04
Graphics::Simple is a simple , device-independent graphics API for Perl. more>>
Graphics::Simple is a simple , device-independent graphics API for Perl.
SYNOPSIS
use Graphics::Simple;
line 100,100,200,200;
circle 50,50,25;
stop(); clear(); # Wait for a button press, clear the page
Ever had a Commodore C-64 or Vic-20 or some other of the machines of that era? Where doing graphics was as simple as
line 20,20,50,30;
and you didnt have to go through things like XOpenDisplay etc.
This module tries to bring back the spirit of that era in a modern environment: this module presents a simple, unified API to several different graphics devices - currently X (using Gtk and Gnome) and PostScript.
The interface is primarily made easy-to-use, starting from the idea that the above line command must work. Therefore, it exports most of the primitives by default (you can turn this off).
However, everything is not sacrificed in the name of simplicity: believing in "simple things simple, complicated things possible", this module also allows multiple windows (all the primitives also work as methods of window objects) as well as raw access to the underlying devices - although the device-independence is then lost. In future plans are some sort of interactions with the devices with which it is possible as well as the addition of more devices.
The use command currently accepts the forms
use Graphics::Simple;
use Graphics::Simple qw/line circle/;
use Graphics::Simple 300,400; # portrait paper
use Graphics::Simple 300,400, qw/line circle/;
i.e. the optional size of the default window first and then normal Exporter arguments.
Graphics::Simple has several different back-ends, currently GnomeCanvas, TkCanvas, PostScript and (not fully working yet) Fig. Other backends are expected.
To start Graphics::Simple with a given backend, you should set the environment variable GSIMPL to the value, e.g. by running your script with the command
GSIMPL=PostScript perl gt1.pl
or by setting the environment variable permanently in your shell, by
GSIMPL=PostScript
export GSIMPL
or
setenv GSIMPL PostScript
<<lessSYNOPSIS
use Graphics::Simple;
line 100,100,200,200;
circle 50,50,25;
stop(); clear(); # Wait for a button press, clear the page
Ever had a Commodore C-64 or Vic-20 or some other of the machines of that era? Where doing graphics was as simple as
line 20,20,50,30;
and you didnt have to go through things like XOpenDisplay etc.
This module tries to bring back the spirit of that era in a modern environment: this module presents a simple, unified API to several different graphics devices - currently X (using Gtk and Gnome) and PostScript.
The interface is primarily made easy-to-use, starting from the idea that the above line command must work. Therefore, it exports most of the primitives by default (you can turn this off).
However, everything is not sacrificed in the name of simplicity: believing in "simple things simple, complicated things possible", this module also allows multiple windows (all the primitives also work as methods of window objects) as well as raw access to the underlying devices - although the device-independence is then lost. In future plans are some sort of interactions with the devices with which it is possible as well as the addition of more devices.
The use command currently accepts the forms
use Graphics::Simple;
use Graphics::Simple qw/line circle/;
use Graphics::Simple 300,400; # portrait paper
use Graphics::Simple 300,400, qw/line circle/;
i.e. the optional size of the default window first and then normal Exporter arguments.
Graphics::Simple has several different back-ends, currently GnomeCanvas, TkCanvas, PostScript and (not fully working yet) Fig. Other backends are expected.
To start Graphics::Simple with a given backend, you should set the environment variable GSIMPL to the value, e.g. by running your script with the command
GSIMPL=PostScript perl gt1.pl
or by setting the environment variable permanently in your shell, by
GSIMPL=PostScript
export GSIMPL
or
setenv GSIMPL PostScript
Download (0.013MB)
Added: 2006-07-19 License: Perl Artistic License Price:
1194 downloads
Graphics::ColorPicker 0.10
Graphics::ColorPicker is a Perl module for WYSIWYG web applications that allow selection of HEX color numbers. more>>
Graphics::ColorPicker is a Perl module for WYSIWYG web applications that allow selection of HEX color numbers.
SYNOPSIS
use Graphics::ColorPicker;
or
require Graphics::ColorPicker;
make_page($path_to_images);
send_page($html_txt,$type);
$time_string = http_date($time);
$name = script_name;
$html_text=frames($websafe);
$html_text = msie_frame;
$html_text=picker($darkimg,$liteimg,$size,$bsize,greyimg);
$html_text=no_picker;
$html_text=cp216_ds($clrdot,$border,$square)
$javascript_text = jslib;
$html=make_buttons(%look_n_feel,$url,$active,@buttons,$xtra);
$html_text=pluck($color);
<<lessSYNOPSIS
use Graphics::ColorPicker;
or
require Graphics::ColorPicker;
make_page($path_to_images);
send_page($html_txt,$type);
$time_string = http_date($time);
$name = script_name;
$html_text=frames($websafe);
$html_text = msie_frame;
$html_text=picker($darkimg,$liteimg,$size,$bsize,greyimg);
$html_text=no_picker;
$html_text=cp216_ds($clrdot,$border,$square)
$javascript_text = jslib;
$html=make_buttons(%look_n_feel,$url,$active,@buttons,$xtra);
$html_text=pluck($color);
Download (0.11MB)
Added: 2007-07-27 License: Perl Artistic License Price:
824 downloads
Bio::Graphics::Feature 1.4
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. more>>
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel.
SYNOPSIS
use Bio::Graphics::Feature;
# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
-stop => 2000,
-type => transcript,
-name => alpha-1 antitrypsin,
-desc => an enzyme inhibitor,
);
# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);
# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.
<<lessSYNOPSIS
use Bio::Graphics::Feature;
# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
-stop => 2000,
-type => transcript,
-name => alpha-1 antitrypsin,
-desc => an enzyme inhibitor,
);
# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
-name => ABC-3,
-type => gapped_alignment,
-subtype => similarity);
# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>exon);
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>exon);
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>exon);
$f = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>gene);
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing.
Download (4.7MB)
Added: 2006-10-21 License: Perl Artistic License Price:
1098 downloads
Graphics::ColorObject 0.5.0
Graphics::ColorObject can convert between color spaces. more>>
Graphics::ColorObject can convert between color spaces.
SYNOPSIS
use Graphics::ColorObject;
# rgb to hsv
$color = Graphics::ColorObject->new_RGB([$r, $g, $b]);
($h, $s, $v) = @{ $color->as_HSV() };
# one rgb space to another (NTSC to PAL)
$color = Graphics::ColorObject->new_RGB([$r, $g, $b], space=>NTSC);
($r, $g, $b) = @{ $color->as_RGB(space=>PAL) };
ABSTRACT
Use this module to convert between all the common color spaces. As a pure Perl module, it is not very fast, and so it you want to convert entire images quickly, this is probably not what you want. The emphasis is on completeness and accurate conversion.
Supported color spaces are: RGB (including sRGB, Apple, Adobe, CIE Rec 601, CIE Rec 709, CIE ITU, and about a dozen other RGB spaces), CMY, CMYK, HSL, HSV, XYZ, xyY, Lab, LCHab, Luv, LCHuv, YPbPr, YCbCr, YUV, YIQ, PhotoYCC.
Conversion between different RGB working spaces, and between different white-points, is fully supported.
For any supported color space XXX, there is one constructor new_XXX that creates a color using data in that color space, and one method as_XXX that returns the current color as expressed in that color space. For example, for RGB there is new_RGB and as_RGB. The color data is always passed as an array reference to a three-element array (four-element in the case of CMYK). Thus, to convert from RGB to HSL, you can use:
$color = Graphics::ColorObject->new_RGB([$r, $g, $b]);
($h, $s, $l) = @{ $color->as_HSL() };
The constructor can always take a hash of optional arguments in addition to the color value, namely the working RGB space and the white point. For example:
$color = Graphics::ColorObject->new_RGB([$r, $g, $b], space=>Adobe, white_point=>D65);
For a list of all supported color spaces, call Graphics::ColorObject->list_colorspaces(). For a list of all RGB working spaces and of all white points that this module supports, call Graphics::ColorObject->list_rgb_spaces() and Graphics::ColorObject->list_white_points().
If not specified, the working RGB space will be sRGB. Many non-RGB conversions also rely on an implicit RGB space, and passing an RGB space as an option (either to the constructor or later) will have an effect on the values.
<<lessSYNOPSIS
use Graphics::ColorObject;
# rgb to hsv
$color = Graphics::ColorObject->new_RGB([$r, $g, $b]);
($h, $s, $v) = @{ $color->as_HSV() };
# one rgb space to another (NTSC to PAL)
$color = Graphics::ColorObject->new_RGB([$r, $g, $b], space=>NTSC);
($r, $g, $b) = @{ $color->as_RGB(space=>PAL) };
ABSTRACT
Use this module to convert between all the common color spaces. As a pure Perl module, it is not very fast, and so it you want to convert entire images quickly, this is probably not what you want. The emphasis is on completeness and accurate conversion.
Supported color spaces are: RGB (including sRGB, Apple, Adobe, CIE Rec 601, CIE Rec 709, CIE ITU, and about a dozen other RGB spaces), CMY, CMYK, HSL, HSV, XYZ, xyY, Lab, LCHab, Luv, LCHuv, YPbPr, YCbCr, YUV, YIQ, PhotoYCC.
Conversion between different RGB working spaces, and between different white-points, is fully supported.
For any supported color space XXX, there is one constructor new_XXX that creates a color using data in that color space, and one method as_XXX that returns the current color as expressed in that color space. For example, for RGB there is new_RGB and as_RGB. The color data is always passed as an array reference to a three-element array (four-element in the case of CMYK). Thus, to convert from RGB to HSL, you can use:
$color = Graphics::ColorObject->new_RGB([$r, $g, $b]);
($h, $s, $l) = @{ $color->as_HSL() };
The constructor can always take a hash of optional arguments in addition to the color value, namely the working RGB space and the white point. For example:
$color = Graphics::ColorObject->new_RGB([$r, $g, $b], space=>Adobe, white_point=>D65);
For a list of all supported color spaces, call Graphics::ColorObject->list_colorspaces(). For a list of all RGB working spaces and of all white points that this module supports, call Graphics::ColorObject->list_rgb_spaces() and Graphics::ColorObject->list_white_points().
If not specified, the working RGB space will be sRGB. Many non-RGB conversions also rely on an implicit RGB space, and passing an RGB space as an option (either to the constructor or later) will have an effect on the values.
Download (0.022MB)
Added: 2006-08-05 License: Perl Artistic License Price:
1175 downloads
PDL::Graphics::TriD 2.4.3
PDL::Graphics::TriD is a PDL 3D interface. more>>
PDL::Graphics::TriD is a PDL 3D interface.
SYNOPSIS
use PDL::Graphics::TriD;
# After each graph, let the user rotate is and # wait for him to press q, then make new graph line3d($coords); # $coords = (3,n,...) line3d($coords,$colors); # $colors = (3,n,...) line3d([$x,$y,$z]); imagrgb([$r,$g,$b]); lattice3d([$x,$y,$z]); # 2-d piddles points3d([$x,$y,$z]);
hold3d(); # the following graphs are on top of each other and the previous line3d([$x,$y,$z]); line3d([$x,$y,$z+1]); $pic = grabpic3d(); # Returns the picture in a (3,$x,$y) float piddle (0..1).
release3d(); # the next graph will again wipe out things.
WARNING
These modules are still in a somewhat unfocused state: dont use them yet if you dont know how to make them work if they happen to do something strange.
This module implements a generic 3D plotting interface for PDL. Points, lines and surfaces (among other objects) are supported.
With OpenGL, it is easy to manipulate the resulting 3D objects with the mouse in real time - this helps data visualization a lot.
<<lessSYNOPSIS
use PDL::Graphics::TriD;
# After each graph, let the user rotate is and # wait for him to press q, then make new graph line3d($coords); # $coords = (3,n,...) line3d($coords,$colors); # $colors = (3,n,...) line3d([$x,$y,$z]); imagrgb([$r,$g,$b]); lattice3d([$x,$y,$z]); # 2-d piddles points3d([$x,$y,$z]);
hold3d(); # the following graphs are on top of each other and the previous line3d([$x,$y,$z]); line3d([$x,$y,$z+1]); $pic = grabpic3d(); # Returns the picture in a (3,$x,$y) float piddle (0..1).
release3d(); # the next graph will again wipe out things.
WARNING
These modules are still in a somewhat unfocused state: dont use them yet if you dont know how to make them work if they happen to do something strange.
This module implements a generic 3D plotting interface for PDL. Points, lines and surfaces (among other objects) are supported.
With OpenGL, it is easy to manipulate the resulting 3D objects with the mouse in real time - this helps data visualization a lot.
Download (2.1MB)
Added: 2007-06-21 License: Perl Artistic License Price:
858 downloads
Bio::Graphics::FeatureFile 1.4
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. more>>
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file.
SYNOPSIS
use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);
# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);
# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;
# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}
# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);
# or create the FeatureFile by hand
# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});
# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.
This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.
<<lessSYNOPSIS
use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);
# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);
# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;
# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}
# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);
# or create the FeatureFile by hand
# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});
# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.
This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.
Download (4.7MB)
Added: 2006-06-12 License: Perl Artistic License Price:
1229 downloads
Bio::Graphics::Glyph::alignment 1.4
Bio::Graphics::Glyph::alignment is the alignment glyph. more>>
Bio::Graphics::Glyph::alignment is the "alignment" glyph.
SYNOPSIS
See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >.
This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is proportionate to the score.
<<lessSYNOPSIS
See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >.
This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is proportionate to the score.
Download (4.7MB)
Added: 2006-10-21 License: Perl Artistic License Price:
1099 downloads
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