Context Independent Sequence Annotator

2015-01-13

azim58 - Context Independent Sequence Annotator

This "Context Independent Sequence Annotator" is a simple program (Java
program) which allows you to annotate a sequence of information. The
sequence of information required is context independent meaning that the
sequence of information can be anything from a timeline, RNA, DNA,
protein, text, etc. The program accepts a text file containing simple
tags to specify how the sequence of information should be annotated, and
then the program outputs an svg (scalable vector graphic) graphic file
which can be viewed and edited in any vector graphics editor such as the
free vector graphics program Inkscape.

Example Use of the Program
The program accepts a text file with the annotation information. The file
would look something like this.

===========================================================================
<information_sequence start_point="0" end_point="100" />
<graphical_line length="200" color="black" />

===========================================================================

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\annotation_information.txt"

Here's a few notes about this annotation information. The
"information_sequence" "start_point" and "end_point" would refer to
arbitrary numbers. Here 0 could mean 0 days and 100 could mean 100 days
(the units of everything would need to be the same to get a correct
looking graphic at the end). The "graphical_line" "length" just refers to
how long you want the information sequence line to visually appear. You
may want to make it longer if you feel that everything is too close
together and/or labels are overlapping eachother, etc. For an
"annotation_graphic", the annotation can be treated as a line or a point.
If you want it to appear as a point, then just make the "start_point" and
"end_point" the same value. Then specify the size you want this square
point to be in the "size_if_point" attribute. If you want it to appear as
a line, just make the "start_point" and "end_point" have different values.

Tracks
The track refers to whether the graphic or label should appear on the
information sequence graphic "0", above it ("1", "2", "3", etc.), or
below it ("-1", "-2", "-3", etc.).

Everything else is fairly self explanatory.

The following information sequence text would produce the following
graphic.

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\example_annotated_sequence.PNG"

Here's another example use of the program to make a dinosaur timeline.

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\dinosaur_timeline.PNG"

Here was the annotation information file needed to make this.

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\dinosaure_annotation_information.t
xt"

Instructions for Using the Program

Files needed
Template svg file

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\CISA_Template.svg"

Context Independent Sequence Annotator Java Class

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\Context_Independent_Sequence_Annot
ator_Class.txt"

Useful Tools Java Class

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\UsefulTools.txt"

Example Annotation Information File

"C:\kurt\storage\CIM Research
Folder\DR\2013\2-8-13\data_download\1104\annotation_information.txt"

* Download the necessary files
* Start a new Java project in Eclipse
* Create a new class called Context_Independent_Sequence_Annotator in
  Eclipse and paste the text from the
  Context_Independent_Sequence_Annotator_Class.txt file into this class
  in Eclipse
* Create a new class called UsefulTools in Eclipse and paste the text
  from the UsefulTools.txt file into this class in Eclipse
* Save the annotation_information.txt file to a place where you know
  where it is
* Save the CISA_Template.svg file to a place where you know where it is
* Edit the annotation_information.txt file the way that you would like
  to so you create your specifications for your annotated sequence
* Change two lines of Code in the
  Context_Independent_Sequence_Annotator in Eclipse. Replace the path on
  the line with "String svg_template_path =" to the path that is
  appropriate for you, and replace the path on the line with "String
  annotation_information_path =" to the path that is appropriate for you.
* Run the program in Eclipse. Then open up your cisa_output.svg file in
  Inkscape or another vector graphics editor to edit it or take a
  picture, etc.

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