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Replace all /wikis references with /wiki
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‎404.html

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@@ -3,32 +3,32 @@
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title: 404 Page Not Found
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---
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<script>
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var allposts = [];
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var allposts = [];
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function redirectToCorrectPage() {
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{% for post in site.pages %}
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allposts.push("{{ post.url }}");
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{% endfor %}
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{% for post in site.wikis %}
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allposts.push("{{ post.url }}");
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{% endfor %}
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{% for post in site.pages %}
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allposts.push("{{ post.url }}");
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{% endfor %}
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{% for post in site.wiki %}
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allposts.push("{{ post.url }}");
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{% endfor %}
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var url = window.location.pathname;
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// strip trailing /
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if (url.slice(-1) === "/") {
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url = url.slice(0, -1);
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if (url.slice(-1) === "/") {
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url = url.slice(0, -1);
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}
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var allpostsUpperCase = allposts.map(function(value) {
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var allpostsUpperCase = allposts.map(function(value) {
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// strip trailing /
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if (value.slice(-1) === "/") {
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value = value.slice(0, -1);
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if (value.slice(-1) === "/") {
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value = value.slice(0, -1);
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}
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return value.toUpperCase();
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});
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var i = allpostsUpperCase.indexOf(url.toUpperCase());
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if (i != -1) {
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console.log(allposts[i]);
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window.location = allposts[i];
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}
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}
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return value.toUpperCase();
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});
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var i = allpostsUpperCase.indexOf(url.toUpperCase());
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if (i != -1) {
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console.log(allposts[i]);
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window.location = allposts[i];
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}
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}
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window.onload = redirectToCorrectPage;
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</script>
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<p>Sorry this page does not exist =(</p>
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<p>Sorry this page does not exist =(</p>

‎_config.yml

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@@ -74,7 +74,7 @@ release:
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version: 4.2.1
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collections:
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wiki :
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wiki:
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output: true
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permalink: /wiki/:path/
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post_dirs: false

‎_wiki/Annotations_List.md

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---
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title: Annotations:List
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permalink: wikis/Annotations%3AList
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permalink: wiki/Annotations%3AList
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---
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How do I List the Annotations in a Sequence?

‎_wiki/BioJava3_Coding_Conventions.md

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---
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title: BioJava3:Coding Conventions
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permalink: wikis/BioJava3%3ACoding_Conventions
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permalink: wiki/BioJava3%3ACoding_Conventions
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---
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- Each file should contain the
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[BioJava3\_license](/wikis/BioJava3_license "wikilink") LGPL copyright
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[BioJava3\_license](/wiki/BioJava3_license "wikilink") LGPL copyright
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statement.
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<!-- -->
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- For Eclipse developers, here a Code template:
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[BioJava3\_eclipse\_template](/wikis/BioJava3_eclipse_template "wikilink")
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[BioJava3\_eclipse\_template](/wiki/BioJava3_eclipse_template "wikilink")
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‎_wiki/BioJava3_Design.md

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@@ -12,7 +12,7 @@ Implementation
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--------------
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For information on the current status of the BioJava 3 implementation go
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to [BioJava3\_project](/wikis/BioJava3_project "wikilink")
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to [BioJava3\_project](/wiki/BioJava3_project "wikilink")
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References
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----------
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It is planned to document BioJava in parallel with development. To do
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this, we want to drive development from a set of [ use
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cases](/wikis/BioJava 3 Use Cases "wikilink").
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cases](/wiki/BioJava 3 Use Cases "wikilink").

‎_wiki/BioJava3_Feature_Requests.md

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@@ -21,5 +21,5 @@ There are also a number of algorithms where we would be interested in
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[Java ports](Algorithm_Java_port "wikilink").
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You can also take a look at the current list of [ BioJava
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Modules](/wikis/BioJava:Modules#BioJava_3.0.X "wikilink") and suggest other
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Modules](/wiki/BioJava:Modules#BioJava_3.0.X "wikilink") and suggest other
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missing features.

‎_wiki/BioJava3_HowTo.md

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---
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title: BioJava3:HowTo
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permalink: wikis/BioJava3%3AHowTo
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permalink: wiki/BioJava3%3AHowTo
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---
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This page is a work-in-progress, describing each of the key areas in

‎_wiki/BioJava3_Proposal.md

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@@ -8,7 +8,7 @@ BioJava 3 has been released
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This page was used while starting the discussions for creating the new
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version. BioJava 3.0 has been released on Dec. 28th 2010.
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[BioJava3\_project](/wikis/BioJava3_project "wikilink")
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[BioJava3\_project](/wiki/BioJava3_project "wikilink")
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Executive Summary
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-----------------

‎_wiki/BioJava3_eclipse.md

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@@ -113,7 +113,7 @@ require SCM handler.*
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files (the maven config files) and will understand that it is a
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maven and a git-tracked project.
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You should now have source to all the biojava modules (/wikis/BioJava3-core,
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You should now have source to all the biojava modules (/wiki/BioJava3-core,
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biojava3-structure, etc). Viewing the history for any file should show
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you all commits since 2009 which have contributed to that file.
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‎_wiki/BioJava3_license.md

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@@ -3,7 +3,7 @@ title: BioJava3 license
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---
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BioJava 3 is using the [standard BioJava
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license](/wikis/BioJava:License "wikilink"): LGPL v 2.1
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license](/wiki/BioJava:License "wikilink"): LGPL v 2.1
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Developers: Please include the following javadoc in the header of every
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class you commit:

‎_wiki/BioJava3_project.md

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@@ -23,7 +23,7 @@ how to check out the code from SVN or get the latest SNAPSHOT builds.
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IDE specific instructions
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-------------------------
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- [BioJava3\_eclipse](/wikis/BioJava3_eclipse "wikilink") how to work with
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- [BioJava3\_eclipse](/wiki/BioJava3_eclipse "wikilink") how to work with
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BioJava3 using eclipse
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Wanted
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------------------
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- We are using Maven to build biojava 3
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- [BioJava3\_license](/wikis/BioJava3_license "wikilink") - All source code
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- [BioJava3\_license](/wiki/BioJava3_license "wikilink") - All source code
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of BioJava 3 is under LGPL.
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- [BioJava3\_logging](/wikis/BioJava3_logging "wikilink") - How to use
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- [BioJava3\_logging](/wiki/BioJava3_logging "wikilink") - How to use
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logging
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Links
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-----
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- [BioJava3\_Proposal](/wikis/BioJava3_Proposal "wikilink")
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- [BioJava3\_Proposal](/wiki/BioJava3_Proposal "wikilink")
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‎_wiki/BioJava;CookBook3_PSA_DNA.md

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---
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title: BioJava;CookBook3:PSA DNA
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permalink: wikis/BioJava;CookBook3%3APSA_DNA
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redirect_to: /_wikis/BioJava:CookBook3:PSA_DNA
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permalink: wiki/BioJava;CookBook3%3APSA_DNA
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redirect_to: /wiki/BioJava:CookBook3:PSA_DNA
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---
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You should automatically be redirected to [BioJava:CookBook3:PSA DNA](/_wikis/BioJava:CookBook3:PSA_DNA)
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You should automatically be redirected to [BioJava:CookBook3:PSA DNA](/wiki/BioJava:CookBook3:PSA_DNA)

‎_wiki/BioJavaKorean_GetStarted.md

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---
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title: BioJavaKorean:GetStarted
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permalink: wikis/BioJavaKorean%3AGetStarted
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permalink: wiki/BioJavaKorean%3AGetStarted
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---
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소개
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You can now compile and run BioJava programs using the *javac* and
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*java* commands. You might like to look at the
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[tutorial](/wikis/BioJava:Tutorial "wikilink"), [API
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[tutorial](/wiki/BioJava:Tutorial "wikilink"), [API
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documentation](http://www.biojava.org/docs/api15b/index.html) and the
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[BioJava in anger](/wikis/BioJava:Cookbook "wikilink") section . Finally, you
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[BioJava in anger](/wiki/BioJava:Cookbook "wikilink") section . Finally, you
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can learn a lot about BioJava by trying the demo programs included in
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the source distribution (see below).

‎_wiki/BioJava_1.5ReleasePlan.md

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---
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title: BioJava:1.5ReleasePlan
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permalink: wikis/BioJava%3A1.5ReleasePlan
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permalink: wiki/BioJava%3A1.5ReleasePlan
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---
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Release plan for BioJava 1.5
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### Documentation
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- Update [Cookbook](/wikis/BioJava:Cookbook "wikilink") code to reflect best
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- Update [Cookbook](/wiki/BioJava:Cookbook "wikilink") code to reflect best
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practices with BioJavaX
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- Should we keep legacy examples in the
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[Cookbook](/wikis/BioJava:Cookbook "wikilink")?
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[Cookbook](/wiki/BioJava:Cookbook "wikilink")?
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- Check for errors in biojavax docbook
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### Javadoc

‎_wiki/BioJava_About.md

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---
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title: BioJava:About
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permalink: wikis/BioJava%3AAbout
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permalink: wiki/BioJava%3AAbout
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About BioJava

‎_wiki/BioJava_BioJavaInside.md

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---
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title: BioJava:BioJavaInside
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permalink: wikis/BioJava%3ABioJavaInside
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permalink: wiki/BioJava%3ABioJavaInside
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---
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**If you use BioJava in an application or publication please cite:**

‎_wiki/BioJava_BioJavaXDocs.md

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---
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title: BioJava:BioJavaXDocs
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permalink: wikis/BioJava%3ABioJavaXDocs
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permalink: wiki/BioJava%3ABioJavaXDocs
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---
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BioJavaX is not BioJava 3 is not BioJavaX.

‎_wiki/BioJava_CambridgeDiscussion.md

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---
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title: BioJava:CambridgeDiscussion
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permalink: wikis/BioJava%3ACambridgeDiscussion
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permalink: wiki/BioJava%3ACambridgeDiscussion
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---
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Background

‎_wiki/BioJava_Community_Portal.md

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---
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title: BioJava:Community Portal
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permalink: wikis/BioJava%3ACommunity_Portal
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permalink: wiki/BioJava%3ACommunity_Portal
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BioJava is an [open source](wp:open_source "wikilink") project developed

‎_wiki/BioJava_CooBook3_HmmerService.md

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---
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title: BioJava:CooBook3:HmmerService
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permalink: wikis/BioJava%3ACooBook3%3AHmmerService
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redirect_to: /_wikis/BioJava:CookBook3:HmmerService
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permalink: wiki/BioJava%3ACooBook3%3AHmmerService
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redirect_to: /wiki/BioJava:CookBook3:HmmerService
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---
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You should automatically be redirected to [BioJava:CookBook3:HmmerService](/_wikis/BioJava:CookBook3:HmmerService)
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You should automatically be redirected to [BioJava:CookBook3:HmmerService](/wiki/BioJava:CookBook3:HmmerService)

‎_wiki/BioJava_CookBook.md

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---
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title: BioJava:CookBook
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permalink: wikis/BioJava%3ACookBook
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redirect_to: /_wikis/BioJava:CookBook4.0
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permalink: wiki/BioJava%3ACookBook
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redirect_to: /wiki/BioJava:CookBook4.0
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---
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You should automatically be redirected to [BioJava:CookBook4.0](/_wikis/BioJava:CookBook4.0)
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You should automatically be redirected to [BioJava:CookBook4.0](/wiki/BioJava:CookBook4.0)

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