wrnap 0.7.0 → 0.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/wrnap/global/rna.rb +10 -0
- data/lib/wrnap/global/rna/context.rb +6 -2
- data/lib/wrnap/global/rna/extensions.rb +16 -0
- data/lib/wrnap/version.rb +1 -1
- metadata +3 -12
- data/.idea/.name +0 -1
- data/.idea/.rakeTasks +0 -7
- data/.idea/encodings.xml +0 -5
- data/.idea/misc.xml +0 -5
- data/.idea/modules.xml +0 -9
- data/.idea/scopes/scope_settings.xml +0 -5
- data/.idea/vcs.xml +0 -7
- data/.idea/workspace.xml +0 -169
- data/.idea/wrnap.iml +0 -49
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
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---
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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metadata.gz: ac1239c0ba7934c50ad98b76df47db8e55fece20
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4
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data.tar.gz: 968842380493afb6092cce95df09d3c4d61bb3c4
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5
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: d3ca46aa20984438b365a325d6a63d0b90f68d8bbd9e238cdfb2927685fe11360a696a9d78dc18d75118ba3a47a1a9e3de0524f0ebf19ec2854aa3620fc2f9cc
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7
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+
data.tar.gz: 0620bed745bc6bed2a2615792422bce97ce31b77e6ad12761dfec85716c8f3577a4c8f7ab7d70934e0cd7c4e49afc1ef8c06fc30a8b8eb9188a11a3582b08168
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data/lib/wrnap/global/rna.rb
CHANGED
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@@ -102,6 +102,12 @@ module Wrnap
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alias :empty_str :empty_structure
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+
def no_structure
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self.class.init_from_string(seq, nil, nil, name)
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end
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+
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alias :no_str :no_structure
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+
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def one_structure(structure_1)
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self.class.init_from_string(seq, structure_1.is_a?(Symbol) ? send(structure_1) : structure_1, nil, name)
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end
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@@ -137,6 +143,10 @@ module Wrnap
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Wrnap::Package.lookup(package_name).run(self, options)
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end
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def ==(other_rna)
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other_rna.kind_of?(Wrnap::Global::Rna) ? [seq, str_1, str_2] == [other_rna.seq, other_rna.str_1, other_rna.str_2] : super
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end
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+
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def method_missing(name, *args, &block)
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if (name_str = "#{name}") =~ /^run_\w+$/
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run(name_str.gsub(/^run_/, ""), *args)
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@@ -40,7 +40,7 @@ module Wrnap
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sequence: self.sequence,
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structure: options[:rna][:structure] || options[:rna][:str_1] || options[:rna][:str],
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second_structure: options[:rna][:second_structure] || options[:rna][:str_2],
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comment: options[:rna][:comment] || options[:rna][:name]
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comment: options[:rna][:comment] || options[:rna][:name] || identifier
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})
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remove_instance_variable(:@sequence)
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@@ -125,8 +125,12 @@ module Wrnap
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end
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end
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def identifier
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"%s %d %s %d" % [accession, from, plus_strand? ? ?+ : ?-, to]
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end
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+
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def inspect
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-
super.gsub(/((\w(::)?)+)>$/) { |_| "%s %
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super.gsub(/((\w(::)?)+)>$/) { |_| "%s %s>" % [identifier, $1] }
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end
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end
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end
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@@ -33,6 +33,10 @@ module Wrnap
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def shuffle(sequence, token_length = 2)
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Shuffle.new(sequence).shuffle(token_length)
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end
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def structure_from_bp_list(length, base_pairs)
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base_pairs.to_a.map(&:to_a).map(&:sort).inject("." * length) { |structure, (i, j)| structure.tap { structure[i] = ?(; structure[j] = ?) } }
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end
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end
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module InstanceMethods
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@@ -50,6 +54,18 @@ module Wrnap
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end
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module OneStructureBasedMethods
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def helices(structure)
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array = base_pairs(structure).sort_by(&:first).map(&:to_a)
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unless array.empty?
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array[1..-1].inject([[array.first]]) do |bins, (i, j)|
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bins.tap { bins[-1][-1] == [i - 1, j + 1] ? bins[-1] << [i, j] : bins << [[i, j]] }
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end
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else
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[]
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end
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end
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def max_bp_distance(structure)
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base_pairs(structure).count + ((structure.length - 3) / 2.0).floor
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end
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data/lib/wrnap/version.rb
CHANGED
metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: wrnap
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.9.0
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platform: ruby
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authors:
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- Evan Senter
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-
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date: 2014-07-03 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -130,15 +130,6 @@ extensions: []
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extra_rdoc_files: []
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files:
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- ".gitignore"
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- ".idea/.name"
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- ".idea/.rakeTasks"
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- ".idea/encodings.xml"
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- ".idea/misc.xml"
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- ".idea/modules.xml"
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- ".idea/scopes/scope_settings.xml"
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- ".idea/vcs.xml"
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- ".idea/workspace.xml"
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- ".idea/wrnap.iml"
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- Gemfile
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- LICENSE.md
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- README.md
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@@ -197,7 +188,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.
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rubygems_version: 2.3.0
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signing_key:
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specification_version: 4
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summary: A comprehensive wrapper (wRNApper) for various RNA CLI programs.
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data/.idea/.name
DELETED
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@@ -1 +0,0 @@
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1
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-
wrnap
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data/.idea/.rakeTasks
DELETED
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@@ -1,7 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<Settings><!--This file was automatically generated by Ruby plugin.
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You are allowed to:
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1. Remove rake task
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2. Add existing rake tasks
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To add existing rake tasks automatically delete this file and reload the project.
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-
--><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build wrnap-0.5.1.gem into the pkg directory" fullCmd="build" taksId="build" /><RakeTask description="Build and install wrnap-0.5.1.gem into system gems" fullCmd="install" taksId="install" /><RakeTask description="Create tag v0.5.1 and build and push wrnap-0.5.1.gem to Rubygems" fullCmd="release" taksId="release" /></RakeGroup></Settings>
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data/.idea/encodings.xml
DELETED
data/.idea/misc.xml
DELETED
data/.idea/modules.xml
DELETED
data/.idea/vcs.xml
DELETED
data/.idea/workspace.xml
DELETED
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@@ -1,169 +0,0 @@
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-
<?xml version="1.0" encoding="UTF-8"?>
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<project version="4">
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-
<component name="ChangeListManager">
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<list default="true" id="f215766d-a45c-47cc-a7d7-9487868cd8b4" name="Default" comment="">
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<change type="MODIFICATION" beforePath="$PROJECT_DIR$/lib/wrnap/package/base.rb" afterPath="$PROJECT_DIR$/lib/wrnap/package/base.rb" />
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</list>
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<ignored path="wrnap.iws" />
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<ignored path=".idea/workspace.xml" />
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<option name="TRACKING_ENABLED" value="true" />
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<option name="SHOW_DIALOG" value="false" />
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<option name="HIGHLIGHT_CONFLICTS" value="true" />
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<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
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<option name="LAST_RESOLUTION" value="IGNORE" />
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</component>
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<component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
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<component name="CreatePatchCommitExecutor">
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<option name="PATCH_PATH" value="" />
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</component>
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<component name="DaemonCodeAnalyzer">
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<disable_hints />
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</component>
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<component name="FavoritesManager">
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<favorites_list name="wrnap" />
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</component>
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<component name="FileEditorManager">
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<leaf>
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<file leaf-file-name="wrnap.rb" pinned="false" current="true" current-in-tab="true">
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<entry file="file://$PROJECT_DIR$/lib/wrnap.rb">
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<provider selected="true" editor-type-id="text-editor">
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<state vertical-scroll-proportion="-0.074179746" vertical-offset="52" max-vertical-offset="1183">
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<caret line="0" column="0" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
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<folding />
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</state>
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</provider>
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</entry>
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</file>
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</leaf>
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</component>
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<component name="FindManager">
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<FindUsagesManager>
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<setting name="OPEN_NEW_TAB" value="true" />
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</FindUsagesManager>
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</component>
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<component name="Git.Settings">
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<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
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</component>
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<component name="ProjectFrameBounds">
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<option name="y" value="22" />
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<option name="width" value="1280" />
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<option name="height" value="774" />
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</component>
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<component name="ProjectLevelVcsManager" settingsEditedManually="false">
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<OptionsSetting value="true" id="Add" />
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<OptionsSetting value="true" id="Remove" />
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<OptionsSetting value="true" id="Checkout" />
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<OptionsSetting value="true" id="Update" />
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<OptionsSetting value="true" id="Status" />
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<OptionsSetting value="true" id="Edit" />
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<ConfirmationsSetting value="0" id="Add" />
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<ConfirmationsSetting value="0" id="Remove" />
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</component>
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<component name="ProjectReloadState">
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<option name="STATE" value="0" />
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</component>
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<component name="ProjectView">
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<navigator currentView="ProjectPane" proportions="" version="1">
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<flattenPackages />
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<showMembers />
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<showModules />
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<showLibraryContents />
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<hideEmptyPackages />
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<abbreviatePackageNames />
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<autoscrollToSource />
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<autoscrollFromSource />
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<sortByType />
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</navigator>
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<panes>
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<pane id="ProjectPane">
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<subPane>
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<PATH>
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<PATH_ELEMENT>
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<option name="myItemId" value="wrnap" />
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<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
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</PATH_ELEMENT>
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</PATH>
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</subPane>
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</pane>
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<pane id="Scope" />
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<component name="PropertiesComponent">
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<property name="options.splitter.main.proportions" value="0.3" />
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<property name="options.splitter.details.proportions" value="0.2" />
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<property name="options.searchVisible" value="true" />
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<property name="FullScreen" value="false" />
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</component>
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<component name="RunManager">
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<component name="ShelveChangesManager" show_recycled="false" />
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<component name="SvnConfiguration">
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<configuration />
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<component name="TaskManager">
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<task active="true" id="Default" summary="Default task">
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<changelist id="f215766d-a45c-47cc-a7d7-9487868cd8b4" name="Default" comment="" />
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<created>1399483991383</created>
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<updated>1399483991383</updated>
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</task>
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<servers />
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<component name="ToolWindowManager">
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<frame x="0" y="22" width="1280" height="774" extended-state="6" />
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<editor active="false" />
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<layout>
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<window_info id="Messages" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.32968536" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
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<window_info id="Changes" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
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<window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
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<window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
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<window_info id="Database" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
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<window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
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<window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" weight="0.16796875" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
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