60 lines
1.6 KiB
Ruby
60 lines
1.6 KiB
Ruby
# the linear index class implementation
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$LOAD_PATH << File.dirname(__FILE__)
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require "Index.rb"
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class LinearIndex < Index
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attr_accessor :nSeq, :sequences
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def initialize(file)
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super(file)
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@nSeq = @file.readInt()
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@sequences = Array.new()
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@nSeq.times {|index|
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@sequences.push(LISeqEntry.new(@file))
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}
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end
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def diff(otherIndex)
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diffHeader(otherIndex)
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if (otherIndex.type != @type)
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print "Indexes are not the same type (#{otherIndex.type} != #{@type})\n"
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return false
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end
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ret = false
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notInOther = @sequences.reject {|item|
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return true if !otherIndex.sequences.include?(item)
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item.diff(otherIndex.sequences[otherIndex.sequences.index(item)])
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}
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notInOther.pretty_print
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end
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end
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class LISeqEntry
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def initialize(file)
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@contig = file.readString()
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@binWidth = file.readInt()
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@binCount = file.readInt()
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@longestFeature = file.readInt()
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@maxBin = file.readInt()
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@totalBin = file.readInt()
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@startPositions = Array.new()
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@binCount.times { |index|
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@startPositions.push(file.readLong())
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}
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@finalPos = file.readLong()
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end
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# print a summary of the index characteristics
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def diff(otherLISeqEntry)
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self.instance_variables.each { |var|
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next if "#{var}" == "@file" or "#{var}" == "@sequences"
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puts "Other LISeqEntry doesn't define #{var}" if !(otherLISeqEntry.instance_variable_defined?(var))
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one = (self.instance_variable_get(var)).to_s
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two = (otherLISeqEntry.instance_variable_get(var)).to_s
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puts "otherLISeqEntry: type #{var} not equal, #{one} != #{two}" if one != two
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}
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end
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end
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