A B C D E F G H I J K L M N O P R S T U V W X Z

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offset - Variable in class org.schwiebert.abl4j.align.Align.StructureThread

operations - Variable in class org.schwiebert.abl4j.align.AllAlignment

operations - Variable in class org.schwiebert.abl4j.distance.EditDistance

options - Variable in class org.schwiebert.abl4j.cluster.Main

org.schwiebert.abl4j - package org.schwiebert.abl4j

org.schwiebert.abl4j.align - package org.schwiebert.abl4j.align

org.schwiebert.abl4j.align.methods - package org.schwiebert.abl4j.align.methods

org.schwiebert.abl4j.cluster - package org.schwiebert.abl4j.cluster

org.schwiebert.abl4j.cluster.methods - package org.schwiebert.abl4j.cluster.methods

org.schwiebert.abl4j.data - package org.schwiebert.abl4j.data

org.schwiebert.abl4j.data.impl.abl - package org.schwiebert.abl4j.data.impl.abl

org.schwiebert.abl4j.distance - package org.schwiebert.abl4j.distance

org.schwiebert.abl4j.examples - package org.schwiebert.abl4j.examples

org.schwiebert.abl4j.io - package org.schwiebert.abl4j.io

org.schwiebert.abl4j.random - package org.schwiebert.abl4j.random

org.schwiebert.abl4j.select - package org.schwiebert.abl4j.select

org.schwiebert.abl4j.select.methods - package org.schwiebert.abl4j.select.methods

org.schwiebert.abl4j.suffixtree - package org.schwiebert.abl4j.suffixtree

org.schwiebert.abl4j.tests - package org.schwiebert.abl4j.tests

org.schwiebert.abl4j.util - package org.schwiebert.abl4j.util

OUTPUT_ENCODING - Static variable in class org.schwiebert.abl4j.util.AblProperties

The encoding of the output stream.

OUTPUT_FILE - Static variable in class org.schwiebert.abl4j.util.AblProperties

The path to the output file.

OUTPUT_STREAM - Static variable in class org.schwiebert.abl4j.util.AblProperties

outputDirectory - Variable in class org.schwiebert.abl4j.tests.AbstractTest

outputHypotheses - Variable in class org.schwiebert.abl4j.select.Main

overallCppTime - Static variable in class org.schwiebert.abl4j.tests.AlignTests

overallCppTime - Static variable in class org.schwiebert.abl4j.tests.ClusterTests

overallCppTime - Static variable in class org.schwiebert.abl4j.tests.SelectTests

overallJavaTime - Static variable in class org.schwiebert.abl4j.tests.AlignTests

overallJavaTime - Static variable in class org.schwiebert.abl4j.tests.ClusterTests

overallJavaTime - Static variable in class org.schwiebert.abl4j.tests.SelectTests

Overlap - Class in org.schwiebert.abl4j.select

Helper class used to calculate overlaps.

Overlap() - Constructor for class org.schwiebert.abl4j.select.Overlap

overlap(IConstituent, IConstituent) - Static method in class org.schwiebert.abl4j.select.Overlap

Returns true if the ranges defined in IConstituent a and IConstituent b do overlap.

OverlapInTree - Class in org.schwiebert.abl4j.select

Helper class that represents an overlap in a tree.

OverlapInTree(ITree<?>) - Constructor for class org.schwiebert.abl4j.select.OverlapInTree

overrideProperties(String[]) - Method in class org.schwiebert.abl4j.util.ABLInitializer