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DNA Sequencing

Scaffolding for student projects that involve evaluating string comparison algorithms in the context of DNA matching

DNA String Comparison Project

Scaffolding for student projects that involve evaluating string comparison algorithms in the context of DNA matching.

How shall we compare algorithms?

There are really two different comparisons we want to think about:

How well an algorithm measures biological/string similarity
How efficiently the algorithm runs

Test Data Provided

DNA_sequence_database.txt - A sample database of labeled DNA sequences
DNA_query.txt - A sample query DNA sequence

Implementations

These are the implementation and test classes provided:

- AlgorithmComparisonManager.java
- DNASearchComparison.java
- DNASearchDemo.java
- DNASequence.java
- ExamplePositionMatchAlgorithm.java
- MatchResult.java
- SequenceMatcher.java
- SequenceMatcherTest.java
- SequenceScoringAlgorithm.java

ExamplePositionMatchAlgorithm is a simple implementation of a SequenceScoringAlgorithm as an example.

(Note: In this project we capitalize the acronym DNA fully in identifiers.)

To add another algorithm:

Create a class implementing SequenceScoringAlgorithm.

Define getName()
Define score(...)
Define higherScoreIsBetter() Add the algorithm to the list in DNASearchDemo.

Usage

To compile:

javac -cp junit17.jar:. *.java

To run:

java DNASearchComparison DNA_query.txt DNA_sequence_database.txt

To run unit tests:

java -jar junit17.jar --class-path . --select-class SequenceMatcherTest

To produce API documentation:

javadoc -cp junit17.jar:. -d docs *.java

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.