DNA String Comparison Project

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

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.

Here are the implementation and test classes:

• DNASearchDemo.java
• DNASequence.java
• MatchResult.java
• SequenceMatcher.java
• SequenceMatcherTest.java
• SequenceScoringAlgorithm.java
• ExamplePositionMatchAlgorithm.java
• AlgorithmComparisonManager.java

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

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Changes 16 March 2026

Added files:

• DNASearchComparison.java
• junit17.jar

To compile:: javac -cp junit17.jar:. *.java

To run:: java DNASearchComparison DNA_query.txt DNA_sequence_database.txt

To run the unit tests:: java -jar junit17.jar --class-path . --select-class SequenceMatcherTest

To produce API documentation:: javadoc -cp junit17.jar:. -d docs *.java

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Copyright (C) 2026 Dr. Jody Paul

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/.