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utilities release version 1.1
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@smdb21
smdb21 committed Sep 11, 2016
1 parent c163559 commit f7b97f7
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6 changes: 6 additions & 0 deletions .gitignore
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/target/
/.settings/
/logs/
.project
.classpath

170 changes: 170 additions & 0 deletions pom.xml
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>utilities</artifactId>
<name>utilities</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<distributionManagement>
<repository>
<id>internal</id>
<url>http://sealion.scripps.edu/archiva/repository/internal/</url>
</repository>
<snapshotRepository>
<id>snapshots</id>
<url>http://sealion.scripps.edu/archiva/repository/snapshots/</url>
</snapshotRepository>
</distributionManagement>
<dependencies>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>dbtoolkit</artifactId>
<version>4.2.5</version>
<exclusions>
<exclusion>
<groupId>batik</groupId>
<artifactId>batik-all</artifactId>
</exclusion>
<exclusion>
<artifactId>pdf-transcoder</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
<exclusion>
<artifactId>ssj</artifactId>
<groupId>umontreal.iro.lecuyer.gof</groupId>
</exclusion>
<exclusion>
<artifactId>jshortcut</artifactId>
<groupId>net.jimmc</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.jcraft</groupId>
<artifactId>jsch</artifactId>
<version>0.1.50</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-exec</artifactId>
<version>1.2</version>
</dependency>


<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>2.0.8</version>
<exclusions>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<version>1.5.5</version>
</dependency>

<dependency>
<groupId>psidev.psi.tools</groupId>
<artifactId>validator</artifactId>
<version>2.0.4</version>
<exclusions>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.5</version>
</dependency>
</dependencies>
<build>
<resources>
<!-- regular resource processsing for everything except logback.xml -->
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<!-- <plugin> -->
<!-- <artifactId>maven-assembly-plugin</artifactId> -->
<!-- <executions> -->
<!-- <execution> -->
<!-- <phase>package</phase> -->
<!-- <goals> -->
<!-- <goal>single</goal> -->
<!-- </goals> -->
<!-- </execution> -->
<!-- </executions> -->
<!-- <configuration> -->
<!-- <descriptorRefs> -->
<!-- <descriptorRef>jar-with-dependencies</descriptorRef> -->
<!-- </descriptorRefs> -->
<!-- </configuration> -->
<!-- </plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<organization>
<name>TSRI</name>
</organization>
<version>1.1</version>
<repositories>
<!-- UGent Genesis Maven 2 repository -->
<repository>
<id>genesis-maven2-repository</id>
<name>Genesis maven2 repository</name>
<url>http://genesis.UGent.be/maven2</url>
<layout>default</layout>
</repository>
</repositories>
<groupId>edu.scripps.yates</groupId>
</project>
104 changes: 104 additions & 0 deletions src/main/java/edu/scripps/yates/utilities/alignment/NeedlemanWunschSimple.java
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package edu.scripps.yates.utilities.alignment;

public class NeedlemanWunschSimple {
char[] mSeqA;
char[] mSeqB;
int[][] mD;
int mScore;
String mAlignmentSeqA = "";
String mAlignmentSeqB = "";

void init(char[] seqA, char[] seqB) {
mSeqA = seqA;
mSeqB = seqB;
mD = new int[mSeqA.length + 1][mSeqB.length + 1];
for (int i = 0; i <= mSeqA.length; i++) {
for (int j = 0; j <= mSeqB.length; j++) {
if (i == 0) {
mD[i][j] = -j;
} else if (j == 0) {
mD[i][j] = -i;
} else {
mD[i][j] = 0;
}
}
}
}

void process() {
for (int i = 1; i <= mSeqA.length; i++) {
for (int j = 1; j <= mSeqB.length; j++) {
int scoreDiag = mD[i - 1][j - 1] + weight(i, j);
int scoreLeft = mD[i][j - 1] - 1;
int scoreUp = mD[i - 1][j] - 1;
mD[i][j] = Math.max(Math.max(scoreDiag, scoreLeft), scoreUp);
}
}
}

void backtrack() {
int i = mSeqA.length;
int j = mSeqB.length;
mScore = mD[i][j];
while (i > 0 && j > 0) {
if (mD[i][j] == mD[i - 1][j - 1] + weight(i, j)) {
mAlignmentSeqA += mSeqA[i - 1];
mAlignmentSeqB += mSeqB[j - 1];
i--;
j--;
continue;
} else if (mD[i][j] == mD[i][j - 1] - 1) {
mAlignmentSeqA += "-";
mAlignmentSeqB += mSeqB[j - 1];
j--;
continue;
} else {
mAlignmentSeqA += mSeqA[i - 1];
mAlignmentSeqB += "-";
i--;
continue;
}
}
mAlignmentSeqA = new StringBuffer(mAlignmentSeqA).reverse().toString();
mAlignmentSeqB = new StringBuffer(mAlignmentSeqB).reverse().toString();
}

private int weight(int i, int j) {
if (mSeqA[i - 1] == mSeqB[j - 1]) {
return 1;
} else {
return -1;
}
}

void printMatrix() {
System.out.println("D =");
for (int i = 0; i < mSeqA.length + 1; i++) {
for (int j = 0; j < mSeqB.length + 1; j++) {
System.out.print(String.format("%4d ", mD[i][j]));
}
System.out.println();
}
System.out.println();
}

void printScoreAndAlignments() {
System.out.println("Score: " + mScore);
System.out.println("Sequence A: " + mAlignmentSeqA);
System.out.println("Sequence B: " + mAlignmentSeqB);
System.out.println();
}

public static void main(String[] args) {
char[] seqA = { 'A', 'C', 'G', 'T', 'C' };
char[] seqB = { 'A', 'G', 'T', 'C' };

NeedlemanWunschSimple nw = new NeedlemanWunschSimple();
nw.init(seqA, seqB);
nw.process();
nw.backtrack();

nw.printMatrix();
nw.printScoreAndAlignments();
}
}
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