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Merge pull request biojava#1 from biojava/master
Updating local fork
2 parents 1116677 + 0012c5f commit ad9b791

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‎.gitignore‎

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*.iml
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/*/target
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*.swp
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target
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target
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*~

‎.travis.yml‎

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language: java
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sudo: false

‎KEYS‎

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uid Spencer Bliven (Code Signing Key) <sbliven@ucsd.edu>
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sig 3 780796DF 2014-07-10 Spencer Bliven (Code Signing Key) <sbliven@ucsd.edu>
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sub 4096R/911B1DCC 2014-07-10 [expires: 2018-07-10]
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sig 780796DF 2014-07-10 Spencer Bliven (Code Signing Key) <sbliven@ucsd.edu>
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‎biojava-aa-prop/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">
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>4.1.1-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-aa-prop</artifactId>
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<name>biojava-aa-prop</name>
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<url>http://www.biojava.org</url>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**.java</exclude>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<configuration>
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<finalName>AAProperties</finalName>
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<archive>
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<manifest>
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<addClasspath>true</addClasspath>
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<mainClass>org.biojava.nbio.aaproperties.CommandPrompt</mainClass>
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</manifest>
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</archive>
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<descriptorRefs>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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<fileSets>
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<fileSet>
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<!-- TODO: use expresssions instead: ${project.build.sourceDirectory},
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etc -->
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<directory>${project.basedir}/src</directory>
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<useDefaultExcludes>true</useDefaultExcludes>
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</fileSet>
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</fileSets>
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</configuration>
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<executions>
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<execution>
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<id>make-assembly</id> <!-- this is used for inheritance merges -->
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<phase>package</phase> <!-- bind to the packaging phase -->
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</build>
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<dependencies>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>4.1.1-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>4.1.1-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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</dependency>
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<!-- binding for log4j2, scope=runTime set in parent pom -->
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-slf4j-impl</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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</dependencies>
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</project>

‎biojava-aa-prop/src/main/assembly/assembly.xml‎

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<assembly
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xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
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<id>AAProperties</id>
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<formats>
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<format>dir</format>
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</formats>
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<moduleSets>
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<moduleSet>
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<!-- <useAllReactorProjects>true</useAllReactorProjects> -->
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<includes>
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<include>org.biojava:biojava-core</include>
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<include>org.biojava:biojava-structure</include>
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</includes>
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<binaries>
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<outputDirectory>modules/${artifactId}</outputDirectory>
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<unpack>false</unpack>
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</binaries>
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</moduleSet>
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</moduleSets>
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<fileSets>
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<fileSet>
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<directory>${project.basedir}/src</directory>
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<outputDirectory>dev</outputDirectory>
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<useDefaultExcludes>true</useDefaultExcludes>
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</fileSet>
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</fileSets>
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</assembly>

‎biojava-aa-prop/src/main/java/demo/BioJavaAADemo.java‎

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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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*/
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package demo;
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import org.biojava.nbio.aaproperties.IPeptideProperties;
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import org.biojava.nbio.aaproperties.PeptidePropertiesImpl;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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/**
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* Created by andreas on 8/9/14.
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*/
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public class BioJavaAADemo {
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public static void main(String[] args) throws CompoundNotFoundException {
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ProteinSequence pSequence = new ProteinSequence("VLSPADKTNVKAAWGKVGAHAG");
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IPeptideProperties pp = new PeptidePropertiesImpl();
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System.out.println("Peptide Properties: " + pp.getIsoelectricPoint(pSequence));
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}
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}

biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/CommandPrompt.java renamed to biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java

Lines changed: 31 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,33 @@
1-
package org.biojava3.aaproperties;
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/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
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* terms of the GNU Lesser General Public Licence. This should
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* be distributed with the code. If you do not have a copy,
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* see:
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*
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* http://www.gnu.org/copyleft/lesser.html
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*
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* Copyright for this code is held jointly by the individual
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* authors. These should be listed in @author doc comments.
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*
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* For more information on the BioJava project and its aims,
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* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.aaproperties;
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import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava.nbio.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.io.*;
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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import java.io.File;
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import java.io.FileInputStream;
@@ -10,17 +39,6 @@
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import java.util.Map;
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import java.util.Map.Entry;
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13-
import org.biojava3.aaproperties.xml.AminoAcidCompositionTable;
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import org.biojava3.aaproperties.xml.CaseFreeAminoAcidCompoundSet;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava3.core.sequence.io.FastaReader;
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import org.biojava3.core.sequence.io.GenbankReader;
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import org.biojava3.core.sequence.io.GenericFastaHeaderParser;
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import org.biojava3.core.sequence.io.GenericGenbankHeaderParser;
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import org.biojava3.core.sequence.io.ProteinSequenceCreator;
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import org.biojava3.core.sequence.template.CompoundSet;
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public class CommandPrompt {
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@@ -232,7 +250,7 @@ private static void printHeader(PrintStream output, List<Character> propertyList
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}
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private static void compute(PrintStream output, String header, String sequence, String delimiter,
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AminoAcidCompositionTable aaTable, List<Character> propertyList, List<Character> specificList, int decimalPlace){
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AminoAcidCompositionTable aaTable, List<Character> propertyList, List<Character> specificList, int decimalPlace) throws CompoundNotFoundException{
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/*
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* 1 Molecular weight
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* 2 Absorbance (assumed Cys reduced and assume Cys to form cystines)

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