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abradleabradle
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Added a new MMTF parsing module in biojava
Updated the dependencies accordingly
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4 files changed

+493
-69
lines changed

4 files changed

+493
-69
lines changed

‎biojava-alignment/pom.xml‎

Lines changed: 37 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
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<?xml version="1.0" encoding="UTF-8"?>
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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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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>biojava</artifactId>
@@ -24,17 +25,18 @@
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<build>
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<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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<!-- Excluding demo package is required for avoiding namespace clashes
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(demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<dependencies>
@@ -53,28 +55,29 @@
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<groupId>org.biojava.thirdparty</groupId>
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<artifactId>forester</artifactId>
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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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<!-- logging dependencies (managed by parent pom, don't set versions or
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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>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>org.biojava</groupId>
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<artifactId>biojava-phylo</artifactId>
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<version>5.0.0-SNAPSHOT</version>
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</dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-phylo</artifactId>
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<version>5.0.0-SNAPSHOT</version>
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</dependency>
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</dependencies>
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</project>

‎biojava-structure/pom.xml‎

Lines changed: 50 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
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<?xml version="1.0" encoding="UTF-8"?>
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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/maven-v4_0_0.xsd">
2+
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>biojava</artifactId>
@@ -19,6 +20,18 @@
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<dependencies>
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<dependency>
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<groupId>org.rcsb</groupId>
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<artifactId>mmtf-api</artifactId>
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<version>0.0.1-SNAPSHOT</version>
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<scope>compile</scope>
28+
</dependency>
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<dependency>
30+
<groupId>org.rcsb</groupId>
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<artifactId>mmtf-decoder</artifactId>
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<version>0.0.1-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
@@ -37,35 +50,36 @@
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<artifactId>vecmath</artifactId>
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<version>1.3.1</version>
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</dependency>
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<dependency>
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<groupId>org.jgrapht</groupId>
43-
<artifactId>jgrapht-core</artifactId>
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<version>0.9.1</version>
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<artifactId>jgrapht-core</artifactId>
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<version>0.9.1</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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<!-- logging dependencies (managed by parent pom, don't set versions or
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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.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>
64-
</dependency>
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<!-- Testing related dependencies -->
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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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<!-- Testing related dependencies -->
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<dependency>
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<groupId>junit</groupId>
@@ -93,16 +107,17 @@
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<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
105-
</plugin>
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<!-- Excluding demo package is required for avoiding namespace clashes
111+
(demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
113+
<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</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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