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Speedup #30

Merged
merged 22 commits into from
Mar 28, 2017
Merged

Speedup #30

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d23bbd9
Modified access to resource files so that it works on Windows and
altaite Feb 28, 2017
9c4052b
Replaced Jackson by MessagePack parsing code from Jmol. Jackson remains
altaite Mar 1, 2017
36d075f
Moving code from getNumBonds() to constructor results in 4-fold speedup
altaite Mar 1, 2017
5ce9fbc
FLOAT64 is now parsed as double, which corresponds to what Jackson did.
altaite Mar 1, 2017
7c10d24
Added a test comparing if results of Jackson and the new MessagePack
altaite Mar 5, 2017
c99723c
Moved MessagePack test into mmtf-codec.
altaite Mar 5, 2017
1570040
Version set to 1.05.
altaite Mar 6, 2017
3822c89
Renaming of mp package to quickmessagepackdeserialization.
altaite Mar 9, 2017
86c7a03
Zipped resource pdb_entry_type.txt. Replaced few other
altaite Mar 17, 2017
06455cb
Replaced zip with gz. Also corrected the loading of file using URL,
altaite Mar 18, 2017
5fc6b9a
Nicer code for reading text files as resources in gz. URL are used
altaite Mar 21, 2017
5f8057f
Minor formatting changes and removal of dead code in comments.
altaite Mar 22, 2017
acf8e1c
Message Pack parsing code from Bob Hanson's Jmol simplified and moved…
altaite Mar 23, 2017
032d454
PDB codes for testing now does not contain missing records (no codes …
altaite Mar 24, 2017
2999e37
Correction of versions to 1.0.4-SNAPSHOT.
altaite Mar 25, 2017
4f69622
Better API for Lines utility.
altaite Mar 26, 2017
ef9034f
Merge branch 'master' into speedup
altaite Mar 27, 2017
2d388ef
Better API for Lines utility. Also number of tested structures
altaite Mar 27, 2017
cd39c88
Merge origin/speedup into speedup
altaite Mar 27, 2017
457bf2c
Replaced Exception for ParseException in MessagePack decoding.
altaite Mar 28, 2017
07425c1
More appropriate name for test.
altaite Mar 28, 2017
72e468e
More descriptive method names in ObjectTree.
altaite Mar 28, 2017
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108 changes: 54 additions & 54 deletions mmtf-api/pom.xml
View file
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Original file line number Diff line number Diff line change
@@ -1,54 +1,54 @@
<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>
<parent>
<groupId>org.rcsb</groupId>
<artifactId>mmtf</artifactId>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>mmtf-api</artifactId>
<packaging>jar</packaging>
<name>mmtf-api</name>
<url>http://maven.apache.org</url>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
</dependencies>
<build>
<plugins>

<!-- Excluding demo package is required for avoiding namespace clashes
(demo package is in all modules) for signing the jar. See issue #387 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<debug>true</debug>
</configuration>
</plugin>
</plugins>
</build>

<reporting>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.3</version>
</plugin>
</plugins>
</reporting>


</project>
<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>
<parent>
<groupId>org.rcsb</groupId>
<artifactId>mmtf</artifactId>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>mmtf-api</artifactId>
<packaging>jar</packaging>
<name>mmtf-api</name>
<url>http://maven.apache.org</url>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
</dependencies>
<build>
<plugins>

<!-- Excluding demo package is required for avoiding namespace clashes
(demo package is in all modules) for signing the jar. See issue #387 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<debug>true</debug>
</configuration>
</plugin>
</plugins>
</build>

<reporting>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.3</version>
</plugin>
</plugins>
</reporting>


</project>
234 changes: 117 additions & 117 deletions mmtf-codec/pom.xml
View file
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Original file line number Diff line number Diff line change
@@ -1,117 +1,117 @@
<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>
<parent>
<groupId>org.rcsb</groupId>
<artifactId>mmtf</artifactId>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>mmtf-codec</artifactId>
<packaging>jar</packaging>

<name>mmtf-codec</name>
<url>http://maven.apache.org</url>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

<dependencies>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-api</artifactId>
<version>1.0.4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-serialization</artifactId>
<version>1.0.4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.4</version>
</dependency>
<!-- TEST DEPENEDENCIES -->
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
</dependency>
<dependency>
<groupId>uk.co.jemos.podam</groupId>
<artifactId>podam</artifactId>
</dependency>
<dependency>
<groupId>org.unitils</groupId>
<artifactId>unitils-core</artifactId>
</dependency>
<!-- junit managed by parent pom, don't set version or scope here -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>

<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>

</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>

<configuration>
<debug>true</debug>
</configuration>
</plugin>
</plugins>
</build>

<reporting>
<plugins>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.1</version>
<configuration>
<aggregate>true</aggregate>
<breakiterator>true</breakiterator>
<quiet>true</quiet>
<source>1.8</source>
<verbose>false</verbose>
<linksource>true</linksource>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.3</version>
</plugin>
</plugins>
</reporting>


</project>
<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>
<parent>
<groupId>org.rcsb</groupId>
<artifactId>mmtf</artifactId>
<version>1.0.4-SNAPSHOT</version>
</parent>
<artifactId>mmtf-codec</artifactId>
<packaging>jar</packaging>

<name>mmtf-codec</name>
<url>http://maven.apache.org</url>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

<dependencies>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-api</artifactId>
<version>1.0.4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-serialization</artifactId>
<version>1.0.4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.4</version>
</dependency>
<!-- TEST DEPENEDENCIES -->
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
</dependency>
<dependency>
<groupId>uk.co.jemos.podam</groupId>
<artifactId>podam</artifactId>
</dependency>
<dependency>
<groupId>org.unitils</groupId>
<artifactId>unitils-core</artifactId>
</dependency>
<!-- junit managed by parent pom, don't set version or scope here -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>

<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<!-- binding for log4j2, scope=runTime set in parent pom -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>

</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>

<configuration>
<debug>true</debug>
</configuration>
</plugin>
</plugins>
</build>

<reporting>
<plugins>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.1</version>
<configuration>
<aggregate>true</aggregate>
<breakiterator>true</breakiterator>
<quiet>true</quiet>
<source>1.8</source>
<verbose>false</verbose>
<linksource>true</linksource>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.3</version>
</plugin>
</plugins>
</reporting>


</project>
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