Skip to content

Commit

Permalink
Opacity slider added.
Browse files Browse the repository at this point in the history 
CSS fixes.
Metadata wizard added.
  • Loading branch information
@antalbalint
antalbalint committed Nov 4, 2015
1 parent 808a5aa commit 6341def
Show file tree
Hide file tree
Showing 20 changed files with 1,077 additions and 240 deletions.
11 changes: 11 additions & 0 deletions docs/install.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,16 @@ Label lines

Each line starting from the second contains a group object ID and a 1 for each annotation assigned to the group object or 0, otherwise.

Wizard
"""""""

Mineoatur also provides a graphical interface to provide the metadata required for a standard data file by starting the wizard from the command line:

java -jar <path_to_jar file> -metadata <data_file> <spearator_character>

.. image:: /images/metadata_wizard.png
:align: center

Options file
------------

Expand All @@ -81,6 +91,7 @@ The following options can be set:
* separator: character used to separate columns in the data and the label files. Default: \\t
* overwrite: whether to overwrite the current instance with the same name. Default: true

Please note that the different object caching methods of the operating systems might affect the performance of Neo4J so it is advised to set the amount of total memory after some experimenting. Under OSX, it is also advised to perform a memory clean from time to time since a lot of object is kept in the memory, leading to performance loss in the long run.

Generation from command line
-------------------------------------
Expand Down
8 changes: 8 additions & 0 deletions docs/scatterplot.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,14 @@ Since scatterplots can be overcrowded, it is might be hardd to find individual o

The highlighting can be reset by using the Reset link.

Setting the opacity
--------------------

To enable the visual inspection of crowded areas, once could use the opacity slider to set the right amount of transparency.

.. image:: /images/opacity.png
:align: center




Expand Down
206 changes: 194 additions & 12 deletions pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,19 +3,102 @@
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>
<profiles>
<profile>
<id>jar</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<project.build.artifcatID>maven-jar-plugin</project.build.artifcatID>
<project.packaging>jar</project.packaging>
<project.build.mainClass>org.mineotaur.application.MineotaurStandalone</project.build.mainClass>
<!--<project.build.exclude>org.mineotaur.application.MineotaurForServer</project.build.exclude>-->
<spring.boot.tomcat.scope>compile</spring.boot.tomcat.scope>
</properties>
</profile>
<profile>
<id>war</id>
<activation>
<property>
<name>pack</name>
<value>war</value>
</property>
</activation>
<properties>
<project.build.artifcatID>maven-war-plugin</project.build.artifcatID>
<project.packaging>war</project.packaging>
<project.build.mainClass>org.mineotaur.application.MineotaurForServer</project.build.mainClass>
<!--<project.build.exclude>org.mineotaur.application.MineotaurStandalone</project.build.exclude>-->
<spring.boot.tomcat.scope>provided</spring.boot.tomcat.scope>
<mineotaur.name>${mineotaurName}</mineotaur.name>
<project.build.exclude></project.build.exclude>
</properties>
</profile>
</profiles>
<packaging>${project.packaging}</packaging>
<build>

<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<executions>
<execution>
<id>copy</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>[ groupId ]</groupId>
<artifactId>[ artifactId ]</artifactId>
<version>[ version ]</version>
<type>[ packaging ]</type>
<classifier> [classifier - optional] </classifier>
<overWrite>[ true or false ]</overWrite>
<outputDirectory>[ output directory ]</outputDirectory>
<destFileName>[ filename ]</destFileName>
</artifactItem>
</artifactItems>
<!-- other configurations here -->
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.kuali.maven.plugins</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>2.0.1</version>
<executions>
<execution>
<phase>process-resources</phase>
<goals>
<goal>write-project-properties</goal>
</goals>
<configuration>
<outputFile>${project.basedir}/src/main/resources/application.properties</outputFile>
<include>mineotaur.name</include>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<artifactId>${project.build.artifcatID}</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>org.mineotaur.application.Mineotaur</mainClass>
<mainClass>${project.build.mainClass}</mainClass>
</manifest>
</archive>

<!--<excludes>
<exclude>${project.build.exclude}</exclude>
</excludes>-->
</configuration>
</plugin>

Expand Down Expand Up @@ -68,15 +151,99 @@
</plugin>
</plugins>
</build>
<properties>
<spring.boot.version>1.1.5.RELEASE</spring.boot.version>
<spring.version>4.0.6.RELEASE</spring.version>
<neo4j.version>2.1.8</neo4j.version>
</properties>
<groupId>Mineotaur</groupId>
<artifactId>Mineotaur</artifactId>
<version>1.0.1</version>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.1.5.RELEASE</version>

</parent>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.context</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.core</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.beans</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.jdbc</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.orm</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.transaction</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.asm</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.expression</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.aop</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.context.support</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-config</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-ldap</artifactId>
<version>4.0.2.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.ldap</groupId>
<artifactId>spring-ldap</artifactId>
<version>1.3.1</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>

<dependency>
Expand All @@ -87,8 +254,13 @@
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<version>1.1.5.RELEASE</version>

<!--<version>${spring.boot.version}</version>-->
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<version>${spring.boot.version}</version>
<scope>${spring.boot.tomcat.scope}</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
Expand Down Expand Up @@ -149,6 +321,14 @@
<groupId>org.springframework</groupId>
<artifactId>org.springframework.context</artifactId>
</exclusion>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.core</artifactId>
</exclusion>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.beans</artifactId>
</exclusion>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>org.springframework.jdbc</artifactId>
Expand Down Expand Up @@ -270,12 +450,14 @@
<artifactId>guice</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>org.springframework.ldap</groupId>
<artifactId>spring-ldap</artifactId>
<version>1.3.0.RELEASE</version>
<classifier>all</classifier>
</dependency>
<!--
<dependency>
<groupId>org.springframework.ldap</groupId>
<artifactId>spring-ldap</artifactId>
<version>1.3.0.RELEASE</version>
<classifier>all</classifier>
</dependency>
-->
<!-- Rather than use the specialized 4510 jar, use Final -->
<dependency>
<groupId>org.hibernate</groupId>
Expand Down

0 comments on commit 6341def

Please sign in to comment.