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rutgervandenbergrutgervandenberg
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Merge branch 'dev'
2 parents 07a1343 + 7c46631 commit 2b4ae79

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‎.travis.yml‎

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language: java
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jdk:
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- oraclejdk8
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- oraclejdk7
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- openjdk7
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notifications:
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webhooks:
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- http://octopull.rmhartog.me/api/travis/webhook

‎pom.xml‎

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<groupId>nl.tudelft</groupId>
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<artifactId>lifetiles</artifactId>
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<packaging>jar</packaging>
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<version>1.0-SNAPSHOT</version>
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<version>1.2-SNAPSHOT</version>
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<name>lifetiles</name>
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<url>http://maven.apache.org</url>
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<properties>
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<version>4.12</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.mockito</groupId>
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<artifactId>mockito-all</artifactId>
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<version>1.9.5</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.jgrapht</groupId>
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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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</dependencies>
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<build>
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<sourceDirectory>../src/main/java</sourceDirectory>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>findbugs-maven-plugin</artifactId>
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<version>3.0.1</version>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>3.3</version>
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<configuration>
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<!--
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Enables analysis which takes more memory but finds more bugs.
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If you run out of memory, changes the value of the effort element
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to 'Low'.
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-->
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<effort>Max</effort>
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<!-- Build doesn't fail if problems are found -->
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<failOnError>false</failOnError>
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<!-- Reports all bugs (other values are medium and max) -->
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<threshold>Low</threshold>
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<!-- Produces XML report -->
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<xmlOutput>true</xmlOutput>
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<!-- Configures the directory in which the XML report is created -->
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<findbugsXmlOutputDirectory>${project.build.directory}/findbugs</findbugsXmlOutputDirectory>
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<source>1.8</source>
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<target>1.8</target>
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</configuration>
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<executions>
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<!--
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Ensures that FindBugs inspects source code when project is compiled.
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-->
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<execution>
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<id>analyze-compile</id>
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<phase>compile</phase>
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<goals>
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<goal>check</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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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>findbugs-maven-plugin</artifactId>
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<version>3.0.1</version>
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<configuration>
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<!-- Enables analysis which takes more memory but finds more bugs. If
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you run out of memory, changes the value of the effort element to 'Low'. -->
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<effort>Max</effort>
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<!-- Build doesn't fail if problems are found -->
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<failOnError>false</failOnError>
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<!-- Reports all bugs (other values are medium and max) -->
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<threshold>Low</threshold>
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<!-- Produces XML report -->
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<xmlOutput>true</xmlOutput>
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<!-- Configures the directory in which the XML report is created -->
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<findbugsXmlOutputDirectory>${project.build.directory}/findbugs</findbugsXmlOutputDirectory>
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</configuration>
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<executions>
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<!-- Ensures that FindBugs inspects source code when project is compiled. -->
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<execution>
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<id>analyze-compile</id>
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<phase>compile</phase>
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<goals>
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<goal>check</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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<reporting>
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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-pmd-plugin</artifactId>
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<version>3.4</version>
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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-checkstyle-plugin</artifactId>
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<version>2.14</version>
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<configuration>
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<failOnViolation>false</failOnViolation>
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<!--<configLocation>checkstyle.xml</configLocation>-->
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>findbugs-maven-plugin</artifactId>
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<version>3.0.1</version>
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<configuration>
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<failOnError>false</failOnError>
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</configuration>
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</plugin>
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</plugins>
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</reporting>
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<reporting>
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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-pmd-plugin</artifactId>
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<version>3.4</version>
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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-checkstyle-plugin</artifactId>
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<version>2.14</version>
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<configuration>
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<failOnViolation>false</failOnViolation>
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<!--<configLocation>checkstyle.xml</configLocation> -->
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>findbugs-maven-plugin</artifactId>
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<version>3.0.1</version>
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<configuration>
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<failOnError>false</failOnError>
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</configuration>
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</plugin>
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</plugins>
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</reporting>
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</project>

‎src/main/java/nl/tudelft/lifetiles/controller/ViewController.java‎

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package nl.tudelft.lifetiles.controller;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Observable;
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import java.util.Set;
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import nl.tudelft.lifetiles.graph.Sequence;
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/**
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* @author Rutger van den Berg
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* Controls what the view modules display.
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*/
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public class ViewController extends Observable {
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/**
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* Map of all sequences currently loaded.
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*/
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private Map<String, Sequence> sequenceMap;
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/**
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* Set containing all sequences currently loaded.
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*/
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private Set<Sequence> allSequences;
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/**
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* Set containing the currently visible sequences.
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*/
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private Set<Sequence> visibleSequences;
27+
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/**
29+
* Creates a new viewcontroller.
30+
*
31+
* @param sequences
32+
* The current sequences.
33+
*/
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public ViewController(final Map<String, Sequence> sequences) {
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sequenceMap = sequences;
36+
allSequences = new HashSet<>();
37+
38+
for (Map.Entry<String, Sequence> map : sequenceMap.entrySet()) {
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Sequence seq = map.getValue();
40+
allSequences.add(seq);
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}
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visibleSequences = new HashSet<>(allSequences);
43+
}
44+
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/**
46+
* Sets the visible sequences in all views to the provided sequences.
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*
48+
* @param sequences
49+
* The sequences to set to visible.
50+
*/
51+
public final void setVisible(final Set<Sequence> sequences) {
52+
visibleSequences = sequences;
53+
if (visibleSequences.retainAll(allSequences)) {
54+
throw new IllegalArgumentException(
55+
"Attempted to set a non-existant sequence to visible");
56+
}
57+
setChanged();
58+
notifyObservers();
59+
}
60+
61+
/**
62+
* @return A set containing all visible sequences.
63+
*/
64+
public final Set<Sequence> getVisible() {
65+
return visibleSequences;
66+
}
67+
68+
}

‎src/main/java/nl/tudelft/lifetiles/graph/DefaultGraphParser.java‎

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package nl.tudelft.lifetiles.graph;
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3+
import java.io.File;
4+
import java.io.IOException;
5+
import java.net.URISyntaxException;
6+
import java.nio.file.Files;
7+
import java.util.HashMap;
8+
import java.util.HashSet;
9+
import java.util.Iterator;
10+
import java.util.Map;
11+
import java.util.Set;
12+
13+
/**
14+
* @author Rutger van den Berg
15+
*
16+
*/
17+
public class DefaultGraphParser implements GraphParser {
18+
/**
19+
* Index of starting position in the vertex descriptor.
20+
*/
21+
private static final int START_POS = 2;
22+
/**
23+
* Index of end position in the vertex descriptor.
24+
*/
25+
private static final int END_POS = 3;
26+
27+
/**
28+
* @param filename
29+
* The basename of the file to parse.
30+
* @param gfact
31+
* The graph factory to use to produce the graph.
32+
* @return a new graph containing the parsed information.
33+
*/
34+
@Override
35+
public final Graph<SequenceSegment> parseFile(final String filename,
36+
final GraphFactory<SequenceSegment> gfact) {
37+
Graph<SequenceSegment> graph = gfact.getGraph();
38+
parseVertices(filename, graph);
39+
parseEdges(filename, graph);
40+
return graph;
41+
}
42+
43+
/**
44+
* @param filename
45+
* name of the file to parse.
46+
* @param graph
47+
* The graph to which the edges will be added.
48+
*/
49+
private void parseEdges(final String filename,
50+
final Graph<SequenceSegment> graph) {
51+
try {
52+
File file = new File(this.getClass()
53+
.getResource("/" + filename + ".edge.graph").toURI());
54+
Iterator<String> it = Files.lines(file.toPath()).iterator();
55+
String line;
56+
while (it.hasNext()) {
57+
line = it.next();
58+
String[] edge = line.split(" ");
59+
graph.addEdge(Integer.parseInt(edge[0]),
60+
Integer.parseInt(edge[1]));
61+
}
62+
} catch (IOException e) {
63+
e.printStackTrace();
64+
} catch (URISyntaxException e) {
65+
e.printStackTrace();
66+
}
67+
}
68+
69+
/**
70+
* @param filename
71+
* name of the file to parse.
72+
* @param graph
73+
* The graph to which the edges will be added.
74+
*/
75+
private void parseVertices(final String filename,
76+
final Graph<SequenceSegment> graph) {
77+
Map<String, Sequence> sequences = new HashMap<>();
78+
try {
79+
File file = new File(this.getClass()
80+
.getResource("/" + filename + ".node.graph").toURI());
81+
Iterator<String> it = Files.lines(file.toPath()).iterator();
82+
while (it.hasNext()) {
83+
graph.addVertex(createSegment(it.next(), it.next(), sequences));
84+
}
85+
} catch (IOException e) {
86+
e.printStackTrace();
87+
} catch (URISyntaxException e) {
88+
e.printStackTrace();
89+
}
90+
}
91+
92+
/**
93+
* @param descriptor
94+
* Description line in the vertex file.
95+
* @param content
96+
* Content line in the vertex file.
97+
* @param sequences
98+
* A map containing sequences that have already been seen.
99+
* @return a new SequenceSegment
100+
*/
101+
private SequenceSegment createSegment(final String descriptor,
102+
final String content, final Map<String, Sequence> sequences) {
103+
if (!descriptor.startsWith(">")) {
104+
throw new IllegalArgumentException();
105+
}
106+
String[] desc = descriptor.split("\\|");
107+
String[] sources = desc[2].split(",");
108+
Set<Sequence> currentSequences = new HashSet<>();
109+
for (String sequencename : sources) {
110+
if (!sequences.containsKey(sequencename.trim())) {
111+
sequences.put(sequencename, new SequenceImplementation(
112+
sequencename));
113+
}
114+
currentSequences.add(sequences.get(sequencename));
115+
}
116+
117+
return new SequenceSegment(currentSequences,
118+
Integer.parseInt(desc[START_POS].trim()),
119+
Integer.parseInt(desc[END_POS].trim()), content.trim());
120+
121+
}
122+
123+
}

‎src/main/java/nl/tudelft/lifetiles/graph/Edge.java‎

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package nl.tudelft.lifetiles.graph;
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/**
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* @author Rutger van den Berg Interface for generic edge.
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* @param <V>
6+
* The type of vertex to use for this Edge.
7+
*/
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public interface Edge<V> {
9+
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}

‎src/main/java/nl/tudelft/lifetiles/graph/EdgeFactory.java‎

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package nl.tudelft.lifetiles.graph;
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/**
4+
* @author Rutger van den Berg
5+
* @param <V> The type of vertex to use.
6+
*/
7+
public interface EdgeFactory<V> {
8+
/**
9+
* @return A new edge from <code>v1</code> to <code>v2</code>
10+
* @param v1 The source vertex.
11+
* @param v2 The destination vertex.
12+
*/
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Edge<V> getEdge(final V v1, final V v2);
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}

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