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‎CHANGELOG

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June 11, 2011 - Release 0.1.0
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* Initial version

‎LICENSE

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Copyright (C) 2011 by Ümit Seren
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.

‎README

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LDViewer - 0.1.0
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a GWT Widget for visualization of LD plots.
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//////////////////////////////////////////////////////////////////////////////
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License MIT (see included LICENSE)
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Original Author Ümit Seren
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Web Site -
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Github Repo. https://github.com/timeu/LDViewer
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Bug Tracking -
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Test Suite -
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//////////////////////////////////////////////////////////////////////////////
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ACKNOWLEDGMENT & THIRD PARTY LIBRARIES
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- processing.js by John Resig (http://processingjs.org)
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- Google Web Toolkit (GWT) by Google (http://code.google.com/webtoolkit/)
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//////////////////////////////////////////////////////////////////////////////
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INTRODUCTION
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LDViewer is a simple Google Web Toolkit (GWT) widget for visualization of LD plots (Heatmap)
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//////////////////////////////////////////////////////////////////////////////
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PLATFORM AND BROWSER COMPATIBILITY
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The LDViewer widget uses processing.js to visualize the LD plots.
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Both widgets rely on the HTML5 canvas element. For browser compatiblity refer to
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the documentation of both libraries.
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In general this widget works with browser that support the HTML5 canvas element.
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In case of Microsoft's IE this only applies to the Internet Explorer 9.0
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//////////////////////////////////////////////////////////////////////////////
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USAGE
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to be written
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//////////////////////////////////////////////////////////////////////////////

‎pom.xml

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<?xml version="1.0"?>
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<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>superpom</artifactId>
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<groupId>at.gmi.nordborglab</groupId>
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<version>0.1</version>
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</parent>
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<groupId>at.gmi.nordborglab.widgets</groupId>
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<artifactId>ldviewer</artifactId>
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<version>0.1.0-SNAPSHOT</version>
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<name>ldviewer</name>
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<url>http://maven.apache.org</url>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
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<gwtVersion>2.4.0</gwtVersion>
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<github.maven.repository>file:///srv/uemit.seren/repository/maven-repository/</github.maven.repository>
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</properties>
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<repositories>
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<repository>
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<id>nordborglab-snapshots</id>
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<url>https://github.com/timeu/maven-repos/raw/master/snapshots/</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>3.8.1</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.google.gwt</groupId>
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<artifactId>gwt-user</artifactId>
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<version>${gwtVersion}</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>at.gmi.nordborglab</groupId>
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<artifactId>processingjs</artifactId>
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<version>0.6.0</version>
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</dependency>
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</dependencies>
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<distributionManagement>
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<repository>
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<id>repo</id>
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<url>${github.maven.repository}/releases/</url>
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</repository>
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<snapshotRepository>
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<id>snapshot-repo</id>
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<url>${github.maven.repository}/snapshots/</url>
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</snapshotRepository>
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</distributionManagement>
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<organization>
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<name>GMI</name>
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<url>http://www.gmi.oeaw.ac.at</url>
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</organization>
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<build>
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<resources>
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<resource>
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<directory>src/main/java</directory>
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</resource>
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<resource>
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<directory>src/main/resources</directory>
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</resource>
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</resources>
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</build>
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<scm>
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<url>https://timeu@github.com/timeu</url>
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<connection>scm:git:https://timeu@github.com/timeu/LDViewer.git</connection>
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<developerConnection>scm:git:https://timeu@github.com/timeu/LDViewer.git</developerConnection>
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</scm>
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</project>

‎src/main/java/at/gmi/nordborglab/widgets/ldviewer/client/LDViewer.java

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package at.gmi.nordborglab.widgets.ldviewer.client;
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import at.gmi.nordborglab.processingjs.client.Processing;
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import at.gmi.nordborglab.widgets.ldviewer.client.datasource.impl.LDDataPoint;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.HasHighlightLDHandlers;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.HasMiddleMouseClickHandlers;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.HasUnhighlightLDHandlers;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.HighlightLDEvent;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.HighlightLDHandler;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.MiddleMouseClickEvent;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.MiddleMouseClickHandler;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.UnhighlightLDEvent;
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import at.gmi.nordborglab.widgets.ldviewer.client.event.UnhighlightLDHandler;
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import com.google.gwt.core.client.GWT;
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import com.google.gwt.core.client.JsArray;
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import com.google.gwt.core.client.JsArrayInteger;
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import com.google.gwt.core.client.JsArrayNumber;
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import com.google.gwt.core.client.Scheduler;
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import com.google.gwt.core.client.Scheduler.ScheduledCommand;
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import com.google.gwt.event.shared.GwtEvent;
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import com.google.gwt.resources.client.ClientBundle;
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import com.google.gwt.resources.client.ExternalTextResource;
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import com.google.gwt.resources.client.ResourceException;
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import com.google.gwt.uibinder.client.UiBinder;
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import com.google.gwt.uibinder.client.UiField;
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import com.google.gwt.user.client.ui.Composite;
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import com.google.gwt.user.client.ui.RequiresResize;
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import com.google.gwt.user.client.ui.Widget;
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import com.google.web.bindery.event.shared.HandlerRegistration;
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public class LDViewer extends Composite implements RequiresResize,
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HasUnhighlightLDHandlers,HasHighlightLDHandlers,
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HasMiddleMouseClickHandlers{
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private static LDViewerUiBinder uiBinder = GWT
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.create(LDViewerUiBinder.class);
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interface LDViewerUiBinder extends UiBinder<Widget, LDViewer> {
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}
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interface Resources extends ClientBundle
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{
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Resources INSTANCE = GWT.create(Resources.class);
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@Source("resources/LDViewer.pde")
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ExternalTextResource getCode();
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}
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@UiField Processing<LDViewerInstance> processing;
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private int start;
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private int end;
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private int zoomStart;
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private int zoomEnd;
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private int width=1024;
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private JsArrayInteger snps;
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private JsArray<JsArrayNumber> r2Values;
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private final ScheduledCommand layoutCmd = new ScheduledCommand() {
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public void execute() {
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layoutScheduled = false;
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forceLayout();
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}
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};
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private boolean layoutScheduled = false;
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public LDViewer() {
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initWidget(uiBinder.createAndBindUi(this));
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}
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public void load(final Runnable onLoad) throws ResourceException {
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Runnable onLoadCode = new Runnable()
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{
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@Override
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public void run() {
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if (!processing.isLoaded())
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return;
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processing.getInstance().setLayoutSize(getElement().getClientWidth(), false);
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if (onLoad != null)
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onLoad.run();
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}
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};
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processing.load(Resources.INSTANCE.getCode(), onLoadCode);
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}
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public void showLDValues(JsArrayInteger SNPs,JsArray<JsArrayNumber> r2Values,int start, int end) {
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this.snps = SNPs;
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this.r2Values = r2Values;
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this.start = start;
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this.end = end;
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this.zoomStart = start;
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this.zoomEnd = end;
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showPlot();
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}
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public void setZoom(int start, int end) {
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zoomStart = zoomStart >= start ? zoomStart : start;
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zoomEnd = zoomEnd <= end ? zoomEnd :end;
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showPlot();
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}
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public int getZoomStart() {
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return zoomStart;
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}
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public int getZoomEnd() {
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return zoomEnd;
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}
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public void resetZoom() {
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zoomStart = start;
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zoomEnd = end;
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showPlot();
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}
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private void showPlot() {
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if (!processing.isLoaded())
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return;
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int[] indices = getFilteredIndices(snps);
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processing.getInstance().setData(filterSNPs(snps,indices),filterR2Values(r2Values,indices),zoomStart,zoomEnd);
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}
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private JsArray<JsArrayNumber> filterR2Values(JsArray<JsArrayNumber> r2Values,int[] indices) {
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if (zoomStart == start && zoomEnd == end)
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return r2Values;
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JsArray<JsArrayNumber> filtered = JsArray.createArray().cast();
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for (int i = indices[0];i<indices[1];i++) {
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JsArrayNumber r2vals = r2Values.get(i);
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JsArrayNumber filteredR2Vals = JsArrayNumber.createArray().cast();
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for (int j=indices[0];j<r2vals.length();j++) {
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filteredR2Vals.push(r2vals.get(j));
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}
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filtered.push(filteredR2Vals);
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}
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return filtered;
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}
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private int[] getFilteredIndices(JsArrayInteger snps) {
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int[] indices = new int[2];
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indices[0] = 0;
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indices[1] = snps.length();
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if (zoomStart == start && zoomEnd == end) {
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return indices;
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}
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for (int i = 0;i<snps.length();i++)
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{
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if (zoomStart > start && indices[0] == 0 && snps.get(i) > zoomStart)
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indices[0] = i;
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if (zoomEnd < end && indices[1] == snps.length() && snps.get(i) > zoomEnd)
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indices[1] = i;
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}
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return indices;
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}
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private JsArrayInteger filterSNPs(JsArrayInteger snps,int[] indices) {
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if (zoomStart == start && zoomEnd == end)
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return snps;
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JsArrayInteger filtered = JsArrayInteger.createArray().cast();
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for (int i = indices[0];i<indices[1];i++) {
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filtered.push(snps.get(i));
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}
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return filtered;
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}
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public boolean isDataValid(int zoomStart,int zoomEnd) {
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return zoomStart >= start && zoomEnd < end;
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}
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public void forceLayout() {
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if (!isAttached())
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return;
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width = getElement().getClientWidth();
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if (processing.isLoaded()) {
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processing.getInstance().setLayoutSize(width,isVisible());
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}
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}
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private void scheduledLayout() {
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if (isAttached() && !layoutScheduled) {
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layoutScheduled = true;
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Scheduler.get().scheduleDeferred(layoutCmd);
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}
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}
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@Override
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public void onResize() {
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scheduledLayout();
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}
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public void setHighlightPosition(Integer position) {
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if (!processing.isLoaded())
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return;
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processing.getInstance().setHighlightPosition(position);
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}
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@Override
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public HandlerRegistration addHighlightLDHandler(HighlightLDHandler handler) {
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sinkEvents(HighlightLDEvent.getType());
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return addHandler(handler, HighlightLDEvent.getType());
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}
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@Override
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public HandlerRegistration addUnhighlightHandler(
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UnhighlightLDHandler handler) {
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sinkEvents(UnhighlightLDEvent.getType());
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return addHandler(handler, UnhighlightLDEvent.getType());
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}
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protected final void sinkEvents(GwtEvent.Type<?> type) {
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String callback = "";
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if (type == HighlightLDEvent.getType())
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callback = "highlightEvent";
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else if (type == UnhighlightLDEvent.getType())
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callback = "unhighlightEvent";
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else if (type == MiddleMouseClickEvent.getType())
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callback = "middleMouseClickEvent";
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processing.getInstance().sinkNativeEvent(this,callback);
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}
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public LDDataPoint[] getHighlightedDataPoints() {
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if (processing.getInstance() != null)
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return processing.getInstance().getHighlightedDataPoints();
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return null;
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}
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@Override
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public HandlerRegistration addMiddleMouseClickHandler(
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MiddleMouseClickHandler handler) {
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sinkEvents(MiddleMouseClickEvent.getType());
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return addHandler(handler, MiddleMouseClickEvent.getType());
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}
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}

‎src/main/java/at/gmi/nordborglab/widgets/ldviewer/client/LDViewer.ui.xml

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<!DOCTYPE ui:UiBinder SYSTEM "http://dl.google.com/gwt/DTD/xhtml.ent">
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<ui:UiBinder xmlns:ui="urn:ui:com.google.gwt.uibinder"
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xmlns:g="urn:import:com.google.gwt.user.client.ui"
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xmlns:pjs="urn:import:at.gmi.nordborglab.processingjs.client">
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<ui:style>
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.ldviewer {
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}
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</ui:style>
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<g:FlowPanel ui:field="container">
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<pjs:Processing ui:field="processing" addStyleNames="{style.ldviewer}"></pjs:Processing>
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</g:FlowPanel>
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</ui:UiBinder>

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