pedvizapi

Install/Use

1. Download pedvizapi
   pedviz_0.15.zip (2d + 2.5d + Rpedviz) OR for *NIX pedviz_0.1.tgz (2d + 2.5d + Rpedviz)
2. Extract the archive
   bin...compiled classes
   doc...java-doc
   src...source code
   pedviz_0.15.jar...java api for 2d visualization
   pedviz_j3d_0.15.jar...java api for 2.5d visualization
   family_32.csv...example pedigree
   
3. Update the Java CLASSPATH
   More information can be found here
   
   or the classpath can be added during compilation
   javac -classpath \pedviz_0.15.jar ...
   
   execution:
   java -classpath \pedviz_0.15.jar ....
   
   
   For 2d visualization only pedviz_0.15.jar is needed.
   
4. Get started!
   
   1. Download GetStarted.java and tutorial_data.csv
   2. Compile
          javac -classpath .\pedviz_0.15.jar GetStarted.java
      Maybe you have to adjust the path.
   3. Executing
          java -classpath .\pedviz_0.15.jar;. GetStarted
      Maybe you have to adjust the path.

File Formats

Overview: Packages

Functions

	Graph graph = new Graph();
         // separator here ","
         CsvGraphLoader loader = new CsvGraphLoader("data.csv", ",");
         //mandatory basic field mapping
         loader.setSettings("PID", "MOM", "DAD");
	loader.load(graph);

	//creates a genotype symbol
	Symbol2D symbol = new SymbolGenotypes("marker1", "marker2"));

	//import files
	MerlinHaplotypes haplotypes = new MerlinHaplotypes("merlin.chr", "pedigree.map");

	//optional with error highlighting
	MerlinErrorChecking merlinErrorChecking = new MerlinErrorChecking("merlin.err");
	haplotypes.setErrors(merlinErrorChecking.getErrors());

	Database db = new HSQLDatabase();
	Graph graph = new Graph();
	if (db.connect("user", "pass", "connection-string")) {
                 //set the table name
		DatabaseGraphLoader loader = new DatabaseGraphLoader(db, "table");
                 //map id,mom id and dad id
                 loader.setSettings("pid-column", "mom-column", "dad-column");
                 //other fields will be loaded and can be used by added "Rules"
                 loader.load(graph);
		db.close();
	}

	Sugiyama s = new Sugiyama(graph);
	s.run();
	GraphView view = new GraphView2D(s.getLayoutedGraph());

	//integrate it into your Swing application
	frame.add(view.getComponent());

         //here random splitting is used
         Sugiyama s = new Sugiyama(graph, new RandomSplitter());
	s.run();
	GraphView view = new GraphView3D(s.getLayoutedGraph());

	//integrate it into your Swing application
	frame.add(view.getComponent());

	//import files
	MerlinHaplotypes haplotypes = new MerlinHaplotypes("merlin.chr", "pedigree.map");

	//optional with error highlighting
	MerlinErrorChecking merlinErrorChecking = new MerlinErrorChecking("merlin.err");
	haplotypes.setErrors(merlinErrorChecking.getErrors());

	//creates a haplotype symbol
	nodeview.addSymbol(new SymbolHaplotypes(haplotypes));

	ErrorChecking errorChecking = new ErrorChecking(graph);
	errorChecking.run();
	//simple output of all errors (see GraphError)
	System.out.println(errorChecking.getErrors());

	Vector log = GraphRepair.repair(graph)

	//creates fisheye-effect
	FisheyeEffect effect = new FisheyeEffect(5, 5, 2);
	effect.setMinSize(4f);
	effect.setAutoUpdateOnMove(false);
	effect.setAutoUpdateOnDrag(true);
	effect.setSpeed(3);

	graphView.setEffect(effect);
	graphView.setZoomEnabled(false);
	graphView.setMovingEnabled(false);

	nodeview.addSymbol(new SymbolSexUndesignated());
	//you can combine different symbols (see Symbol.getPriority())
	nodeview.addSymbol(new SymbolDeceased());

	graphView.addRule(new ShapeRule("sex", "2", new SymbolSexMale()));
	graphView.addRule(new ShapeRule("sex", "1", new SymbolSexFemale()));
	graphView.addRule(new ShapeRule("dead", "1", new SymbolDeceased()));
	graphView.addRule(new ShapeRule("adopted", "1", new SymbolAdopted()));

	nodeview.addSymbol(new SymbolSexUndesignated3d());
	//you can combine different symbols (see Symbol.getPriority())
	nodeview.addSymbol(new SymbolDeceased3d());

	graphView.addRule(new ShapeRule("sex", "1", new SymbolSexFemale3d()));
	graphView.addRule(new ShapeRule("sex", "2", new SymbolSexMale3d()));
	graphView.addRule(new ShapeRule("dead", "1", new SymbolDeceased3d()));
	graphView.addRule(new ShapeRule("adopted", "1", new SymbolAdopted3d()));

	//ShapeRule
	graphView.addRule(new ShapeRule("sex", "1", new SymbolSexFemale()));
	graphView.addRule(new ShapeRule(
		new SymbolQualitativeTrait("Energie", 0, 13, 6, 0)));

	//ColorRule
	graphView.addRule(new ColorRule("trait1", "1", Color.RED));

	//GradientRule
	HashMap colors = new HashMap();
	colors.put(0.0, Color.blue);
	colors.put(6.0, Color.green);
	colors.put(13.0, Color.red);
	graphView.addRule(new GradientRule("Energie", colors));

	nodeview.addHintAttribute("ID");
	nodeview.addHintAttribute("SEX");
	nodeview.addHintAttribute("...");

	graphView.addRule(new HintRule() {
		//use \n for new line and {line} for a horizontal line
		@Override
		public String getHint(NodeView n) {
			return n.getNode().getId() + "\n{line}\nsex: "
				+ n.getNode().getUserData("SEX")
				+ "\ndad: "
				+ n.getNode().getIdDad()
				+ "\nmom:"
				+ n.getNode().getIdMom();
		}
	});

	//mode = Highlighter.MATERNAL | Highlighter.PATERNAL | Highlighter.MATERNAL_AND_PATERNAL |
	//Highlighter.ANCESTORS | Highlighter.SUCCESSORS | Highlighter.SUCCESSORS_AND_ANCESTORS
	LODHighlighter lodHighlighter = new LODHighlighter(mode);
	graphView.addNodeListener(lodHighlighter);

	graphView.addNodeListener(new PathHighlighter());