import ca.ualberta.stothard.cgview.*; import java.io.*; public class CgviewTest0 implements CgviewConstants { public static void main( String args[] ) { int length = 9000; Cgview cgview = new Cgview(length); //some optional settings cgview.setWidth(600); cgview.setHeight(600); cgview.setBackboneRadius(160.0f); cgview.setTitle("Example"); cgview.setLabelPlacementQuality(10); cgview.setShowWarning(true); cgview.setLabelLineLength(8.0d); cgview.setLabelLineThickness(0.5f); //create a FeatureSlot to hold sequence features FeatureSlot featureSlot = new FeatureSlot(cgview, DIRECT_STRAND); //create random sequence features for (int i = 1; i <= 100; i = i + 1) { int j = Math.round((float)((float)(length - 2) * Math.random())) + 1; //a Feature to add to our FeatureSlot Feature feature = new Feature(featureSlot, "label"); //a single FeatureRange to add the Feature FeatureRange featureRange = new FeatureRange (feature, j, j + 1); featureRange.setDecoration(DECORATION_CLOCKWISE_ARROW); } try { //create a PNG file CgviewIO.writeToPNGFile(cgview, "test_maps/CgviewTest0.png"); //create an SVG file CgviewIO.writeToSVGFile(cgview, "test_maps/CgviewTest0.svg", false); } catch (IOException e) { e.printStackTrace(System.err); System.exit(1); } } }

import ca.ualberta.stothard.cgview.*; import java.io.*; import java.awt.*; public class CgviewTest1 implements CgviewConstants { public static void main( String args[] ) { int length = 12078; Cgview cgview = new Cgview(length); //some optional settings cgview.setWidth(600); cgview.setHeight(600); cgview.setBackboneRadius(140.0f); cgview.setTitle("Example 2"); cgview.setLabelPlacementQuality(5); cgview.setShowWarning(false); cgview.setLabelLineLength(15.0d); cgview.setLabelLineThickness(1.0f); cgview.setUseInnerLabels(INNER_LABELS_SHOW); cgview.setMoveInnerLabelsToOuter(true); cgview.setMinimumFeatureLength(1.0d); Legend legend = new Legend(cgview); legend.setPosition(LEGEND_UPPER_CENTER); LegendItem legendItem = new LegendItem(legend); legendItem.setLabel("An example"); legendItem.setFont(new Font("SansSerif", Font.BOLD + Font.ITALIC, 22)); //create FeatureSlots to hold sequence features FeatureSlot directSlot0 = new FeatureSlot(cgview, DIRECT_STRAND); FeatureSlot directSlot1 = new FeatureSlot(cgview, DIRECT_STRAND); FeatureSlot reverseSlot0 = new FeatureSlot(cgview, REVERSE_STRAND); //Features to add to the FeatureSlots Feature feature0 = new Feature(directSlot0, "A"); feature0.setColor(Color.blue); Feature feature1 = new Feature(directSlot1, "B"); feature1.setColor(Color.red); Feature feature2 = new Feature(reverseSlot0, "C"); feature2.setColor(Color.green); //create random sequence features for (int i = 1; i <= 100; i = i + 1) { int j = Math.round((float)((float)(length - 2) * Math.random())) + 1; int k = Math.round((float)((float)(length - 2) * Math.random())) + 1; int l = Math.round((float)((float)(length - 2) * Math.random())) + 1; //a single FeatureRange to add the Feature FeatureRange featureRange0 = new FeatureRange (feature0, j, j + 1); FeatureRange featureRange1 = new FeatureRange (feature1, k, k + 1); FeatureRange featureRange2 = new FeatureRange (feature2, l, l + 1); } try { //create a PNG file CgviewIO.writeToPNGFile(cgview, "test_maps/CgviewTest1.png"); //create an SVG file CgviewIO.writeToSVGFile(cgview, "test_maps/CgviewTest1.svg", false); } catch (IOException e) { e.printStackTrace(System.err); System.exit(1); } } }

import ca.ualberta.stothard.cgview.*; import java.io.*; import java.awt.*; public class CgviewTest2 implements CgviewConstants { public static void main( String args[] ) { int length = 9000; Cgview cgview = new Cgview(length); //some optional settings cgview.setWidth(600); cgview.setHeight(600); cgview.setBackboneRadius(140.0f); cgview.setBackboneColor(Color.red); cgview.setTitle("Example"); cgview.setLabelPlacementQuality(10); cgview.setShowWarning(true); cgview.setLabelLineLength(8.0d); cgview.setLabelLineThickness(1.5f); cgview.setRulerTextPadding(6.0f); //create a FeatureSlot to hold sequence features FeatureSlot featureSlot = new FeatureSlot(cgview, DIRECT_STRAND); //create random sequence features for (int i = 1; i <= 100; i = i + 1) { int j = Math.round((float) ((float) (length - 2) * Math.random())) + 1; //a Feature to add to our FeatureSlot Feature feature = new Feature(featureSlot, "label"); feature.setColor(Color.black); //a single FeatureRange to add the Feature FeatureRange featureRange = new FeatureRange(feature, j, j + 1); featureRange.setDecoration(DECORATION_CLOCKWISE_ARROW); } //zoom in cgview.setDesiredZoom(5.0d); cgview.setDesiredZoomCenter(100); cgview.setLabelLineLength(50.0d); try { //create a PNG file CgviewIO.writeToPNGFile(cgview, "test_maps/CgviewTest2.png"); //create an SVG file CgviewIO.writeToSVGFile(cgview, "test_maps/CgviewTest2.svg", false); } catch (IOException e) { e.printStackTrace(System.err); System.exit(1); } } }

import ca.ualberta.stothard.cgview.*; import java.io.*; import java.awt.*; public class CgviewTest3 implements CgviewConstants { public static void main( String args[] ) { int length = 9000; Cgview cgview = new Cgview(length); //some optional settings cgview.setWidth(750); cgview.setHeight(750); cgview.setBackboneRadius(150.0f); cgview.setBackboneColor(Color.blue); cgview.setTitle("Example"); cgview.setLabelPlacementQuality(5); cgview.setShowWarning(true); cgview.setLabelLineThickness(1.5f); cgview.setRulerTextPadding(6.0f); Legend legend = new Legend(cgview); legend.setPosition(LEGEND_UPPER_CENTER); LegendItem legendItem = new LegendItem(legend); legendItem.setLabel("Point to labels to view mouseover information."); legendItem.setFont(new Font("SansSerif", Font.PLAIN, 20)); legendItem.setTextAlignment(LEGEND_ITEM_ALIGN_CENTER); legendItem = new LegendItem(legend); legendItem.setLabel("Click on labels to test hyperlinks."); legendItem.setFont(new Font("SansSerif", Font.PLAIN, 20)); legendItem.setTextAlignment(LEGEND_ITEM_ALIGN_CENTER); //create a FeatureSlot to hold sequence features FeatureSlot featureSlot = new FeatureSlot(cgview, DIRECT_STRAND); //create random sequence features for (int i = 1; i <= 50; i = i + 1) { int j = Math.round((float)((float)(length - 2) * Math.random())) + 1; //a Feature to add to our FeatureSlot Feature feature = new Feature(featureSlot, "label"); feature.setColor(Color.gray); //a single FeatureRange to add the Feature FeatureRange featureRange = new FeatureRange (feature, j, j + 1); featureRange.setDecoration(DECORATION_CLOCKWISE_ARROW); //add a link and mouseover. Normally you would use a link to a specific //gene or protein featureRange.setHyperlink("https://www.ncbi.nlm.nih.gov/entrez/query.fcgi"); featureRange.setMouseover("Start = " + j + ", stop = " + (j + 1)); } try { //create a PNG map. CgviewIO.writeToPNGFile(cgview, "test_maps/CgviewTest3.png"); //for PNG and JPG files the mouseover and link information //can be placed in an image map. To generate the image map, //use the CgviewIO.writeHTMLFile() method after the image //has been written to file. //the overLIB javascript library (https://github.com/overlib/overlib) //can be used for displaying mouseovers. You will need to make overlib.js //available to the html file by placing overlib.js inside an 'includes' //directory boolean useOverlib = true; CgviewIO.writeHTMLFile( cgview, "CgviewTest3.png", "png", "test_maps/CgviewTest3.html", useOverlib ); //create an SVG file. The mouseover and links are included in the SVG. boolean useCompression = false; //The previous call to writeToPNGFile generated and positioned //the feature labels in a non-overlapping arrangement. //Label positioning can be slow. Supplying usePreviousDrawnLabels //set to true tells CgviewIO to use the previously arranged labels //instead of generating and positioning new labels. boolean usePreviouslyDrawnLabels = true; CgviewIO.writeToSVGFile( cgview, "test_maps/CgviewTest3.svg", useCompression, usePreviouslyDrawnLabels ); System.exit(0); } catch (IOException e) { e.printStackTrace(System.err); System.exit(1); } } }

• Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.