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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("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi");
featureRange.setMouseover("Start = " + j + ", stop = " + (j + 1));
}
try {
//create a PNG map.
CgviewIO.writeToPNGFile(cgview, "mouseover_links.png");
//for PNG and JPG files the mouseover and link information
//must 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 (http://www.bosrup.com/web/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, "mouseover_links.png", "png", "mouseover_links.html", useOverlib);
//create an SVG file. The mouseover and links are included in the SVG.
boolean embedFonts = true;
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,
"mouseover_links.svg",
embedFonts,
useCompression,
usePreviouslyDrawnLabels);
}
catch (Exception e) {
e.printStackTrace(System.err);
System.exit(1);
}
}
}
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