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package annotationfilter; |
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import basefile.BASEFileReader; |
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import basefile.BASEFileSection; |
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import java.io.File; |
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/** |
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* The main class for AnnotationFilter. |
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* |
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* @author Johan Enell |
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* |
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*/ |
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public class Main |
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{ |
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|
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public static void main(String[] args) |
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{ |
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try |
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{ |
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BASEFileReader bfr = null; |
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if (args.length == 1) |
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{ |
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bfr = new BASEFileReader(new File(args[0])); |
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} |
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else if (args.length == 0) |
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{ |
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bfr = new BASEFileReader(new File("stdin.txt")); |
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} |
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else |
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{ |
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System.err.println("AnnotatinoFilter: invalid input given"); |
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System.exit(-1); |
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} |
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System.out.println("BASEfile"); |
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|
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Filter filter = new Filter(); |
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BASEFileSection section = bfr.readSection(true); |
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while (section != null) |
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{ |
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if (section.isType("annFilter settings")) |
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{ |
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filter.extractSettings(section); |
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} |
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else if (section.isType("assays")) |
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{ |
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filter.extractAssays(section, bfr); |
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} |
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else if (section.isType("spots")) |
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{ |
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filter.extractSpots(section, bfr); |
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} |
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section = bfr.readSection(); |
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} |
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} |
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catch (OutOfMemoryError e) |
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{ |
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System.err.println("No more memory in the java virtual machine. Try to start the application with the flag '-Xmx256m' or '-Xmx512m'. If you need even more memory, duplicate the digit"); |
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e.printStackTrace(); |
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System.exit(-1); |
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} |
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catch (Exception e) |
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{ |
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e.printStackTrace(); |
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System.exit(-1); |
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} |
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} |
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} |