List of loadAnnotation() Examples

Examples of loadAnnotation()

bnGUI.OBOES.loadAnnotation()
"ftp://" prefix. @param AnnotationFile the path to the file containing annotations @param ontology_name the name of the ontology for which to create accession-to-term and term-to-accession mappings @return true if the annotation was read in successfully; false otherwise. @see loadBackgroundAnnotation @see Ontology

Examples of bnGUI.OBOES.loadAnnotation()

        myOB.setMinimumCount(2);


        //This loads the data in
        myOB.loadOntology(ontology.getAbsolutePath(), "gene ontology");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "gene ontology");
        } catch (Exception ex) {
            System.out.println(ex.toString());
        }

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Examples of bnGUI.OBOES.loadAnnotation()


        //This loads the data in
        myOB.loadOntology(ontology.getAbsolutePath(), "gene ontology");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "gene ontology");
        } catch (Exception ex) {
            System.out.println(ex.toString());
        }

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Examples of bnGUI.OBOES.loadAnnotation()

        //This loads the data in
        myOB.loadOntology(ontology.getAbsolutePath(), "gene ontology");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "gene ontology");
        } catch (Exception ex) {
            System.out.println(ex.toString());
        }


        try {

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Examples of bnGUI.OBOES.loadAnnotation()

        myOB.setCorrectionMethod("benjamini_hochberg");
        myOB.setMaximumPvalue(.99);
        myOB.setMinimumCount(1);
        myOB.loadOntology(ontology.getAbsolutePath(), "geneo");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "geneo");
        } catch (Exception ex) {
            System.out.println(ex.toString());
        }

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Examples of bnGUI.OBOES.loadAnnotation()

        myOB.setMaximumPvalue(.99);
        myOB.setMinimumCount(1);
        myOB.loadOntology(ontology.getAbsolutePath(), "geneo");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "geneo");
        } catch (Exception ex) {
            System.out.println(ex.toString());
        }
        SimpleEnrichment[] enr = null;

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Examples of bnGUI.OBOES.loadAnnotation()

        myOB.setMinimumCount(1);
        myOB.loadOntology(ontology.getAbsolutePath(), "geneo");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "geneo");
        } catch (Exception ex) {
            System.out.println(ex.toString());
        }
        SimpleEnrichment[] enr = null;
        try {

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