Package org.openbel.framework.common.model

Examples of org.openbel.framework.common.model.Header

35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
    /**
     * Tests that statement triples in two {@link Document documents} will
     * produce the same merged result regardless of document sequence.
     */
    public void commutative_simple() {
        Document a = make_document(new Header("Doc 1", "Doc 1", "1.0"),
                new NamespaceGroup(URL, null),
                parse("g(AKT2) -> r(AKT3)"),
                parse("p(AKT1) => complex(p(DUSP1), p(WRN))"));
        Document b = make_document(new Header("Doc 2", "Doc 2", "1.0"),
                new NamespaceGroup(URL, null),
                parse("m(AKT1) =| p(AKT2)"),
                parse("cat(g(AKT2)) -| p(PARP1)"));

        // merge in different orders
View Full Code Here
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
    /**
     * Tests that subject-only statements in two {@link Document documents}
     * will produce the same merged result regardless of document sequence.
     */
    public void commutative_subject_only() {
        Document a = make_document(new Header("Doc 1", "Doc 1", "1.0"),
                new NamespaceGroup(URL, null),
                parse("r(AKT3)"),
                parse("p(AKT1)"));
        Document b = make_document(new Header("Doc 2", "Doc 2", "1.0"),
                new NamespaceGroup(URL, null),
                parse("m(AKT1)"),
                parse("g(AKT2)"));

        // merge in different orders
View Full Code Here
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
    /**
     * Tests that nested statements in two {@link Document documents} will
     * produce the same merged result regardless of document sequence.
     */
    public void commutative_nested() {
        Document a = make_document(new Header("Doc 1", "Doc 1", "1.0"),
                new NamespaceGroup(URL, null),
                parse("r(AKT3) => (g(PARP1) -| cat(p(AKT2)))"),
                parse("p(AKT1) -> (kin(p(PARP1)) -| p(AKT3))"));
        Document b = make_document(new Header("Doc 2", "Doc 2", "1.0"),
                new NamespaceGroup(URL, null),
                parse("m(AKT1) => (g(PARP1) -| p(AKT2))"),
                parse("g(AKT2) -> (r(AKT1) => p(PARP1))"));

        // merge in different orders
View Full Code Here
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
        String name = source.getName();
        String description = source.getDescription();
        String version = source.getVersion();

        // Destination type
        Header dest = new Header(name, description, version);

        if (source.isSetAuthorGroup()) {
            List<String> author = source.getAuthorGroup().getAuthor();
            dest.setAuthors(author);
        }

        if (source.isSetLicenseGroup()) {
            List<String> license = source.getLicenseGroup().getLicense();
            dest.setLicenses(license);
        }

        String copyright = source.getCopyright();
        dest.setCopyright(copyright);

        String disclaimer = source.getDisclaimer();
        dest.setDisclaimer(disclaimer);

        String contactInfo = source.getContactInfo();
        dest.setContactInfo(contactInfo);

        return dest;
    }
View Full Code Here
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
    @Override
    public Header convert(BELDocumentHeader bdh) {
        String name = bdh.getName();
        String desc = bdh.getDescription();
        String version = bdh.getVersion();
        Header h = new Header(name, desc, version);
        h.setAuthors(Arrays.asList(bdh.getAuthor()));
        h.setContactInfo(bdh.getContactInfo());
        h.setCopyright(bdh.getCopyright());
        h.setDisclaimer(bdh.getDisclaimer());
        h.setLicenses(bdh.getLicense() == null ? null : Arrays.asList(bdh
                .getLicense()));

        return h;
    }
View Full Code Here
72
73
74
75
76
77
78
79
80
81
82
    public Document convert(BELDocument bd) {
        if (bd == null) {
            return null;
        }

        final Header header = dhc.convert(bd.getDocumentHeader());

        // handle annotation definitions
        Set<BELAnnotationDefinition> badlist = bd.getAnnotationDefinitions();
        List<AnnotationDefinition> adlist = null;
        if (badlist != null) {
View Full Code Here
164
165
166
167
168
169
170
171
172
173
174
                }
            }
            xd.setAnnotationDefinitionGroup(xadGroup);
        }

        Header header = source.getHeader();
        HeaderConverter hConverter = new HeaderConverter();
        // Defer to HeaderConverter
        xd.setHeader(hConverter.convert(header));

        NamespaceGroup nsGroup = source.getNamespaceGroup();
View Full Code Here
TOP

Related Classes of org.openbel.framework.common.model.Header

  • org.openbel.framework.common.bel.converters.BELDocumentConverter
  • org.openbel.framework.common.bel.converters.BELDocumentHeaderConverter
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.xbel.converters.DocumentConverter
  • org.openbel.framework.common.xbel.converters.HeaderConverter
  • org.openbel.framework.core.protonetwork.ProtoNetworkMerge_CommutativeTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.