Package org.openbel.framework.common.model

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

453
454
455
456
457
458
459
460
461
462
463
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        long t2 = currentTimeMillis();
        Document pfDoc = output.getDocument();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
View Full Code Here
677
678
679
680
681
682
683
684
685
686
687
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        long t2 = currentTimeMillis();
        Document ncDoc = output.getDocument();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
View Full Code Here
876
877
878
879
880
881
882
883
884
885
886
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        long t2 = currentTimeMillis();
        Document gsDoc = output.getDocument();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
View Full Code Here
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
            throws ProtoNetworkError {
        final Index resourceIndex = ResourceIndex.INSTANCE.getIndex();
        final ResourceLocation pfResource = resourceIndex
                .getProteinFamilyResource();

        final Document pfdoc = readResource(pfResource);
        p3.pruneFamilies(false, pfdoc, orthoPn);
        p3.inferFamilies(pfdoc, orthoPn);
        final ProtoNetwork pfpn = p3.compile(pfdoc);
        p3.merge(orthoPn, pfpn);

        final ResourceLocation ncResource = resourceIndex
                .getNamedComplexesResource();
        final Document ncdoc = readResource(ncResource);
        p3.pruneComplexes(false, ncdoc, orthoPn);
        final ProtoNetwork ncpn = p3.compile(ncdoc);
        p3.merge(orthoPn, ncpn);

        final ResourceLocation gsResource = resourceIndex
                .getGeneScaffoldingResource();
        final Document gsdoc = readResource(gsResource);
        p3.pruneGene(gsdoc, orthoPn);
        final ProtoNetwork gspn = p3.compile(gsdoc);
        p3.merge(orthoPn, gspn);
    }
View Full Code Here
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
        p3.merge(orthoPn, gspn);
    }

    private ProtoNetwork pruneResource(final ProtoNetwork pn,
            final ResourceLocation resource) {
        Document doc = readResource(resource);

        long t1 = currentTimeMillis();

        stageOutput(format("Processing orthology document '%s'", doc.getName()));
        p3.pruneOrthologyDocument(doc, pn);
        final ProtoNetwork opn = p3.compile(doc);

        long t2 = currentTimeMillis();
View Full Code Here
1152
1153
1154
1155
1156
1157
1158
1159
            return null; // Dead code
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        Document doc = output.getDocument();
        return doc;
    }
View Full Code Here
128
129
130
131
132
133
134
135
136
137
138
        } catch (ValidationError ve) {
            reportable.error(ve.getUserFacingMessage());
            bail(ExitCode.NO_VALID_DOCUMENTS);
        }

        Document document = null;
        try {
            document = convert(file);
        } catch (ConversionError ce) {
            reportable.error("Failed converting file to BEL model");
            reportable.error(ce.getUserFacingMessage());
View Full Code Here
172
173
174
175
176
177
178
179
180
181
182
        }
    }

    private Document convert(final File f) throws ConversionError {
        try {
            Document document = converter.toCommon(f);
            return document;
        } catch (JAXBException e) {
            final String name = f.getAbsolutePath();
            final String msg = e.getMessage();
            final Throwable cause = e;
View Full Code Here
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
        output.addValidationErrors(validator.validateWithErrors(file));
        if (output.hasValidationErrors()) {
            return output;
        }

        Document d = null;
        try {
            d = converter.toCommon(file);
            output.setDocument(d);
        } catch (JAXBException e) {
            final String name = file.toString();
            final String msg = e.getMessage();
            final Throwable cause = e;
            output.setConversionError(new ConversionError(name, msg, cause));
            return output;
        } catch (IOException e) {
            final String name = file.toString();
            final String msg = e.getMessage();
            final Throwable cause = e;
            output.setConversionError(new ConversionError(name, msg, cause));
            return output;
        }

        List<AnnotationDefinition> definitions = d.getDefinitions();
        if (definitions == null) {
            return output;
        }

        verifyAnnotations(output, d, definitions);
View Full Code Here
197
198
199
200
201
202
203
204
205
206
207
208
209
210
                output.addValidationError(ve);
            }
            return output;
        }

        final Document d = belConverter.toCommon(rslts.getDocument());
        output.setDocument(d);

        List<AnnotationDefinition> definitions = d.getDefinitions();
        if (definitions == null) {
            return output;
        }

        verifyAnnotations(output, d, definitions);
View Full Code Here
TOP

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

  • org.openbel.framework.common.bel.converters.BELDocumentConverter
  • org.openbel.framework.common.bel.converters.BELDocumentConverterTest
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.xbel.converters.DocumentConverter
  • org.openbel.framework.compiler.PhaseOneImpl
  • org.openbel.framework.core.protonetwork.ProtoNetworkMerge_CommutativeTest
  • org.openbel.framework.tools.Backtrack
  • org.openbel.framework.tools.BelCheck
  • org.openbel.framework.tools.DocumentConverter
  • org.openbel.framework.tools.PhaseOneApplication
    • 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.