Package org.openbel.framework.compiler.DefaultPhaseThree

Examples of org.openbel.framework.compiler.DefaultPhaseThree.DocumentModificationResult

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        stageOutput(bldr.toString());

        stageOutput("Pruning protein families");
        boolean expand = withProteinFamilyExpansion();
        t1 = currentTimeMillis();
        DocumentModificationResult r = p3.pruneFamilies(expand, pfDoc, pn);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());

        if (r.isFailure()) {
            for (final String error : r.getErrors()) {
                stageError(error);
            }
            return pn;
        }
        for (final String warning : r.getWarnings()) {
            stageError(warning);
        }

        if (r.getRemainingStatements() == 0) {
            bldr.setLength(0);
            bldr.append("No statements remain after pruning");
            markEndStage(bldr);
            stageOutput(bldr.toString());
            return pn;
        }

        bldr.setLength(0);
        bldr.append(r.getRemainingStatements());
        bldr.append(" of ");
        bldr.append(r.getTotalStatements());
        bldr.append(" statements remain after pruning");
        stageOutput(bldr.toString());

        stageOutput("Inferring protein family relationships");
        t1 = currentTimeMillis();
        r = p3.inferFamilies(pfDoc, pn);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());

        if (r.isFailure()) {
            for (final String error : r.getErrors()) {
                stageError(error);
            }
            return pn;
        }
        for (final String warning : r.getWarnings()) {
            stageError(warning);
        }

        bldr.setLength(0);
        if (r.getDeltaStatements() == 0) {
            bldr.append("No statements inferred for protein families");
        } else {
            bldr.append(r.getDeltaStatements());
            bldr.append(" of ");
            bldr.append(r.getTotalStatements());
            bldr.append(" statements inferred for protein families");
        }
        stageOutput(bldr.toString());

        stageOutput("Compiling pruned protein families");
View Full Code Here
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        stageOutput(bldr.toString());

        stageOutput("Pruning named complexes");
        boolean expand = withNamedComplexExpansion();
        t1 = currentTimeMillis();
        DocumentModificationResult pr = p3.pruneComplexes(expand, ncDoc, pn);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());

        if (pr.isFailure()) {
            for (final String error : pr.getErrors()) {
                stageError(error);
            }
            return pn;
        }
        for (final String warning : pr.getWarnings()) {
            stageError(warning);
        }

        if (pr.getRemainingStatements() == 0) {
            bldr.setLength(0);
            bldr.append("No statements remain after pruning");
            markEndStage(bldr);
            stageOutput(bldr.toString());
            return pn;
        }

        bldr.setLength(0);
        bldr.append(pr.getRemainingStatements());
        bldr.append(" of ");
        bldr.append(pr.getTotalStatements());
        bldr.append(" statements remain after pruning");
        stageOutput(bldr.toString());

        stageOutput("Compiling named complexes proto-network");
        t1 = currentTimeMillis();
View Full Code Here
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        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());

        stageOutput("Pruning gene scaffolding");
        t1 = currentTimeMillis();
        DocumentModificationResult pr = p3.pruneGene(gsDoc, pn);
        t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());

        if (pr.isFailure()) {
            for (final String error : pr.getErrors()) {
                stageError(error);
            }
        }
        for (final String warning : pr.getWarnings()) {
            stageError(warning);
        }

        if (pr.getRemainingStatements() == 0) {
            bldr.setLength(0);
            bldr.append("No statements remain after pruning");
            markEndStage(bldr);
            stageOutput(bldr.toString());
            return pn;
        }

        bldr.setLength(0);
        bldr.append(pr.getRemainingStatements());
        bldr.append(" of ");
        bldr.append(pr.getTotalStatements());
        bldr.append(" statements remain after pruning");
        stageOutput(bldr.toString());

        stageOutput("Compiling gene scaffolding proto-network");
        t1 = currentTimeMillis();
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Related Classes of org.openbel.framework.compiler.DefaultPhaseThree.DocumentModificationResult

  • org.openbel.framework.tools.PhaseThreeApplication
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