Examples with Component org.powerbot.script.rt4.Component used on opensource projects

Example 6 with Component

use of org.powerbot.script.rt4.Component in project libSBOLj by SynBioDex.

the class ComponentDefinitionOutput method createComponentDefinitionOutput.

public static SBOLDocument createComponentDefinitionOutput() throws SBOLValidationException {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    SBOLDocument document = new SBOLDocument();
    document.setTypesInURIs(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    document.setDefaultURIprefix(prURI);
    Sequence seqpTetR = document.createSequence("BBa_R0040", "", "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqRbs = document.createSequence("BBa_B0034", "", "aaagaggagaaa", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqCds = document.createSequence("BBa_C0062", "", "atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattctatggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgatcctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaatgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgcttagttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctctagttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggcatgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaatgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaataacactgatagtgctagtgtagatcac", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqTer = document.createSequence("BBa_B0015", "", "ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    Sequence seqPluxR = document.createSequence("BBa_R0062", "", "acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    ComponentDefinition pTetR = document.createComponentDefinition("BBa_R0040", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    pTetR.addRole(SequenceOntology.PROMOTER);
    pTetR.setName("pTetR");
    pTetR.setDescription("TetR repressible promoter");
    pTetR.addSequence(seqpTetR.getIdentity());
    ComponentDefinition rbs = document.createComponentDefinition("BBa_B0034", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    rbs.addRole(SequenceOntology.RIBOSOME_ENTRY_SITE);
    rbs.setName("BBa_B0034");
    rbs.setDescription("RBS based on Elowitz repressilator");
    rbs.addSequence(seqRbs.getIdentity());
    ComponentDefinition cds = document.createComponentDefinition("BBa_C0062", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    cds.addRole(SequenceOntology.CDS);
    cds.setName("luxR");
    cds.setDescription("luxR coding sequence");
    cds.addSequence(seqCds.getIdentity());
    ComponentDefinition ter = document.createComponentDefinition("BBa_B0015", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    ter.addRole(URI.create("http://identifiers.org/so/SO:0000141"));
    ter.setName("BBa_B0015");
    ter.setDescription("Double terminator");
    ter.addSequence(seqTer.getIdentity());
    ComponentDefinition pluxR = document.createComponentDefinition("BBa_R0062", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    // 
    pluxR.addRole(SequenceOntology.PROMOTER);
    pluxR.setName("pLuxR");
    pluxR.setDescription("LuxR inducible promoter");
    pluxR.addSequence(seqPluxR.getIdentity());
    ComponentDefinition device = document.createComponentDefinition("BBa_F2620", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    // biological region
    device.addRole(URI.create("http://identifiers.org/so/SO:00001411"));
    device.setName("BBa_F2620");
    device.setDescription("3OC6HSL -> PoPS Receiver");
    Component comPtetR = device.createComponent("pTetR", AccessType.PUBLIC, pTetR.getIdentity());
    Component comRbs = device.createComponent("rbs", AccessType.PUBLIC, rbs.getIdentity());
    Component comCds = device.createComponent("luxR", AccessType.PUBLIC, cds.getIdentity());
    Component comTer = device.createComponent("ter", AccessType.PUBLIC, ter.getIdentity());
    Component comPluxR = device.createComponent("pLuxR", AccessType.PUBLIC, pluxR.getIdentity());
    int start = 1;
    int end = seqPluxR.getElements().length();
    SequenceAnnotation anno = device.createSequenceAnnotation("anno1", "location1", start, end, OrientationType.INLINE);
    anno.setComponent(comPtetR.getIdentity());
    start = end + 1;
    end = seqRbs.getElements().length() + end + 1;
    SequenceAnnotation anno2 = device.createSequenceAnnotation("anno2", "location2", start, end, OrientationType.INLINE);
    anno2.setComponent(comRbs.getIdentity());
    start = end + 1;
    end = seqCds.getElements().length() + end + 1;
    SequenceAnnotation anno3 = device.createSequenceAnnotation("anno3", "location3", start, end, OrientationType.INLINE);
    anno3.setComponent(comCds.getIdentity());
    start = end + 1;
    end = seqTer.getElements().length() + end + 1;
    SequenceAnnotation anno4 = device.createSequenceAnnotation("anno4", "location4", start, end, OrientationType.INLINE);
    anno4.setComponent(comTer.getIdentity());
    start = end + 1;
    end = seqPluxR.getElements().length() + end + 1;
    SequenceAnnotation anno5 = device.createSequenceAnnotation("anno5", "location5", start, end, OrientationType.INLINE);
    anno5.setComponent(comPluxR.getIdentity());
    return document;
}

Example 7 with Component

use of org.powerbot.script.rt4.Component in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method addSubComponents.

private static void addSubComponents(SBOLDocument document, ComponentDefinition componentDef, List<ComponentDefinition> subComponents) throws Exception {
    int i = 1;
    int start = 0;
    int end = 0;
    for (ComponentDefinition subComponent : subComponents) {
        Component component = componentDef.createComponent(subComponent.getDisplayId(), AccessType.PUBLIC, subComponent.getIdentity());
        start = end + 1;
        end = start + getSequenceLength(document, subComponent);
        SequenceAnnotation annotation = componentDef.createSequenceAnnotation("anno" + i, "location" + i, start, end, OrientationType.INLINE);
        annotation.setComponent(component.getIdentity());
        i++;
    }
}

Example 8 with Component

use of org.powerbot.script.rt4.Component in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method getSequenceLength.

private static int getSequenceLength(SBOLDocument document, ComponentDefinition componentDef) throws Exception {
    if (componentDef.getSequences() != null && componentDef.getSequences().size() > 0) {
        Sequence sequence = componentDef.getSequences().iterator().next();
        return sequence.getElements().length();
    } else {
        int total = 0;
        for (SequenceAnnotation annotation : componentDef.getSequenceAnnotations()) {
            if (annotation.getComponent() != null) {
                Component component = annotation.getComponent();
                ComponentDefinition subComponentDef = component.getDefinition();
                total = total + getSequenceLength(document, subComponentDef);
            } else {
                throw new Exception("Can't get sequence length for an incomplete design");
            }
        }
        return total;
    }
}

Example 9 with Component

use of org.powerbot.script.rt4.Component in project libSBOLj by SynBioDex.

the class SequenceConstraintOutput method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_K174004", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("pspac promoter");
    promoter.setDescription("LacI repressible promoter");
    ComponentDefinition constPromoter = document.createComponentDefinition("pspac", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    constPromoter.addRole(SequenceOntology.PROMOTER);
    constPromoter.setName("constitutive promoter");
    constPromoter.setDescription("pspac core promoter region");
    ComponentDefinition operator = document.createComponentDefinition("LacI_operator", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    operator.addRole(SequenceOntology.OPERATOR);
    operator.setName("LacI operator");
    operator.setDescription("LacI binding site");
    Component promoterComponent = promoter.createComponent("promoter", AccessType.PUBLIC, constPromoter.getIdentity());
    Component operatorComponent = promoter.createComponent("operator", AccessType.PUBLIC, operator.getIdentity());
    promoter.createSequenceConstraint("r1", RestrictionType.PRECEDES, promoterComponent.getIdentity(), operatorComponent.getIdentity());
    SBOLWriter.write(document, (System.out));
}

Example 10 with Component

use of org.powerbot.script.rt4.Component in project powerbot by powerbot.

the class WidgetCloser method poll.

@Override
public void poll() {
    if (ctx.widgets.component(Constants.INFO_BANWARNING >> 16, Constants.INFO_BANWARNING & 0xffff).visible()) {
        final Component c = ctx.widgets.component(Constants.INFO_BANWARNING >> 16, Constants.INFO_BANWARNING_CLOSE);
        GoogleAnalytics.getInstance().pageview("scripts/0/login/warning", c.valid() ? c.text() : "");
    }
    final List<Integer> w = new ArrayList<Integer>();
    if (!ctx.properties.getProperty("widget.closer.disable", "").equals("true")) {
        for (final int e : ctx.bank.opened() ? Constants.WIDGETCLOSER_ACTIVE : Constants.WIDGETCLOSER_ITEMS) {
            w.add(e);
        }
    }
    if (!ctx.bot().allowTrades()) {
        for (final int e : Constants.WIDGETCLOSER_TRADE_ITEMS) {
            w.add(e);
        }
    }
    for (final int id : w) {
        final AtomicInteger a = attempts.get(id);
        if (a.get() >= 3) {
            continue;
        }
        final Component c = ctx.widgets.component(id >> 16, id & 0xffff);
        final Point p = c.screenPoint();
        if (c.visible() && c.click()) {
            if (Condition.wait(new Condition.Check() {

                @Override
                public boolean poll() {
                    return !c.visible() || !c.screenPoint().equals(p);
                }
            })) {
                a.set(0);
            } else {
                a.incrementAndGet();
            }
        }
    }
    for (final int id : Constants.WIDGETCLOSER_FATAL) {
        if (ctx.widgets.component(id >> 16, id & 0xffff).visible()) {
            ctx.controller.stop();
            return;
        }
    }
}