Examples with BeautiConnector beast.app.beauti.BeautiConnector used on opensource projects

Example 1 with BeautiConnector

use of beast.app.beauti.BeautiConnector in project beast2 by CompEvol.

the class BeautiSubTemplateTest method testBeautiSubTemplateIfElement.

@Test
public void testBeautiSubTemplateIfElement() throws Exception {
    // minimal template
    BeautiSubTemplate t = new BeautiSubTemplate();
    // minimal template + connector + name + condition
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'><if cond='kappa/estimate=true'><parameter id='kappa' name='stateNode' value='1.0'/></if></state>");
    assertEquals(1, t.connectorsInput.get().size());
    BeautiConnector c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    String xml = t.xMLInput.get();
    assertEquals("<![CDATA[\n<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n]]>", xml);
}

Example 2 with BeautiConnector

use of beast.app.beauti.BeautiConnector in project beast2 by CompEvol.

the class BeautiSubTemplateTest method testBeautiSubTemplateIfMultipleElement.

@Test
public void testBeautiSubTemplateIfMultipleElement() throws Exception {
    BeautiSubTemplate t = new BeautiSubTemplate();
    // minimal template + connector + name + condition for 2 entries
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'>" + "<if cond='kappa/estimate=true'>" + "<parameter id='kappa' name='stateNode' value='1.0'/>" + "<parameter id='gamma' value='3.0'/>" + "</if></state>");
    assertEquals(2, t.connectorsInput.get().size());
    BeautiConnector c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(1);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("parameter", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    String xml = t.xMLInput.get();
    assertEquals("<![CDATA[\n" + "<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n" + "<parameter id=\"gamma\" value=\"3.0\"/>\n" + "]]>", xml);
    t = new BeautiSubTemplate();
    // minimal template + connector + name + condition for 2 entries
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'>" + "<if cond='kappa/estimate=true'>" + "<parameter id='kappa' name='stateNode' value='1.0'/>" + "<parameter idref='gamma'/>" + "</if></state>");
    assertEquals(2, t.connectorsInput.get().size());
    c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(1);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("parameter", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    xml = t.xMLInput.get();
    assertEquals("<![CDATA[\n" + "<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n" + "]]>", xml);
    t = new BeautiSubTemplate();
    // minimal template + connector + name + condition for 2 entries
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'>" + "<if cond='kappa/estimate=true'>" + "<parameter idref='gamma'/>" + "<parameter id='kappa' name='stateNode' value='1.0'/>" + "</if></state>");
    assertEquals(2, t.connectorsInput.get().size());
    c = t.connectorsInput.get().get(1);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(0);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("parameter", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    xml = t.xMLInput.get();
    assertEquals("<![CDATA[\n" + "<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n" + "]]>", xml);
}

Example 3 with BeautiConnector

use of beast.app.beauti.BeautiConnector in project beast2 by CompEvol.

the class BeautiSubTemplateTest method testBeautiSubTemplateCombined2.

@Test
public void testBeautiSubTemplateCombined2() throws Exception {
    BeautiSubTemplate t = new BeautiSubTemplate();
    // minimal template + connector + name + condition for 2 entries
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'>" + "    <parameter id='kappa' name='stateNode' value='1.0' beauti:if='kappa/estimate=true'/>" + "    <parameter id='gamma' value='3.0'  beauti:if='gamma/estimate=true'/>" + "</state>" + "<logger idref='tracer'>" + "    <log idref='kappa' beauti:if='kappa/estimate=true'/>" + "    <log idref='gamma' beauti:if='gamma/estimate=true'/>" + "</logger>");
    assertEquals(4, t.connectorsInput.get().size());
    BeautiConnector c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(1);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("parameter", c.inputNameInput.get());
    assertEquals("gamma/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(2);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("tracer", c.targetIDInput.get());
    assertEquals("log", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(3);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("tracer", c.targetIDInput.get());
    assertEquals("log", c.inputNameInput.get());
    assertEquals("gamma/estimate=true", c.conditionInput.get());
    String xml = t.xMLInput.get().replaceAll("\\s+", " ");
    assertEquals("<![CDATA[ <parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/> <parameter id=\"gamma\" value=\"3.0\"/> ]]>", xml);
}

Example 4 with BeautiConnector

use of beast.app.beauti.BeautiConnector in project beast2 by CompEvol.

the class BeautiSubTemplateTest method testBeautiSubTemplate.

@Test
public void testBeautiSubTemplate() throws Exception {
    // minimal template
    BeautiSubTemplate t = new BeautiSubTemplate();
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<parameter id='kappa' value='1.0'/>");
    assertEquals(0, t.connectorsInput.get().size());
    String xml = t.xMLInput.get().replaceAll("\\s+", " ");
    assertEquals("<![CDATA[ <parameter id=\"kappa\" value=\"1.0\"/> ]]>", xml);
    // minimal template + connector
    t = new BeautiSubTemplate();
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'><parameter id='kappa' value='1.0'/></state>");
    assertEquals(1, t.connectorsInput.get().size());
    BeautiConnector c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("parameter", c.inputNameInput.get());
    assertEquals(null, c.conditionInput.get());
    xml = t.xMLInput.get().replaceAll("\\s+", " ");
    assertEquals("<![CDATA[ <parameter id=\"kappa\" value=\"1.0\"/> ]]>", xml);
    // minimal template + connector + name
    t = new BeautiSubTemplate();
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'><parameter id='kappa' name='stateNode' value='1.0'/></state>");
    assertEquals(1, t.connectorsInput.get().size());
    c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals(null, c.conditionInput.get());
    xml = t.xMLInput.get().replaceAll("\\s+", " ");
    assertEquals("<![CDATA[ <parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/> ]]>", xml);
    // minimal template + connector + name + condition
    t = new BeautiSubTemplate();
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'><parameter id='kappa' name='stateNode' value='1.0' beauti:if='kappa/estimate=true'/></state>");
    assertEquals(1, t.connectorsInput.get().size());
    c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    xml = t.xMLInput.get().replaceAll("\\s+", " ");
    assertEquals("<![CDATA[ <parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/> ]]>", xml);
}

Example 5 with BeautiConnector

use of beast.app.beauti.BeautiConnector in project beast2 by CompEvol.

the class BeautiSubTemplateTest method testBeautiSubTemplateCombined.

@Test
public void testBeautiSubTemplateCombined() throws Exception {
    BeautiSubTemplate t = new BeautiSubTemplate();
    // minimal template + connector + name + condition for 2 entries
    t.initByName("class", RealParameter.class.getName(), "mainid", "kappa", "value", "<state idref='thestate'>" + "  <if cond='kappa/estimate=true'>" + "    <parameter id='kappa' name='stateNode' value='1.0'/>" + "    <parameter id='gamma' value='3.0'/>" + "  </if>" + "</state>" + "<logger idref='tracer'>" + "  <if cond='gamma/estimate=true'>" + "    <log idref='kappa'/>" + "    <log idref='gamma'/>" + "  </if>" + "</logger>");
    assertEquals(4, t.connectorsInput.get().size());
    BeautiConnector c = t.connectorsInput.get().get(0);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("stateNode", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(1);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("thestate", c.targetIDInput.get());
    assertEquals("parameter", c.inputNameInput.get());
    assertEquals("kappa/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(2);
    assertEquals("kappa", c.sourceIDInput.get());
    assertEquals("tracer", c.targetIDInput.get());
    assertEquals("log", c.inputNameInput.get());
    assertEquals("gamma/estimate=true", c.conditionInput.get());
    c = t.connectorsInput.get().get(3);
    assertEquals("gamma", c.sourceIDInput.get());
    assertEquals("tracer", c.targetIDInput.get());
    assertEquals("log", c.inputNameInput.get());
    assertEquals("gamma/estimate=true", c.conditionInput.get());
    String xml = t.xMLInput.get();
    assertEquals("<![CDATA[      <parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>    <parameter id=\"gamma\" value=\"3.0\"/>              ]]>", xml);
}