diff --git a/buildCodonSM.sh b/buildCodonSM.sh index f308452..85bc1cd 100755 --- a/buildCodonSM.sh +++ b/buildCodonSM.sh @@ -3,12 +3,16 @@ BEASTV="2.7" PKG="CodonSubstModels" VERSION="2.0.0" -# mkdir ~/Library/Application\ Support/BEAST/$BEASTV/$PKG +if [ ! -d "~/Library/Application Support/BEAST/$BEASTV/$PKG" ]; then + mkdir ~/Library/Application\ Support/BEAST/$BEASTV/$PKG +fi ant build cp dist/$PKG.v$VERSION.zip ~/Library/Application\ Support/BEAST/$BEASTV/$PKG/tmp.zip cd ~/Library/Application\ Support/BEAST/$BEASTV/$PKG/ unzip -o tmp.zip cd ~/WorkSpace/$PKG +ls -l ~/Library/Application\ Support/BEAST/$BEASTV/$PKG + echo "----Done----" diff --git a/fxtemplates/CodonSubstModels.xml b/fxtemplates/CodonSubstModels.xml index 9fd51b8..946b900 100644 --- a/fxtemplates/CodonSubstModels.xml +++ b/fxtemplates/CodonSubstModels.xml @@ -104,7 +104,7 @@ codonmodels.M0Model.rates, codonmodels.M0Model.eigenSystem, codonmodels.M0Model.verbose' - buttonLabelMap='beast.app.beauti.BeautiInitDlg.>> details=Edit parameters' + buttonLabelMap='beastfx.app.beauti.BeautiInitDlg.>> details=Edit parameters' > <!--disableMenus='Mode'--> @@ -169,7 +169,7 @@ <alignmentProvider id="Codon Alignment" spec='codonmodels.app.beauti.CodonAlignmentProvider' template='@CodonPartitionTemplate'/> - <partitiontemplate id='CodonPartitionTemplate' spec='BeautiSubTemplate' class='beast.base.evolution.likelihood.ThreadedTreeLikelihood' mainid='mcmc'> + <partitiontemplate id='CodonPartitionTemplate' spec='beastfx.app.inputeditor.BeautiSubTemplate' class='beast.base.evolution.likelihood.ThreadedTreeLikelihood' mainid='mcmc'> <![CDATA[ <!-- site model --> <plugin spec='SiteModel' id="SiteModel.s:$(n)" gammaCategoryCount='0'> @@ -247,7 +247,7 @@ <connect srcID='treelog.t:$(n)' targetID='mcmc' inputName='logger' if='inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/> <connect srcID='RandomTree.t:$(n)' targetID='mcmc' inputName='init' if='isInitializing'/> - <connect method="beast.app.beauti.StateNodeInitialiserListInputEditor.customConnector"/> + <connect method="beastfx.app.beauti.StateNodeInitialiserListInputEditor.customConnector"/> <connect srcID='ClockPrior.c:$(n)' targetID='prior' inputName='distribution' if='inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true'/> <!-- when FixMeanMutationRatesOperator, the prior is uniform due to the operator --> diff --git a/src/codonmodels/evolution/alignment/CodonAlignment.java b/src/codonmodels/evolution/alignment/CodonAlignment.java index e70e218..6c3e645 100644 --- a/src/codonmodels/evolution/alignment/CodonAlignment.java +++ b/src/codonmodels/evolution/alignment/CodonAlignment.java @@ -92,8 +92,8 @@ public CodonAlignment(Alignment alignment, GeneticCode geneticCode) { if (this.m_dataType == null || !this.m_dataType.getTypeDescription().equals(Codon.CODON)) { DataType oldType = this.m_dataType; this.m_dataType = new Codon(geneticCode); - Log.warning.println("Warning: CodonAlignment (" + this.getID() + ") original data type was " + - oldType + ", is corrected to " + this.m_dataType + " - " + geneticCode.getDescription() + " !"); + Log.warning.println("Warning: find CodonAlignment (" + this.getID() + ") is not a Codon data type (" + + oldType + "), so set it to : " + this.m_dataType + " - " + geneticCode.getDescription() + " !"); } initAndValidate(); } diff --git a/src/codonmodels/evolution/datatype/Codon.java b/src/codonmodels/evolution/datatype/Codon.java index b2a46c6..f7e02e8 100644 --- a/src/codonmodels/evolution/datatype/Codon.java +++ b/src/codonmodels/evolution/datatype/Codon.java @@ -28,9 +28,10 @@ import beast.base.core.Input; import beast.base.core.Log; +import beast.base.evolution.datatype.DataType; +import beast.base.evolution.datatype.Nucleotide; import java.util.Arrays; -import beast.base.evolution.datatype.DataType; /** * Implements DataType for codon, diff --git a/test/codonmodels/evolution/alignment/CodonAlignmentTest.java b/test/codonmodels/evolution/alignment/CodonAlignmentTest.java index 843accd..a6e33ed 100644 --- a/test/codonmodels/evolution/alignment/CodonAlignmentTest.java +++ b/test/codonmodels/evolution/alignment/CodonAlignmentTest.java @@ -2,13 +2,18 @@ import beast.base.evolution.alignment.Alignment; import beast.base.evolution.alignment.Sequence; +import beast.base.evolution.datatype.DataType; +import beast.pkgmgmt.BEASTClassLoader; import codonmodels.evolution.CodonData; import codonmodels.evolution.datatype.Codon; import org.junit.Test; import java.util.List; +import java.util.Set; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; -import static junit.framework.Assert.assertEquals; /** * @author Walter Xie @@ -30,6 +35,13 @@ public void testGetSequence() { } } + @Test + public void testGettingDataType() { + Set<String> dataTypes = BEASTClassLoader.loadService(DataType.class); + System.out.println(dataTypes); + assertTrue("Cannot load Codon data type !", dataTypes.contains(Codon.CODON)); + } + @Test public void testCodonUsage() { Alignment data = CodonData.getAlig6T333(); diff --git a/test/codonmodels/evolution/datatype/CodonTest.java b/test/codonmodels/evolution/datatype/CodonTest.java index 497f15b..23acb65 100644 --- a/test/codonmodels/evolution/datatype/CodonTest.java +++ b/test/codonmodels/evolution/datatype/CodonTest.java @@ -10,7 +10,7 @@ import java.util.Arrays; import java.util.List; -import static junit.framework.Assert.*; +import static org.junit.Assert.*; /** * @author Walter Xie diff --git a/test/codonmodels/evolution/datatype/GeneticCodeTest.java b/test/codonmodels/evolution/datatype/GeneticCodeTest.java index b6af0e1..866a1ae 100644 --- a/test/codonmodels/evolution/datatype/GeneticCodeTest.java +++ b/test/codonmodels/evolution/datatype/GeneticCodeTest.java @@ -6,7 +6,6 @@ import java.util.Arrays; -import static junit.framework.Assert.assertEquals; import static org.junit.Assert.*; /** diff --git a/test/codonmodels/evolution/likelihood/DALikelihoodTest.java b/test/codonmodels/evolution/likelihood/DALikelihoodTest.java index c81eb98..9d2bc97 100644 --- a/test/codonmodels/evolution/likelihood/DALikelihoodTest.java +++ b/test/codonmodels/evolution/likelihood/DALikelihoodTest.java @@ -14,7 +14,7 @@ import java.util.Arrays; -import static junit.framework.Assert.assertEquals; +import static org.junit.Assert.assertEquals; /** diff --git a/test/codonmodels/evolution/likelihood/DAStatesLikelihoodCoreIndexTest.java b/test/codonmodels/evolution/likelihood/DAStatesLikelihoodCoreIndexTest.java index b9166e8..f53ae0f 100644 --- a/test/codonmodels/evolution/likelihood/DAStatesLikelihoodCoreIndexTest.java +++ b/test/codonmodels/evolution/likelihood/DAStatesLikelihoodCoreIndexTest.java @@ -6,7 +6,7 @@ import java.util.Arrays; -import static junit.framework.Assert.assertEquals; +import static org.junit.Assert.assertEquals; /** * Build transition probability matrices under 3-node tree, diff --git a/test/codonmodels/evolution/likelihood/M0TreeLikelihoodTest.java b/test/codonmodels/evolution/likelihood/M0TreeLikelihoodTest.java index d1b8f84..27a4c5e 100644 --- a/test/codonmodels/evolution/likelihood/M0TreeLikelihoodTest.java +++ b/test/codonmodels/evolution/likelihood/M0TreeLikelihoodTest.java @@ -8,7 +8,7 @@ import org.junit.Before; import org.junit.Test; -import static junit.framework.Assert.assertEquals; +import static org.junit.Assert.assertEquals; /** * @author Walter Xie diff --git a/test/codonmodels/evolution/substmodel/M0ModelTest.java b/test/codonmodels/evolution/substmodel/M0ModelTest.java index 5f00adc..7ba1ae6 100644 --- a/test/codonmodels/evolution/substmodel/M0ModelTest.java +++ b/test/codonmodels/evolution/substmodel/M0ModelTest.java @@ -14,7 +14,7 @@ import java.util.Arrays; import java.util.stream.DoubleStream; -import static junit.framework.Assert.assertEquals; +import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; /** diff --git a/version.xml b/version.xml index 9a29608..2dce05f 100644 --- a/version.xml +++ b/version.xml @@ -12,6 +12,7 @@ <provider classname="codonmodels.CodonSubstitutionModel"/> <provider classname="codonmodels.evolution.alignment.CodonAlignment"/> <provider classname="codonmodels.evolution.datatype.Codon"/> +<!-- <provider classname="codonmodels.evolution.datatype.GeneticCode"/>--> <provider classname="codonmodels.evolution.likelihood.DataAugTreeLikelihood"/> <provider classname="codonmodels.evolution.likelihood.GenericDATreeLikelihood"/> <provider classname="codonmodels.evolution.operators.GibbsSamplingOperator"/>