From 98f450ebdaf248f0e6598ff6760c69fc472152b3 Mon Sep 17 00:00:00 2001 From: Denise Date: Fri, 18 Mar 2016 13:45:14 +0100 Subject: [PATCH] Up to date with beast 2.4. --- src/bdsky/MultiSkyline.java | 2 +- src/bdsky/SimpleSkyline.java | 2 +- src/beast/evolution/speciation/CanonicalParameterization.java | 2 +- src/beast/evolution/speciation/OUPrior.java | 2 +- .../speciation/ParameterizedBirthDeathSkylineModel.java | 2 +- src/beast/evolution/speciation/R0Parameterization.java | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/bdsky/MultiSkyline.java b/src/bdsky/MultiSkyline.java index 23ab6c5..21a942d 100644 --- a/src/bdsky/MultiSkyline.java +++ b/src/bdsky/MultiSkyline.java @@ -25,7 +25,7 @@ public MultiSkyline(SimpleSkyline... skyline) { } @Override - public void initAndValidate() throws Exception {} + public void initAndValidate() {} @Override public List getSegments() { diff --git a/src/bdsky/SimpleSkyline.java b/src/bdsky/SimpleSkyline.java index 2d204a1..9584673 100644 --- a/src/bdsky/SimpleSkyline.java +++ b/src/bdsky/SimpleSkyline.java @@ -29,7 +29,7 @@ public class SimpleSkyline extends CalculationNode implements Skyline { "Should be the same length as time vector", (RealParameter) null); @Override - public void initAndValidate() throws Exception { + public void initAndValidate() { Double[] times = getTimes(); diff --git a/src/beast/evolution/speciation/CanonicalParameterization.java b/src/beast/evolution/speciation/CanonicalParameterization.java index e3a20ae..3252aca 100644 --- a/src/beast/evolution/speciation/CanonicalParameterization.java +++ b/src/beast/evolution/speciation/CanonicalParameterization.java @@ -22,7 +22,7 @@ public class CanonicalParameterization extends BDSParameterization { new Input<>("removalProbability", "The probability of an individual to become noninfectious immediately after the sampling"); @Override - public void initAndValidate() throws Exception { + public void initAndValidate() { MultiSkyline multiSkyline = new MultiSkyline( birthRate.get(), diff --git a/src/beast/evolution/speciation/OUPrior.java b/src/beast/evolution/speciation/OUPrior.java index 8b9916f..5d7b3c4 100644 --- a/src/beast/evolution/speciation/OUPrior.java +++ b/src/beast/evolution/speciation/OUPrior.java @@ -41,7 +41,7 @@ public class OUPrior extends Distribution { public Input logSpace = new Input<>("logspace", "true if prior should be applied to log(x).", false); - public double calculateLogP() throws Exception { + public double calculateLogP() { double mu = meanInput.get().getValue(); double sigma = sigmaInput.get().getValue(); diff --git a/src/beast/evolution/speciation/ParameterizedBirthDeathSkylineModel.java b/src/beast/evolution/speciation/ParameterizedBirthDeathSkylineModel.java index ebd066f..a37d187 100644 --- a/src/beast/evolution/speciation/ParameterizedBirthDeathSkylineModel.java +++ b/src/beast/evolution/speciation/ParameterizedBirthDeathSkylineModel.java @@ -127,7 +127,7 @@ enum ConditionOn {NONE, SURVIVAL, RHO_SAMPLING}; public Boolean printTempResults; @Override - public void initAndValidate() throws Exception { + public void initAndValidate() { super.initAndValidate(); if (!originIsRootEdge.get() && treeInput.get().getRoot().getHeight() >= origin()) diff --git a/src/beast/evolution/speciation/R0Parameterization.java b/src/beast/evolution/speciation/R0Parameterization.java index 6bf5b9d..ff43c3d 100644 --- a/src/beast/evolution/speciation/R0Parameterization.java +++ b/src/beast/evolution/speciation/R0Parameterization.java @@ -23,7 +23,7 @@ public class R0Parameterization extends BDSParameterization { "If 1.0 then no sampled ancestors are produced in that interval."); @Override - public void initAndValidate() throws Exception { + public void initAndValidate() { MultiSkyline multiSkyline = new MultiSkyline( R0.get(),