Fixed permutation function in BayesTree to properly update the nodes listing. Added assertion to removeClique() to fail under malformed bayes trees.

.cproject

@@ -1,7 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?fileVersion 4.0.0?>
+<?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">
-
-<cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">
 	<storageModule moduleId="org.eclipse.cdt.core.settings">
 		<cconfiguration id="cdt.managedbuild.toolchain.gnu.macosx.base.1359703544">
 			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.macosx.base.1359703544" moduleId="org.eclipse.cdt.core.settings" name="MacOSX GCC">
@@ -309,14 +307,6 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testGaussianFactor.run" path="linear/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testGaussianFactor.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
 			<target name="all" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j2</buildArguments>
@@ -343,6 +333,7 @@
 			</target>
 			<target name="tests/testBayesTree.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>tests/testBayesTree.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -350,6 +341,7 @@
 			</target>
 			<target name="testBinaryBayesNet.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testBinaryBayesNet.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -397,6 +389,7 @@
 			</target>
 			<target name="testSymbolicBayesNet.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testSymbolicBayesNet.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -404,6 +397,7 @@
 			</target>
 			<target name="tests/testSymbolicFactor.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>tests/testSymbolicFactor.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -411,6 +405,7 @@
 			</target>
 			<target name="testSymbolicFactorGraph.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testSymbolicFactorGraph.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -426,11 +421,20 @@
 			</target>
 			<target name="tests/testBayesTree" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>tests/testBayesTree</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
+			<target name="testGaussianFactor.run" path="linear/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testGaussianFactor.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
 			<target name="testPoseRTV.run" path="build/gtsam_unstable/dynamics" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j5</buildArguments>
@@ -519,22 +523,6 @@
 				<useDefaultCommand>false</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="all" path="CppUnitLite" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>all</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="clean" path="CppUnitLite" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>clean</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
 			<target name="tests/testPose2.run" path="build_retract/gtsam/geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j2</buildArguments>
@@ -551,6 +539,22 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
+			<target name="all" path="CppUnitLite" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>all</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="clean" path="CppUnitLite" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>clean</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
 			<target name="all" path="spqr_mini" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j2</buildArguments>
@@ -575,34 +579,26 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testValues.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="all" path="build_wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>testValues.run</buildTarget>
+				<buildTarget>all</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testOrdering.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="check" path="build_wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>testOrdering.run</buildTarget>
+				<buildTarget>check</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testKey.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="clean" path="build_wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>testKey.run</buildTarget>
+				<buildTarget>clean</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testLinearContainerFactor.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
-				<buildTarget>testLinearContainerFactor.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
@@ -687,26 +683,34 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="all" path="build_wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="testValues.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
+				<buildArguments>-j5</buildArguments>
-				<buildTarget>all</buildTarget>
+				<buildTarget>testValues.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="check" path="build_wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="testOrdering.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
+				<buildArguments>-j5</buildArguments>
-				<buildTarget>check</buildTarget>
+				<buildTarget>testOrdering.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="clean" path="build_wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="testKey.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
+				<buildArguments>-j5</buildArguments>
-				<buildTarget>clean</buildTarget>
+				<buildTarget>testKey.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testLinearContainerFactor.run" path="build/gtsam/nonlinear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j5</buildArguments>
+				<buildTarget>testLinearContainerFactor.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
@@ -887,6 +891,14 @@
 				<useDefaultCommand>false</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
+			<target name="testBayesTree.run" path="build/gtsam/inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j5</buildArguments>
+				<buildTarget>testBayesTree.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
 			<target name="vSFMexample.run" path="build/examples/vSLAMexample" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j2</buildArguments>
@@ -1049,6 +1061,7 @@
 			</target>
 			<target name="testGraph.run" path="build/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testGraph.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1056,6 +1069,7 @@
 			</target>
 			<target name="testJunctionTree.run" path="build/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testJunctionTree.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1063,6 +1077,7 @@
 			</target>
 			<target name="testSymbolicBayesNetB.run" path="build/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testSymbolicBayesNetB.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1222,6 +1237,7 @@
 			</target>
 			<target name="testErrors.run" path="linear" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
+				<buildArguments/>
 				<buildTarget>testErrors.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1267,14 +1283,6 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testGaussianFactor.run" path="build/linear/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testGaussianFactor.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
 			<target name="check" path="base" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j2</buildArguments>
@@ -1355,6 +1363,14 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
+			<target name="testGaussianFactor.run" path="build/linear/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testGaussianFactor.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
 			<target name="check" path="build/inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j2</buildArguments>
@@ -1677,7 +1693,6 @@
 			</target>
 			<target name="testSimulated2DOriented.run" path="slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments/>
 				<buildTarget>testSimulated2DOriented.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1717,7 +1732,6 @@
 			</target>
 			<target name="testSimulated2D.run" path="slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments/>
 				<buildTarget>testSimulated2D.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1725,7 +1739,6 @@
 			</target>
 			<target name="testSimulated3D.run" path="slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments/>
 				<buildTarget>testSimulated3D.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1957,7 +1970,6 @@
 			</target>
 			<target name="tests/testGaussianISAM2" path="build/slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments/>
 				<buildTarget>tests/testGaussianISAM2</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -1979,102 +1991,6 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testRot3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testRot3.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testRot2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testRot2.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testPose3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testPose3.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="timeRot3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>timeRot3.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testPose2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testPose2.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testCal3_S2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testCal3_S2.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testSimpleCamera.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testSimpleCamera.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testHomography2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testHomography2.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testCalibratedCamera.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testCalibratedCamera.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="check" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>check</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="clean" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>clean</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
-			<target name="testPoint2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
-				<buildCommand>make</buildCommand>
-				<buildArguments>-j2</buildArguments>
-				<buildTarget>testPoint2.run</buildTarget>
-				<stopOnError>true</stopOnError>
-				<useDefaultCommand>true</useDefaultCommand>
-				<runAllBuilders>true</runAllBuilders>
-			</target>
 			<target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
 				<buildArguments>-j3</buildArguments>
@@ -2276,6 +2192,7 @@
 			</target>
 			<target name="Generate DEB Package" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>cpack</buildCommand>
+				<buildArguments/>
 				<buildTarget>-G DEB</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -2283,6 +2200,7 @@
 			</target>
 			<target name="Generate RPM Package" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>cpack</buildCommand>
+				<buildArguments/>
 				<buildTarget>-G RPM</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -2290,6 +2208,7 @@
 			</target>
 			<target name="Generate TGZ Package" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>cpack</buildCommand>
+				<buildArguments/>
 				<buildTarget>-G TGZ</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -2297,6 +2216,7 @@
 			</target>
 			<target name="Generate TGZ Source Package" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>cpack</buildCommand>
+				<buildArguments/>
 				<buildTarget>--config CPackSourceConfig.cmake</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -2422,34 +2342,98 @@
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testSpirit.run" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="testRot3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>testSpirit.run</buildTarget>
+				<buildTarget>testRot3.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="testWrap.run" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="testRot2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>testWrap.run</buildTarget>
+				<buildTarget>testRot2.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="check.wrap" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="testPose3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>check.wrap</buildTarget>
+				<buildTarget>testPose3.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
-			<target name="wrap" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+			<target name="timeRot3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>make</buildCommand>
-				<buildArguments>-j5</buildArguments>
+				<buildArguments>-j2</buildArguments>
-				<buildTarget>wrap</buildTarget>
+				<buildTarget>timeRot3.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testPose2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testPose2.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testCal3_S2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testCal3_S2.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testSimpleCamera.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testSimpleCamera.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testHomography2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testHomography2.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testCalibratedCamera.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testCalibratedCamera.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="check" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>check</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="clean" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>clean</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testPoint2.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j2</buildArguments>
+				<buildTarget>testPoint2.run</buildTarget>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>true</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
@@ -2493,6 +2477,38 @@
 				<useDefaultCommand>false</useDefaultCommand>
 				<runAllBuilders>true</runAllBuilders>
 			</target>
+			<target name="testSpirit.run" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j5</buildArguments>
+				<buildTarget>testSpirit.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="testWrap.run" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j5</buildArguments>
+				<buildTarget>testWrap.run</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="check.wrap" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j5</buildArguments>
+				<buildTarget>check.wrap</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
+			<target name="wrap" path="build/wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
+				<buildCommand>make</buildCommand>
+				<buildArguments>-j5</buildArguments>
+				<buildTarget>wrap</buildTarget>
+				<stopOnError>true</stopOnError>
+				<useDefaultCommand>true</useDefaultCommand>
+				<runAllBuilders>true</runAllBuilders>
+			</target>
 		</buildTargets>
 	</storageModule>
 </cproject>

gtsam/inference/BayesTree-inl.h

@@ -201,6 +201,25 @@ namespace gtsam {
     return new_clique;
   }
 
+  /* ************************************************************************* */
+  template<class CONDITIONAL, class CLIQUE>
+  void BayesTree<CONDITIONAL,CLIQUE>::permuteWithInverse(const Permutation& inversePermutation) {
+    // recursively permute the cliques and internal conditionals
+    if (root_)
+      root_->permuteWithInverse(inversePermutation);
+
+    // need to know what the largest key is to get the right number of cliques
+    Index maxIndex = *std::max_element(inversePermutation.begin(), inversePermutation.end());
+
+    // Update the nodes structure
+    typename BayesTree<CONDITIONAL,CLIQUE>::Nodes newNodes(maxIndex+1);
+//    inversePermutation.applyToCollection(newNodes, nodes_); // Uses the forward, rather than inverse permutation
+    for(size_t i = 0; i < nodes_.size(); ++i)
+      newNodes[inversePermutation[i]] = nodes_[i];
+
+    nodes_ = newNodes;
+  }
+
   /* ************************************************************************* */
   template<class CONDITIONAL, class CLIQUE>
   inline void BayesTree<CONDITIONAL,CLIQUE>::addToCliqueFront(BayesTree<CONDITIONAL,CLIQUE>& bayesTree, const sharedConditional& conditional, const sharedClique& clique) {
@@ -242,6 +261,7 @@ namespace gtsam {
       child->parent_ = typename Clique::weak_ptr();
 
     BOOST_FOREACH(Index j, (*clique->conditional())) {
+      assert(j < nodes_.size()); // Don't want to overrun nodes list
       nodes_[j].reset();
     }
   }

gtsam/inference/BayesTree.h

@@ -236,10 +236,8 @@ namespace gtsam {
       root_->deleteCachedShortcuts();
     }
 
-    /** Apply a permutation to all cliques */
+    /** Apply a permutation to the full tree - also updates the nodes structure */
-    void permuteWithInverse(const Permutation& inversePermutation) {
+    void permuteWithInverse(const Permutation& inversePermutation);
-      root_->permuteWithInverse(inversePermutation);
-    }
 
     /**
      * Remove path from clique to root and return that path as factors

gtsam/inference/Permutation.h

@@ -189,7 +189,9 @@ protected:
 
 
 namespace internal {
-  // An internal class used for storing and applying a permutation from a map
+  /**
+   * An internal class used for storing and applying a permutation from a map
+   */
   class Reduction : public gtsam::FastMap<Index,Index> {
   public:
     typedef gtsam::FastMap<Index,Index> Base;
@@ -205,8 +207,9 @@ namespace internal {
     bool equals(const Reduction& other, double tol = 1e-9) const;
   };
 
-  // Reduce the variable indices so that those in the set are mapped to start at zero
+  /**
+   * Reduce the variable indices so that those in the set are mapped to start at zero
+   */
   Permutation createReducingPermutation(const std::set<Index>& indices);
-}
+} // \namespace internal
-
+} // \namespace gtsam
-}

gtsam/inference/tests/testBayesTree.cpp

@@ -19,6 +19,7 @@
 
 #include <boost/assign/std/list.hpp> // for operator +=
 #include <boost/assign/std/vector.hpp>
+#include <boost/assign/std/set.hpp>
 #include <boost/assign/list_of.hpp>
 using namespace boost::assign;
 
@@ -309,8 +310,6 @@ TEST( BayesTree, shortcutCheck )
 //  }
 }
 
-
-
 /* ************************************************************************* */
 TEST( BayesTree, removeTop )
 {
@@ -408,6 +407,99 @@ TEST( BayesTree, removeTop3 )
 
   CHECK(orphans.size() == 0);
 }
+
+/* ************************************************************************* */
+TEST( BayesTree, permute )
+{
+  // creates a permutation and ensures that the nodes listing is updated
+
+  // initial keys - more than just 6 variables - for a system with 9 variables
+  const Index _A0_=8, _B0_=7, _C0_=6, _D0_=5, _E0_=4, _F0_=0;
+
+  // reduced keys - back to just 6 variables
+  const Index _A_=5, _B_=4, _C_=3, _D_=2, _E_=1, _F_=0;
+
+  // Create and verify the permutation
+  std::set<Index> indices; indices += _A0_, _B0_, _C0_, _D0_, _E0_, _F0_;
+  Permutation actReducingPermutation = gtsam::internal::createReducingPermutation(indices);
+  Permutation expReducingPermutation(6);
+  expReducingPermutation[_A_] = _A0_;
+  expReducingPermutation[_B_] = _B0_;
+  expReducingPermutation[_C_] = _C0_;
+  expReducingPermutation[_D_] = _D0_;
+  expReducingPermutation[_E_] = _E0_;
+  expReducingPermutation[_F_] = _F0_;
+  EXPECT(assert_equal(expReducingPermutation, actReducingPermutation));
+
+  // Invert the permutation
+  gtsam::internal::Reduction inv_reduction = gtsam::internal::Reduction::CreateAsInverse(expReducingPermutation);
+
+  // Build a bayes tree around reduced keys as if just eliminated from subset of factors/variables
+  IndexConditional::shared_ptr
+      A(new IndexConditional(_A_)),
+      B(new IndexConditional(_B_, _A_)),
+      C(new IndexConditional(_C_, _A_)),
+      D(new IndexConditional(_D_, _C_)),
+      E(new IndexConditional(_E_, _B_)),
+      F(new IndexConditional(_F_, _E_));
+  SymbolicBayesTree bayesTreeReduced;
+  SymbolicBayesTree::insert(bayesTreeReduced, A);
+  SymbolicBayesTree::insert(bayesTreeReduced, B);
+  SymbolicBayesTree::insert(bayesTreeReduced, C);
+  SymbolicBayesTree::insert(bayesTreeReduced, D);
+  SymbolicBayesTree::insert(bayesTreeReduced, E);
+  SymbolicBayesTree::insert(bayesTreeReduced, F);
+
+//  bayesTreeReduced.print("Reduced bayes tree");
+//  P( 4 5)
+//    P( 3 | 5)
+//      P( 2 | 3)
+//    P( 1 | 4)
+//      P( 0 | 1)
+
+  // Apply the permutation - should add placeholders for variables not present in nodes
+  SymbolicBayesTree actBayesTree = *bayesTreeReduced.clone();
+  actBayesTree.permuteWithInverse(expReducingPermutation);
+
+//  actBayesTree.print("Full bayes tree");
+//  P( 7 8)
+//    P( 6 | 8)
+//      P( 5 | 6)
+//    P( 4 | 7)
+//      P( 0 | 4)
+
+  // check keys in cliques
+  std::vector<Index> expRootIndices; expRootIndices += _B0_, _A0_;
+  IndexConditional::shared_ptr
+    expRoot(new IndexConditional(expRootIndices, 2)), // root
+    A0(new IndexConditional(_A0_)),
+    B0(new IndexConditional(_B0_, _A0_)),
+    C0(new IndexConditional(_C0_, _A0_)), // leaf level 1
+    D0(new IndexConditional(_D0_, _C0_)), // leaf level 2
+    E0(new IndexConditional(_E0_, _B0_)), // leaf level 2
+    F0(new IndexConditional(_F0_, _E0_)); // leaf level 3
+
+  CHECK(actBayesTree.root());
+  EXPECT(assert_equal(*expRoot, *actBayesTree.root()->conditional()));
+  EXPECT(assert_equal(*C0, *actBayesTree.root()->children().front()->conditional()));
+  EXPECT(assert_equal(*D0, *actBayesTree.root()->children().front()->children().front()->conditional()));
+  EXPECT(assert_equal(*E0, *actBayesTree.root()->children().back()->conditional()));
+  EXPECT(assert_equal(*F0, *actBayesTree.root()->children().back()->children().front()->conditional()));
+
+  // check nodes structure
+  LONGS_EQUAL(9, actBayesTree.nodes().size());
+
+  SymbolicBayesTree expFullTree;
+  SymbolicBayesTree::insert(expFullTree, A0);
+  SymbolicBayesTree::insert(expFullTree, B0);
+  SymbolicBayesTree::insert(expFullTree, C0);
+  SymbolicBayesTree::insert(expFullTree, D0);
+  SymbolicBayesTree::insert(expFullTree, E0);
+  SymbolicBayesTree::insert(expFullTree, F0);
+
+  EXPECT(assert_equal(expFullTree, actBayesTree));
+}
+
 ///* ************************************************************************* */
 ///**
 // *  x2 - x3 - x4 - x5
@@ -463,10 +555,7 @@ TEST( BayesTree, removeTop3 )
 //  CHECK(assert_equal(expected, actual));
 //
 //}
-/* ************************************************************************* */
 
-int main() {
+/* ************************************************************************* */
-  TestResult tr;
+int main() { TestResult tr; return TestRegistry::runAllTests(tr); }
-  return TestRegistry::runAllTests(tr);
-}
 /* ************************************************************************* */