Examples with SortedSet java.util.SortedSet used on opensource projects

Example 66 with SortedSet

use of java.util.SortedSet in project uPortal by Jasig.

the class PortletExecutionStatisticsController method createColumnDiscriminatorMap.

protected Map<PortletExecutionAggregationDiscriminator, SortedSet<PortletExecutionAggregation>> createColumnDiscriminatorMap(PortletExecutionReportForm form) {
    // Collections used to track the queried groups and the results
    final Map<PortletExecutionAggregationDiscriminator, SortedSet<PortletExecutionAggregation>> groupedAggregations = new TreeMap<PortletExecutionAggregationDiscriminator, SortedSet<PortletExecutionAggregation>>(PortletExecutionAggregationDiscriminatorImpl.Comparator.INSTANCE);
    // Get concrete group mapping objects that are being queried for
    List<Long> groups = form.getGroups();
    Set<String> portletFNames = form.getPortlets();
    Set<String> executionTypes = form.getExecutionTypeNames();
    for (final Long queryGroupId : groups) {
        AggregatedGroupMapping groupMapping = this.aggregatedGroupLookupDao.getGroupMapping(queryGroupId);
        for (final String portletFName : portletFNames) {
            AggregatedPortletMapping tabMapping = this.aggregatedPortletLookupDao.getMappedPortletForFname(portletFName);
            for (String executionType : executionTypes) {
                final PortletExecutionAggregationDiscriminator mapping = new PortletExecutionAggregationDiscriminatorImpl(groupMapping, tabMapping, ExecutionType.valueOf(executionType));
                // Create the set the aggregations for this report column will be stored in,
                // sorted chronologically
                final SortedSet<PortletExecutionAggregation> aggregations = new TreeSet<PortletExecutionAggregation>(BaseAggregationDateTimeComparator.INSTANCE);
                // Map the group to the set
                groupedAggregations.put(mapping, aggregations);
            }
        }
    }
    return groupedAggregations;
}

Example 67 with SortedSet

use of java.util.SortedSet in project uPortal by Jasig.

the class TabRenderStatisticsController method createColumnDiscriminatorMap.

protected Map<TabRenderAggregationDiscriminator, SortedSet<TabRenderAggregation>> createColumnDiscriminatorMap(TabRenderReportForm form) {
    // Collections used to track the queried groups and the results
    final Map<TabRenderAggregationDiscriminator, SortedSet<TabRenderAggregation>> groupedAggregations = new TreeMap<TabRenderAggregationDiscriminator, SortedSet<TabRenderAggregation>>(TabRenderAggregationDiscriminatorImpl.Comparator.INSTANCE);
    // Get concrete group mapping objects that are being queried for
    List<Long> groups = form.getGroups();
    List<Long> tabs = form.getTabs();
    for (final Long queryGroupId : groups) {
        AggregatedGroupMapping groupMapping = this.aggregatedGroupDao.getGroupMapping(queryGroupId);
        for (final Long tabId : tabs) {
            AggregatedTabMapping tabMapping = this.aggregatedTabLookupDao.getTabMapping(tabId);
            final TabRenderAggregationDiscriminator mapping = new TabRenderAggregationDiscriminatorImpl(groupMapping, tabMapping);
            // Create the set the aggregations for this report column will be stored in, sorted
            // chronologically
            final SortedSet<TabRenderAggregation> aggregations = new TreeSet<TabRenderAggregation>(BaseAggregationDateTimeComparator.INSTANCE);
            // Map the group to the set
            groupedAggregations.put(mapping, aggregations);
        }
    }
    return groupedAggregations;
}

Example 68 with SortedSet

use of java.util.SortedSet in project vcell by virtualcell.

the class SmoldynFileWriter method writeSurfaces.

private void writeSurfaces() throws SolverException, ImageException, PropertyVetoException, GeometryException, ExpressionException {
    GeometrySurfaceDescription geometrySurfaceDescription = resampledGeometry.getGeometrySurfaceDescription();
    SurfaceClass[] surfaceClasses = geometrySurfaceDescription.getSurfaceClasses();
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    SubVolume[] surfaceGeometrySubVolumes = geometrySpec.getSubVolumes();
    GeometricRegion[] AllGeometricRegions = resampledGeometry.getGeometrySurfaceDescription().getGeometricRegions();
    ArrayList<SurfaceGeometricRegion> surfaceRegionList = new ArrayList<SurfaceGeometricRegion>();
    ArrayList<VolumeGeometricRegion> volumeRegionList = new ArrayList<VolumeGeometricRegion>();
    for (GeometricRegion geometricRegion : AllGeometricRegions) {
        if (geometricRegion instanceof SurfaceGeometricRegion) {
            surfaceRegionList.add((SurfaceGeometricRegion) geometricRegion);
        } else if (geometricRegion instanceof VolumeGeometricRegion) {
            volumeRegionList.add((VolumeGeometricRegion) geometricRegion);
        } else {
            throw new SolverException("unsupported geometric region type " + geometricRegion.getClass());
        }
    }
    printWriter.println("# geometry");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.dim + " " + dimension);
    if (bHasNoSurface) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + surfaceGeometrySubVolumes.length);
    } else {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + (surfaceGeometrySubVolumes.length + 1));
        // plus the surface which are bounding walls
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_surface + " " + (surfaceClasses.length + dimension));
    }
    printWriter.println();
    // write boundaries and wall surfaces
    writeWallSurfaces();
    // for 3D ... smoldyn normal convension is triangle right-hand-rule normal points to the outside compartment subdomain.
    if (!bHasNoSurface) {
        membraneSubdomainTriangleMap = new HashMap<MembraneSubDomain, ArrayList<TrianglePanel>>();
        // write surfaces
        printWriter.println("# surfaces");
        int triangleGlobalCount = 0;
        int membraneIndex = -1;
        SurfaceCollection surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
        // pre-allocate collections used repeatedly in following loops; clear before reusing
        HashMap<Node, Set<String>> nodeTriMap = new HashMap<>();
        ArrayList<TrianglePanel> triList = new ArrayList<TrianglePanel>();
        // use a sorted set to ensure neighbors written out is same order for reproducibility
        SortedSet<String> neighborsForCurrentNode = new TreeSet<String>();
        for (int sci = 0; sci < surfaceClasses.length; sci++) {
            nodeTriMap.clear();
            triList.clear();
            int triLocalCount = 0;
            SurfaceClass surfaceClass = surfaceClasses[sci];
            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(surfaceClass);
            for (GeometricRegion gr : geometricRegions) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) gr;
                VolumeGeometricRegion volRegion0 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[0];
                VolumeGeometricRegion volRegion1 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[1];
                SubVolume subVolume0 = volRegion0.getSubVolume();
                SubVolume subVolume1 = volRegion1.getSubVolume();
                CompartmentSubDomain compart0 = mathDesc.getCompartmentSubDomain(subVolume0.getName());
                CompartmentSubDomain compart1 = mathDesc.getCompartmentSubDomain(subVolume1.getName());
                MembraneSubDomain membraneSubDomain = mathDesc.getMembraneSubDomain(compart0, compart1);
                if (membraneSubDomain == null) {
                    throw new SolverException(VCellErrorMessages.getSmoldynUnexpectedSurface(compart0, compart1));
                }
                int exteriorRegionID = volRegion0.getRegionID();
                int interiorRegionID = volRegion1.getRegionID();
                if (membraneSubDomain.getInsideCompartment() == compart0) {
                    exteriorRegionID = volRegion1.getRegionID();
                    interiorRegionID = volRegion0.getRegionID();
                }
                for (int j = 0; j < surfaceCollection.getSurfaceCount(); j++) {
                    Surface surface = surfaceCollection.getSurfaces(j);
                    if ((surface.getInteriorRegionIndex() == exteriorRegionID && surface.getExteriorRegionIndex() == interiorRegionID) || (surface.getInteriorRegionIndex() == interiorRegionID && surface.getExteriorRegionIndex() == exteriorRegionID)) {
                        // Polygon polygon = surface.getPolygons(k);
                        for (Polygon polygon : surface) {
                            if (polygonMembaneElementMap != null) {
                                membraneIndex = polygonMembaneElementMap.get(polygon).getMembraneIndex();
                            }
                            Node[] nodes = polygon.getNodes();
                            if (dimension == 2) {
                                // ignore z
                                Vect3d unitNormal = new Vect3d();
                                polygon.getUnitNormal(unitNormal);
                                unitNormal.set(unitNormal.getX(), unitNormal.getY(), 0);
                                int point0 = 0;
                                Vect3d v0 = new Vect3d(nodes[point0].getX(), nodes[point0].getY(), 0);
                                int point1 = 1;
                                Vect3d v1 = null;
                                for (point1 = 1; point1 < nodes.length; point1++) {
                                    if (v0.getX() != nodes[point1].getX() || v0.getY() != nodes[point1].getY()) {
                                        v1 = new Vect3d(nodes[point1].getX(), nodes[point1].getY(), 0);
                                        break;
                                    }
                                }
                                if (v1 == null) {
                                    throw new RuntimeException("failed to generate surface");
                                }
                                Vect3d v01 = Vect3d.sub(v1, v0);
                                Vect3d unit01n = v01.cross(unitNormal);
                                unit01n.unit();
                                if (Math.abs(unit01n.getZ() - 1.0) < 1e-6) {
                                    // v0 to v1 opposes vcell surface normal. it's already flipped.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        // we have to flipped it back
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    } else {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else if (Math.abs(unit01n.getZ() + 1.0) < 1e-6) {
                                    // v0 to v1 is in direction of vcell surface normal.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    } else {
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else {
                                    throw new RuntimeException("failed to generate surface");
                                }
                            } else if (dimension == 3) {
                                Triangle triangle1;
                                Triangle triangle2;
                                if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                    // interior
                                    triangle1 = new Triangle(nodes[0], nodes[1], nodes[2]);
                                    triangle2 = new Triangle(nodes[0], nodes[2], nodes[3]);
                                } else {
                                    triangle1 = new Triangle(nodes[2], nodes[1], nodes[0]);
                                    triangle2 = new Triangle(nodes[3], nodes[2], nodes[0]);
                                }
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle1));
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle2));
                            }
                        }
                    }
                }
            }
            // add triangles to node hash
            for (TrianglePanel triPanel : triList) {
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    Set<String> triNameSet = nodeTriMap.get(node);
                    if (triNameSet == null) {
                        triNameSet = new HashSet<String>();
                        nodeTriMap.put(node, triNameSet);
                    }
                    triNameSet.add(triPanel.name);
                }
            }
            SubVolume[] adjacentSubvolums = surfaceClass.getAdjacentSubvolumes().toArray(new SubVolume[0]);
            CompartmentSubDomain csd0 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[0].getName());
            CompartmentSubDomain csd1 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[1].getName());
            MembraneSubDomain membraneSubDomain = simulation.getMathDescription().getMembraneSubDomain(csd0, csd1);
            membraneSubdomainTriangleMap.put(membraneSubDomain, triList);
            final boolean initialMoleculesOnMembrane = (closestTriangles != null);
            if (initialMoleculesOnMembrane) {
                findClosestTriangles(membraneSubDomain, triList);
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + surfaceClass.getName());
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.all + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
            // printWriter.println(SmoldynKeyword.action + " " + SmoldynKeyword.all + "(" + SmoldynKeyword.up + ") " + SmoldynKeyword.both + " " + SmoldynKeyword.reflect);
            // get color after species
            Color c = colors[sci + particleVariableList.size()];
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + c.getRed() / 255.0 + " " + c.getGreen() / 255.0 + " " + c.getBlue() / 255.0 + " 0.1");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.tri + " " + triList.size());
            for (TrianglePanel trianglePanel : triList) {
                Triangle triangle = trianglePanel.triangle;
                printWriter.print(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.tri);
                switch(dimension) {
                    case 1:
                        printWriter.print(" " + triangle.getNodes(0).getX());
                        break;
                    case 2:
                        printWriter.print(" " + triangle.getNodes(0).getX() + " " + triangle.getNodes(0).getY());
                        printWriter.print(" " + triangle.getNodes(1).getX() + " " + triangle.getNodes(1).getY());
                        break;
                    case 3:
                        for (Node node : triangle.getNodes()) {
                            printWriter.print(" " + node.getX() + " " + node.getY() + " " + node.getZ());
                        }
                        break;
                }
                printWriter.println(" " + trianglePanel.name);
            }
            for (TrianglePanel triPanel : triList) {
                neighborsForCurrentNode.clear();
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    neighborsForCurrentNode.addAll(nodeTriMap.get(node));
                }
                neighborsForCurrentNode.remove(triPanel.name);
                // printWriter.print(SmoldynKeyword.neighbors + " " +triPanel.name);
                // to allow smoldyn read line length as 256, chop the neighbors to multiple lines
                int maxNeighborCount = 4;
                // 
                int count = 0;
                for (String neigh : neighborsForCurrentNode) {
                    if (count % maxNeighborCount == 0) {
                        printWriter.println();
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.neighbors + " " + triPanel.name);
                    }
                    printWriter.print(" " + neigh);
                    count++;
                }
            }
            printWriter.println();
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
            printWriter.println();
        }
    // write compartment
    // printWriter.println("# bounding wall compartment");
    // printWriter.println(SmoldynKeyword.start_compartment + " " + VCellSmoldynKeyword.bounding_wall_compartment);
    // printWriter.println(SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_X);
    // if (dimension > 1) {
    // printWriter.println(SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Y);
    // if (dimension > 2) {
    // printWriter.println(SmoldynKeyword.surface + " " + VCellSmoldynKeyword.bounding_wall_surface_Z);
    // }
    // }
    // printWriter.println(SmoldynKeyword.end_compartment);
    // printWriter.println();
    }
}

Example 69 with SortedSet

use of java.util.SortedSet in project vcell by virtualcell.

the class SmoldynSurfaceTessellator method writeSurfaces.

protected void writeSurfaces() throws SolverException, ImageException, PropertyVetoException, GeometryException, ExpressionException {
    GeometrySurfaceDescription geometrySurfaceDescription = resampledGeometry.getGeometrySurfaceDescription();
    SurfaceClass[] surfaceClasses = geometrySurfaceDescription.getSurfaceClasses();
    GeometrySpec geometrySpec = resampledGeometry.getGeometrySpec();
    SubVolume[] surfaceGeometrySubVolumes = geometrySpec.getSubVolumes();
    GeometricRegion[] AllGeometricRegions = resampledGeometry.getGeometrySurfaceDescription().getGeometricRegions();
    ArrayList<SurfaceGeometricRegion> surfaceRegionList = new ArrayList<SurfaceGeometricRegion>();
    ArrayList<VolumeGeometricRegion> volumeRegionList = new ArrayList<VolumeGeometricRegion>();
    for (GeometricRegion geometricRegion : AllGeometricRegions) {
        if (geometricRegion instanceof SurfaceGeometricRegion) {
            surfaceRegionList.add((SurfaceGeometricRegion) geometricRegion);
        } else if (geometricRegion instanceof VolumeGeometricRegion) {
            volumeRegionList.add((VolumeGeometricRegion) geometricRegion);
        } else {
            throw new SolverException("unsupported geometric region type " + geometricRegion.getClass());
        }
    }
    printWriter.println("# geometry");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.dim + " " + dimension);
    if (bHasNoSurface) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + surfaceGeometrySubVolumes.length);
    } else {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_compartment + " " + (surfaceGeometrySubVolumes.length + 1));
        // plus the surface which are bounding walls
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_surface + " " + (surfaceClasses.length + dimension));
    }
    printWriter.println();
    // write boundaries and wall surfaces
    writeWallSurfaces();
    // for 3D ... smoldyn normal convension is triangle right-hand-rule normal points to the outside compartment subdomain.
    if (!bHasNoSurface) {
        membraneSubdomainTriangleMap = new HashMap<MembraneSubDomain, ArrayList<TrianglePanel>>();
        // write surfaces
        printWriter.println("# surfaces");
        int triangleGlobalCount = 0;
        int membraneIndex = -1;
        SurfaceCollection surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
        // pre-allocate collections used repeatedly in following loops; clear before reusing
        HashMap<Node, Set<String>> nodeTriMap = new HashMap<>();
        ArrayList<TrianglePanel> triList = new ArrayList<TrianglePanel>();
        // use a sorted set to ensure neighbors written out is same order for reproducibility
        SortedSet<String> neighborsForCurrentNode = new TreeSet<String>();
        for (int sci = 0; sci < surfaceClasses.length; sci++) {
            nodeTriMap.clear();
            triList.clear();
            int triLocalCount = 0;
            SurfaceClass surfaceClass = surfaceClasses[sci];
            GeometricRegion[] geometricRegions = geometrySurfaceDescription.getGeometricRegions(surfaceClass);
            for (GeometricRegion gr : geometricRegions) {
                SurfaceGeometricRegion sgr = (SurfaceGeometricRegion) gr;
                VolumeGeometricRegion volRegion0 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[0];
                VolumeGeometricRegion volRegion1 = (VolumeGeometricRegion) sgr.getAdjacentGeometricRegions()[1];
                SubVolume subVolume0 = volRegion0.getSubVolume();
                SubVolume subVolume1 = volRegion1.getSubVolume();
                CompartmentSubDomain compart0 = mathDesc.getCompartmentSubDomain(subVolume0.getName());
                CompartmentSubDomain compart1 = mathDesc.getCompartmentSubDomain(subVolume1.getName());
                MembraneSubDomain membraneSubDomain = mathDesc.getMembraneSubDomain(compart0, compart1);
                if (membraneSubDomain == null) {
                    throw new SolverException(VCellErrorMessages.getSmoldynUnexpectedSurface(compart0, compart1));
                }
                int exteriorRegionID = volRegion0.getRegionID();
                int interiorRegionID = volRegion1.getRegionID();
                if (membraneSubDomain.getInsideCompartment() == compart0) {
                    exteriorRegionID = volRegion1.getRegionID();
                    interiorRegionID = volRegion0.getRegionID();
                }
                for (int j = 0; j < surfaceCollection.getSurfaceCount(); j++) {
                    Surface surface = surfaceCollection.getSurfaces(j);
                    if ((surface.getInteriorRegionIndex() == exteriorRegionID && surface.getExteriorRegionIndex() == interiorRegionID) || (surface.getInteriorRegionIndex() == interiorRegionID && surface.getExteriorRegionIndex() == exteriorRegionID)) {
                        // Polygon polygon = surface.getPolygons(k);
                        for (Polygon polygon : surface) {
                            if (polygonMembaneElementMap != null) {
                                membraneIndex = polygonMembaneElementMap.get(polygon).getMembraneIndex();
                            }
                            Node[] nodes = polygon.getNodes();
                            if (dimension == 2) {
                                // ignore z
                                Vect3d unitNormal = new Vect3d();
                                polygon.getUnitNormal(unitNormal);
                                unitNormal.set(unitNormal.getX(), unitNormal.getY(), 0);
                                int point0 = 0;
                                Vect3d v0 = new Vect3d(nodes[point0].getX(), nodes[point0].getY(), 0);
                                int point1 = 1;
                                Vect3d v1 = null;
                                for (point1 = 1; point1 < nodes.length; point1++) {
                                    if (v0.getX() != nodes[point1].getX() || v0.getY() != nodes[point1].getY()) {
                                        v1 = new Vect3d(nodes[point1].getX(), nodes[point1].getY(), 0);
                                        break;
                                    }
                                }
                                if (v1 == null) {
                                    throw new RuntimeException("failed to generate surface");
                                }
                                Vect3d v01 = Vect3d.sub(v1, v0);
                                Vect3d unit01n = v01.cross(unitNormal);
                                unit01n.unit();
                                if (Math.abs(unit01n.getZ() - 1.0) < 1e-6) {
                                    // v0 to v1 opposes vcell surface normal. it's already flipped.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        // we have to flipped it back
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    } else {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else if (Math.abs(unit01n.getZ() + 1.0) < 1e-6) {
                                    // v0 to v1 is in direction of vcell surface normal.
                                    Triangle triangle;
                                    if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                        triangle = new Triangle(nodes[point0], nodes[point1], null);
                                    } else {
                                        triangle = new Triangle(nodes[point1], nodes[point0], null);
                                    }
                                    triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle));
                                } else {
                                    throw new RuntimeException("failed to generate surface");
                                }
                            } else if (dimension == 3) {
                                Triangle triangle1;
                                Triangle triangle2;
                                if (surface.getInteriorRegionIndex() == interiorRegionID) {
                                    // interior
                                    triangle1 = new Triangle(nodes[0], nodes[1], nodes[2]);
                                    triangle2 = new Triangle(nodes[0], nodes[2], nodes[3]);
                                } else {
                                    triangle1 = new Triangle(nodes[2], nodes[1], nodes[0]);
                                    triangle2 = new Triangle(nodes[3], nodes[2], nodes[0]);
                                }
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle1));
                                triList.add(new TrianglePanel(triLocalCount++, triangleGlobalCount++, membraneIndex, triangle2));
                            }
                        }
                    }
                }
            }
            // add triangles to node hash
            for (TrianglePanel triPanel : triList) {
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    Set<String> triNameSet = nodeTriMap.get(node);
                    if (triNameSet == null) {
                        triNameSet = new HashSet<String>();
                        nodeTriMap.put(node, triNameSet);
                    }
                    triNameSet.add(triPanel.name);
                }
            }
            SubVolume[] adjacentSubvolums = surfaceClass.getAdjacentSubvolumes().toArray(new SubVolume[0]);
            CompartmentSubDomain csd0 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[0].getName());
            CompartmentSubDomain csd1 = simulation.getMathDescription().getCompartmentSubDomain(adjacentSubvolums[1].getName());
            MembraneSubDomain membraneSubDomain = simulation.getMathDescription().getMembraneSubDomain(csd0, csd1);
            membraneSubdomainTriangleMap.put(membraneSubDomain, triList);
            final boolean initialMoleculesOnMembrane = (closestTriangles != null);
            if (initialMoleculesOnMembrane) {
                findClosestTriangles(membraneSubDomain, triList);
            }
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.start_surface + " " + surfaceClass.getName());
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.action + " " + SmoldynVCellMapper.SmoldynKeyword.all + "(" + SmoldynVCellMapper.SmoldynKeyword.all + ") " + SmoldynVCellMapper.SmoldynKeyword.both + " " + SmoldynVCellMapper.SmoldynKeyword.reflect);
            // printWriter.println(SmoldynKeyword.action + " " + SmoldynKeyword.all + "(" + SmoldynKeyword.up + ") " + SmoldynKeyword.both + " " + SmoldynKeyword.reflect);
            Color c = colorForSurface(sci);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.color + " " + SmoldynVCellMapper.SmoldynKeyword.both + " " + c.getRed() / 255.0 + " " + c.getGreen() / 255.0 + " " + c.getBlue() / 255.0 + " 0.1");
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.front + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.polygon + " " + SmoldynVCellMapper.SmoldynKeyword.back + " " + SmoldynVCellMapper.SmoldynKeyword.edge);
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_panels + " " + SmoldynVCellMapper.SmoldynKeyword.tri + " " + triList.size());
            for (TrianglePanel trianglePanel : triList) {
                Triangle triangle = trianglePanel.triangle;
                printWriter.print(SmoldynVCellMapper.SmoldynKeyword.panel + " " + SmoldynVCellMapper.SmoldynKeyword.tri);
                switch(dimension) {
                    case 1:
                        printWriter.print(" " + triangle.getNodes(0).getX());
                        break;
                    case 2:
                        printWriter.print(" " + triangle.getNodes(0).getX() + " " + triangle.getNodes(0).getY());
                        printWriter.print(" " + triangle.getNodes(1).getX() + " " + triangle.getNodes(1).getY());
                        break;
                    case 3:
                        for (Node node : triangle.getNodes()) {
                            printWriter.print(" " + node.getX() + " " + node.getY() + " " + node.getZ());
                        }
                        break;
                }
                printWriter.println(" " + trianglePanel.name);
            }
            for (TrianglePanel triPanel : triList) {
                neighborsForCurrentNode.clear();
                for (Node node : triPanel.triangle.getNodes()) {
                    if (node == null) {
                        continue;
                    }
                    neighborsForCurrentNode.addAll(nodeTriMap.get(node));
                }
                neighborsForCurrentNode.remove(triPanel.name);
                // printWriter.print(SmoldynKeyword.neighbors + " " +triPanel.name);
                // to allow smoldyn read line length as 256, chop the neighbors to multiple lines
                int maxNeighborCount = 4;
                // 
                int count = 0;
                for (String neigh : neighborsForCurrentNode) {
                    if (count % maxNeighborCount == 0) {
                        printWriter.println();
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.neighbors + " " + triPanel.name);
                    }
                    printWriter.print(" " + neigh);
                    count++;
                }
            }
            printWriter.println();
            printWriter.println(SmoldynVCellMapper.SmoldynKeyword.end_surface);
            printWriter.println();
        }
    }
}

Example 70 with SortedSet

use of java.util.SortedSet in project hadoop by apache.

the class TestLayoutVersion method testNameNodeFeatureMinimumCompatibleLayoutVersionOutOfOrder.

/**
   * Tests that attempting to add a new NameNode feature out of order with
   * respect to minimum compatible layout version will fail fast.
   */
@Test(expected = AssertionError.class)
public void testNameNodeFeatureMinimumCompatibleLayoutVersionOutOfOrder() {
    FeatureInfo ancestorF = LayoutVersion.Feature.RESERVED_REL2_4_0.getInfo();
    LayoutFeature f = mock(LayoutFeature.class);
    when(f.getInfo()).thenReturn(new FeatureInfo(ancestorF.getLayoutVersion() - 1, ancestorF.getLayoutVersion(), ancestorF.getMinimumCompatibleLayoutVersion() + 1, "Invalid feature.", false));
    Map<Integer, SortedSet<LayoutFeature>> features = new HashMap<>();
    LayoutVersion.updateMap(features, LayoutVersion.Feature.values());
    LayoutVersion.updateMap(features, new LayoutFeature[] { f });
}