public final class EnvelopeCalculation
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private AtomData |
atomData |
private java.util.BitSet |
bsIgnore |
private java.util.BitSet |
bsMySelected |
private java.util.BitSet |
bsSurface |
private javax.vecmath.Point3f |
centerI |
private javax.vecmath.Point3f |
centerT |
private javax.vecmath.Point3f[] |
currentPoints |
private float |
diameterP |
private boolean |
disregardNeighbors |
private FastBitSet[] |
dotsConvexMaps |
private int |
dotsConvexMax |
private FastBitSet |
emptySet |
private int |
geodesicCount |
private FastBitSet |
geodesicMap |
private int |
indexI |
private boolean |
isSurface |
private short[] |
mads |
private FastBitSet |
mapT |
static int |
MAX_LEVEL |
private float |
maxRadius |
private boolean |
modelZeroBased |
private boolean |
multiModel |
private javax.vecmath.Point3f[] |
neighborCenters |
private int |
neighborCount |
private int[] |
neighborIndices |
private float[] |
neighborPlusProbeRadii2 |
private float[] |
neighborRadii2 |
private boolean |
onlySelectedDots |
private javax.vecmath.Point3f |
pointT |
private static int[] |
power4 |
private float |
radiiIP2 |
private float |
radiusI |
private float |
radiusP |
static float |
SURFACE_DISTANCE_FOR_CALCULATION |
private javax.vecmath.Point3f[] |
vertexTest |
private AtomDataServer |
viewer |
Constructor and Description |
---|
EnvelopeCalculation(AtomDataServer viewer,
int atomCount,
short[] mads,
boolean asJavaBitSet) |
Modifier and Type | Method and Description |
---|---|
private void |
addIncompleteFaces(FastBitSet points) |
void |
allocDotsConvexMaps(int max) |
private void |
calcConvexBits() |
private void |
calcConvexMap(boolean isSurface) |
void |
calculate(RadiusData rd,
float maxRadius,
java.util.BitSet bsSelected,
java.util.BitSet bsIgnore,
boolean disregardNeighbors,
boolean onlySelectedDots,
boolean isSurface,
boolean multiModel) |
void |
deleteAtoms(int firstAtomDeleted,
int nAtomsDeleted,
java.util.BitSet bsAtoms) |
float |
getAppropriateRadius(int atomIndex) |
java.util.BitSet |
getBsSurfaceClone() |
FastBitSet[] |
getDotsConvexMaps() |
int |
getDotsConvexMax() |
private AtomIndexIterator |
getNeighbors(AtomIndexIterator iter) |
javax.vecmath.Point3f[] |
getPoints() |
float |
getRadius(int atomIndex) |
void |
newSet() |
void |
reCalculate(java.util.BitSet bs) |
private void |
setAtomI(int indexI) |
private void |
setDotsConvexMax() |
void |
setFromBits(int index,
java.util.BitSet bs) |
void |
setMads(short[] mads) |
private FastBitSet geodesicMap
private FastBitSet mapT
private short[] mads
private AtomData atomData
private AtomDataServer viewer
private int atomCount
private FastBitSet emptySet
public static final float SURFACE_DISTANCE_FOR_CALCULATION
public static final int MAX_LEVEL
private float maxRadius
private boolean modelZeroBased
private boolean disregardNeighbors
private java.util.BitSet bsMySelected
private FastBitSet[] dotsConvexMaps
private int dotsConvexMax
private int geodesicCount
private java.util.BitSet bsSurface
private float radiusP
private float diameterP
private java.util.BitSet bsIgnore
private boolean onlySelectedDots
private boolean isSurface
private boolean multiModel
private javax.vecmath.Point3f[] currentPoints
private int indexI
private javax.vecmath.Point3f centerI
private float radiusI
private float radiiIP2
private final javax.vecmath.Point3f pointT
private javax.vecmath.Point3f centerT
private final javax.vecmath.Point3f[] vertexTest
private static int[] power4
private int neighborCount
private int[] neighborIndices
private javax.vecmath.Point3f[] neighborCenters
private float[] neighborPlusProbeRadii2
private float[] neighborRadii2
public EnvelopeCalculation(AtomDataServer viewer, int atomCount, short[] mads, boolean asJavaBitSet)
public FastBitSet[] getDotsConvexMaps()
public int getDotsConvexMax()
public void allocDotsConvexMaps(int max)
public java.util.BitSet getBsSurfaceClone()
public void setMads(short[] mads)
public void setFromBits(int index, java.util.BitSet bs)
public void newSet()
public void reCalculate(java.util.BitSet bs)
public void calculate(RadiusData rd, float maxRadius, java.util.BitSet bsSelected, java.util.BitSet bsIgnore, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel)
rd
- maxRadius
- bsSelected
- bsIgnore
- disregardNeighbors
- onlySelectedDots
- isSurface
- multiModel
- public float getRadius(int atomIndex)
public javax.vecmath.Point3f[] getPoints()
private void setDotsConvexMax()
public float getAppropriateRadius(int atomIndex)
private void setAtomI(int indexI)
private void calcConvexMap(boolean isSurface)
private void addIncompleteFaces(FastBitSet points)
private void calcConvexBits()
private AtomIndexIterator getNeighbors(AtomIndexIterator iter)
public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted, java.util.BitSet bsAtoms)