public final class EnvelopeCalculation
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private AtomData |
atomData |
private BS |
bsIgnore |
private BS |
bsMySelected |
private BS |
bsSurface |
private BS |
bsTemp |
private P3 |
centerI |
private P3 |
centerT |
private P3[] |
currentPoints |
private float |
diameterP |
private boolean |
disregardNeighbors |
private BS[] |
dotsConvexMaps |
private int |
dotsConvexMax |
private static BS |
EMPTY_SET |
private int |
geodesicCount |
private BS |
geodesicMap |
private int |
indexI |
private boolean |
isSurface |
private short[] |
mads |
private BS |
mapT |
static int |
MAX_LEVEL |
private float |
maxRadius |
private boolean |
modelZeroBased |
private boolean |
multiModel |
private P3[] |
neighborCenters |
private int |
neighborCount |
private int[] |
neighborIndices |
private float[] |
neighborPlusProbeRadii2 |
private float[] |
neighborRadii2 |
private boolean |
onlySelectedDots |
private P3 |
pointT |
private static int[] |
power4 |
private float |
radiiIP2 |
private float |
radiusI |
private float |
radiusP |
static float |
SURFACE_DISTANCE_FOR_CALCULATION |
private P3[] |
vertexTest |
private AtomDataServer |
viewer |
Constructor and Description |
---|
EnvelopeCalculation(AtomDataServer viewer,
int atomCount,
short[] mads) |
Modifier and Type | Method and Description |
---|---|
private void |
addIncompleteFaces(BS points) |
void |
allocDotsConvexMaps(int max) |
private void |
calcConvexBits() |
private void |
calcConvexMap(boolean isSurface) |
void |
calculate(RadiusData rd,
float maxRadius,
BS bsSelected,
BS bsIgnore,
boolean disregardNeighbors,
boolean onlySelectedDots,
boolean isSurface,
boolean multiModel) |
void |
deleteAtoms(int firstAtomDeleted,
int nAtomsDeleted) |
float |
getAppropriateRadius(int atomIndex) |
BS |
getBsSurfaceClone() |
BS[] |
getDotsConvexMaps() |
int |
getDotsConvexMax() |
private AtomIndexIterator |
getNeighbors(AtomIndexIterator iter) |
P3[] |
getPoints() |
float |
getRadius(int atomIndex) |
void |
newSet() |
void |
reCalculate(BS bs,
Matrix3f m)
problem prior to 12.3.18 was that dots once on the deodesic were not being moved.
|
private void |
setAtomI(int indexI) |
private void |
setDotsConvexMax() |
void |
setFromBits(int index,
BS bs) |
void |
setMads(short[] mads) |
private BS geodesicMap
private BS mapT
private short[] mads
private AtomData atomData
private AtomDataServer viewer
private int atomCount
private static BS EMPTY_SET
public static final float SURFACE_DISTANCE_FOR_CALCULATION
public static final int MAX_LEVEL
private float maxRadius
private boolean modelZeroBased
private boolean disregardNeighbors
private BS bsMySelected
private BS[] dotsConvexMaps
private int dotsConvexMax
private int geodesicCount
private BS bsSurface
private float radiusP
private float diameterP
private BS bsTemp
private BS bsIgnore
private boolean onlySelectedDots
private boolean isSurface
private boolean multiModel
private P3[] currentPoints
private int indexI
private P3 centerI
private float radiusI
private float radiiIP2
private final P3 pointT
private P3 centerT
private final P3[] vertexTest
private static int[] power4
private int neighborCount
private int[] neighborIndices
private P3[] neighborCenters
private float[] neighborPlusProbeRadii2
private float[] neighborRadii2
public EnvelopeCalculation(AtomDataServer viewer, int atomCount, short[] mads)
viewer
- atomCount
- mads
- public BS[] getDotsConvexMaps()
public int getDotsConvexMax()
public void allocDotsConvexMaps(int max)
public BS getBsSurfaceClone()
public void setMads(short[] mads)
public void setFromBits(int index, BS bs)
public void newSet()
public void reCalculate(BS bs, Matrix3f m)
bs
- m
- public void calculate(RadiusData rd, float maxRadius, BS bsSelected, BS bsIgnore, boolean disregardNeighbors, boolean onlySelectedDots, boolean isSurface, boolean multiModel)
rd
- maxRadius
- bsSelected
- bsIgnore
- disregardNeighbors
- onlySelectedDots
- isSurface
- multiModel
- public float getRadius(int atomIndex)
public P3[] getPoints()
private void setDotsConvexMax()
public float getAppropriateRadius(int atomIndex)
private void setAtomI(int indexI)
private void calcConvexMap(boolean isSurface)
private void addIncompleteFaces(BS points)
private void calcConvexBits()
private AtomIndexIterator getNeighbors(AtomIndexIterator iter)
public void deleteAtoms(int firstAtomDeleted, int nAtomsDeleted)
firstAtomDeleted
- nAtomsDeleted
-