private static void computeLofK(
final ExactACset set,
final List<double[]> genotypeLikelihoods,
final double[] log10AlleleFrequencyPriors,
final StateTracker stateTracker) {
set.getLog10Likelihoods()[0] = 0.0; // the zero case
final int totalK = set.getACsum();
// special case for k = 0 over all k
if (totalK == 0) {
for (int j = 1; j < set.getLog10Likelihoods().length; j++) {
set.getLog10Likelihoods()[j] =
set.getLog10Likelihoods()[j - 1] + genotypeLikelihoods.get(j)[HOM_REF_INDEX];
}
final double log10Lof0 = set.getLog10Likelihoods()[set.getLog10Likelihoods().length - 1];
stateTracker.setLog10LikelihoodOfAFzero(log10Lof0);
stateTracker.setLog10PosteriorOfAFzero(log10Lof0 + log10AlleleFrequencyPriors[0]);
return;
}
// if we got here, then k > 0 for at least one k.
// the non-AA possible conformations were already dealt with by pushes from dependent sets;
// now deal with the AA case (which depends on previous cells in this column) and then update
// the L(j,k) value
for (int j = 1; j < set.getLog10Likelihoods().length; j++) {
if (totalK < 2 * j - 1) {
final double[] gl = genotypeLikelihoods.get(j);
final double conformationValue =
MathUtils.log10(2 * j - totalK)
+ MathUtils.log10(2 * j - totalK - 1)
+ set.getLog10Likelihoods()[j - 1]
+ gl[HOM_REF_INDEX];
set.getLog10Likelihoods()[j] =
MathUtils.approximateLog10SumLog10(set.getLog10Likelihoods()[j], conformationValue);
}
final double logDenominator = MathUtils.log10(2 * j) + MathUtils.log10(2 * j - 1);
set.getLog10Likelihoods()[j] = set.getLog10Likelihoods()[j] - logDenominator;
}
double log10LofK = set.getLog10Likelihoods()[set.getLog10Likelihoods().length - 1];
// update the MLE if necessary
stateTracker.updateMLEifNeeded(log10LofK, set.getACcounts().getCounts());
// apply the priors over each alternate allele
for (final int ACcount : set.getACcounts().getCounts()) {
if (ACcount > 0) {
log10LofK += log10AlleleFrequencyPriors[ACcount];
}
}
stateTracker.updateMAPifNeeded(log10LofK, set.getACcounts().getCounts());
}
public static void glWeightPointerARB(int size, int stride, FloatBuffer pPointer) {
ContextCapabilities caps = GLContext.getCapabilities();
long function_pointer = caps.glWeightPointerARB;
BufferChecks.checkFunctionAddress(function_pointer);
GLChecks.ensureArrayVBOdisabled(caps);
BufferChecks.checkDirect(pPointer);
if (LWJGLUtil.CHECKS)
StateTracker.getReferences(caps).ARB_vertex_blend_glWeightPointerARB_pPointer = pPointer;
nglWeightPointerARB(
size, GL11.GL_FLOAT, stride, MemoryUtil.getAddress(pPointer), function_pointer);
}
public static void glVertexAttribIPointerEXT(
int index, int size, int type, int stride, ShortBuffer buffer) {
ContextCapabilities caps = GLContext.getCapabilities();
long function_pointer = caps.glVertexAttribIPointerEXT;
BufferChecks.checkFunctionAddress(function_pointer);
GLChecks.ensureArrayVBOdisabled(caps);
BufferChecks.checkDirect(buffer);
if (LWJGLUtil.CHECKS)
StateTracker.getReferences(caps).EXT_gpu_shader4_glVertexAttribIPointerEXT_buffer = buffer;
nglVertexAttribIPointerEXT(
index, size, type, stride, buffer, buffer.position() << 1, function_pointer);
}
public void stopScrolling(boolean now) {
if (now) {
DragSortListView.this.removeCallbacks(this);
mScrolling = false;
} else {
mAbort = true;
}
if (mTrackDragScroll) {
mStateTracker.stopTracking();
}
// Debug.stopMethodTracing();
}
@Override
protected void updateState() {
mState = sWifiApState.getTriState(mView.getContext());
switch (mState) {
case STATE_DISABLED:
mIcon = R.drawable.stat_wifi_ap_off;
break;
case STATE_ENABLED:
mIcon = R.drawable.stat_wifi_ap_on;
break;
case STATE_INTERMEDIATE:
// In the transitional state, the bottom green bar
// shows the tri-state (on, off, transitioning), but
// the top dark-gray-or-bright-white logo shows the
// user's intent. This is much easier to see in
// sunlight.
if (sWifiApState.isTurningOn()) {
mIcon = R.drawable.stat_wifi_ap_on;
} else {
mIcon = R.drawable.stat_wifi_ap_off;
}
break;
}
}
public void startScrolling(int dir) {
if (!mScrolling) {
// Debug.startMethodTracing("dslv-scroll");
if (mTrackDragScroll) {
mStateTracker.startTracking();
Log.d("mobeta", "scroll tracking started");
}
mAbort = false;
mScrolling = true;
tStart = SystemClock.uptimeMillis();
mPrevTime = tStart;
mLastHeader = getHeaderViewsCount() - 1;
mFirstFooter = getCount() - getFooterViewsCount();
scrollDir = dir;
post(this);
}
}
@Override
public void onReceive(Context context, Intent intent) {
sWifiApState.onActualStateChange(context, intent);
}
@Override
protected void toggleState() {
sWifiApState.toggleState(mView.getContext());
}
private double calculateAlleleCountConformation(
final ExactACset set,
final List<double[]> genotypeLikelihoods,
final int numChr,
final Deque<ExactACset> ACqueue,
final Map<ExactACcounts, ExactACset> indexesToACset,
final double[] log10AlleleFrequencyPriors,
final StateTracker stateTracker) {
// compute the log10Likelihoods
computeLofK(set, genotypeLikelihoods, log10AlleleFrequencyPriors, stateTracker);
final double log10LofK = set.getLog10Likelihoods()[set.getLog10Likelihoods().length - 1];
// can we abort early because the log10Likelihoods are so small?
if (stateTracker.abort(log10LofK, set.getACcounts(), true, false)) {
return log10LofK;
}
// iterate over higher frequencies if possible
final int ACwiggle = numChr - set.getACsum();
if (ACwiggle
== 0) { // all alternate alleles already sum to 2N so we cannot possibly go to higher
// frequencies
return log10LofK;
}
final int numAltAlleles = set.getACcounts().getCounts().length;
// add conformations for the k+1 case
for (int allele = 0; allele < numAltAlleles; allele++) {
final int[] ACcountsClone = set.getACcounts().getCounts().clone();
ACcountsClone[allele]++;
// to get to this conformation, a sample would need to be AB (remember that ref=0)
final int PLindex = GenotypeLikelihoods.calculatePLindex(0, allele + 1);
updateACset(
ACcountsClone, numChr, set, PLindex, ACqueue, indexesToACset, genotypeLikelihoods);
}
// add conformations for the k+2 case if it makes sense; note that the 2 new alleles may be the
// same or different
if (ACwiggle > 1) {
final List<DependentSet> differentAlleles = new ArrayList<>(numAltAlleles * numAltAlleles);
final List<DependentSet> sameAlleles = new ArrayList<>(numAltAlleles);
for (int allele_i = 0; allele_i < numAltAlleles; allele_i++) {
for (int allele_j = allele_i; allele_j < numAltAlleles; allele_j++) {
final int[] ACcountsClone = set.getACcounts().getCounts().clone();
ACcountsClone[allele_i]++;
ACcountsClone[allele_j]++;
// to get to this conformation, a sample would need to be BB or BC (remember that ref=0,
// so add one to the index)
final int PLindex = GenotypeLikelihoods.calculatePLindex(allele_i + 1, allele_j + 1);
if (allele_i == allele_j) {
sameAlleles.add(new DependentSet(ACcountsClone, PLindex));
} else {
differentAlleles.add(new DependentSet(ACcountsClone, PLindex));
}
}
}
// IMPORTANT: we must first add the cases where the 2 new alleles are different so that the
// queue maintains its ordering
for (final DependentSet dependent : differentAlleles) {
updateACset(
dependent.ACcounts,
numChr,
set,
dependent.PLindex,
ACqueue,
indexesToACset,
genotypeLikelihoods);
}
for (final DependentSet dependent : sameAlleles) {
updateACset(
dependent.ACcounts,
numChr,
set,
dependent.PLindex,
ACqueue,
indexesToACset,
genotypeLikelihoods);
}
}
return log10LofK;
}
public void run() {
if (mAbort) {
mScrolling = false;
return;
}
if (mTrackDragScroll) {
mStateTracker.appendState();
}
if (scrollDir == UP) {
mScrollSpeed =
mScrollProfile.getSpeed((mUpScrollStartYF - mLastY) / mDragUpScrollHeight, mPrevTime);
} else {
mScrollSpeed =
-mScrollProfile.getSpeed(
(mLastY - mDownScrollStartYF) / mDragDownScrollHeight, mPrevTime);
}
dt = SystemClock.uptimeMillis() - mPrevTime;
// dy is change in View position of a list item; i.e. positive dy
// means user is scrolling up (list item moves down the screen,
// remember
// y=0 is at top of View).
dy = (int) Math.round(mScrollSpeed * dt);
// Log.d("mobeta", "scrolling by " + dy);
// don't bail if dy=0, touch might be at edge of scroll region; but,
// don't do any work
if (dy == 0) {
mPrevTime += dt;
post(this);
return;
}
final int first = getFirstVisiblePosition();
final int last = getLastVisiblePosition();
final int count = getCount();
final int padTop = getPaddingTop();
final int listHeight = getHeight() - padTop - getPaddingBottom();
int movePosition;
if (dy > 0) {
if (first == 0 && getChildAt(0).getTop() == padTop) {
mScrolling = false;
return;
}
movePosition = first;
dy = Math.min(listHeight, dy);
} else {
if (last == count - 1 && getChildAt(last - first).getBottom() <= listHeight + padTop) {
mScrolling = false;
return;
}
movePosition = last;
dy = Math.max(-listHeight, dy);
}
// what if movePosition is a position to be expanded/collapsed?
final int oldTop = getChildAt(movePosition - first).getTop();
int newTop = oldTop + dy;
// Log.d("mobeta",
// "movePos="+movePosition+" newTop="+newTop+" oldTop="+(newTop-dy)+" lvheight="+getHeight()+"
// fvheight="+mFloatViewHeight+" oldBottom="+getChildAt(movePosition-first).getBottom());
// Where will floating view end up given current list state?
// newFloatPos is a visual position
int newFloatPos = getFloatPosition(mLastY, movePosition, newTop);
if (newFloatPos != mExpDragPos) {
// scroll induces shuffle; adjust scroll for smoothness
if (scrollDir == DOWN && newFloatPos == movePosition) {
newTop -= mFloatViewHeight + getDividerHeight();
} else if (newFloatPos < movePosition) {
if (scrollDir == UP || (scrollDir == DOWN && movePosition == mExpDragPos)) {
newTop += mFloatViewHeight + getDividerHeight();
}
}
}
// Schedule expand/collapse where needed and update list state.
// Important that this goes before the following underscroll move.
shuffleItems(newFloatPos);
// Do underscroll (assumes/uses new list state)
// Log.d("mobeta", "viewTop=" + viewTop + " pos=" + pos +
// " itemTop=" + itemTop);
// Log.d("mobeta", "dy="+(newTop - oldTop));
setSelectionFromTop(movePosition, newTop - getPaddingTop());
DragSortListView.super.layoutChildren();
mPrevTime += dt;
post(this);
}
