void THISTimeline::exportEntireSequence()
{
exporter->startFrame = 0;
exporter->endFrame = getSequenceLength()-1;
startExport();
}
unsigned char* THISTimeline::getSourcePixelsForFrame(int offset, bool thumb)
{
float channel = sourcekeys->sampleTimelineAt(offset/(getSequenceLength()-1.0f));
if(channel > .5){
return sourceA->getPixelsForFrame(offset, thumb);
}
else{
return sourceB->getPixelsForFrame(offset, thumb);
}
}
void Genome::copySequence(Genome *dest) const
{
DNAIteratorConstPtr inDna = getDNAIterator();
DNAIteratorPtr outDna = dest->getDNAIterator();
hal_size_t n = getSequenceLength();
assert(n == dest->getSequenceLength());
for (; (hal_size_t)inDna->getArrayIndex() < n; inDna->toRight(),
outDna->toRight())
{
outDna->setChar(inDna->getChar());
}
}
float* THISTimeline::getBlendedDistortionFrame(float percent, bool thumb)
{
int index = distortion->getIndexAtPercent(percent);
if(index < 0 || index >= blendedDistortionThumbnails.size() || index >= blendedDistortion.size()){
ofLog(OF_LOG_ERROR, "THISTimeline -- Asking for index %d when we only have %d frames", index, blendedDistortion.size());
return NULL;
}
//cout << "asking for distortion at index " << index << " percent " << percent << endl;
BlendedDistortionFrame* bdf = thumb ? &blendedDistortionThumbnails[index] : &blendedDistortion[index];
int fullDistortionWidth = getDistortionWidth(percent);
int taperedDistortionWidth = MAX(fullDistortionWidth * blendkeys->sampleTimelineAt(percent), 1);
if(!bdf->loaded || bdf->distortionWidth != taperedDistortionWidth){
int imgwidth = thumb ? distortion->getThumbWidth() : distortion->getImageWidth();
int imgheight = thumb ? distortion->getThumbHeight() : distortion->getImageHeight();
if(bdf->pixels == NULL){
bdf->pixels = new float[imgwidth*imgheight];
}
memset(bdf->pixels, 0, sizeof(float)*imgwidth*imgheight);
int midIndex = getWindowStartFrame(percent) + fullDistortionWidth/2;
int startIndex = midIndex - (taperedDistortionWidth / 2);
int endIndex = midIndex + ((1+taperedDistortionWidth) / 2);
if(startIndex >= endIndex){
endIndex = startIndex+1;
}
//add all the images together...
for(int i = startIndex; i < MIN(endIndex, getSequenceLength()-1); i++){
unsigned char* distortionPixels = distortion->getPixelsForFrame(i, thumb);
for(int y = 0; y < imgheight; y++){
for(int x = 0; x < imgwidth; x++){
bdf->pixels[y*imgwidth+x] += distortionPixels[y*imgwidth+x];
}
}
}
//average
for(int i = 0; i < imgwidth*imgheight; i++){
bdf->pixels[i] /= (taperedDistortionWidth*255.0);
}
bdf->loaded = true;
bdf->distortionWidth = taperedDistortionWidth;
}
bdf->lastUsedTime = ofGetElapsedTimef();
return bdf->pixels;
}
void THISTimeline::togglePlayback()
{
if(exporting) return;
if(isPlayingBack){
isPlayingBack = false;
}
else{
isPlayingBack = true;
rollingOverPlayhead = true;
playbackStartTime = ofGetElapsedTimef();
percentPerFrame = 1. / getSequenceLength();
}
}
void ReadsLayout::getVcoverage(size_t listIndex, bool direction, vector<unsigned int> &cov)
{
unsigned int pos;
unsigned int sequenceLength=getSequenceLength(listIndex);
int rl=R->getReadsLength();
size_t index;
cov.clear();
cov.assign(sequenceLength,0);
vector<unsigned int> tmp;
tmp.assign(sequenceLength,0);
if (direction)
{
index = getBegin(listIndex);
while (index != 0)
{
pos = getPosition(index);
cov[pos - 1]++;
index = getNext(index);
}
}
else
{
index = listIndex;
sequenceLength-= (rl-1);
while (index != 0)
{
pos = getPosition(index);
pos=sequenceLength-pos;
cov[pos]++;
index = getPrevious(index);
}
}
tmp[0]=cov[0];
for (size_t i=1; i<cov.size(); i++)
{
cov[i]=cov[i]+cov[i-1];
tmp[i]=cov[i];
}
for (size_t i=rl; i<cov.size(); i++)
cov[i]-=tmp[i-rl];
}
float* THISTimeline::getBlendedDistortionFrame(int index, bool thumb)
{
return getBlendedDistortionFrame(index/(getSequenceLength()-1.0f), thumb);
}
int THISTimeline::getDistortionWidth(int baseFrame)
{
return getDistortionWidth(baseFrame/(getSequenceLength()-1.0f));
}
int THISTimeline::getWindowEndFrame(float percent)
{
return MIN(getWindowStartFrame(percent) + getDistortionWidth( percent ), getSequenceLength()-1);
}
int THISTimeline::getWindowEndFrame(int baseFrame)
{
return getWindowEndFrame( (baseFrame+.5f)/(getSequenceLength()-1.0f) );
}
void THISTimeline::draw()
{
//update keyframers
minwidthkeys->setZoomBounds(zoomer->getViewRange());
maxwidthkeys->setZoomBounds(zoomer->getViewRange());
sourcekeys->setZoomBounds(zoomer->getViewRange());
blendkeys->setZoomBounds(zoomer->getViewRange());
if(!zoomer->isActive()){
sourceA->setDrawRange(zoomer->getViewRange());
sourceB->setDrawRange(zoomer->getViewRange());
distortion->setDrawRange(zoomer->getViewRange());
}
if(exporting && !exporter->isExporting()){
exporting = false;
minwidthkeys->enable();
maxwidthkeys->enable();
sourcekeys->enable();
blendkeys->enable();
zoomer->enable();
}
if(isPlayingBack){
zoomedPlayheadFloatPosition = ofMap(ofGetElapsedTimef(), playbackStartTime, playbackStartTime+(getLastFrameInView()-getFirstFrameInView())/25., 0, zoomer->getViewRange().max-zoomer->getViewRange().min, false);
zoomedPlayheadFloatPosition = zoomer->getViewRange().min + fmod(zoomedPlayheadFloatPosition, zoomer->getViewRange().max-zoomer->getViewRange().min);
}
//-------- POSITION ALL ELEMENTS
//-------- COMP ELEMENTS
newCompButton->setPos(uiposition.x, uiposition.y);
newCompButton->setSize(BIG_BUTTON_WIDTH, BIG_BUTTON_HEIGHT);
loadCompButton->setPos(uiposition.x, uiposition.y+BIG_BUTTON_HEIGHT+ELEMENT_SPACER);
loadCompButton->setSize(BIG_BUTTON_WIDTH, BIG_BUTTON_HEIGHT);
// loadSourceBButton->setPos(uiposition.x, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*2);
// loadSourceBButton->setSize(BIG_BUTTON_WIDTH, BIG_BUTTON_HEIGHT);
//
// loadDistortionButton->setPos(uiposition.x, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*3);
// loadDistortionButton->setSize(BIG_BUTTON_WIDTH, BIG_BUTTON_HEIGHT);
//
// setOutputDirectoryButton->setPos(uiposition.x, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*4);
// setOutputDirectoryButton->setSize(BIG_BUTTON_WIDTH, BIG_BUTTON_HEIGHT);
//------------- EXPORT BUTTONS
exportCurrentViewButton->setPos(uiposition.x, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*5);
exportCurrentViewButton->setSize(BIG_BUTTON_WIDTH/3.0, BIG_BUTTON_HEIGHT);
exportEntireSequenceButton->setPos(uiposition.x+BIG_BUTTON_WIDTH/3.0, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*5);
exportEntireSequenceButton->setSize(BIG_BUTTON_WIDTH/3.0, BIG_BUTTON_HEIGHT);
cancelExportButton->setPos(uiposition.x+2*BIG_BUTTON_WIDTH/3.0, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*5);
cancelExportButton->setSize(BIG_BUTTON_WIDTH/3.0, BIG_BUTTON_HEIGHT);
//---------- TIMELINE ELEMENTS
THISSequence* loadedReferenceSource = NULL;
if(sourceA->isLoaded()) loadedReferenceSource = sourceA;
else if(sourceB->isLoaded()) loadedReferenceSource = sourceB;
else if(distortion->isLoaded()) loadedReferenceSource = distortion;
float sourcePreviewHeight = SOURCE_PREVIEW_HEIGHT;
if(loadedReferenceSource != NULL){
sourcePreviewHeight = loadedReferenceSource->heightPerFrame;
}
//frame ticker //3 previews //5 keyframes //A-B Switch //zoomer
float totalHeight = FRAME_TICKER_HEIGHT + sourcePreviewHeight*3 + KEYFRAME_HEIGHT*4 + GRAPH_HEIGHT + SWITCHER_HEIGHT + FRAME_TICKER_HEIGHT + ELEMENT_SPACER*4;
float totalWidth = width-BUTTON_WIDTH*2;
playheadBar->setPos(position.x+BUTTON_WIDTH, position.y);
playheadBar->setSize(totalWidth, totalHeight);
//---------- KEYFRAME POSITIONS
float keyframeStartY = position.y+FRAME_TICKER_HEIGHT+sourcePreviewHeight*3+ELEMENT_SPACER;
maxwidthkeys->setDrawRect(ofRectangle(BUTTON_WIDTH, keyframeStartY, totalWidth, KEYFRAME_HEIGHT));
//inbetween is the min/max visualizer
minwidthkeys->setDrawRect(ofRectangle(BUTTON_WIDTH, keyframeStartY+KEYFRAME_HEIGHT+GRAPH_HEIGHT, totalWidth, KEYFRAME_HEIGHT));
sourcekeys->setDrawRect(ofRectangle(BUTTON_WIDTH, keyframeStartY+KEYFRAME_HEIGHT*2+GRAPH_HEIGHT+ELEMENT_SPACER, totalWidth, SWITCHER_HEIGHT));
blendkeys->setDrawRect(ofRectangle(BUTTON_WIDTH, keyframeStartY+KEYFRAME_HEIGHT*2+GRAPH_HEIGHT+SWITCHER_HEIGHT+ELEMENT_SPACER*2, totalWidth, KEYFRAME_HEIGHT));
zoomer->setDrawRect(ofRectangle(BUTTON_WIDTH, keyframeStartY+KEYFRAME_HEIGHT*3+GRAPH_HEIGHT+SWITCHER_HEIGHT+ELEMENT_SPACER*3, totalWidth, FRAME_TICKER_HEIGHT));
// cout << "CHECK 3: cur comp " << currentCompFolder << endl;
//----------- BEGIN DRAWING
ofPushStyle();
//draw UI elements
ofNoFill();
ofSetColor(80, 80, 80);
ofRect(newCompButton->x,newCompButton->y, newCompButton->width, newCompButton->height );
ofDrawBitmapString("new comp", newCompButton->x + 10, newCompButton->y + 15);
ofRect(loadCompButton->x,loadCompButton->y, loadCompButton->width,loadCompButton->height);
ofDrawBitmapString("load comp", loadCompButton->x + 10, loadCompButton->y + 15);
float yStart = loadCompButton->y+loadCompButton->height+20;
ofRect(loadCompButton->x,yStart, loadCompButton->width, 80);
ofDrawBitmapString("Comp " + currentCompFolder +
"\nSource A " + sourceA->directory +
"\nSource B " + sourceB->directory +
"\nDistortion " + distortion->directory +
"\nOutput " + exporter->pathPrefix,
loadCompButton->x + 10, yStart + 15);
ofRect(exportCurrentViewButton->x,exportCurrentViewButton->y, exportCurrentViewButton->width,exportCurrentViewButton->height);
ofDrawBitmapString("export\ncurrent view", exportCurrentViewButton->x + 10, exportCurrentViewButton->y + 15);
ofRect(exportEntireSequenceButton->x,exportEntireSequenceButton->y, exportEntireSequenceButton->width,exportEntireSequenceButton->height);
ofDrawBitmapString("export\nentire sequence", exportEntireSequenceButton->x + 10, exportEntireSequenceButton->y + 15);
ofRect(cancelExportButton->x,cancelExportButton->y, cancelExportButton->width,cancelExportButton->height);
ofDrawBitmapString("cancel export", cancelExportButton->x + 10, cancelExportButton->y + 15);
ofPopStyle();
//draw frame ticker
//TODO: put into timeline object
int firstFrame = getFirstFrameInView();
int lastFrame = getLastFrameInView();
int totalFrames = (lastFrame - firstFrame);
ofDrawBitmapString("First Frame: " + ofToString(firstFrame) + "\n"+
"Last Frame: " + ofToString(lastFrame) + "\n" +
"Total Frames: " + ofToString(totalFrames), frameInfoPosition);
if(!allSequencesLoaded()){
return;
}
ofPushStyle();
//---------- PROGRESS
ofNoFill();
ofRect(uiposition.x, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*6, BIG_BUTTON_WIDTH, BIG_BUTTON_HEIGHT/2);
if(exporting){
float percentDone = exporter->getPercentDone();
ofFill();
ofSetColor(200, 200, 100, 40);
ofRect(uiposition.x, uiposition.y+(BIG_BUTTON_HEIGHT+ELEMENT_SPACER)*6, BIG_BUTTON_WIDTH*percentDone, BIG_BUTTON_HEIGHT/2);
}
//draw frame numbers
//---------- frame Info
float pixelsPerFrame = (width-BUTTON_WIDTH*2.0) / totalFrames;
int frameStep = 1;
bool drawFullRect = false;
if(pixelsPerFrame < .5){
frameStep = 20;
drawFullRect = true;
}
else if(pixelsPerFrame < 1.0){
frameStep = 10;
drawFullRect = true;
}
else if(pixelsPerFrame < 2.0){
frameStep = 5;
}
else if(pixelsPerFrame < 4.0){
frameStep = 2;
}
if(drawFullRect){
ofSetColor(200, 200, 100, 40);
ofRect(BUTTON_WIDTH, position.y+FRAME_TICKER_HEIGHT/2., totalWidth, FRAME_TICKER_HEIGHT/2);
}
ofSetColor(200, 200, 100, 100);
for(int i = 0; i <= totalFrames; i+=frameStep){
float xPixelPos = ofMap(i, 0, totalFrames, BUTTON_WIDTH, width-BUTTON_WIDTH, true);
ofLine(xPixelPos, position.y+FRAME_TICKER_HEIGHT/2., xPixelPos, position.y+FRAME_TICKER_HEIGHT);
}
ofSetColor(255, 255, 255);
sourceA->setDrawWidth(totalWidth);
sourceB->setDrawWidth(totalWidth);
distortion->setDrawWidth(totalWidth);
//backgroup
ofSetColor(0, 0, 0);
ofRect(position.x + BUTTON_WIDTH, position.y+FRAME_TICKER_HEIGHT, totalWidth, sourcePreviewHeight*3);
ofSetColor(255, 255, 255);
sourceA->draw(position.x + BUTTON_WIDTH, position.y+FRAME_TICKER_HEIGHT);
sourceB->draw(position.x + BUTTON_WIDTH, position.y+FRAME_TICKER_HEIGHT+sourcePreviewHeight);
distortion->draw(position.x + BUTTON_WIDTH, position.y+FRAME_TICKER_HEIGHT+sourcePreviewHeight*2);
ofEnableSmoothing();
ofEnableAlphaBlending();
ofSetColor(40, 40, 40);
//---------- DRAW .5 LINE
ofLine(BUTTON_WIDTH, sourcekeys->getDrawRect().y + .5*sourcekeys->getDrawRect().height,
BUTTON_WIDTH+totalWidth, sourcekeys->getDrawRect().y + .5*sourcekeys->getDrawRect().height);
//--------DRAW MIN-MAX GRAPH VISUALIZATION
float minMaxVisualizerOffset = keyframeStartY + KEYFRAME_HEIGHT;
ofSetColor(200, 120, 0);
for(int i = 0; i <= totalWidth; i+=4){
//draw lines, then blank out with bars
ofLine(BUTTON_WIDTH+i, minMaxVisualizerOffset, BUTTON_WIDTH+i, minMaxVisualizerOffset+GRAPH_HEIGHT);
}
ofSetColor(20, 20, 20);
ofFill();
for(int i = 0; i <= totalWidth; i+=2){
float samplepos = ofMap(1.0f*i/totalWidth,0,1.0, zoomer->getViewRange().min, zoomer->getViewRange().max, true);
//toprect
ofRect(BUTTON_WIDTH+i, minMaxVisualizerOffset, 2, (1-maxwidthkeys->sampleTimelineAt(samplepos))*GRAPH_HEIGHT);
//bottomrect
float bottomheight = minwidthkeys->sampleTimelineAt(samplepos)*GRAPH_HEIGHT;
ofRect(BUTTON_WIDTH+i, minMaxVisualizerOffset + (GRAPH_HEIGHT-bottomheight), 2, bottomheight);
}
//---------- DRAW KEYFRAMES
maxwidthkeys->draw();
minwidthkeys->draw();
sourcekeys->draw();
blendkeys->draw();
zoomer->draw();
if(loadedReferenceSource != NULL){
ofSetColor(200, 200, 100, 100);
//draw lines for preview points
for(int i = 0; i < loadedReferenceSource->previewTextures.size(); i++){
float xPixelPos = loadedReferenceSource->previewTextures[i].bounds.x + BUTTON_WIDTH;
ofLine(xPixelPos, position.y, xPixelPos, position.y+FRAME_TICKER_HEIGHT+sourcePreviewHeight*3);
ofDrawBitmapString(ofToString(loadedReferenceSource->previewTextures[i].frameIndex), xPixelPos+3, position.y+5);
}
}
//--------------- DRAW PLAYHEAD
if(rollingOverPlayhead){
ofSetColor(255, 0, 0, 100);
float playheadX = position.x + BUTTON_WIDTH + totalWidth*playheadFloatPosition;
ofLine(playheadX, position.y,
playheadX, position.y+totalHeight-FRAME_TICKER_HEIGHT-ELEMENT_SPACER);
//draw distortion width
if(loadedReferenceSource != NULL){
ofSetColor(255, 0, 0, 50);
float minXPercent = ofMap(getCurrentWindowStartFrame(), 0, getSequenceLength()-1, 0.0, 1.0, true);
float maxXPercent = ofMap(getCurrentWindowEndFrame(), 0, getSequenceLength()-1, 0.0, 1.0, true);
float minX = BUTTON_WIDTH + ofMap(minXPercent, zoomer->getViewRange().min, zoomer->getViewRange().max, 0, totalWidth, true);
float maxX = BUTTON_WIDTH + ofMap(maxXPercent, zoomer->getViewRange().min, zoomer->getViewRange().max, 0, totalWidth, true);
ofRect(minX, position.y+FRAME_TICKER_HEIGHT, (maxX-minX), totalHeight-FRAME_TICKER_HEIGHT*2-ELEMENT_SPACER);
ofSetColor(255, 200, 20);
//draw frame ticker
ofDrawBitmapString(ofToString(getCurrentWindowStartFrame()), ofPoint(minX, position.y-10)) ;
//draw frame ticker
ofDrawBitmapString(ofToString(getCurrentWindowEndFrame()), ofPoint(maxX, position.y+10)) ;
}
ofSetColor(255, 200, 20);
//draw frame ticker
ofDrawBitmapString(ofToString(loadedReferenceSource->getIndexAtPercent(zoomedPlayheadFloatPosition)), ofPoint(playheadX, position.y)) ;
}
ofPopStyle();
return;
ofSetColor(255, 255, 0, 255);
ofLine(position.x + BUTTON_WIDTH + totalWidth*playheadPosition, position.y,
position.x + BUTTON_WIDTH + totalWidth*playheadPosition, position.y+totalHeight-FRAME_TICKER_HEIGHT-ELEMENT_SPACER);
ofNoFill();
ofSetColor(255,0,255);
ofRect(position.x + BUTTON_WIDTH, position.y+FRAME_TICKER_HEIGHT, totalWidth, sourcePreviewHeight*3);
//------ DRAW DISABLED FIELD
if(exporting){
ofFill();
ofSetColor(200, 200, 200, 20);
ofRect(position.x+BUTTON_WIDTH, position.y, totalWidth, totalHeight);
}
ofPopStyle();
sourceA->purgeThumbs();
sourceB->purgeThumbs();
distortion->purgeThumbs();
}
int main( int argc, char *argv[] ) {
char seqChar[MAXSEQLENGTH];
int seqNum[MAXSEQLENGTH+1];
DBL_TYPE pf;
int complexity = 3;
int length, tmpLength;
char inputFile[ MAXLINE];
int vs;
char sampleFile[MAXLINE];
//permAvgPairs stores the expected value of each
//class of base pairs, grouped by permutation or complex, respectively
int inputFileSpecified;
FILE *F_sample = NULL; // ppairs file
int index;
strcpy( inputFile, "");
nupack_sample = 1;
nupack_num_samples = 10;
struct timeval rand_time;
gettimeofday(&rand_time,0);
nupack_random_seed = (rand_time.tv_sec)*1000000 + rand_time.tv_usec;
inputFileSpecified = ReadCommandLineNPK( argc, argv, inputFile);
if(NupackShowHelp) {
printf("Usage: sample [OPTIONS] PREFIX\n");
printf("Randomly sample unpseudoknotted structures from the equilibrium distribution\n");
printf("Example: sample -multi -T 25 -material dna -samples 100 example\n");
PrintNupackThermoHelp();
PrintNupackUtilitiesHelp();
exit(1);
}
if( !inputFileSpecified ) {
printf("Enter output file prefix: ");
scanf("%s", inputFile);
strcat(inputFile,".in"); // Here, .in is just a placeholder
}
if(!inputFileSpecified ||
!ReadInputFile( inputFile, seqChar, &vs, NULL, NULL, NULL) ) {
if (inputFileSpecified==0) getUserInput( seqChar, &vs, NULL, NULL);
else abort();
}
strncpy(sampleFile,inputFile,strlen(inputFile)-3);
sampleFile[strlen(inputFile)-3] = '\0';
strcat(sampleFile,".sample");
header( argc, argv, "sample", sampleFile);
printInputs( argc, argv, seqChar, vs, NULL, NULL,sampleFile);
tmpLength = length = strlen( seqChar);
convertSeq(seqChar, seqNum, tmpLength);
int ns1,ns2;
getSequenceLength(seqChar, &ns1);
getSequenceLengthInt(seqNum, &ns2);
init_genrand(nupack_random_seed);
pairPr = NULL;
if (complexity != 3) {
printf("Sampling supported only for complexity = 3. Exiting\n");
exit(1);
}
nupack_sample_list = (char **)calloc(nupack_num_samples, sizeof(char *));
printf("Number of Samples = %i\n",nupack_num_samples);
for(index = 0 ; index < nupack_num_samples ; index++) {
nupack_sample_list[index] = (char *) calloc(tmpLength+1,sizeof(char));
}
printf("Started Calculation\n");
pf = pfuncFull(seqNum, complexity, DNARNACOUNT, DANGLETYPE, TEMP_K - ZERO_C_IN_KELVIN, 0,
SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
printf("Finished Calculation\n");
if ((F_sample = fopen(sampleFile,"a")) == NULL) {
printf("Error opening file %s!\n",sampleFile);
exit(1);
}
// Print the free energy to the output file
fprintf(F_sample,"%s Free energy: %.8Le kcal/mol\n",
COMMENT_STRING,-kB*TEMP_K*logl(pf));
fprintf(F_sample,"%s Number of Samples: %i\n",COMMENT_STRING,nupack_num_samples);
// Put newline for stylistic reasons
fprintf(F_sample,"\n");
for(index = 0 ; index < nupack_num_samples ; index++) {
fprintf(F_sample, "%s\n",nupack_sample_list[index]);
free(nupack_sample_list[index]);
nupack_sample_list[index] = NULL;
}
free(nupack_sample_list);
#ifdef GC_DEBUG
CHECK_LEAKS();
#endif
return 0;
}
updateSize();
updateVisibleRange();
}
void DetView::setDisabledDetViewActions(bool t){
showTranslationAction->setDisabled(t);
showComplementAction->setDisabled(t);
wrapSequenceAction->setDisabled(t);
}
int DetView::getShift() const {
return isWrapMode() ? currentShiftsCounter * getDetViewRenderArea()->getShiftHeight() : 0;
}
void DetView::ensurePositionVisible(int pos) {
CHECK(pos >= 0 && pos <= getSequenceLength(), );
DetViewRenderArea* detViewRenderArea = getDetViewRenderArea();
if (isWrapMode()) {
if (!visibleRange.contains(pos)) {
if (pos < visibleRange.startPos) {
// scroll up till the line is visible
int line = pos / getSymbolsPerLine();
int listStartPos = line * getSymbolsPerLine();
visibleRange.startPos = listStartPos;
currentShiftsCounter = detViewRenderArea->getDirectLine() + 1;
} else {
// scroll down till the line becomes visible
const int line = pos / getSymbolsPerLine();
const int visibleShiftsCount = detViewRenderArea->height() / detViewRenderArea->getShiftHeight();
const int shiftToEnsureIsVisible = line * numShiftsInOneLine + detViewRenderArea->getDirectLine() + 1;
unsigned int ReadsLayout::sampleOH(size_t listIndex,
bool dir,
unsigned int maxD,
unsigned int maxN,
unsigned int *distr)
{
unsigned int index;
unsigned int pos;
int nodeLength=getSequenceLength(listIndex);
unsigned int rl=R->getReadsLength();
unsigned int nOverlap=0;
unsigned int mult;
int oh; //overhang
if (dir)
{
index = getBegin(listIndex);
pos = 1;
index = getNext(index);
while (index != 0)
{
if (pos > maxD && maxD!=0)
break;
if (nOverlap > maxN && nOverlap!=0)
break;
mult = 1;
oh = getPosition(index) - pos;
while (oh == 0)
{
mult++;
index = getNext(index);
if (index == 0)
break;
oh = getPosition(index) - pos;
}
if (mult > 1)
{
nOverlap += mult - 1;
mult = (mult * mult) - mult;
distr[0] += mult;
if (index == 0)
break;
}
distr[oh]++;
nOverlap++;
pos += oh;
index = getNext(index);
}
}
else
{
pos=nodeLength-rl+1;
index = getPrevious(listIndex);
while (index != 0)
{
if (nodeLength - (pos+rl-1) > maxD && maxD!=0)
break;
if (nOverlap > maxN && nOverlap!=0)
break;
mult = 1;
oh = pos - getPosition(index);
while (oh == 0)
{
mult++;
index = getPrevious(index);
if (index == 0)
break;
oh = pos - getPosition(index);
}
if (mult > 1)
{
nOverlap += mult - 1;
mult = (mult * mult) - mult;
distr[0] += mult;
if (index == 0)
break;
}
distr[oh]++;
nOverlap++;
pos -= oh;
index = getPrevious(index);
}
}
return nOverlap;
}