/* only call on an exon position */
private char getPeptide(int bp, SeqFeatureI sf) {
char base = '\0';
SequenceI peptides = null;
FeatureSetI parent = sf.getParent();
int pepPos = -1;
if (parent != null && parent.hasPeptideSequence()) {
peptides = parent.getPeptideSequence();
if (parent instanceof FeatureSet) {
FeatureSet fs = (FeatureSet) parent;
pepPos = fs.getPeptidePosForGenomicPos(bp);
}
if (pepPos >= 0 && pepPos < peptides.getLength()) {
base = peptides.getBaseAt(pepPos);
}
}
return base;
}
/**
* @param position
* @param tier
* @return
*/
public static int getOffset(int position, TierI tier) {
SeqFeatureI sf = null;
int offset = 0;
if (tier.featureExsitsAt(position, Level.BOTTOM)) {
sf = tier.featureAt(position, Level.BOTTOM);
ReadingFrame exonFrame = ReadingFrame.valueOf(sf.getFrame());
ReadingFrame tierFrame = tier.getReadingFrame();
if (exonFrame == ReadingFrame.NONE
&& sf.getParent() != null
&& sf.getParent().isTranscript()) {
FeatureSetI parent = sf.getParent();
Transcript parentClone = (Transcript) sf.getParent().clone();
int start = parentClone.getEnd();
// the transcript start might be different than the lowest exon start
// when in the middle of an edit
if (parentClone.canHaveChildren()) {
for (int i = 0; i < parentClone.size(); i++) {
SeqFeatureI f = parentClone.getFeatureAt(i);
if ((Strand.valueOf(f.getStrand()) == Strand.FORWARD && f.getStart() < start)
|| (Strand.valueOf(f.getStrand()) == Strand.REVERSE && f.getStart() > start))
start = f.getStart();
}
}
int translationStart = parentClone.getTranslationStart();
int translationPos = parentClone.getFeaturePosition(translationStart);
int oldstart = start;
start += ((translationPos - 1) % 3) * parentClone.getStrand();
parentClone.setTranslationStart(start);
parentClone.setTranslationEnd(parentClone.getEnd());
parentClone.setPeptideSequence(null);
String translation = parentClone.translate();
SequenceI sequence = parentClone.getPeptideSequence();
int index = parent.getFeatureIndex(sf);
exonFrame = ReadingFrame.valueOf(parentClone.getFeatureAt(index).getFrame());
}
if (tierFrame != exonFrame && sf.getParent() != null && sf.getParent().isTranscript()) {
if (tierFrame == ReadingFrame.THREE) {
offset = exonFrame == ReadingFrame.ONE ? -2 : -1;
} else if (tierFrame == ReadingFrame.TWO) {
offset = exonFrame == ReadingFrame.ONE ? -1 : 1;
} else if (tierFrame == ReadingFrame.ONE) {
offset = exonFrame == ReadingFrame.TWO ? 1 : 2;
}
}
if (exonFrame == ReadingFrame.NONE) {
offset = 0;
}
}
return offset;
}
/**
* Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset
* currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and
* set isExon flag
*/
public Component getBaseComponent(int position, TierI tier, Orientation o) {
transcript = null;
int bp = tier.getBasePair(position);
int oldPos = position;
// We need to change the position if dealing with aa view
if (tier.getType() == SequenceType.AA) {
int offset = getOffset(position, tier);
bp += offset * tier.getStrand().toInt();
position = tier.getPosition(bp);
}
char base = tier.charAt(position);
if (tier.featureExsitsAt(position, TierI.Level.BOTTOM)) {
this.state = State.EXON;
SeqFeatureI feature = tier.featureAt(position, TierI.Level.BOTTOM);
Transcript parentClone = null;
Transcript otherParentClone = null;
if (tier.getType() == SequenceType.AA
&& feature.getParent() != null
&& feature.getParent().isTranscript()) {
FeatureSetI parent = feature.getParent();
int index = parent.getFeatureIndex(feature);
int start = parent.getEnd();
// the transcript start might be different than the lowest exon start
// when in the middle of an edit
if (parent.canHaveChildren()) {
for (int i = 0; i < parent.size(); i++) {
SeqFeatureI sf = parent.getFeatureAt(i);
if ((Strand.valueOf(sf.getStrand()) == Strand.FORWARD && sf.getStart() < start)
|| (Strand.valueOf(sf.getStrand()) == Strand.REVERSE && sf.getStart() > start))
start = sf.getStart();
}
}
int translationStart = parent.getTranslationStart();
int translationEnd = parent.getTranslationEnd();
int translationPos = parent.getFeaturePosition(translationStart);
int oldstart = start;
start += ((translationPos - 1) % 3) * parent.getStrand();
// Tring to avoid all the recalculation...
if (feature.getParent() == currentParent
&& start == currentStart
&& featureStart == feature.getStart()
&& featureEnd == feature.getEnd()) {
parentClone = currentParentClone;
otherParentClone = currentParentClone2;
} else {
// need to get a full translation so that we can get the amino acids
// in the UTR region
parentClone = (Transcript) feature.getParent().clone();
otherParentClone = (Transcript) feature.getParent().clone();
if (!parentClone.setTranslationStart(start)) {
start = oldstart;
TranslationI cds = otherParentClone.getTranslation();
cds.calcTranslationStartForLongestPeptide();
translationStart = otherParentClone.getTranslationStart();
translationPos = otherParentClone.getFeaturePosition(translationStart);
start += ((translationPos - 1) % 3) * otherParentClone.getStrand();
parentClone.setTranslationStart(start);
}
parentClone.setTranslationEnd(parentClone.getEnd());
parentClone.setPeptideSequence(null);
String translation = parentClone.translate();
SequenceI sequence = parentClone.getPeptideSequence();
currentParent = (Transcript) feature.getParent();
currentParentClone = parentClone;
currentParentClone2 = otherParentClone;
currentStart = start;
featureStart = feature.getStart();
featureEnd = feature.getEnd();
if (otherParentClone.getFeatureContaining(translationEnd) == null) {
TranslationI cds = otherParentClone.getTranslation();
cds.setTranslationEndFromStart();
}
}
SeqFeatureI sf = parentClone.getFeatureAt(index);
if (bp >= sf.getLow() && bp <= sf.getHigh()) {
base = getPeptide(bp, sf);
} else {
base = '\0';
}
if (otherParentClone != null) {
feature = otherParentClone.getFeatureAt(index);
}
} else if (tier.getType() == SequenceType.AA
&& feature.getParent() != null
&& !feature.getParent().isTranscript()) {
base = '\0';
}
if (isUTR(bp, feature, tier)) {
this.state = State.UTR;
}
if (isTranslationStart(bp, feature)) {
this.state = State.TRANSLATION_START;
}
if (isTranslationEnd(bp, feature)) {
this.state = State.TRANSLATION_END;
}
// Can have an error or a shift on a position but not both
if (isSequencingErrorPosition(bp, feature, tier.getType())) {
this.state = State.ERROR;
// set base to the base of the new sequence?
}
if (isShiftPosition(bp, feature, tier.getType())) {
this.state = State.SHIFT;
}
} else if (tier.featureExsitsAt(position, TierI.Level.TOP)) {
SeqFeatureI feature = tier.featureAt(position, Level.TOP);
this.state = State.INTRON;
if (tier.getType() == SequenceType.AA) {
base = '\0';
}
int start = feature.getEnd();
int end = feature.getStart();
if (feature.canHaveChildren()) {
for (int i = 0; i < feature.size(); i++) {
SeqFeatureI sf = feature.getFeatureAt(i);
if ((Strand.valueOf(sf.getStrand()) == Strand.FORWARD && sf.getStart() < start)
|| (Strand.valueOf(sf.getStrand()) == Strand.REVERSE && sf.getStart() > start))
start = sf.getStart();
if ((Strand.valueOf(sf.getStrand()) == Strand.FORWARD && sf.getEnd() > end)
|| (Strand.valueOf(sf.getStrand()) == Strand.REVERSE && sf.getEnd() < end))
end = sf.getEnd();
}
}
if (bp <= Math.min(start, end) || bp >= Math.max(start, end)) {
this.state = State.OUT;
base = '\0';
}
} else {
this.state = State.OUT;
base = '\0';
}
if (!(state == State.SHIFT || state == State.ERROR)
&& getRegionLow() <= position
&& position <= getRegionHigh()) {
this.state = State.SELECTED;
base = tier.charAt(oldPos);
}
init(base);
return this;
}