public virtual GtfTranscriptItem Next(bool exonOnly = true)
{
CheckFileOpened();
GtfTranscriptItem result = new GtfTranscriptItem();
if (this.last != null)
{
result.Add(last);
}
Func<GtfItem> getItem;
if (exonOnly)
{
getItem = () => file.NextExon();
}
else
{
getItem = () => file.Next();
}
while ((last = getItem()) != null)
{
if (result.IsSameTranscript(last))
{
if (last.Strand == '-')
{
result.Insert(0, last);
}
else
{
result.Add(last);
}
}
else
{
break;
}
}
if (result.Count > 0)
{
return result;
}
else
{
return null;
}
}
public void MatchGtfTranscriptItem(GtfTranscriptItem gtItem)
{
int index = gtItem.FindItemIndex(this.Start, this.End - 1);
if (-1 == index)
{
return;
}
GtfItem gitem = gtItem[index];
MatchExon exon = new MatchExon();
this.exons.Add(exon);
exon.TranscriptId = gitem.TranscriptId;
exon.TranscriptCount = 1;
exon.TranscriptType = gitem.Source;
Location ml = new Location();
exon.Add(ml);
if (gitem.Start > this.Start)
{
//if the peak range is out of the exon range, that peak range may be potential exon which
//is detected by RNASeq data, so just extend the peak range to expect length rather than
//extend by prior exon range
ml.Start = this.ExpectStart;
exon.IntronSize = gitem.Start - this.Start;
exon.RetainedIntron = true;
}
else if (gitem.Start <= this.ExpectStart)
{
//the exon has enough base pair
ml.Start = this.ExpectStart;
}
else
{
//the exon has no enough base pair
ml.Start = gitem.Start;
long expectLength = ml.Start - this.ExpectStart;
int curindex = index - 1;
while (expectLength > 0 && curindex >= 0)
{
Location lp = new Location();
exon.Insert(0, lp);
GtfItem prior = gtItem[curindex];
lp.End = prior.End;
if (prior.Length >= expectLength)
{
lp.Start = prior.End - expectLength + 1;
break;
}
else
{
lp.Start = prior.Start;
expectLength = expectLength - prior.Length;
curindex--;
}
}
}
if (gitem.End < this.End - 1)
{
ml.End = this.ExpectEnd;
exon.IntronSize = this.End - 1 - gitem.End;
exon.RetainedIntron = true;
}
else if (gitem.End >= this.ExpectEnd)
{
ml.End = this.ExpectEnd;
}
else
{
ml.End = gitem.End;
long expectLength = this.ExpectEnd - ml.End;
int curindex = index + 1;
while (expectLength > 0 && curindex < gtItem.Count)
{
Location lp = new Location();
exon.Add(lp);
GtfItem next = gtItem[curindex];
lp.Start = next.Start;
if (next.Length >= expectLength)
{
lp.End = next.Start + expectLength - 1;
break;
}
else
{
lp.End = next.End;
expectLength = expectLength - next.Length;
curindex++;
}
}
}
}
public void MatchGtfTranscriptItem(GtfTranscriptItem gtItem)
{
int index = gtItem.FindItemIndex(this.Start, this.End - 1);
if (-1 == index)
{
return;
}
GtfItem gitem = gtItem[index];
MatchExon exon = new MatchExon();
this.exons.Add(exon);
exon.TranscriptId = gitem.TranscriptId;
exon.TranscriptCount = 1;
exon.TranscriptType = gitem.Source;
Location ml = new Location();
exon.Add(ml);
if (gitem.Start > this.Start)
{
//if the peak range is out of the exon range, that peak range may be potential exon which
//is detected by RNASeq data, so just extend the peak range to expect length rather than
//extend by prior exon range
ml.Start = this.ExpectStart;
exon.IntronSize = gitem.Start - this.Start;
exon.RetainedIntron = true;
}
else if (gitem.Start <= this.ExpectStart)
{
//the exon has enough base pair
ml.Start = this.ExpectStart;
}
else
{
//the exon has no enough base pair
ml.Start = gitem.Start;
long expectLength = ml.Start - this.ExpectStart;
int curindex = index - 1;
while (expectLength > 0 && curindex >= 0)
{
Location lp = new Location();
exon.Insert(0, lp);
GtfItem prior = gtItem[curindex];
lp.End = prior.End;
if (prior.Length >= expectLength)
{
lp.Start = prior.End - expectLength + 1;
break;
}
else
{
lp.Start = prior.Start;
expectLength = expectLength - prior.Length;
curindex--;
}
}
}
if (gitem.End < this.End - 1)
{
ml.End = this.ExpectEnd;
exon.IntronSize = this.End - 1 - gitem.End;
exon.RetainedIntron = true;
}
else if (gitem.End >= this.ExpectEnd)
{
ml.End = this.ExpectEnd;
}
else
{
ml.End = gitem.End;
long expectLength = this.ExpectEnd - ml.End;
int curindex = index + 1;
while (expectLength > 0 && curindex < gtItem.Count)
{
Location lp = new Location();
exon.Add(lp);
GtfItem next = gtItem[curindex];
lp.Start = next.Start;
if (next.Length >= expectLength)
{
lp.End = next.Start + expectLength - 1;
break;
}
else
{
lp.End = next.End;
expectLength = expectLength - next.Length;
curindex++;
}
}
}
}