jkOwnLib/trans3.c File Reference

#include "common.h"
#include "dnaseq.h"
#include "trans3.h"

Include dependency graph for trans3.c:

Go to the source code of this file.

Functions
trans3 *	trans3New (struct dnaSeq *seq)
void	trans3Free (struct trans3 **pT3)
void	trans3FreeList (struct trans3 **pList)
trans3 *	trans3Find (struct hash *t3Hash, char *name, int start, int end)
void	trans3Offset (struct trans3 *t3List, AA *aa, int *retOffset, int *retFrame)
int	trans3GenoPos (char *pt, bioSeq *seq, struct trans3 *t3List, boolean isEnd)
int	trans3Frame (char *pt, struct trans3 *t3List)
Variables
static char const	rcsid [] = "$Id: trans3.c,v 1.5 2007/04/20 22:43:37 kent Exp $"

---

Function Documentation

struct trans3* trans3Find	(	struct hash *	t3Hash,
		char *	name,
		int	start,
		int	end
	)			[read]

Definition at line 62 of file trans3.c.

References trans3::end, hashFindVal(), internalErr, trans3::next, and trans3::start.

Referenced by gfAlignTrans(), gfAlignTransTrans(), and untranslateRangeList().

{
struct trans3 *t3;
for (t3 = hashFindVal(t3Hash, name); t3 != NULL; t3 = t3->next)
    {
    if (t3->start <= start && t3->end >= end)
        return t3;
    }
internalErr();
return NULL;
}

Here is the call graph for this function:

Here is the caller graph for this function:

int trans3Frame	(	char *	pt,
		struct trans3 *	t3List
	)

Definition at line 126 of file trans3.c.

References FALSE, and trans3GenoPos().

Referenced by saveAxtBundle().

{
if (t3List == NULL)
    return 0;
else
    return 1 + trans3GenoPos(pt, NULL, t3List, FALSE)%3;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void trans3Free

(

struct trans3 **

pT3

)

Definition at line 36 of file trans3.c.

References freeDnaSeq(), freez(), and trans3::trans.

Referenced by gfAlignTrans(), gfAlignTransTrans(), gfMakeOoc(), gfTransTransFindBundles(), trans3FreeList(), transCountBothStrands(), transIndexBothStrands(), and transTransQuery().

{
struct trans3 *t3 = *pT3;
if (t3 != NULL)
    {
    freeDnaSeq(&t3->trans[0]);
    freeDnaSeq(&t3->trans[1]);
    freeDnaSeq(&t3->trans[2]);
    freez(pT3);
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void trans3FreeList

(

struct trans3 **

pList

)

Definition at line 49 of file trans3.c.

References trans3::next, and trans3Free().

Referenced by bigBlat().

{
struct trans3 *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    trans3Free(&el);
    }
*pList = NULL;
}

Here is the call graph for this function:

Here is the caller graph for this function:

int trans3GenoPos	(	char *	pt,
		bioSeq *	seq,
		struct trans3 *	t3List,
		boolean	isEnd
	)

Definition at line 99 of file trans3.c.

References dnaSeq::dna, trans3::seq, and trans3Offset().

Referenced by ffNextBreak(), saveAxtBundle(), savePslx(), scoreAli(), and trans3Frame().

{
int offset, frame;
if (t3List != NULL)
    {
    /* Special processing at end. The end coordinate is
     * not included.  In most cases this makes things
     * easier.  Here we have to move it back one
     * amino acid, so that in the edge case it will
     * be included in the block that's loaded.  Then
     * we move it back. */
    if (isEnd)
        pt -= 1;
    trans3Offset(t3List, pt, &offset, &frame);
    if (isEnd)
        offset += 1;
    return 3*offset + frame;
    }
else
   {
   return pt - seq->dna;
   }
}

Here is the call graph for this function:

Here is the caller graph for this function:

struct trans3* trans3New

(

struct dnaSeq *

seq

)

[read]

Definition at line 10 of file trans3.c.

References AllocVar, trans3::end, FALSE, trans3::name, dnaSeq::name, trans3::seq, dnaSeq::size, trans3::trans, and translateSeq().

Referenced by gfAlignTransTrans(), gfMakeOoc(), gfTransTransFindBundles(), loadHashT3Ranges(), seqListToTrans3List(), transCountBothStrands(), transIndexBothStrands(), and transTransQuery().

{
struct trans3 *t3;
int frame;
int lastPos = seq->size - 1;

AllocVar(t3);
t3->name = seq->name;
t3->seq = seq;
t3->end = seq->size;
for (frame=0; frame<3; ++frame)
    {
    /* Position and frame are the same except in the
     * very rare case where we are trying to translate 
     * something less than 3 bases.  In this case this
     * somewhat cryptic construction will force it to
     * return empty sequences for the missing frames
     * avoiding an assert in translateSeq. */
    int pos = frame;
    if (pos > lastPos) pos = lastPos;
    t3->trans[frame] = translateSeq(seq, pos, FALSE);
    }
return t3;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void trans3Offset	(	struct trans3 *	t3List,
		AA *	aa,
		int *	retOffset,
		int *	retFrame
	)

Definition at line 76 of file trans3.c.

References dnaSeq::dna, trans3::next, trans3::seq, dnaSeq::size, trans3::start, and trans3::trans.

Referenced by trans3GenoPos().

{
struct trans3 *t3;
int frame;
aaSeq *seq;

for (t3 = t3List; t3 != NULL; t3 = t3->next)
    {
    for (frame = 0; frame < 3; ++frame)
        {
        seq = t3->trans[frame];
        if (seq->dna <= aa && aa < seq->dna + seq->size)
            {
            *retOffset = aa - seq->dna + t3->start/3;
            *retFrame = frame;
            return;
            }
        }
    }
internalErr();
}

Here is the caller graph for this function:

---

Variable Documentation

char const rcsid[] = "$Id: trans3.c,v 1.5 2007/04/20 22:43:37 kent Exp $" [static]

Definition at line 8 of file trans3.c.

---