diff --git a/blxGff3Parser.c b/blxGff3Parser.c
index b7645e7064237149da5c0de4b6e4eb22cacf26b9..16ea2e705c08242b6860f6c8d501b55159301475 100644
--- a/blxGff3Parser.c
+++ b/blxGff3Parser.c
@@ -292,7 +292,9 @@ static void createBlixemObject(BlxGffData *gffData,
if (tmpError)
{
/* style errors are not critical */
- reportAndClearIfError(&tmpError, G_LOG_LEVEL_WARNING);
+ //reportAndClearIfError(&tmpError, G_LOG_LEVEL_WARNING);
+ g_error_free(tmpError);
+ tmpError = NULL;
}
/* populate the gaps array */
diff --git a/blxwindow.c b/blxwindow.c
index fbda7c0f2f4dbdc9ea02b48149bd8ad8a88a6d40..658d6b2e496d53d3b98960b98bddb886eaa63da7 100755
--- a/blxwindow.c
+++ b/blxwindow.c
@@ -5234,43 +5234,33 @@ static void calcReadingFrame(MSP *msp, const BlxViewContext *bc)
* used to pass the reading frame in exblx files seemed to occasionally pass an incorrect reading frame. */
if (!mspIsIntron(msp))
{
- if (msp->phase != UNSET_INT || msp->qFrame == UNSET_INT)
- {
- if (msp->phase == UNSET_INT)
- {
- g_warning("Phase is not specified for MSP '%s' (q=%d-%d; s=%d-%d) - assuming phase 0.\n", mspGetSName(msp), msp->qRange.min, msp->qRange.max, msp->sRange.min, msp->sRange.max);
- msp->phase = 0;
- }
-
- /* Get the first coord of the first complete codon. This is the start coord (5' end) of the match
- * plus the phase (if non-zero), which initially gets stored in the qFrame field in the MSP... */
- const int coord = mspGetQStart(msp) + msp->phase;
+ /* Get the first coord of the first complete codon. This is the start coord (5' end) of the match
+ * plus (or minus) the phase (if non-zero), which initially gets stored in the qFrame field in the MSP... */
+ const int direction = (msp->qStrand == BLXSTRAND_FORWARD ? 1 : -1);
+ const int coord = mspGetQStart(msp) + (direction * msp->phase);
- /* Find the reading frame that this coord belongs in. This is the same as the base number within
- * reading frame 1. */
- int frame = UNSET_INT;
- const gboolean invertCoords = (mspGetRefStrand(msp) == BLXSTRAND_REVERSE);
+ /* Find the reading frame that this coord belongs in. This is the same as the base number within
+ * reading frame 1. */
+ int frame = UNSET_INT;
+ const gboolean invertCoords = (mspGetRefStrand(msp) == BLXSTRAND_REVERSE);
- convertDnaIdxToDisplayIdx(coord, bc->seqType, 1, bc->numFrames, invertCoords, &bc->refSeqRange, &frame);
-
- if (frame != UNSET_INT)
- {
- if (msp->qFrame != UNSET_INT && msp->qFrame != frame && bc->seqType == BLXSEQ_PEPTIDE)
- {
- g_warning("Calculated reading frame '%d' differs from parsed reading frame '%d'; using calculated frame (%s).\n", frame, msp->qFrame, mspGetSName(msp));
- }
-
- msp->qFrame = frame;
- }
+ convertDnaIdxToDisplayIdx(coord, bc->seqType, 1, bc->numFrames, invertCoords, &bc->refSeqRange, &frame);
+
+ if (frame != UNSET_INT)
+ {
+ msp->qFrame = frame;
}
if (msp->qFrame == UNSET_INT)
{
- g_warning("Reading frame is not set for MSP '%s' (q=%d-%d; s=%d-%d) - setting to 1.\n", mspGetSName(msp), msp->qRange.min, msp->qRange.max, msp->sRange.min, msp->sRange.max);
+ g_warning("Reading frame could not be calculated for MSP '%s' (q=%d-%d; s=%d-%d) - setting to 1.\n", mspGetSName(msp), msp->qRange.min, msp->qRange.max, msp->sRange.min, msp->sRange.max);
msp->qFrame = 1;
}
-
- /* Messy, for backwards compatibility... set the frame number in the qframe string */
+ }
+
+ /* Messy, for backwards compatibility... set the frame number in the qframe string */
+ if (msp->qFrame != UNSET_INT)
+ {
char *frameStr = convertIntToString(msp->qFrame);
msp->qframe[2] = frameStr[0];
g_free(frameStr);
@@ -5278,6 +5268,7 @@ static void calcReadingFrame(MSP *msp, const BlxViewContext *bc)
}
+
/* Calculate the ID and q frame for the given MSP and store
* them in the MSP struct. Returns the calculated ID (or UNSET_INT if this msp
* is not a blast match). */
diff --git a/utilities.c b/utilities.c
index 9e6acaedda03937b79a9aee1769e4c7141b99b00..cc6914644c75f83a2b7ae2b28b2ff304c53117c0 100644
--- a/utilities.c
+++ b/utilities.c
@@ -1700,46 +1700,50 @@ static BlxSequence* blxSequenceFindByName(const char *name, GList *allSeqs)
BlxSequence* blxSequenceGetVariantParent(const BlxSequence *variant, GList *allSeqs)
{
BlxSequence *result = NULL;
-
+
const char *variantName = blxSequenceGetFullName(variant);
- char *parentName = g_strdup(variantName);
- char *insertPoint = strchr(parentName, '-');
- if (insertPoint)
+ if (variantName)
{
- /* Replace '-' by terminating char, in case there's nothing else to copy in. */
- *insertPoint = '\0';
-
- /* The insert point is where we'll copy into. Create another pointer that we'll increment
- * until we find a '.' and then we'll copy from that point. */
- char *copyPoint = insertPoint;
- ++copyPoint;
-
- gboolean foundRestartPoint = FALSE; /* set to true when we find where to start copying from again */
-
- while (copyPoint && *copyPoint != '\0')
+ char *parentName = g_strdup(variantName);
+ char *insertPoint = strchr(parentName, '-');
+
+ if (insertPoint)
{
- if (foundRestartPoint)
- {
- *insertPoint = *copyPoint;
- ++insertPoint;
- }
- else if (*copyPoint == '.')
- {
- foundRestartPoint = TRUE;
- *insertPoint = *copyPoint;
- ++insertPoint;
- }
+ /* Replace '-' by terminating char, in case there's nothing else to copy in. */
+ *insertPoint = '\0';
+ /* The insert point is where we'll copy into. Create another pointer that we'll increment
+ * until we find a '.' and then we'll copy from that point. */
+ char *copyPoint = insertPoint;
++copyPoint;
+
+ gboolean foundRestartPoint = FALSE; /* set to true when we find where to start copying from again */
+
+ while (copyPoint && *copyPoint != '\0')
+ {
+ if (foundRestartPoint)
+ {
+ *insertPoint = *copyPoint;
+ ++insertPoint;
+ }
+ else if (*copyPoint == '.')
+ {
+ foundRestartPoint = TRUE;
+ *insertPoint = *copyPoint;
+ ++insertPoint;
+ }
+
+ ++copyPoint;
+ }
+
+ *insertPoint = '\0';
+
+ result = blxSequenceFindByName(parentName, allSeqs);
+ g_free(parentName);
}
-
- *insertPoint = '\0';
-
- result = blxSequenceFindByName(parentName, allSeqs);
- g_free(parentName);
}
-
+
return result;
}