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-rw-r--r--sequin/sequin3.c617
1 files changed, 257 insertions, 360 deletions
diff --git a/sequin/sequin3.c b/sequin/sequin3.c
index 29a08245..e7157a87 100644
--- a/sequin/sequin3.c
+++ b/sequin/sequin3.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.825 $
+* $Revision: 6.861 $
*
* File Description:
*
@@ -74,7 +74,8 @@
#include <asn2gnbi.h>
#include <alignval.h>
#include <cdrgn.h>
-
+#include <macrodlg.h>
+#include <macroapi.h>
/* For converting primer names to primer seqs and vice versa */
static void PrimerSeqToPrimerNameCallback (BioSourcePtr biop, Pointer userdata)
@@ -153,6 +154,7 @@ typedef struct fndeldata {
Int4 gap_count;
Int4 bsp_length;
Boolean in_gap;
+ Boolean unk_gap;
ValNodePtr head;
ValNodePtr last;
} DelData, PNTR DelDataPtr;
@@ -163,6 +165,7 @@ static void AddNextBlock (
{
ByteStorePtr bs;
+ IntFuzzPtr ifp;
SeqLitPtr slitp;
CharPtr str;
ValNodePtr vnp;
@@ -173,6 +176,13 @@ static void AddNextBlock (
if (slitp != NULL) {
slitp->length = ddp->gap_count;
ddp->bsp_length += slitp->length;
+ if (ddp->unk_gap) {
+ ifp = IntFuzzNew ();
+ if (ifp != NULL) {
+ ifp->choice = 4;
+ slitp->fuzz = ifp;
+ }
+ }
vnp = ValNodeAddPointer (&(ddp->last), 2, (Pointer) slitp);
if (ddp->head == NULL) {
ddp->head = vnp;
@@ -222,10 +232,11 @@ static void LIBCALLBACK FarToNearCallback (
str = ddp->curr;
while (ch != '\0') {
- if (ch != '-') {
+ if (ch != '-' && ch != '+') {
if (ddp->in_gap) {
AddNextBlock (ddp);
ddp->in_gap = FALSE;
+ ddp->unk_gap = FALSE;
ddp->gap_count = 0;
ddp->curr = ddp->buffer;
ddp->seqlen = 0;
@@ -246,6 +257,7 @@ static void LIBCALLBACK FarToNearCallback (
if (! ddp->in_gap) {
AddNextBlock (ddp);
ddp->in_gap = TRUE;
+ ddp->unk_gap = (Boolean) (ch == '-');
ddp->gap_count = 0;
ddp->curr = ddp->buffer;
ddp->seqlen = 0;
@@ -272,7 +284,7 @@ static void FarToNearProc (BioseqPtr bsp, Pointer userdata)
if (dd.buffer == NULL) return;
dd.curr = dd.buffer;
dd.seqlen = 0;
- SeqPortStream (bsp, EXPAND_GAPS_TO_DASHES, (Pointer) &dd, FarToNearCallback);
+ SeqPortStream (bsp, EXPAND_GAPS_TO_DASHES | KNOWN_GAP_AS_PLUS, (Pointer) &dd, FarToNearCallback);
AddNextBlock (&dd);
MemFree (dd.buffer);
olddelta = bsp->seq_ext;
@@ -1107,7 +1119,8 @@ static void AddEnvironmentalSampleQual (BioSourcePtr biop, Pointer userdata)
if (biop == NULL || biop->org == NULL || biop->org->orgname == NULL) return;
- if (StringISearch (biop->org->orgname->lineage, "environmental sample") == NULL)
+ if (StringISearch (biop->org->orgname->lineage, "environmental sample") == NULL
+ && StringCmp (biop->org->orgname->div, "ENV") != 0)
{
return;
}
@@ -1340,6 +1353,45 @@ static void ReassignFeatIDs (IteM i)
Update ();
}
+static void UniqifyFeatIDs (IteM i)
+
+{
+ MsgAnswer ans;
+ BaseFormPtr bfp;
+ BioseqSetPtr bssp;
+ Int4 count;
+ Int4 offset = 0;
+ SeqEntryPtr sep;
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+
+ if (! IS_Bioseq_set (sep)) return;
+ bssp = (BioseqSetPtr) sep->data.ptrvalue;
+ if (bssp == NULL || bssp->_class != BioseqseqSet_class_genbank) return;
+
+ ans = Message (MSG_OKC, "Are you sure you want to make merged feature identifiers unique?");
+ if (ans == ANS_CANCEL) return;
+
+ for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+ count = FindHighestFeatureID (sep);
+ OffsetFeatureIDs (sep, offset);
+ OffsetFeatureIDXrefs (sep, offset);
+ offset += count;
+ }
+
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+ ObjMgrDeSelect (0, 0, 0, 0, NULL);
+ Update ();
+}
+
static void ClearFeatIDsAndLinks (IteM i)
{
@@ -1687,6 +1739,25 @@ static void ForceTaxonFixup (IteM i)
ForceTaxonFixupBtn (i, NULL);
}
+static void JustTaxonFixup (IteM i)
+
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+ Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
static void DupFeatRemovalWarning (SeqFeatPtr sfp)
{
@@ -4665,7 +4736,7 @@ ConvertRawBioseqToDelta
sep = GetTopSeqEntryForEntityID (bsp->idx.entityID);
- VisitFeaturesInSep (sep, bsp, AdjustCDSLocationsForUnknownGapsCallback);
+ VisitFeaturesInSep (sep, (Pointer) Sequin_GlobalAlign2Seq, AdjustCDSLocationsForUnknownGapsCallback);
}
@@ -4909,7 +4980,7 @@ static void DoConvertRawToDeltaWithGapLocations (ButtoN b)
if (GetStatus (dcp->adjust_CDS_locations))
{
- VisitFeaturesInSep (sep, NULL, AdjustCDSLocationsForUnknownGapsCallback);
+ VisitFeaturesInSep (sep, (Pointer)Sequin_GlobalAlign2Seq, AdjustCDSLocationsForUnknownGapsCallback);
DeleteMarkedObjects (dcp->input_entityID, 0, NULL);
}
@@ -7617,7 +7688,7 @@ static void DoConvertPubDescStringConstraint (ButtoN b)
Remove (cpdp->form);
}
-static void CreateConvertPubDescStringConstraintDialog (IteM i)
+static void CreateConvertPubDescStringConstraintDialogX (IteM i)
{
BaseFormPtr bfp;
ConvertPubDescPtr cpdp;
@@ -8032,6 +8103,27 @@ static void UpdateECnumbers (IteM i)
ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
}
+
+static void ParseGoTermsFromUserFieldsItem (IteM i)
+
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+ ParseGoTermsFromFields (sep);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+
/*---------------------------------------------------------------------*/
/* */
/* HasInternalStops () -- Checks to see if a given protein has */
@@ -10010,24 +10102,11 @@ static void FreeMolInfoBlockData (MolInfoBlockPtr mibp)
}
-typedef struct sequenceconstraint
-{
- Boolean nucs_ok;
- Boolean prots_ok;
-
- Int4 other_constraint_type;
- StringConstraintPtr string_constraint;
- ChoiceConstraintPtr source_constraint;
- ValNodePtr feature_list;
-
-} SequenceConstraintData, PNTR SequenceConstraintPtr;
-
-
-static SequenceConstraintPtr SequenceConstraintFree (SequenceConstraintPtr scp)
+extern SequenceConstraintXPtr SequenceConstraintXFree (SequenceConstraintXPtr scp)
{
if (scp != NULL)
{
- scp->string_constraint = StringConstraintFree (scp->string_constraint);
+ scp->string_constraint = StringConstraintXFree (scp->string_constraint);
scp->source_constraint = ChoiceConstraintFree (scp->source_constraint);
scp->feature_list = ValNodeFree (scp->feature_list);
scp = MemFree (scp);
@@ -10046,7 +10125,7 @@ typedef struct sequenceconstraintdlg
DialoG feature_string_constraint;
DialoG id_string_constraint;
-} SequenceConstraintDlgData, PNTR SequenceConstraintDlgPtr;
+} SequenceConstraintXDlgData, PNTR SequenceConstraintXDlgPtr;
enum sequenceconstraintothertype
@@ -10058,12 +10137,12 @@ enum sequenceconstraintothertype
};
-static void ChangeSequenceConstraintType (GrouP g)
+static void ChangeSequenceConstraintXType (GrouP g)
{
- SequenceConstraintDlgPtr scdp;
+ SequenceConstraintXDlgPtr scdp;
Int4 other_constraint_type;
- scdp = (SequenceConstraintDlgPtr) GetObjectExtra (g);
+ scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (g);
if (scdp == NULL)
{
return;
@@ -10086,11 +10165,11 @@ static void ChangeSequenceConstraintType (GrouP g)
}
}
-static void ResetSequenceConstraintDialog (DialoG d)
+static void ResetSequenceConstraintXDialog (DialoG d)
{
- SequenceConstraintDlgPtr scdp;
+ SequenceConstraintXDlgPtr scdp;
- scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+ scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
if (scdp == NULL)
{
return;
@@ -10098,25 +10177,25 @@ static void ResetSequenceConstraintDialog (DialoG d)
SetValue (scdp->seq_type_constraint, 1);
SetValue (scdp->other_constraint_type, SEQ_CONSTRAINT_ANY + 1);
- ChangeSequenceConstraintType (scdp->other_constraint_type);
+ ChangeSequenceConstraintXType (scdp->other_constraint_type);
}
-static void SequenceConstraintToDialog (DialoG d, Pointer data)
+static void SequenceConstraintXToDialog (DialoG d, Pointer data)
{
- SequenceConstraintPtr scp;
- SequenceConstraintDlgPtr scdp;
+ SequenceConstraintXPtr scp;
+ SequenceConstraintXDlgPtr scdp;
- scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+ scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
if (scdp == NULL)
{
return;
}
- scp = (SequenceConstraintPtr) data;
+ scp = (SequenceConstraintXPtr) data;
if (scp == NULL)
{
- ResetSequenceConstraintDialog (d);
+ ResetSequenceConstraintXDialog (d);
}
else
{
@@ -10146,23 +10225,23 @@ static void SequenceConstraintToDialog (DialoG d, Pointer data)
PointerToDialog (scdp->id_string_constraint, scp->string_constraint);
break;
}
- ChangeSequenceConstraintType (scdp->other_constraint_type);
+ ChangeSequenceConstraintXType (scdp->other_constraint_type);
}
}
-static Pointer DialogToSequenceConstraint (DialoG d)
+static Pointer DialogToSequenceConstraintX (DialoG d)
{
- SequenceConstraintPtr scp;
- SequenceConstraintDlgPtr scdp;
+ SequenceConstraintXPtr scp;
+ SequenceConstraintXDlgPtr scdp;
- scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+ scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
if (scdp == NULL)
{
return NULL;
}
- scp = (SequenceConstraintPtr) MemNew (sizeof (SequenceConstraintData));
+ scp = (SequenceConstraintXPtr) MemNew (sizeof (SequenceConstraintXData));
if (scp != NULL)
{
switch (GetValue (scdp->seq_type_constraint))
@@ -10198,16 +10277,16 @@ static Pointer DialogToSequenceConstraint (DialoG d)
}
-static void SequenceConstraintMessage (DialoG d, Int2 mssg)
+static void SequenceConstraintXMessage (DialoG d, Int2 mssg)
{
- SequenceConstraintDlgPtr scdp;
+ SequenceConstraintXDlgPtr scdp;
- scdp = (SequenceConstraintDlgPtr) GetObjectExtra (d);
+ scdp = (SequenceConstraintXDlgPtr) GetObjectExtra (d);
if (scdp != NULL) {
switch (mssg) {
case VIB_MSG_INIT :
- ResetSequenceConstraintDialog (d);
+ ResetSequenceConstraintXDialog (d);
break;
case VIB_MSG_ENTER :
Select (scdp->other_constraint_type);
@@ -10218,19 +10297,19 @@ static void SequenceConstraintMessage (DialoG d, Int2 mssg)
}
}
-static ValNodePtr TestSequenceConstraintDialog (DialoG d)
+static ValNodePtr TestSequenceConstraintXDialog (DialoG d)
{
return NULL;
}
-static DialoG SequenceConstraintDialog (GrouP g)
+extern DialoG SequenceConstraintXDialog (GrouP g)
{
- SequenceConstraintDlgPtr dlg;
+ SequenceConstraintXDlgPtr dlg;
GrouP p, k;
- dlg = (SequenceConstraintDlgPtr) MemNew (sizeof (SequenceConstraintDlgData));
+ dlg = (SequenceConstraintXDlgPtr) MemNew (sizeof (SequenceConstraintXDlgData));
if (dlg == NULL) return NULL;
p = HiddenGroup (g, -1, 0, NULL);
@@ -10238,10 +10317,10 @@ static DialoG SequenceConstraintDialog (GrouP g)
SetGroupSpacing (p, 10, 10);
dlg->dialog = (DialoG) p;
- dlg->todialog = SequenceConstraintToDialog;
- dlg->fromdialog = DialogToSequenceConstraint;
- dlg->dialogmessage = SequenceConstraintMessage;
- dlg->testdialog = TestSequenceConstraintDialog;
+ dlg->todialog = SequenceConstraintXToDialog;
+ dlg->fromdialog = DialogToSequenceConstraintX;
+ dlg->dialogmessage = SequenceConstraintXMessage;
+ dlg->testdialog = TestSequenceConstraintXDialog;
dlg->seq_type_constraint = HiddenGroup (p, 4, 0, NULL);
RadioButton (dlg->seq_type_constraint, "All Sequences");
@@ -10249,21 +10328,21 @@ static DialoG SequenceConstraintDialog (GrouP g)
RadioButton (dlg->seq_type_constraint, "Proteins");
SetValue (dlg->seq_type_constraint, 2);
- dlg->other_constraint_type = HiddenGroup (p, 2, 0, ChangeSequenceConstraintType);
+ dlg->other_constraint_type = HiddenGroup (p, 2, 0, ChangeSequenceConstraintXType);
RadioButton (dlg->other_constraint_type, "Any sequence");
StaticPrompt (dlg->other_constraint_type, "", 0, dialogTextHeight, systemFont, 'l');
RadioButton (dlg->other_constraint_type, "Where sequence source");
- dlg->source_constraint = SourceConstraintDialog (dlg->other_constraint_type, FALSE);
+ dlg->source_constraint = SourceConstraintDialogX (dlg->other_constraint_type, FALSE);
RadioButton (dlg->other_constraint_type, "Where feature text");
k = HiddenGroup (dlg->other_constraint_type, 2, 0, NULL);
SetGroupSpacing (k, 10, 10);
dlg->feature_list = FeatureSelectionDialog (k, TRUE, NULL, NULL);
- dlg->feature_string_constraint = StringConstraintDialog (k, NULL, FALSE);
+ dlg->feature_string_constraint = StringConstraintDialogX (k, NULL, FALSE);
RadioButton (dlg->other_constraint_type, "Where sequence ID");
- dlg->id_string_constraint = StringConstraintDialog (dlg->other_constraint_type, NULL, FALSE);
+ dlg->id_string_constraint = StringConstraintDialogX (dlg->other_constraint_type, NULL, FALSE);
SetValue (dlg->other_constraint_type, CHOICE_CONSTRAINT_ANY);
SetObjectExtra (dlg->other_constraint_type, dlg, NULL);
@@ -10280,7 +10359,7 @@ static DialoG SequenceConstraintDialog (GrouP g)
}
-extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr string_constraint)
+extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintXPtr string_constraint)
{
Char id [41];
CharPtr cp, cp_dst;
@@ -10303,7 +10382,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
sip->next = NULL;
id [0] = '\0';
SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
- match = DoesStringMatchConstraint (id, string_constraint);
+ match = DoesStringMatchConstraintX (id, string_constraint);
if (!match)
{
changed = FALSE;
@@ -10330,7 +10409,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
}
if (changed)
{
- match = DoesStringMatchConstraint (id, string_constraint);
+ match = DoesStringMatchConstraintX (id, string_constraint);
}
/* if search text doesn't have ., try ID without version */
@@ -10340,7 +10419,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
if (cp != NULL)
{
*cp = 0;
- match = DoesStringMatchConstraint (id, string_constraint);
+ match = DoesStringMatchConstraintX (id, string_constraint);
}
}
}
@@ -10370,7 +10449,7 @@ extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr
}
-static Boolean DoesSequenceMatchSequenceConstraint (BioseqPtr bsp, SequenceConstraintPtr scp)
+extern Boolean DoesSequenceMatchSequenceConstraintX (BioseqPtr bsp, SequenceConstraintXPtr scp)
{
SeqDescrPtr sdp;
SeqMgrDescContext dcontext;
@@ -10392,7 +10471,7 @@ static Boolean DoesSequenceMatchSequenceConstraint (BioseqPtr bsp, SequenceConst
}
break;
case SEQ_CONSTRAINT_FEATURE_TEXT:
- return DoBioseqFeaturesMatchSequenceConstraint (bsp, scp->feature_list, scp->string_constraint);
+ return DoBioseqFeaturesMatchSequenceConstraintX (bsp, scp->feature_list, scp->string_constraint);
break;
case SEQ_CONSTRAINT_ID:
return DoesIDListMeetStringConstraint(bsp->id, scp->string_constraint);
@@ -10407,7 +10486,7 @@ typedef struct molinfoedit {
MolInfoBlock from;
MolInfoBlock to;
DialoG sequence_constraint;
- SequenceConstraintPtr scp;
+ SequenceConstraintXPtr scp;
Boolean allow_existing;
} MolInfoEdit, PNTR MolInfoEditPtr;
@@ -10487,7 +10566,7 @@ static void EditMolInfoCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, In
if (IS_Bioseq (sep)) {
bsp = (BioseqPtr) sep->data.ptrvalue;
- if (DoesSequenceMatchSequenceConstraint (bsp, miep->scp)) {
+ if (DoesSequenceMatchSequenceConstraintX (bsp, miep->scp)) {
if ((Uint1)GetValNodePopup (miep->from.molPopup,
miep->from.mol_values) == bsp->mol
|| GetValue (miep->from.molPopup) == 1)
@@ -10593,7 +10672,7 @@ static void DoProcessEditMolInfo (ButtoN b)
SeqEntryExplore (miep->sep, (Pointer) miep, EditMolInfoCallback);
FreeMolInfoBlockData (&(miep->from));
FreeMolInfoBlockData (&(miep->to));
- miep->scp = SequenceConstraintFree (miep->scp);
+ miep->scp = SequenceConstraintXFree (miep->scp);
ArrowCursor ();
Update ();
ObjMgrSetDirtyFlag (miep->input_entityID, TRUE);
@@ -10639,7 +10718,7 @@ static void EditMolInfoFields (IteM i)
StaticPrompt (h, "To", 0, 0, programFont, 'c');
CreateMolInfoBlock (&miep->to, h, TRUE);
- miep->sequence_constraint = SequenceConstraintDialog (w);
+ miep->sequence_constraint = SequenceConstraintXDialog (w);
c = HiddenGroup (w, 2, 0, NULL);
b = DefaultButton (c, "Accept", DoProcessEditMolInfo);
@@ -10717,14 +10796,14 @@ static void RibosomalRNAToGenomicDNAToolBtn (ButtoN b)
RibosomalRNAToGenomicDNA (bfp);
}
-static Boolean MolInfoOkForSeqEntry (SeqEntryPtr sep, SequenceConstraintPtr scp)
+static Boolean MolInfoOkForSeqEntry (SeqEntryPtr sep, SequenceConstraintXPtr scp)
{
BioseqSetPtr bssp;
SeqEntryPtr seq_set;
if (IS_Bioseq (sep))
{
- return DoesSequenceMatchSequenceConstraint(sep->data.ptrvalue, scp);
+ return DoesSequenceMatchSequenceConstraintX(sep->data.ptrvalue, scp);
}
else if (IS_Bioseq_set (sep))
{
@@ -10843,7 +10922,7 @@ static void DoApplyMolInfo (SeqEntryPtr sep, MolInfoEditPtr miep)
if (IS_Bioseq (sep)) {
bsp = (BioseqPtr) sep->data.ptrvalue;
- if (DoesSequenceMatchSequenceConstraint(bsp, miep->scp)) {
+ if (DoesSequenceMatchSequenceConstraintX(bsp, miep->scp)) {
DoApplyMolInfoToBioseq (bsp, miep);
} else return;
} else if (IS_Bioseq_set (sep)) {
@@ -10902,7 +10981,7 @@ static Boolean WillEditMolInfo (MolInfoEditPtr miep)
}
typedef struct molinfocheck {
- SequenceConstraintPtr scp;
+ SequenceConstraintXPtr scp;
Int4 num_with;
Int4 num_without;
} MolInfoCheckData, PNTR MolInfoCheckPtr;
@@ -11077,7 +11156,7 @@ static void DoProcessApplyMolInfo (ButtoN b)
DoApplyMolInfo (miep->sep, miep);
FreeMolInfoBlockData (&miep->to);
- miep->scp = SequenceConstraintFree (miep->scp);
+ miep->scp = SequenceConstraintXFree (miep->scp);
ArrowCursor ();
Update ();
ObjMgrSetDirtyFlag (miep->input_entityID, TRUE);
@@ -11119,7 +11198,7 @@ static void ApplyMolInfo (IteM i)
h = HiddenGroup (g, 0, 2, NULL);
CreateMolInfoBlock (&miep->to, h, TRUE);
- miep->sequence_constraint = SequenceConstraintDialog (w);
+ miep->sequence_constraint = SequenceConstraintXDialog (w);
c = HiddenGroup (w, 2, 0, NULL);
b = DefaultButton (c, "Accept", DoProcessApplyMolInfo);
@@ -12055,7 +12134,9 @@ static void CaptureFFLineEx (
MemSet (subcip, 0, sizeof (ClickableItemData));
subcip->clickable_item_type = blocktype;
subcip->description = StringSave (ptr);
- ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+ if (item_list != NULL) {
+ ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+ }
ValNodeAddPointer (&(cip->subcategories), 0, subcip);
/* iterate to add the rest of the lines of the qual */
while (ch != 0 && tmp != NULL && (qual_name = StartsWithQualOrFeat (tmp + 1)) == NULL) {
@@ -12070,7 +12151,9 @@ static void CaptureFFLineEx (
MemSet (subcip, 0, sizeof (ClickableItemData));
subcip->clickable_item_type = blocktype;
subcip->description = StringSave (ptr);
- ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+ if (item_list != NULL) {
+ ValNodeAddPointer (&(subcip->item_list), item_list->choice, item_list->data.ptrvalue);
+ }
ValNodeAddPointer (&(cip->subcategories), 0, subcip);
}
}
@@ -12160,6 +12243,7 @@ extern ValNodePtr GetSUCCommonList (SeqEntryPtr sep, Boolean reverse, Boolean by
ErrSev level;
Boolean okay;
SeqEntryPtr oldscope;
+ Uint2 entityID;
if (sep == NULL) return NULL;
@@ -12191,6 +12275,8 @@ extern ValNodePtr GetSUCCommonList (SeqEntryPtr sep, Boolean reverse, Boolean by
oldscope = SeqEntrySetScope (sep);
okay = SeqEntryToGnbk (sep, NULL, GENBANK_FMT, SEQUIN_MODE, NORMAL_STYLE,
SHOW_CONTIG_FEATURES, 0, 0, &xtra, NULL);
+ entityID = SeqMgrGetEntityIDForSeqEntry (sep);
+ SeqMgrIndexFeatures (entityID, NULL);
SeqEntrySetScope (oldscope);
ErrSetMessageLevel (level);
if (okay) {
@@ -15723,6 +15809,7 @@ static void UnsetPartialForTruncatedProteins (SeqFeatPtr sfp, Pointer userdata)
change_name = (BoolPtr) userdata;
CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
SetSeqLocPartial (sfp->location, partial5, FALSE);
+ sfp->partial = partial5;
if (*change_name) {
prp = sfp->data.value.ptrvalue;
if (prp != NULL && prp->name != NULL
@@ -15754,6 +15841,7 @@ static void UnsetCDSPartialForTruncatedProteins (SeqFeatPtr sfp, Pointer userdat
if (product_bsp == prot_bsp) {
CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
SetSeqLocPartial (sfp->location, partial5, FALSE);
+ sfp->partial = partial5;
cds_len = (prot_bsp->length + 1) * 3 ;
crp = (CdRegionPtr) sfp->data.value.ptrvalue;
@@ -15903,6 +15991,7 @@ static void TruncProtsCallback (BioseqPtr bsp, Pointer userdata)
SetSeqLocPartial (slp, partial5, partial3);
SeqLocFree (gene->location);
gene->location = slp;
+ gene->partial = partial5 || partial3;
}
else
{
@@ -18801,271 +18890,6 @@ static void ReverseNameOrderInAuthor (AuthorPtr pAuthor)
}
-typedef struct replaceitempair {
- CharPtr FindString;
- CharPtr ReplaceString;
-} ReplaceItemPair, PNTR ReplaceItemPairPtr;
-
-
-ReplaceItemPair AbbreviationList[] = {
- { "arabidopsis thaliana", "Arabidopsis thaliana" },
- { "adp", "ADP" },
- { "adp-", "ADP-" },
- { "atp", "ATP" },
- { "atp-", "ATP-" },
- { "bac", "BAC" },
- { "caenorhabditis elegans", "Caenorhabditis elegans" },
- { "cdna", "cDNA" },
- { "cdnas", "cDNAs" },
- { "coa", "CoA" },
- { "coi", "COI" },
- { "coii", "COII" },
- { "danio rerio", "Danio rerio" },
- { "dna", "DNA" },
- { "dna-", "DNA-" },
- { "drosophila melanogaster", "Drosophila melanogaster" },
- { "dsrna", "dsRNA" },
- { "escherichia coli", "Escherichia coli" },
- { "hiv", "HIV" },
- { "hiv-1", "HIV-1" },
- { "hiv-2", "HIV-2" },
- { "hnrna", "hnRNA" },
- { "homo sapiens", "Homo sapiens" },
- { "mhc", "MHC" },
- { "mrna", "mRNA" },
- { "mtdna", "mtDNA" },
- { "mus musculus", "Mus musculus" },
- { "nadh", "NADH" },
- { "nov.", "nov." },
- { "nov..", "nov.." },
- { "pcr", "PCR" },
- { "pcr-", "PCR-" },
- { "rattus norvegicus", "Rattus norvegicus" },
- { "rapd", "RAPD" },
- { "rdna", "rDNA" },
- { "rna", "RNA" },
- { "rna-", "RNA-" },
- { "rrna", "rRNA" },
- { "rt-pcr", "RT-PCR" },
- { "saccharomyces cerevisiae", "Saccharomyces cerevisiae" },
- { "scrna", "scRNA" },
- { "siv-1", "SIV-1" },
- { "snp", "SNP" },
- { "snps", "SNPs" },
- { "snrna", "snRNA" },
- { "sp.", "sp." },
- { "sp..", "sp.." },
- { "ssp.", "ssp." },
- { "ssp..", "ssp.." },
- { "ssrna", "ssRNA" },
- { "subsp.", "subsp." },
- { "subsp..", "subsp.." },
- { "trna", "tRNA" },
- { "trna-", "tRNA-" },
- { "var.", "var." },
- { "var..", "var.." },
- { "usa", "USA" },
- { "U.S.A.", "USA" },
- { "U.S.A", "USA" },
- { "United States of America", "USA" },
- {"(hiv)", "(HIV)" },
- {"(hiv1)", "(HIV1)" },
- {"(hiv-1)", "(HIV-1)" }
-};
-
-ReplaceItemPair SpecialAbbreviationList[] = {
- { "sp.", "sp." },
- { "nov.", "nov." },
- { "ssp.", "ssp." },
- { "var.", "var." },
- { "subsp.", "subsp." }
-};
-
-static void FixAbbreviationsInElement (CharPtr PNTR pEl)
-{
- int i;
- CharPtr NewPtr;
- Boolean whole_word;
-
- if (pEl == NULL) return;
- if (*pEl == NULL) return;
-
- for (i = 0; i < sizeof (AbbreviationList) / sizeof (ReplaceItemPair); i++)
- {
- if (AbbreviationList[i].FindString[StringLen (AbbreviationList[i].FindString) - 1] == '-')
- {
- whole_word = FALSE;
- }
- else
- {
- whole_word = TRUE;
- }
- FindReplaceString (pEl, AbbreviationList[i].FindString,
- AbbreviationList[i].ReplaceString, FALSE, whole_word);
- }
- for (i = 0; i < sizeof (SpecialAbbreviationList) / sizeof (ReplaceItemPair); i++)
- {
- FindReplaceString (pEl, SpecialAbbreviationList[i].FindString,
- SpecialAbbreviationList[i].ReplaceString, FALSE, TRUE);
- if (StringLen (*pEl) >= StringLen (SpecialAbbreviationList[i].ReplaceString)
- && StringCmp ((*pEl) + StringLen (*pEl) - StringLen (SpecialAbbreviationList[i].ReplaceString), SpecialAbbreviationList[i].ReplaceString) == 0)
- {
- NewPtr = MemNew (StringLen (*pEl) + 2);
- if (NewPtr == NULL) return;
- StringCpy (NewPtr, *pEl);
- StringCat (NewPtr, ".");
- MemFree (*pEl);
- *pEl = NewPtr;
- }
- }
-}
-
-ReplaceItemPair ShortWordList[] = {
- { "A", "a" },
- { "About", "about" },
- { "And", "and" },
- { "At", "at" },
- { "But", "but" },
- { "By", "by" },
- { "For", "for" },
- { "In", "in" },
- { "Is", "is" },
- { "Of", "of" },
- { "On", "on" },
- { "Or", "or" },
- { "The", "the" },
- { "To", "to" },
- { "With", "with" }
-};
-
-static void FixShortWordsInElement (CharPtr PNTR pEl)
-{
- Int2 i;
-
- if (pEl == NULL) return;
- if (*pEl == NULL) return;
-
- for (i = 0; i < sizeof (ShortWordList) / sizeof (ReplaceItemPair); i++)
- {
- FindReplaceString (pEl, ShortWordList[i].FindString,
- ShortWordList[i].ReplaceString, FALSE, TRUE);
- }
- if (isalpha ((Int4)((*pEl)[0])))
- {
- (*pEl)[0] = toupper ((*pEl)[0]);
- }
-}
-
-static void
-FixCapitalizationInElement
-(CharPtr PNTR pEl,
- Boolean bAbbrev,
- Boolean bShortWords,
- Boolean bApostrophes)
-{
- CharPtr pCh;
- Boolean bSendToLower;
-
- if(pEl == NULL) return;
- if(*pEl == NULL) return;
-
- bSendToLower = FALSE;
- for(pCh = *pEl; *pCh != 0; pCh++)
- {
- if(isalpha((Int4)(*pCh)))
- {
- if(bSendToLower)
- {
- *pCh = tolower(*pCh);
- }
- else
- {
- *pCh = toupper(*pCh);
- bSendToLower = TRUE;
- }
- }
- else if (bApostrophes || *pCh != '\'')
- {
- bSendToLower = FALSE;
- }
- }
- if (bShortWords)
- FixShortWordsInElement (pEl);
- if (bAbbrev)
- FixAbbreviationsInElement (pEl);
-}
-
-
-static void FixOrgNamesInString (CharPtr str, ValNodePtr org_names)
-{
- ValNodePtr vnp;
- CharPtr cp, taxname;
- Int4 taxname_len;
-
- if (StringHasNoText (str) || org_names == NULL) return;
- for (vnp = org_names; vnp != NULL; vnp = vnp->next)
- {
- taxname = (CharPtr) org_names->data.ptrvalue;
- taxname_len = StringLen (taxname);
- cp = StringISearch (str, taxname);
- while (cp != NULL)
- {
- StringNCpy (cp, taxname, taxname_len);
- cp = StringISearch (cp + taxname_len, taxname);
- }
- }
-}
-
-
-extern void ResetCapitalization (Boolean first_is_upper, CharPtr pString)
-{
- CharPtr pCh;
- Boolean was_digit = FALSE;
-
- pCh = pString;
- if (pCh == NULL) return;
- if (*pCh == '\0') return;
-
- if (first_is_upper)
- {
- /* Set first character to upper */
- *pCh = toupper (*pCh);
- }
- else
- {
- /* set first character to lower */
- *pCh = tolower (*pCh);
- }
-
- if (isdigit ((Int4)(*pCh)))
- {
- was_digit = TRUE;
- }
- pCh++;
- /* Set rest of characters to lower */
- while (*pCh != '\0')
- {
- if (was_digit
- && (*pCh == 'S' || *pCh == 's')
- && (isspace ((Int4)(*(pCh + 1))) || *(pCh + 1) == 0))
- {
- *pCh = toupper (*pCh);
- was_digit = FALSE;
- }
- else if (isdigit ((Int4)(*pCh)))
- {
- was_digit = TRUE;
- }
- else
- {
- was_digit = FALSE;
- *pCh = tolower (*pCh);
- }
- pCh++;
- }
-}
-
-
extern void
FixCapitalizationInTitle
(CharPtr PNTR pTitle,
@@ -19142,7 +18966,7 @@ static void TruncateAuthorMiddleInitials (AuthorPtr pAuthor)
}
}
-static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstraintPtr author_scp)
+static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstraintXPtr author_scp)
{
NameStdPtr pNameStandard;
CharPtr consortium;
@@ -19160,7 +18984,7 @@ static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstrain
len = StringLen (pNameStandard->names[0]);
if (len > 0)
{
- if (DoesStringMatchConstraint (pNameStandard->names[0], author_scp))
+ if (DoesStringMatchConstraintX (pNameStandard->names[0], author_scp))
{
consortium = (CharPtr) MemNew ((len + 1) * sizeof (Char));
if (consortium != NULL)
@@ -19190,7 +19014,7 @@ static void ChangeAuthorLastNameToConsortium (AuthorPtr pAuthor, StringConstrain
typedef struct fixpubdesc
{
Int4 iType;
- StringConstraintPtr author_scp;
+ StringConstraintXPtr author_scp;
ValNodePtr org_names;
} FixPubdescData, PNTR FixPubdescPtr;
@@ -19336,7 +19160,7 @@ extern void GetOrgNamesInRecordCallback (BioSourcePtr biop, Pointer userdata)
/* This function is used to apply fixes to citations */
-static void FixPubs (Uint2 entityID, Int4 iType, StringConstraintPtr author_scp)
+static void FixPubs (Uint2 entityID, Int4 iType, StringConstraintXPtr author_scp)
{
SeqEntryPtr sep;
SelStructPtr sel;
@@ -19477,7 +19301,7 @@ static void ChangeAllAuthorNameToConsortium (IteM i)
static void ChangeAuthorNameWithConsortiumToConsortium (IteM i)
{
BaseFormPtr bfp;
- StringConstraintPtr scp;
+ StringConstraintXPtr scp;
#ifdef WIN_MAC
bfp = currentFormDataPtr;
@@ -19487,7 +19311,7 @@ static void ChangeAuthorNameWithConsortiumToConsortium (IteM i)
if (bfp == NULL) return;
- scp = (StringConstraintPtr) MemNew (sizeof (StringConstraintData));
+ scp = (StringConstraintXPtr) MemNew (sizeof (StringConstraintData));
if (scp == NULL)
{
return;
@@ -19500,7 +19324,7 @@ static void ChangeAuthorNameWithConsortiumToConsortium (IteM i)
scp->not_present = FALSE;
FixPubs (bfp->input_entityID, FIX_PUB_SWAP_NAME_CONSORTIUM, scp);
- scp = StringConstraintFree (scp);
+ scp = StringConstraintXFree (scp);
}
typedef struct authornamestringconstraintform
@@ -19512,7 +19336,7 @@ typedef struct authornamestringconstraintform
static void DoChangeAuthorNameToConsortiumWithConstraint (ButtoN b)
{
AuthorNameStringConstraintFormPtr frm;
- StringConstraintPtr scp;
+ StringConstraintXPtr scp;
frm = (AuthorNameStringConstraintFormPtr) GetObjectExtra (b);
if (frm == NULL)
@@ -19520,14 +19344,14 @@ static void DoChangeAuthorNameToConsortiumWithConstraint (ButtoN b)
return;
}
- scp = (StringConstraintPtr) DialogToPointer (frm->author_name_constraint_dlg);
+ scp = (StringConstraintXPtr) DialogToPointer (frm->author_name_constraint_dlg);
Hide (frm->form);
WatchCursor ();
Update ();
FixPubs (frm->input_entityID, FIX_PUB_SWAP_NAME_CONSORTIUM, scp);
- scp = StringConstraintFree (scp);
+ scp = StringConstraintXFree (scp);
Remove ((WindoW)frm->form);
ArrowCursor ();
Update ();
@@ -19563,7 +19387,7 @@ static void ChangeAuthorNameToConsortiumWithConstraint (IteM i)
h = HiddenGroup (w, -1, 0, NULL);
SetGroupSpacing (h, 10, 10);
- frm->author_name_constraint_dlg = StringConstraintDialog (h, "Where author last name", TRUE);
+ frm->author_name_constraint_dlg = StringConstraintDialogX (h, "Where author last name", TRUE);
c = HiddenGroup (h, 2, 0, NULL);
SetGroupSpacing (h, 10, 10);
@@ -19873,6 +19697,35 @@ static void RenormalizeNucProtSetsMenuItem (IteM i)
}
+static void AddAllDbxrefsBioseqCallback (BioseqPtr bsp, Pointer data)
+{
+ AddAllDbxrefsToBioseq (bsp);
+}
+
+
+static void AddAllDbxrefsMenuItem (IteM i)
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+
+ /* Get the current data */
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+
+ if (bfp == NULL)
+ return;
+
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+
+ VisitBioseqsInSep (sep, NULL, AddAllDbxrefsBioseqCallback);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
extern void LookupAllPubs (IteM i);
extern void ResolveExistingLocalIDs (IteM i);
extern void PromoteAlignsToBestIDProc (IteM i);
@@ -19945,7 +19798,7 @@ static void ShowDiscrepancyReport (IteM i)
if (bfp == NULL) return;
- CreateDiscrepancyReportWindow (bfp);
+ CreateDiscrepancyReportWindow (/* bfp */);
}
static void TestTax3 (IteM i, Int4 taxid, CharPtr name)
@@ -20224,7 +20077,7 @@ static void MakeSpecialOrganismMenu (MenU m, BaseFormPtr bfp)
MenU x;
s = SubMenu (m, "Organism/ G");
- i = CommandItem (s, "Parse Text", ParseTaxnameToSourceQual);
+ i = CommandItem (s, "Parse Text After Bionomial", ParseTaxnameToSourceQual);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
i = CommandItem (s, "Parse ATCC Strain to Xref", AtccStrainToXref);
@@ -20249,6 +20102,8 @@ static void MakeSpecialOrganismMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Lat-lon Tool", LatLonTool);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (s, "Lat-Lon Country Conflict Tool", LatLonCountryTool);
+ SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Fix Specific-Host Values", FixSpecificHostValues);
SetObjectExtra (i, bfp, NULL);
@@ -20288,6 +20143,8 @@ static void MakeSpecialOrganismMenu (MenU m, BaseFormPtr bfp)
x = SubMenu(s, "Parse Organism Modifiers");
i = CommandItem (x, "Load From File", LoadOrganismModifierTable);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Load Tax Consult File", LoadTaxConsult);
+ SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Export To File", ExportOrganismTable);
SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Export Last Lineage Table", ExportLastLineage);
@@ -20371,6 +20228,9 @@ static void MakeSpecialProjectsMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Apply BARCODE Dbxrefs", ApplyBarcodeDbxrefs);
SetObjectExtra (i, bfp, NULL);
+ SeparatorItem (s);
+ i = CommandItem (s, "Add Note to Coding Regions in Source Features", ApplyTagToCodingRegionsInSourceFeatures);
+ SetObjectExtra (i, bfp, NULL);
}
}
@@ -20680,7 +20540,7 @@ static void MakeSpecialConvertMenu (MenU m, BaseFormPtr bfp)
z = SubMenu (y, "Publication");
i = CommandItem (z, "All", ConvertPubDescToFeat);
SetObjectExtra (i, bfp, NULL);
- i = CommandItem (z, "By Constraint", CreateConvertPubDescStringConstraintDialog);
+ i = CommandItem (z, "By Constraint", CreateConvertPubDescStringConstraintDialogX);
SetObjectExtra (i, bfp, NULL);
y = SubMenu (x, "Convert Full Length Feature to Descriptor");
@@ -20718,6 +20578,8 @@ static void MakeSpecialConvertMenu (MenU m, BaseFormPtr bfp)
x = SubMenu (s, "Convert IDs, Accessions, or GenBank.names");
i = CommandItem (x, "LocalIDs to GeneralIDs", ConvertLocalToGeneral);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Convert GeneralIDs to LocalIDs", ConvertGeneralIdToLocalID);
+ SetObjectExtra (i, bfp, NULL);
y = SubMenu (x, "Accession to LocalIDs");
i = CommandItem (y, "For All Sequences", ConvertToLocalProcAll);
SetObjectExtra (i, bfp, NULL);
@@ -20756,7 +20618,7 @@ static void MakeSpecialEditMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Exception", FeatureExceptionEditor);
SetObjectExtra (i, bfp, NULL);
- i = CommandItem (x, "Partial", FeaturePartialEditor);
+ i = CommandItem (x, "Location", FeaturePartialEditor);
SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Strand", FeatureStrandEditor);
SetObjectExtra (i, bfp, NULL);
@@ -20770,6 +20632,10 @@ static void MakeSpecialEditMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Reverse Location Interval Order", ReverseFeatureIntervals);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Resolve Intersecting Feature Locations", ResolveFeatureOverlaps);
+ SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Update Features", UpdateFeatures);
+ SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
x = SubMenu (s, "Bulk Edit");
@@ -20786,8 +20652,12 @@ static void MakeSpecialEditMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
- i = CommandItem (s, "Extend Partial Features", ExtendPartialFeatures);
+ x = SubMenu (s, "Extend Partial Features");
+ i = CommandItem (x, "All", ExtendPartialFeatures);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "With Constraint", ExtendPartialFeaturesWithConstraint);
+ SetObjectExtra (i, bfp, NULL);
+
i = CommandItem (s, "Extend Gene", ExtendGeneReg);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
@@ -20912,6 +20782,9 @@ static void MakeSpecialGapSequencesMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Remove Unnecessary Gap Features", RemoveUnnecessaryGapFeatures);
SetObjectExtra (i, bfp, NULL);
+ SeparatorItem (s);
+ i = CommandItem (s, "Flip Intervals Between Gaps", FlipSequenceIntervals);
+ SetObjectExtra (i, bfp, NULL);
}
static void MakeSpecialSelectMenu (MenU m, BaseFormPtr bfp)
@@ -20947,6 +20820,8 @@ static void MakeSpecialLinkMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Reassign", ReassignFeatIDs);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Unique in Merged Set", UniqifyFeatIDs);
+ SetObjectExtra (i, bfp, NULL);
i = CommandItem (x, "Clear IDs and Links", ClearFeatIDsAndLinks);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
@@ -20967,7 +20842,6 @@ static void MakeSpecialLinkMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
}
-
extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
{
@@ -21095,6 +20969,11 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
i = CommandItem (s, "Load Feature Fields from File", LoadFeatureFieldTable);
SetObjectExtra (i, bfp, NULL);
+#if 1
+ i = CommandItem (s, "New Load Feature Fields from File", NewLoadFeatureQualifierTable);
+ SetObjectExtra (i, bfp, NULL);
+#endif
+
MakeSpecialRemoveMenu (m, bfp);
@@ -21216,6 +21095,8 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Add Cit-sub for update", AddCitSubForUpdate);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (s, "Fix USA and States", AbbreviateCitSubAffilStates);
+ SetObjectExtra (i, bfp, NULL);
MakeSpecialGapSequencesMenu (m, bfp);
@@ -21376,11 +21257,18 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
i = CommandItem (s, "Force Locus Fixup", ForceLocusFixup);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
+ /*
+ i = CommandItem (s, "Just Taxonomy Fixup", JustTaxonFixup);
+ SetObjectExtra (i, bfp, NULL);
+ SeparatorItem (s);
+ */
i = CommandItem (s, "Correct CDS Genetic Codes", CorrectCDSGenCodes);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
i = CommandItem (s, "Update Replace EC_numbers", UpdateECnumbers);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (s, "Parse GO Terms from User Fields", ParseGoTermsFromUserFieldsItem);
+ SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
i = CommandItem (s, "NC_Cleanup", DoNCCleanup);
SetObjectExtra (i, bfp, NULL);
@@ -21461,11 +21349,20 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
#endif
+#if 0
SeparatorItem (m);
- i = CommandItem (m, "Discrepancy Report", ShowDiscrepancyReport);
+ i = CommandItem (m, "Add All Dbxrefs", AddAllDbxrefsMenuItem);
SetObjectExtra (i, bfp, NULL);
+#endif
}
+ SeparatorItem (m);
+ i = CommandItem (m, "Discrepancy Report", ShowDiscrepancyReport);
+ SetObjectExtra (i, bfp, NULL);
+ SeparatorItem (m);
+ i = CommandItem (m, "Macro Editor", LaunchMacroEditor);
+ SetObjectExtra (i, bfp, NULL);
+
/*#ifdef INTERNAL_NCBI_SEQUIN*/
/*#ifdef NEW_TAXON_SERVICE*/
/*
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 11:37:14 +0000