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authorAaron M. Ucko <ucko@debian.org>2005-06-17 02:24:46 +0000
committerAaron M. Ucko <ucko@debian.org>2005-06-17 02:24:46 +0000
commitd76c50353c9e74f6915ca6352afb29ae53d45777 (patch)
tree9045ebb0b61573bfa4ff3d8778899c5a2cb76d6c /sequin/sequin2.c
parent402b112099aa816a02fd502b7f0261a99fe7126a (diff)
Load /tmp/.../ncbi-tools6-6.1.20050605 into
branches/upstream/current.
Diffstat (limited to 'sequin/sequin2.c')
-rw-r--r--sequin/sequin2.c2889
1 files changed, 1868 insertions, 1021 deletions
diff --git a/sequin/sequin2.c b/sequin/sequin2.c
index a1ff4f10..3850cc57 100644
--- a/sequin/sequin2.c
+++ b/sequin/sequin2.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.377 $
+* $Revision: 6.402 $
*
* File Description:
*
@@ -69,6 +69,7 @@
#include <netscape.h>
#endif
#include <actutils.h>
+#include <salpanel.h>
extern EnumFieldAssoc orgmod_subtype_alist [];
extern EnumFieldAssoc subsource_subtype_alist [];
@@ -117,18 +118,6 @@ static Boolean PackageTypeIsSingle (Int2 seqPackage)
}
}
-static Boolean PackageTypeDefaultMolTypeIsDNA (Int2 seqPackage)
-{
- if (PackageTypeIsSet (seqPackage) || seqPackage == SEQ_PKG_GENOMICCDNA)
- {
- return TRUE;
- }
- else
- {
- return FALSE;
- }
-}
-
/* These functions are used to find titles in SeqEntries */
static void FindFirstTitle (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent)
@@ -500,7 +489,7 @@ static CharPtr GetModValueFromSeqEntry (SeqEntryPtr sep, CharPtr mod_name)
if (!LookForSearchString (ttl, lookfor, value, value_len - 1))
{
- if (StringICmp (mod_name, "organism"))
+ if (StringICmp (mod_name, "organism") == 0)
{
MakeSearchStringFromAlist (lookfor, "org");
if (!LookForSearchString (ttl, lookfor, value, value_len - 1))
@@ -508,7 +497,7 @@ static CharPtr GetModValueFromSeqEntry (SeqEntryPtr sep, CharPtr mod_name)
value = MemFree (value);
}
}
- else if (StringICmp (mod_name, "org"))
+ else if (StringICmp (mod_name, "org") == 0)
{
MakeSearchStringFromAlist (lookfor, "organism");
if (!LookForSearchString (ttl, lookfor, value, value_len - 1))
@@ -536,6 +525,37 @@ return to the Sequence Format form and choose the proper submission type.\n\n";
#define FastaFormatBufLen 1000
+static Int4 CountSegSetSegments (SeqEntryPtr sep)
+{
+ BioseqSetPtr bssp;
+
+ if (sep == NULL || sep->data.ptrvalue == NULL || ! IS_Bioseq_set (sep))
+ {
+ return 0;
+ }
+
+ bssp = (BioseqSetPtr) sep->data.ptrvalue;
+ if (bssp->_class != BioseqseqSet_class_segset)
+ {
+ return 0;
+ }
+ sep = bssp->seq_set;
+
+ while (sep != NULL)
+ {
+ if (IS_Bioseq_set (sep) && sep->data.ptrvalue != NULL)
+ {
+ bssp = (BioseqSetPtr) sep->data.ptrvalue;
+ if (bssp->_class == BioseqseqSet_class_parts)
+ {
+ return ValNodeLen (bssp->seq_set);
+ }
+ }
+ sep = sep->next;
+ }
+ return 0;
+}
+
static void FormatFastaDoc (FastaPagePtr fpp)
{
@@ -557,6 +577,7 @@ static void FormatFastaDoc (FastaPagePtr fpp)
CharPtr ttl;
CharPtr tmp;
ValNodePtr vnp;
+ Int4 num_seg;
if (fpp != NULL) {
str = MemNew (sizeof (char) * FastaFormatBufLen);
@@ -595,7 +616,7 @@ static void FormatFastaDoc (FastaPagePtr fpp)
label = "Message";
measure = "nucleotides";
} else if (fpp->is_na) {
- label = "Segment";
+ label = "Sequence";
measure = "nucleotides";
} else {
label = "Sequence";
@@ -605,7 +626,7 @@ static void FormatFastaDoc (FastaPagePtr fpp)
sprintf (str, "%d transcript sequence%s, total length %ld %s\n",
(int) num, plural, (long) len, measure);
} else if (fpp->is_na) {
- sprintf (str, "%d nucleotide segment%s, total length %ld %s\n",
+ sprintf (str, "%d nucleotide sequence%s, total length %ld %s\n",
(int) num, plural, (long) len, measure);
} else {
sprintf (str, "%d protein sequence%s, total length %ld %s\n",
@@ -619,6 +640,7 @@ static void FormatFastaDoc (FastaPagePtr fpp)
for (sep = fpp->list; sep != NULL; sep = sep->next) {
num++;
len = 0;
+ num_seg = CountSegSetSegments (sep);
sip = NULL;
tmp [0] = '\0';
if (IS_Bioseq (sep)) {
@@ -628,6 +650,7 @@ static void FormatFastaDoc (FastaPagePtr fpp)
sip = SeqIdFindWorst (bsp->id);
SeqIdWrite (sip, tmp, PRINTID_REPORT, FastaFormatBufLen);
}
+ nsep = sep;
} else if (IS_Bioseq_set (sep)) {
nsep = FindNucSeqEntry (sep);
if (nsep != NULL && IS_Bioseq (nsep)) {
@@ -639,10 +662,20 @@ static void FormatFastaDoc (FastaPagePtr fpp)
}
}
}
- sprintf (str, "\n%s %d\nLength: %ld %s\nSequence ID: %s\n", label,
- (int) num, (long) len, measure, tmp);
+
+ /* if segmented set, show number of segments */
+ if (num_seg > 0)
+ {
+ sprintf (str, "\nSegset %d\nLength: %ld %s (%d segments)\nSequence ID: %s\n",
+ (int) num, (long) len, measure, num_seg, tmp);
+ }
+ else
+ {
+ sprintf (str, "\n%s %d\nLength: %ld %s\nSequence ID: %s\n", label,
+ (int) num, (long) len, measure, tmp);
+ }
ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
title = StringSaveNoNull (ttl);
if (title != NULL && (! fpp->is_na)) {
if (LookForSearchString (title, "[gene=", tmp, FastaFormatBufLen - 1)) {
@@ -732,7 +765,7 @@ static void FormatFastaDoc (FastaPagePtr fpp)
}
MemFree (title);
ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
title = StringSaveNoNull (ttl);
if (title != NULL) {
if (! fpp->is_na) {
@@ -962,7 +995,7 @@ static SeqEntryPtr ReadOneSegSet (FILE *fp, Boolean parse_id, ValNodePtr PNTR er
ValNodeAddPointer (err_msg_list, 0, errormsg);
errormsg = NULL;
}
- nextsep = SequinFastaToSeqEntryEx (fp, FALSE, &errormsg, FALSE, &lastchar);
+ nextsep = SequinFastaToSeqEntryEx (fp, TRUE, &errormsg, FALSE, &lastchar);
}
nextsep = SegsetFromSeqEntryList (seg_list);
return nextsep;
@@ -978,14 +1011,7 @@ static void AddDefaultMoleculeTypeAndLocation (SeqEntryPtr seq_list, Int2 seqPac
old_value = GetModValueFromSeqEntry (sep, "moltype");
if (StringHasNoText (old_value))
{
- if (PackageTypeIsSet (seqPackage) || seqPackage == SEQ_PKG_GENOMICCDNA)
- {
- ApplyOneModToSeqEntry (sep, "moltype", "dna");
- }
- else
- {
- ApplyOneModToSeqEntry (sep, "moltype", "rna");
- }
+ ApplyOneModToSeqEntry (sep, "moltype", "dna");
}
old_value = MemFree (old_value);
old_value = GetModValueFromSeqEntry (sep, "location");
@@ -994,6 +1020,13 @@ static void AddDefaultMoleculeTypeAndLocation (SeqEntryPtr seq_list, Int2 seqPac
ApplyOneModToSeqEntry (sep, "location", "genomic");
}
old_value = MemFree (old_value);
+
+ old_value = GetModValueFromSeqEntry (sep, "topology");
+ if (StringHasNoText (old_value))
+ {
+ ApplyOneModToSeqEntry (sep, "topology", "Linear");
+ }
+ old_value = MemFree (old_value);
}
}
@@ -1116,6 +1149,7 @@ ImportSequencesFromFile
last->next = new_sep_list;
}
+
return sep_list;
}
@@ -1388,10 +1422,77 @@ static Boolean RejectExtraSequences (SeqEntryPtr new_list, FastaPagePtr fpp)
}
}
+static void ShowImportHelp (ButtoN b)
+{
+ CharPtr help_msg;
+
+ help_msg = (CharPtr) GetObjectExtra (b);
+ if (help_msg == NULL)
+ {
+ return;
+ }
+
+ Message (MSG_OK, help_msg);
+}
+
+static Boolean OkToImport (CharPtr msg, CharPtr help_msg)
+{
+ WindoW w;
+ GrouP h, c;
+ PrompT p;
+ ButtoN b;
+ ModalAcceptCancelData acd;
+
+ if (msg == NULL)
+ {
+ return TRUE;
+ }
+ acd.accepted = FALSE;
+ acd.cancelled = FALSE;
+
+ w = ModalWindow(-20, -13, -10, -10, NULL);
+ h = HiddenGroup (w, -1, 0, NULL);
+
+ p = StaticPrompt (h, msg, 0, 0, programFont, 'l');
+ c = HiddenGroup (h, 3, 0, NULL);
+ b = PushButton (c, "Yes", ModalAcceptButton);
+ SetObjectExtra (b, &acd, NULL);
+ b = PushButton (c, "No", ModalCancelButton);
+ SetObjectExtra (b, &acd, NULL);
+ if (help_msg != NULL)
+ {
+ b = PushButton (c, "Help", ShowImportHelp);
+ SetObjectExtra (b, help_msg, NULL);
+ }
+ AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, NULL);
+
+ Show(w);
+ Select (w);
+ while (!acd.accepted && ! acd.cancelled)
+ {
+ ProcessExternalEvent ();
+ Update ();
+ }
+ ProcessAnEvent ();
+ Remove (w);
+ if (acd.accepted)
+ {
+ return TRUE;
+ }
+ else
+ {
+ return FALSE;
+ }
+}
+
+static CharPtr segset_import_help_str = "Segmented sequence: a collection of non-overlapping, non-contiguous sequences that cover a specified genetic region. A standard example is a set of genomic DNA sequences that encode exons from a gene along with fragments of their flanking introns.";
+static CharPtr gapped_import_help_str = "Gapped sequence: a sequence with one or more gaps of known or unknown length.";
+
+
static Boolean ImportedSequenceTypeOk (SeqEntryPtr list, Int2 seqPackage)
{
BioseqPtr bsp;
- MsgAnswer ans = ANS_YES;
+ Boolean rval = TRUE;
if (list == NULL || seqPackage != SEQ_PKG_SINGLE)
{
@@ -1402,21 +1503,18 @@ static Boolean ImportedSequenceTypeOk (SeqEntryPtr list, Int2 seqPackage)
bsp = (BioseqPtr) list->data.ptrvalue;
if (bsp != NULL && bsp->repr == Seq_repr_delta)
{
- ans = Message (MSG_YN, "You have imported a gapped (delta) sequence. Did you mean to do that?");
+ SendHelpScrollMessage (helpForm, "Sequence Format Form", NULL);
+ rval = OkToImport ("You have imported a gapped sequence. Did you mean to do that?",
+ gapped_import_help_str);
}
}
else if (list->choice == 2)
{
- ans = Message (MSG_YN, "You have imported a segmented sequence. Did you mean to do that?");
- }
- if (ans == ANS_YES)
- {
- return TRUE;
- }
- else
- {
- return FALSE;
+ SendHelpScrollMessage (helpForm, "Sequence Format Form", NULL);
+ rval = OkToImport ("You have imported a segmented sequence. Did you mean to do that?",
+ segset_import_help_str);
}
+ return rval;
}
static Boolean ImportFastaDialog (DialoG d, CharPtr filename)
@@ -1783,6 +1881,7 @@ static void FormatPhylipDoc (PhylipPagePtr ppp)
if (bssp != NULL && (bssp->_class == 7 ||
(IsPopPhyEtcSet (bssp->_class)))) {
for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+ nsep = NULL;
num++;
len = 0;
sip = NULL;
@@ -1808,7 +1907,7 @@ static void FormatPhylipDoc (PhylipPagePtr ppp)
sprintf (str, "\n%s %d\nLength: %ld %s\nSequence ID: %s\n", label,
(int) num, (long) len, measure, tmp);
ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
title = StringSaveNoNull (ttl);
if (title != NULL) {
if (LookForSearchString (title, "[org=", tmp, PhylipFormatBufLen - 1)) {
@@ -1850,7 +1949,7 @@ static void FormatPhylipDoc (PhylipPagePtr ppp)
}
MemFree (title);
ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
title = StringSaveNoNull (ttl);
if (title != NULL) {
ExciseString (title, "[org=", "]");
@@ -5198,6 +5297,7 @@ static Pointer FastaSequencesFormToSeqEntryPtr (ForM f)
ObjectIdPtr oip;
UserFieldPtr ufp;
UserObjectPtr uop;
+ SeqEntryPtr oldscope;
sep = NULL;
sqfp = (SequencesFormPtr) GetObjectExtra (f);
@@ -5429,6 +5529,7 @@ static Pointer FastaSequencesFormToSeqEntryPtr (ForM f)
sqfp->seqPackage != SEQ_PKG_GENOMICCDNA) {
annotType = GetValue (sqfp->annotType);
if (annotType > 0) {
+ oldscope = SeqEntrySetScope (sep);
switch (annotType) {
case 1 :
ApplyAnnotationToAll (ADD_IMP, sep, sqfp->partialLft, sqfp->partialRgt,
@@ -5457,6 +5558,7 @@ static Pointer FastaSequencesFormToSeqEntryPtr (ForM f)
default :
break;
}
+ SeqEntrySetScope (oldscope);
}
}
ArrowCursor ();
@@ -5823,10 +5925,35 @@ static void ReplaceMolNamesWithMolBracketsInDefinitionLines (SeqEntryPtr sep);
static Boolean CheckSequencesForOrganisms (SequencesFormPtr sqfp);
static void SequencesFormDeleteProc (Pointer formDataPtr);
+static void SetDefaultMolTypesAndTopologies (SeqEntryPtr seq_list)
+{
+ SeqEntryPtr sep, nsep;
+ CharPtr ttl = NULL;
+ Char tmp[128];
+
+ for (sep = seq_list; sep != NULL; sep = sep->next)
+ {
+ nsep = FindNucSeqEntry (sep);
+ ttl = NULL;
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
+
+ if (!LookForSearchString (ttl, "[moltype=", tmp, sizeof (tmp) - 1))
+ {
+ ApplyOneModToSeqEntry (nsep, "moltype", "Genomic DNA");
+ }
+ ttl = NULL;
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
+ if (!LookForSearchString (ttl, "[topology=", tmp, sizeof (tmp) - 1))
+ {
+ ApplyOneModToSeqEntry (nsep, "topology", "Linear");
+ }
+ }
+}
+
static void NucleotideImportFinish (SequencesFormPtr sqfp)
{
- FastaPagePtr fpp;
- PhylipPagePtr ppp;
+ FastaPagePtr fpp = NULL;
+ PhylipPagePtr ppp = NULL;
SeqEntryPtr sep = NULL;
ValNodePtr fixes = NULL;
Boolean cancelled = FALSE;
@@ -5859,6 +5986,15 @@ static void NucleotideImportFinish (SequencesFormPtr sqfp)
FixDefinitionLines (sep, &cancelled, &fixes);
fixes = FreeStringPairList (fixes);
+
+ SetDefaultMolTypesAndTopologies (sep);
+
+ if (fpp != NULL)
+ {
+ Reset (fpp->doc);
+ FormatFastaDoc (fpp);
+ }
+
if (cancelled)
{
SequencesFormDeleteProc (sqfp);
@@ -7822,69 +7958,6 @@ static SeqEntryPtr GetSeqEntryFromSequencesForm (SequencesFormPtr sqfp)
return list;
}
-static Boolean HasNoMoreThanOneOrganismName (SeqEntryPtr seq_list, CharPtr PNTR org_name)
-{
- SeqEntryPtr sep;
- CharPtr ttl;
- CharPtr title;
- Char text [128];
- Char last_org [128];
- Char lookfor [128];
- Char lookfor2 [128];
- Boolean found_org;
- Boolean found_diff_org = FALSE;
-
- MakeSearchStringFromAlist (lookfor, "Org");
- MakeSearchStringFromAlist (lookfor2, "Organism");
- last_org [0] = 0;
-
- for (sep = seq_list; sep != NULL && !found_diff_org; sep = sep->next)
- {
- ttl = NULL;
- found_org = TRUE;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
- title = StringSaveNoNull (ttl);
- text [0] = '\0';
- if (! LookForSearchString (title, lookfor, text, sizeof (text) - 1))
- {
- if (! LookForSearchString (title, lookfor2, text, sizeof (text) - 1))
- {
- found_org = FALSE;
- }
- }
- if (found_org)
- {
- if (last_org [0] == 0)
- {
- StringCpy (last_org, text);
- }
- else if (StringCmp (last_org, text) != 0)
- {
- found_diff_org = TRUE;
- }
- }
- }
- if (found_diff_org)
- {
- return FALSE;
- }
- else
- {
- if (org_name != NULL)
- {
- if (last_org [0] == 0)
- {
- *org_name = 0;
- }
- else
- {
- *org_name = StringSave (last_org);
- }
- }
- return TRUE;
- }
-}
-
extern Boolean IsNonTextModifier (CharPtr mod_name)
{
@@ -7918,126 +7991,167 @@ static Int4 GetValForEnumName (EnumFieldAssocPtr eap, CharPtr mod_value)
return 0;
}
-static void AddSeqIDAndValueToTagList
-(CharPtr id,
- CharPtr title,
- CharPtr lookfor,
- CharPtr mod_name,
- Int2 seqPackage,
- ValNodePtr PNTR head,
- ValNodePtr PNTR found_modifiers)
+static CharPtr
+TagListStringFromDefLineValue
+(CharPtr defline_val,
+ Boolean is_nontext,
+ Int2 mod_type)
{
+ CharPtr taglist_str = NULL;
Char text [128];
- CharPtr str;
- Int4 len;
- Int4 mod_type;
- Boolean is_nontext;
-
- if (head == NULL)
- {
- return;
- }
-
- if (found_modifiers != NULL)
- {
- *found_modifiers = BuildModifierTypeList (*found_modifiers, title);
- }
- is_nontext = IsNonTextModifier (mod_name);
- mod_type = GetModifierType (mod_name);
-
- text [0] = '\0';
if (is_nontext)
{
- if (LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ if (StringHasNoText (defline_val))
{
- StringCpy (text, "1");
+ taglist_str = StringSave ("0");
}
else
{
- StringCpy (text, "0");
+ taglist_str = StringSave ("1");
}
}
else if (mod_type == eModifierType_Organism)
{
- if (! LookForSearchString (title, (CharPtr) short_org, text, sizeof (text) - 1))
- {
- if (! LookForSearchString (title, (CharPtr) long_org, text, sizeof (text) - 1))
- {
- StringCpy (text, " ");
- }
- }
+ taglist_str = StringSave (defline_val);
}
else if (mod_type == eModifierType_Location)
{
- if (LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ if (StringHasNoText (defline_val))
{
- sprintf (text, "%d", GetValForEnumName (biosource_genome_simple_alist, text));
+ taglist_str = StringSave ("1");
}
else
{
- StringCpy (text, "1");
+ sprintf (text, "%d", GetValForEnumName (biosource_genome_simple_alist,
+ defline_val));
+ taglist_str = StringSave (text);
}
}
else if (mod_type == eModifierType_NucGeneticCode
|| mod_type == eModifierType_MitoGeneticCode)
{
- if (LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ if (StringHasNoText (defline_val))
{
- sprintf (text, "%d", GeneticCodeFromString (text));
+ taglist_str = StringSave ("0");
}
else
{
- StringCpy (text, "0");
+ sprintf (text, "%d", GeneticCodeFromString (defline_val));
+ taglist_str = StringSave (text);
}
}
else if (mod_type == eModifierType_MolType)
{
- if (LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ if (StringHasNoText (defline_val))
{
- sprintf (text, "%d", MolTypeFromString (text));
+ taglist_str = StringSave ("253");
}
else
{
- if (PackageTypeIsSet (seqPackage) || seqPackage == SEQ_PKG_GENOMICCDNA)
- {
- sprintf (text, "%d", 253);
- }
- else
- {
- sprintf (text, "%d", 254);
- }
+ sprintf (text, "%d", MolTypeFromString (defline_val));
+ taglist_str = StringSave (text);
}
}
else if (mod_type == eModifierType_Topology)
{
- if (LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ if (StringHasNoText (defline_val))
{
- sprintf (text, "%d", TopologyFromString (text));
+ sprintf (text, "%d", TopologyFromString (""));
}
else
{
- sprintf (text, "%d", TopologyFromString (""));
+ sprintf (text, "%d", TopologyFromString (defline_val));
}
+ taglist_str = StringSave (text);
}
else
{
- if (! LookForSearchString (title, lookfor, text, sizeof (text) - 1)) {
+ if (StringHasNoText (defline_val))
+ {
+ taglist_str = StringSave (" ");
+ }
+ else
+ {
+ taglist_str = StringSave (defline_val);
+ }
+ }
+ return taglist_str;
+}
+
+static void AddSeqIDAndValueToTagList
+(CharPtr id,
+ CharPtr title,
+ CharPtr lookfor,
+ CharPtr mod_name,
+ Int2 seqPackage,
+ ValNodePtr PNTR head,
+ ValNodePtr PNTR found_modifiers)
+{
+ Char text [128];
+ CharPtr str;
+ Int4 len;
+ Int4 mod_type;
+ Boolean is_nontext;
+ CharPtr taglist_str = NULL;
+
+ if (head == NULL)
+ {
+ return;
+ }
+
+ if (found_modifiers != NULL)
+ {
+ *found_modifiers = BuildModifierTypeList (*found_modifiers, title);
+ }
+
+ is_nontext = IsNonTextModifier (mod_name);
+ mod_type = GetModifierType (mod_name);
+
+ text [0] = '\0';
+
+ if (is_nontext)
+ {
+ if (LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ {
+ sprintf (text, "2");
+ }
+ else
+ {
+ text [0] = '\0';
+ }
+ }
+ else if (mod_type == eModifierType_Organism)
+ {
+ if (! LookForSearchString (title, (CharPtr) short_org, text, sizeof (text) - 1))
+ {
+ if (! LookForSearchString (title, (CharPtr) long_org, text, sizeof (text) - 1))
+ {
+ StringCpy (text, " ");
+ }
+ }
+ }
+ else
+ {
+ if (!LookForSearchString (title, lookfor, text, sizeof (text) - 1))
+ {
StringCpy (text, " ");
}
}
- len = StringLen (id) + StringLen (text);
+
+ taglist_str = TagListStringFromDefLineValue (text, is_nontext, mod_type);
+ len = StringLen (id) + StringLen (taglist_str);
str = MemNew (len + 4);
if (str != NULL) {
StringCpy (str, id);
StringCat (str, "\t");
- StringCat (str, text);
+ StringCat (str, taglist_str);
StringCat (str, "\n");
}
+ taglist_str = MemFree (taglist_str);
ValNodeAddPointer (head, 0, str);
-
}
static void AddSeqIDAndValueFromSeqEntryToTagList
@@ -8224,6 +8338,92 @@ static Boolean HasAnySourceInformation (ValNodePtr header_list, ValNodePtr colum
return has_any;
}
+static Boolean OrganismMatchesAnotherRow (Int4 row, ValNodePtr row_list, Pointer userdata)
+{
+ ValNodePtr header_vnp, column_list, check_column_list, row_vnp;
+ Int4 row_num;
+
+ if (row_list == NULL || row < 1)
+ {
+ return FALSE;
+ }
+
+ /* we start with the header of the second column, because the first column
+ * is the sequence ID */
+ header_vnp = row_list->data.ptrvalue;
+ if (header_vnp == NULL) return FALSE;
+ header_vnp = header_vnp->next;
+ if (header_vnp == NULL) return FALSE;
+
+ /* find the row we're interested in */
+ for (row_vnp = row_list->next, row_num = 1;
+ row_vnp != NULL && row_num != row;
+ row_vnp = row_vnp->next, row_num++)
+ {
+ }
+ if (row_vnp == NULL)
+ {
+ return FALSE;
+ }
+
+ column_list = (ValNodePtr) row_vnp->data.ptrvalue;
+ if (!HasAnySourceInformation (row_list->data.ptrvalue, column_list))
+ {
+ return FALSE;
+ }
+
+ if (column_list == NULL || column_list->next == NULL)
+ {
+ return FALSE;
+ }
+
+ /* now check it against the other rows */
+ for (row_vnp = row_list->next, row_num = 1;
+ row_vnp != NULL;
+ row_vnp = row_vnp->next, row_num++)
+ {
+ if (row_num == row)
+ {
+ continue;
+ }
+
+ check_column_list = (ValNodePtr) row_vnp->data.ptrvalue;
+ if (check_column_list == NULL || check_column_list->next == NULL)
+ {
+ continue;
+ }
+
+ /* we compare the column lists, starting with the second column
+ * because the first column contains the sequence ID
+ */
+ if (DoColumnlistsHaveIdenticalSourceInformation (column_list->next,
+ check_column_list->next,
+ header_vnp))
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
+
+static Boolean AnySequencesHaveIdenticalOrganisms (ValNodePtr row_list)
+{
+ Int4 i, num_rows;
+ Boolean have_match = FALSE;
+
+ if (row_list == NULL || row_list->next == NULL)
+ {
+ return FALSE;
+ }
+ num_rows = ValNodeLen (row_list);
+
+ for (i = 1; i < num_rows && ! have_match; i++)
+ {
+ have_match = OrganismMatchesAnotherRow (i, row_list, NULL);
+ }
+ return have_match;
+}
+
static void ReportIdenticalOrganisms (ValNodePtr row_list, DoC doc)
{
ValNodePtr checked_list = NULL;
@@ -8320,7 +8520,7 @@ static void ReportIdenticalOrganisms (ValNodePtr row_list, DoC doc)
}
}
-static void SummarizeModifiers (ValNodePtr row_list, DoC summary_doc)
+static void SummarizeModifiers (ValNodePtr row_list, DialoG summary_dlg)
{
ValNodePtr header_vnp, row_vnp, column_vnp;
Int4 column_offset, col_pos;
@@ -8330,16 +8530,25 @@ static void SummarizeModifiers (ValNodePtr row_list, DoC summary_doc)
CharPtr first_value_seen;
Boolean all_unique;
ValNodePtr values_seen;
- CharPtr status;
+ CharPtr row_status;
Int4 line_len;
CharPtr modifier_line = NULL;
Int4 num_missing;
+ ValNodePtr summary_row_list = NULL;
+ ValNodePtr summary_col_list = NULL, summary_header_list = NULL;
- if (row_list == NULL || row_list->next == NULL || summary_doc == NULL)
+ if (row_list == NULL || row_list->next == NULL || summary_dlg == NULL)
{
return;
}
+ summary_col_list = NULL;
+ ValNodeAddPointer (&summary_col_list, 8, StringSave ("Modifier"));
+ ValNodeAddPointer (&summary_col_list, 6, StringSave ("Status"));
+ ValNodeAddPointer (&summary_col_list, 11, StringSave ("First Value"));
+ ValNodeAddPointer (&summary_row_list, 0, summary_col_list);
+ summary_header_list = summary_col_list;
+
header_vnp = row_list->data.ptrvalue;
/* skip over sequence ID column */
header_vnp = header_vnp->next;
@@ -8404,57 +8613,85 @@ static void SummarizeModifiers (ValNodePtr row_list, DoC summary_doc)
/* add summary line for this modifier */
if (! any_present)
{
- status = "%s: All missing (%d sequences). ";
+ row_status = "All missing (%d sequences)";
}
else if (all_present && all_unique)
{
- status = "%s: All present, all unique values. ";
+ row_status = "All present, all unique values";
}
else if (all_present && is_unique)
{
- status = "%s: All present, one unique value. ";
+ row_status = "All present, one unique value";
}
else if (all_present && ! is_unique)
{
- status = "%s: All present, mixed values. ";
+ row_status = "All present, mixed values";
}
else if (! all_present && all_unique)
{
- status = "%s: %d missing, all unique values. ";
+ row_status = "%d missing, all unique values";
}
else if (! all_present && is_unique)
{
- status = "%s: %d missing, one unique value present. ";
+ row_status = "%d missing, one unique value present";
}
else if (! all_present && ! is_unique)
{
- status = "%s: %d missing, mixed values. ";
+ row_status = "%d missing, mixed values";
}
- line_len = StringLen (header_vnp->data.ptrvalue)
- + StringLen (status)
- + StringLen (first_value_seen)
- + 30;
+ line_len = StringLen (row_status) + 30;
modifier_line = (CharPtr) MemNew (line_len * sizeof (Char));
if (modifier_line != NULL)
{
+
+ /* add summary row for this modifier */
+ summary_col_list = NULL;
+ /* add modifier name */
+ ValNodeAddPointer (&summary_col_list,
+ 0,
+ StringSave (header_vnp->data.ptrvalue));
+ /* show up to the first fifteen characters of the modifier name */
+ summary_header_list->choice = MAX (summary_header_list->choice,
+ StringLen (header_vnp->data.ptrvalue));
+ summary_header_list->choice = MIN (summary_header_list->choice,
+ 15);
+
+ /* add status */
if (all_present)
{
- sprintf (modifier_line, status, header_vnp->data.ptrvalue);
+ ValNodeAddPointer (&summary_col_list,
+ 0,
+ StringSave (row_status));
+ summary_header_list->next->choice = MAX (summary_header_list->next->choice,
+ StringLen (row_status));
}
else
{
- sprintf (modifier_line, status, header_vnp->data.ptrvalue, num_missing);
+ sprintf (modifier_line, row_status, num_missing);
+ ValNodeAddPointer (&summary_col_list,
+ 0,
+ StringSave (modifier_line));
+ summary_header_list->next->choice = MAX (summary_header_list->next->choice,
+ StringLen (modifier_line));
}
- if (!StringHasNoText (first_value_seen))
+ /* add sample value */
+ if (StringHasNoText (first_value_seen))
+ {
+ ValNodeAddPointer (&summary_col_list, 0, StringSave (""));
+ }
+ else
{
- StringCat (modifier_line, "(");
- StringCat (modifier_line, first_value_seen);
- StringCat (modifier_line, ")");
+ ValNodeAddPointer (&summary_col_list,
+ 0,
+ StringSave (first_value_seen));
+ summary_header_list->next->next->choice = MAX (summary_header_list->next->next->choice,
+ StringLen (first_value_seen));
}
- AppendText (summary_doc, modifier_line, NULL, NULL, programFont);
+ ValNodeAddPointer (&summary_row_list, 0, summary_col_list);
+
modifier_line = MemFree (modifier_line);
}
@@ -8465,11 +8702,33 @@ static void SummarizeModifiers (ValNodePtr row_list, DoC summary_doc)
header_vnp = header_vnp->next;
column_offset++;
}
+
+ PointerToDialog (summary_dlg, summary_row_list);
+ summary_row_list = FreeTableDisplayRowList (summary_row_list);
+
+}
+
+static ValNodePtr GetListOfCurrentModifiers (SeqEntryPtr seq_list)
+{
+ ValNodePtr found_modifiers = NULL;
+ SeqEntryPtr sep, nsep;
+ CharPtr ttl;
+
+ /* get list of modifiers */
+ ValNodeAddPointer (&found_modifiers, 0, StringSave ("Organism"));
+ for (sep = seq_list; sep != NULL; sep = sep->next)
+ {
+ ttl = NULL;
+ nsep = FindNucSeqEntry (sep);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
+ found_modifiers = BuildModifierTypeList (found_modifiers, ttl);
+ }
+ return found_modifiers;
}
static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
{
- SeqEntryPtr seq_list, sep;
+ SeqEntryPtr seq_list, sep, nsep;
ValNodePtr found_modifiers = NULL, vnp;
CharPtr ttl;
CharPtr mod_name;
@@ -8487,7 +8746,6 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
if (sqfp == NULL) return;
Reset (sqfp->org_doc);
- Reset (sqfp->summary_doc);
ObjectRect (sqfp->org_doc, &r);
InsetRect (&r, 4, 4);
faColFmt.pixWidth = r.right - r.left;
@@ -8498,23 +8756,22 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
AppendText (sqfp->org_doc,
"You must create sequences before you can add source information.",
&faParFmt, &faColFmt, programFont);
+ Show (sqfp->org_doc);
+ Hide (sqfp->ident_org_btn);
+ Hide (sqfp->summary_dlg);
}
else
{
+ Show (sqfp->summary_dlg);
/* get list of modifiers */
- for (sep = seq_list, seq_num = 0; sep != NULL; sep = sep->next, seq_num++)
- {
- ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
- found_modifiers = BuildModifierTypeList (found_modifiers, ttl);
- }
+ found_modifiers = GetListOfCurrentModifiers (seq_list);
/* create header line for table */
/* store max column width in choice */
column_list = NULL;
ValNodeAddPointer (&column_list, 6, StringSave ("Seq ID"));
ValNodeAddPointer (&column_list, 8, StringSave ("Organism"));
- for (vnp = found_modifiers; vnp != NULL; vnp = vnp->next)
+ for (vnp = found_modifiers->next; vnp != NULL; vnp = vnp->next)
{
ValNodeAddPointer (&column_list, StringLen (vnp->data.ptrvalue), StringSave ((CharPtr) vnp->data.ptrvalue));
}
@@ -8527,6 +8784,8 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
{
column_list = NULL;
header_vnp = header_list;
+ nsep = FindNucSeqEntry (sep);
+
/* add Sequence ID */
bsp = FindNucBioseq (sep);
if (bsp != NULL)
@@ -8544,7 +8803,7 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
/* get title */
ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
/* add organism name */
header_vnp = header_vnp->next;
@@ -8554,7 +8813,7 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
ValNodeAddPointer (&column_list, 0, org_name);
/* get remaining modifiers */
- for (vnp = found_modifiers; vnp != NULL; vnp = vnp->next)
+ for (vnp = found_modifiers->next; vnp != NULL; vnp = vnp->next)
{
header_vnp = header_vnp->next;
mod_name = (CharPtr) vnp->data.ptrvalue;
@@ -8565,9 +8824,19 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
}
ValNodeAddPointer (&row_list, 0, column_list);
}
+ if (AnySequencesHaveIdenticalOrganisms (row_list))
+ {
+ Show (sqfp->ident_org_btn);
+ Show (sqfp->org_doc);
+ }
+ else
+ {
+ Hide (sqfp->ident_org_btn);
+ Hide (sqfp->org_doc);
+ }
ReportIdenticalOrganisms (row_list, sqfp->org_doc);
- SummarizeModifiers (row_list, sqfp->summary_doc);
+ SummarizeModifiers (row_list, sqfp->summary_dlg);
/* free table text */
for (row_vnp = row_list; row_vnp != NULL; row_vnp = row_vnp->next)
@@ -8581,7 +8850,6 @@ static void SeqEntryPtrToOrgDoc (SequencesFormPtr sqfp)
}
/* update document */
InvalDocRows (sqfp->org_doc, 0, 0, 0);
- InvalDocRows (sqfp->summary_doc, 0, 0, 0);
}
static void SeqEntryPtrToSourceTab (SequencesFormPtr sqfp)
@@ -10231,6 +10499,7 @@ static DialoG MultiOrganismSelectionDialog (GrouP parent)
RecT r1, r2, r3;
ValNodePtr gencodelist;
ButtoN b;
+ PrompT p1;
dlg = (MultiOrganismSelectionDialogPtr) MemNew (sizeof (MultiOrganismSelectionDialogData));
@@ -10250,7 +10519,8 @@ static DialoG MultiOrganismSelectionDialog (GrouP parent)
dlg->geneticcodelist = GetGeneticCodeValNodeList ();
dlg->org_select_dlg = OrganismSelectionDialog (grp, "");
-
+ p1 = StaticPrompt (grp, "You can use the Copy buttons to populate the organism field from the selector above.",
+ 0, 0, programFont, 'l');
scroll_grp = NormalGroup (grp, 2, 0, "", NULL, NULL);
id_grp = HiddenGroup (scroll_grp, 5, 0, NULL);
@@ -10304,7 +10574,7 @@ static DialoG MultiOrganismSelectionDialog (GrouP parent)
dlg->id_scroll = ScrollBar4 (scroll_grp, 0, 10, MultiOrgScroll);
SetObjectExtra (dlg->id_scroll, dlg, NULL);
- AlignObjects (ALIGN_CENTER, (HANDLE) dlg->org_select_dlg, (HANDLE) scroll_grp, NULL);
+ AlignObjects (ALIGN_CENTER, (HANDLE) dlg->org_select_dlg, (HANDLE) p1, (HANDLE) scroll_grp, NULL);
ObjectRect (dlg->copy_btn [0], &r1);
ObjectRect (dlg->copy_btn [4], &r2);
@@ -10443,6 +10713,54 @@ GetTagListValue (TagListPtr tlp, Int4 seq_num)
return GetTagListValueEx (tlp, seq_num, 1);
}
+static void SetTagListValue (TagListPtr tlp, Int4 row, Int4 column, CharPtr new_value)
+{
+ ValNodePtr vnp;
+ Int4 row_num;
+ CharPtr new_val;
+
+ if (tlp == NULL)
+ {
+ return;
+ }
+
+ for (vnp = tlp->vnp, row_num = 0;
+ vnp != NULL && row_num != row;
+ vnp = vnp->next, row_num++)
+ {
+ }
+ if (vnp == NULL)
+ {
+ return;
+ }
+
+ new_val = ReplaceTagListColumn (vnp->data.ptrvalue, new_value, column);
+ if (new_val != vnp->data.ptrvalue)
+ {
+ vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
+ vnp->data.ptrvalue = new_val;
+ }
+}
+
+static void SetTagListColumnValue (TagListPtr tlp, Int4 column, CharPtr new_value)
+{
+ ValNodePtr vnp;
+ CharPtr new_val;
+
+ for (vnp = tlp->vnp;
+ vnp != NULL;
+ vnp = vnp->next)
+ {
+ new_val = ReplaceTagListColumn (vnp->data.ptrvalue, new_value, column);
+ if (new_val != vnp->data.ptrvalue)
+ {
+ vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue);
+ vnp->data.ptrvalue = new_val;
+ }
+ }
+}
+
+
static void
ReplaceValueInDefLines
(SourceAssistantPtr sap,
@@ -10575,9 +10893,9 @@ static GrouP MakeGeneticCodeCommentInstructionGroup (GrouP parent)
instr_grp = HiddenGroup (parent, 1, 0, NULL);
StaticPrompt (instr_grp, "When a genetic code is determined automatically from the organism name and location,",
0, 0, programFont, 'l');
- StaticPrompt (instr_grp, "you cannot edit the genetic code directly. You may add information about the ",
+ StaticPrompt (instr_grp, "you cannot edit the genetic code directly. You may provide an alternate genetic code",
0, 0, programFont, 'l');
- StaticPrompt (instr_grp, "genetic code here if you wish.",
+ StaticPrompt (instr_grp, "and the evidence to support it here if you wish.",
0, 0, programFont, 'l');
return instr_grp;
@@ -10611,6 +10929,315 @@ static GrouP MakeLocationInstructionGroup (GrouP parent)
return instr_grp;
}
+static GrouP MakeInstructionGroup (GrouP parent, Boolean is_nontext, Int2 mod_type)
+{
+ GrouP instr_grp = NULL;
+
+ if (is_nontext)
+ {
+ instr_grp = MakeNontextInstructionGroup (parent);
+ }
+ else if (mod_type == eModifierType_Location)
+ {
+ instr_grp = MakeLocationInstructionGroup (parent);
+ }
+ else if (mod_type == eModifierType_Organism)
+ {
+ instr_grp = MakeSourceInstructionGroup (parent);
+ }
+ else if (mod_type == eModifierType_NucGeneticCode
+ || mod_type == eModifierType_MitoGeneticCode
+ || mod_type == eModifierType_GeneticCode)
+ {
+ instr_grp = MakeGeneticCodeInstructionGroup (parent);
+ }
+ else if (mod_type == eModifierType_GeneticCodeComment)
+ {
+ instr_grp = MakeGeneticCodeCommentInstructionGroup (parent);
+ }
+ return instr_grp;
+}
+
+
+/* This section of code prepares a dialog for editing one value for
+ * the specified modifier type. It can be used for setting the value
+ * for a single sequence or the values for all sequences.
+ */
+typedef struct singlemodvaldlg
+{
+ DIALOG_MESSAGE_BLOCK
+ Boolean is_nontext;
+ Int2 mod_type;
+ Int2 seqPackage;
+
+ PopuP nontext_popup;
+ DialoG strvalue_dlg;
+ DialoG org_dlg;
+ TexT text_txt;
+} SingleModValDlgData, PNTR SingleModValDlgPtr;
+
+static void SingleModValToDialog (DialoG d, Pointer userdata)
+{
+ SingleModValDlgPtr dlg;
+ CharPtr suggested_value;
+ ValNode vn;
+ ValNodePtr gencodelist;
+
+ dlg = (SingleModValDlgPtr) GetObjectExtra (d);
+
+ if (dlg == NULL)
+ {
+ return;
+ }
+
+ suggested_value = (CharPtr) userdata;
+
+ if (dlg->is_nontext)
+ {
+ if (StringICmp (suggested_value, "TRUE") == 0)
+ {
+ SetValue (dlg->nontext_popup, 2);
+ }
+ else
+ {
+ SetValue (dlg->nontext_popup, 1);
+ }
+ }
+ else if (dlg->mod_type == eModifierType_Location)
+ {
+ if (StringHasNoText (suggested_value))
+ {
+ vn.choice = 1;
+ vn.data.ptrvalue = "genomic";
+ }
+ else
+ {
+ vn.choice = GetValForEnumName (biosource_genome_simple_alist, suggested_value);
+ vn.data.ptrvalue = suggested_value;
+ }
+ vn.next = NULL;
+ PointerToDialog (dlg->strvalue_dlg, &vn);
+ }
+ else if (dlg->mod_type == eModifierType_Organism)
+ {
+ PointerToDialog (dlg->org_dlg, suggested_value);
+ }
+ else if (dlg->mod_type == eModifierType_NucGeneticCode
+ || dlg->mod_type == eModifierType_MitoGeneticCode
+ || dlg->mod_type == eModifierType_GeneticCode)
+ {
+ gencodelist = GetGeneticCodeValNodeList ();
+ if (StringHasNoText (suggested_value))
+ {
+ vn.choice = 0;
+ }
+ else if (isdigit (suggested_value[0]))
+ {
+ vn.choice = atoi (suggested_value);
+ }
+ else
+ {
+ vn.choice = GeneticCodeFromStringAndList (suggested_value, gencodelist);
+ }
+ vn.next = NULL;
+ vn.data.ptrvalue = suggested_value;
+ PointerToDialog (dlg->strvalue_dlg, &vn);
+ gencodelist = ValNodeFreeData (gencodelist);
+ }
+ else if (dlg->mod_type == eModifierType_MolType)
+ {
+ if (StringHasNoText (suggested_value))
+ {
+ vn.choice = 253;
+ }
+ else if (isdigit (suggested_value[0]))
+ {
+ vn.choice = atoi (suggested_value);
+ }
+ else
+ {
+ vn.choice = MolTypeFromString (suggested_value);
+ }
+ vn.next = NULL;
+ vn.data.ptrvalue = suggested_value;
+ PointerToDialog (dlg->strvalue_dlg, &vn);
+ }
+ else if (dlg->mod_type == eModifierType_Topology)
+ {
+ if (StringHasNoText (suggested_value))
+ {
+ vn.choice = 1;
+ }
+ else if (isdigit (suggested_value[0]))
+ {
+ vn.choice = atoi (suggested_value);
+ }
+ else
+ {
+ vn.choice = TopologyFromString (suggested_value);
+ }
+ vn.next = NULL;
+ vn.data.ptrvalue = suggested_value;
+ PointerToDialog (dlg->strvalue_dlg, &vn);
+ }
+ else
+ {
+ if (StringHasNoText (suggested_value))
+ {
+ SetTitle (dlg->text_txt, "");
+ }
+ else
+ {
+ SetTitle (dlg->text_txt, suggested_value);
+ }
+ }
+}
+
+static Pointer DialogToSingleModVal (DialoG d)
+{
+ SingleModValDlgPtr dlg;
+ CharPtr new_value = NULL;
+ ValNodePtr value_vnp;
+
+ dlg = (SingleModValDlgPtr) GetObjectExtra (d);
+
+ if (dlg == NULL)
+ {
+ return;
+ }
+
+ /* prepare value */
+ if (dlg->is_nontext)
+ {
+ if (GetValue (dlg->nontext_popup) == 2)
+ {
+ new_value = StringSave ("2");
+ }
+ }
+ else if (dlg->mod_type == eModifierType_Location
+ || dlg->mod_type == eModifierType_NucGeneticCode
+ || dlg->mod_type == eModifierType_MitoGeneticCode
+ || dlg->mod_type == eModifierType_GeneticCode
+ || dlg->mod_type == eModifierType_MolType
+ || dlg->mod_type == eModifierType_Topology)
+ {
+ value_vnp = DialogToPointer (dlg->strvalue_dlg);
+ new_value = value_vnp->data.ptrvalue;
+ if (dlg->mod_type == eModifierType_Location)
+ {
+ StringToLower (new_value);
+ }
+ value_vnp = ValNodeFree (value_vnp);
+ if (dlg->mod_type == eModifierType_MolType
+ && StringICmp (new_value, "mRNA [cDNA]") == 0)
+ {
+ new_value = MemFree (new_value);
+ new_value = StringSave ("mRNA");
+ }
+ }
+ else if (dlg->mod_type == eModifierType_Organism)
+ {
+ new_value = DialogToPointer (dlg->org_dlg);
+ }
+ else
+ {
+ new_value = SaveStringFromText (dlg->text_txt);
+ }
+ return (Pointer) new_value;
+}
+
+
+static DialoG SingleModValDialog (GrouP parent, Boolean is_nontext, Int2 mod_type, Int2 seqPackage)
+{
+ SingleModValDlgPtr dlg;
+ GrouP grp;
+ ValNodePtr gencodelist;
+
+ dlg = (SingleModValDlgPtr) MemNew (sizeof (SingleModValDlgData));
+ if (dlg == NULL)
+ {
+ return NULL;
+ }
+
+ grp = HiddenGroup (parent, 1, 0, NULL);
+ SetObjectExtra (grp, dlg, StdCleanupExtraProc);
+ SetGroupSpacing (grp, 10, 10);
+
+ dlg->dialog = (DialoG) grp;
+ dlg->todialog = SingleModValToDialog;
+ dlg->fromdialog = DialogToSingleModVal;
+ dlg->dialogmessage = NULL;
+ dlg->testdialog = NULL;
+
+ dlg->is_nontext = is_nontext;
+ dlg->mod_type = mod_type;
+ dlg->nontext_popup = NULL;
+ dlg->strvalue_dlg = NULL;
+ dlg->org_dlg = NULL;
+ dlg->text_txt = NULL;
+
+
+ if (dlg->is_nontext)
+ {
+ dlg->nontext_popup = PopupList (grp, TRUE, NULL);
+ PopupItem (dlg->nontext_popup, "FALSE");
+ PopupItem (dlg->nontext_popup, "TRUE");
+ }
+ else if (dlg->mod_type == eModifierType_Location)
+ {
+ dlg->strvalue_dlg = EnumAssocSelectionDialog (grp, biosource_genome_simple_alist,
+ "location", FALSE, NULL, NULL);
+ }
+ else if (dlg->mod_type == eModifierType_Organism)
+ {
+ dlg->org_dlg = OrganismSelectionDialog (grp, "");
+ }
+ else if (dlg->mod_type == eModifierType_NucGeneticCode
+ || dlg->mod_type == eModifierType_MitoGeneticCode
+ || dlg->mod_type == eModifierType_GeneticCode)
+ {
+ gencodelist = GetGeneticCodeValNodeList ();
+ dlg->strvalue_dlg = ValNodeSelectionDialog (grp, gencodelist, 6,
+ ValNodeStringName,
+ ValNodeSimpleDataFree,
+ ValNodeStringCopy,
+ ValNodeChoiceMatch,
+ "genetic code",
+ NULL, NULL, FALSE);
+ }
+ else if (dlg->mod_type == eModifierType_MolType)
+ {
+ if (seqPackage == SEQ_PKG_GENOMICCDNA)
+ {
+ dlg->strvalue_dlg = EnumAssocSelectionDialog (grp, biomol_nucGen_alist,
+ "moltype", FALSE, NULL, NULL);
+ }
+ else
+ {
+ dlg->strvalue_dlg = EnumAssocSelectionDialog (grp, biomol_nucX_alist,
+ "moltype", FALSE, NULL, NULL);
+ }
+ }
+ else if (dlg->mod_type == eModifierType_Topology)
+ {
+ dlg->strvalue_dlg = EnumAssocSelectionDialog (grp, topology_nuc_alist,
+ "topology", FALSE, NULL, NULL);
+ }
+ else
+ {
+ if (dlg->mod_type == eModifierType_GeneticCodeComment)
+ {
+ dlg->text_txt = DialogText (grp, "", 40, NULL);
+ }
+ else
+ {
+ dlg->text_txt = DialogText (grp, "", 20, NULL);
+ }
+ }
+
+ return (DialoG) grp;
+}
+
static CharPtr
GetValueFromTagList
(TagListPtr tlp,
@@ -10743,7 +11370,7 @@ static void AddSeqIDAndValueFromSeqEntryToRowList
(SeqEntryPtr sep,
ValNodePtr PNTR row_list)
{
- BioseqPtr bsp;
+ BioseqPtr bsp = NULL;
SeqDescrPtr sdp;
Char id_txt [128];
@@ -10801,7 +11428,14 @@ static void EditOrganismColumn (SourceAssistantPtr sap, SeqEntryPtr seq_list)
return;
}
- w = MovableModalWindow (-20, -13, -10, -10, "Organisms", NULL);
+ if ((sap != NULL && sap->num_deflines > 1) || (seq_list != NULL && seq_list->next != NULL))
+ {
+ w = MovableModalWindow (-20, -13, -10, -10, "Organism Editor", NULL);
+ }
+ else
+ {
+ w = MovableModalWindow (-20, -13, -10, -10, "Multiple Organism Editor", NULL);
+ }
h = HiddenGroup(w, -1, 0, NULL);
SetGroupSpacing (h, 10, 10);
@@ -10944,85 +11578,76 @@ static void EditOrganismColumn (SourceAssistantPtr sap, SeqEntryPtr seq_list)
}
-typedef struct clearcolumnvaluesdata
+typedef struct setcolumnvaluesdata
{
- SourceAssistantPtr sap;
- SeqEntryPtr seq_list;
- TagListPtr tlp;
- CharPtr lookfor;
- CharPtr mod_name;
- Int2 seqPackage;
-} ClearColumnValuesData, PNTR ClearColumnValuesPtr;
+ TagListPtr tlp;
+ DialoG all_val_dlg;
+ Boolean is_nontext;
+ Int2 mod_type;
+} SetColumnValuesData, PNTR SetColumnValuesPtr;
-static void ClearColumnValues (ButtoN b)
-{
- BioseqPtr bsp;
- Char id_txt [128];
- ValNodePtr head, vnp;
- SeqEntryPtr sep, nsep;
- ClearColumnValuesPtr ccvp;
- Int4 j;
+static void SetAllColumnValues (SetColumnValuesPtr scvp, CharPtr new_value)
+{
+ CharPtr taglist_str;
+ Int4 j;
+ ValNodePtr vnp;
- ccvp = (ClearColumnValuesPtr) GetObjectExtra (b);
- if (ccvp == NULL || (ccvp->sap == NULL && ccvp->seq_list == NULL) || ccvp->tlp == NULL)
+ if (scvp == NULL || scvp->tlp == NULL)
{
return;
}
- head = NULL;
- if (ccvp->sap == NULL)
- {
- for (sep = ccvp->seq_list; sep != NULL; sep = sep->next)
- {
- if (IS_Bioseq (sep))
- {
- bsp = (BioseqPtr) sep->data.ptrvalue;
- }
- else if (IS_Bioseq_set (sep))
- {
- nsep = FindNucSeqEntry (sep);
- if (nsep != NULL && IS_Bioseq (nsep))
- {
- bsp = (BioseqPtr) nsep->data.ptrvalue;
- }
- }
-
- if (bsp == NULL)
- {
- continue;
- }
+ taglist_str = TagListStringFromDefLineValue (new_value, scvp->is_nontext, scvp->mod_type);
+ SetTagListColumnValue (scvp->tlp, 1, taglist_str);
+ taglist_str = MemFree (taglist_str);
+
+ SendMessageToDialog (scvp->tlp->dialog, VIB_MSG_REDRAW);
+ for (j = 0, vnp = scvp->tlp->vnp; vnp != NULL; j++, vnp = vnp->next) {
+ }
+ scvp->tlp->max = MAX ((Int2) 0, (Int2) (j - scvp->tlp->rows));
+ CorrectBarMax (scvp->tlp->bar, scvp->tlp->max);
+ CorrectBarPage (scvp->tlp->bar, scvp->tlp->rows - 1, scvp->tlp->rows - 1);
+ if (scvp->tlp->max > 0) {
+ SafeShow (scvp->tlp->bar);
+ } else {
+ SafeHide (scvp->tlp->bar);
+ }
+ SendMessageToDialog (scvp->tlp->dialog, VIB_MSG_ENTER);
+}
+
+static void ClearColumnValues (ButtoN b)
+{
+ SetColumnValuesPtr scvp;
- SeqIdWrite (SeqIdFindWorst (bsp->id), id_txt, PRINTID_REPORT, sizeof (id_txt));
+ scvp = (SetColumnValuesPtr) GetObjectExtra (b);
- AddSeqIDAndValueToTagList (id_txt, NULL,
- ccvp->lookfor, ccvp->mod_name, ccvp->seqPackage,
- &head, NULL);
- }
- }
- else
+ if (ANS_NO == Message (MSG_YN, "Are you sure you want to clear all the values?"))
{
- for (j = 0; j < ccvp->sap->num_deflines; j++)
- {
- AddSeqIDAndValueToTagList (ccvp->sap->id_list[j], NULL,
- ccvp->lookfor, ccvp->mod_name, ccvp->seqPackage,
- &head, NULL);
- }
+ return;
}
- SendMessageToDialog (ccvp->tlp->dialog, VIB_MSG_RESET);
- ccvp->tlp->vnp = head;
- SendMessageToDialog (ccvp->tlp->dialog, VIB_MSG_REDRAW);
- for (j = 0, vnp = ccvp->tlp->vnp; vnp != NULL; j++, vnp = vnp->next) {
+ SetAllColumnValues (scvp, NULL);
+}
+
+static void EditOrgModApplyAll (ButtoN b)
+{
+ SetColumnValuesPtr scvp;
+ CharPtr new_value;
+
+ scvp = (SetColumnValuesPtr) GetObjectExtra (b);
+ if (scvp == NULL || scvp->all_val_dlg == NULL || scvp->tlp == NULL)
+ {
+ return;
}
- ccvp->tlp->max = MAX ((Int2) 0, (Int2) (j - ccvp->tlp->rows));
- CorrectBarMax (ccvp->tlp->bar, ccvp->tlp->max);
- CorrectBarPage (ccvp->tlp->bar, ccvp->tlp->rows - 1, ccvp->tlp->rows - 1);
- if (ccvp->tlp->max > 0) {
- SafeShow (ccvp->tlp->bar);
- } else {
- SafeHide (ccvp->tlp->bar);
+
+ if (ANS_NO == Message (MSG_YN, "Are you sure you want to set all the values?"))
+ {
+ return;
}
- SendMessageToDialog (ccvp->tlp->dialog, VIB_MSG_ENTER);
+
+ new_value = DialogToPointer (scvp->all_val_dlg);
+ SetAllColumnValues (scvp, new_value);
+ new_value = MemFree (new_value);
}
static void
@@ -11050,9 +11675,10 @@ EditOrgModColumn
EnumFieldAssocPtr gencode_alist = NULL;
EnumFieldAssocPtr edit_alists [2];
GrouP instr_grp = NULL;
- ClearColumnValuesData ccvd;
+ SetColumnValuesData scvd;
ButtoN clear_btn;
CharPtr mod_label;
+ ButtoN apply_all_btn;
if (StringHasNoText (mod_name) || (sap == NULL && seq_list == NULL))
{
@@ -11082,6 +11708,15 @@ EditOrgModColumn
w = MovableModalWindow (-20, -13, -10, -10, mod_label, NULL);
h = HiddenGroup(w, -1, 0, NULL);
SetGroupSpacing (h, 10, 10);
+
+ instr_grp = MakeInstructionGroup (h, is_nontext, mod_type);
+
+ scvd.all_val_dlg = SingleModValDialog (h, is_nontext, mod_type, seqPackage);
+ PointerToDialog (scvd.all_val_dlg, NULL);
+ scvd.is_nontext = is_nontext;
+ scvd.mod_type = mod_type;
+ apply_all_btn = PushButton (h, "Apply above value to all sequences", EditOrgModApplyAll);
+ SetObjectExtra (apply_all_btn, &scvd, NULL);
k = HiddenGroup (h, 1, 0, NULL);
g = HiddenGroup (k, 2, 0, NULL);
@@ -11111,14 +11746,12 @@ EditOrgModColumn
dlg = CreateTagListDialogEx (k, rows_shown, 2, 2,
nontextmodedittypes, modedit_widths,
nontextmodedit_alists, TRUE, TRUE, NULL, NULL);
- instr_grp = MakeNontextInstructionGroup (h);
}
else if (mod_type == eModifierType_Location)
{
dlg = CreateTagListDialogEx (k, rows_shown, 2, 2,
locationmodedittypes, modedit_widths,
locationmodedit_alists, TRUE, TRUE, NULL, NULL);
- instr_grp = MakeLocationInstructionGroup (h);
}
else if (mod_type == eModifierType_NucGeneticCode
|| mod_type == eModifierType_MitoGeneticCode)
@@ -11129,7 +11762,6 @@ EditOrgModColumn
dlg = CreateTagListDialogEx (k, rows_shown, 2, 2,
locationmodedittypes, modedit_widths,
edit_alists, TRUE, TRUE, NULL, NULL);
- instr_grp = MakeGeneticCodeInstructionGroup (h);
}
else if (mod_type == eModifierType_MolType)
{
@@ -11162,7 +11794,6 @@ EditOrgModColumn
dlg = CreateTagListDialogEx (k, rows_shown, 2, 2,
modedit_types, modedit_widths,
NULL, TRUE, TRUE, NULL, NULL);
- instr_grp = MakeSourceInstructionGroup (h);
}
else
{
@@ -11212,15 +11843,21 @@ EditOrgModColumn
}
SendMessageToDialog (tlp->dialog, VIB_MSG_ENTER);
- ccvd.sap = sap;
- ccvd.seq_list = seq_list;
- ccvd.tlp = tlp;
- ccvd.lookfor = lookfor;
- ccvd.mod_name = mod_name;
- ccvd.seqPackage = seqPackage;
+ scvd.tlp = tlp;
- clear_btn = PushButton (h, "Clear All Values", ClearColumnValues);
- SetObjectExtra (clear_btn, &ccvd, NULL);
+ if (mod_type == eModifierType_MolType)
+ {
+ clear_btn = PushButton (h, "Reset All to Genomic DNA", ClearColumnValues);
+ }
+ else if (mod_type == eModifierType_Topology)
+ {
+ clear_btn = PushButton (h, "Reset All to Linear", ClearColumnValues);
+ }
+ else
+ {
+ clear_btn = PushButton (h, "Clear All Values", ClearColumnValues);
+ }
+ SetObjectExtra (clear_btn, &scvd, NULL);
c = HiddenGroup (h, 2, 0, NULL);
b = PushButton (c, "Accept", ModalAcceptButton);
@@ -11228,15 +11865,13 @@ EditOrgModColumn
b = PushButton (c, "Cancel", ModalCancelButton);
SetObjectExtra (b, &acd, NULL);
- if (instr_grp == NULL)
- {
- AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) clear_btn, (HANDLE) c, (HANDLE) NULL);
- }
- else
- {
- AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) instr_grp, (HANDLE) clear_btn,
- (HANDLE) c, (HANDLE) NULL);
- }
+ AlignObjects (ALIGN_CENTER, (HANDLE) scvd.all_val_dlg,
+ (HANDLE) apply_all_btn,
+ (HANDLE) k,
+ (HANDLE) clear_btn,
+ (HANDLE) c,
+ (HANDLE) instr_grp,
+ NULL);
Show (w);
Select (w);
@@ -11535,6 +12170,7 @@ ContinueWithAutopopulatedGeneticCodes
return rval;
}
+
static void
ApplyOrgModColumnOrCell
(CharPtr mod_name,
@@ -11547,13 +12183,11 @@ ApplyOrgModColumnOrCell
Int2 seqPackage)
{
WindoW w;
- GrouP h, g, c;
- TexT text_txt;
- PopuP nontext_popup;
+ GrouP h, c;
GrouP instr_grp = NULL;
Boolean found_value = FALSE;
Int4 j;
- ValNodePtr head = NULL, value_vnp;
+ ValNodePtr head = NULL;
ModalAcceptCancelData acd;
ButtoN b;
Boolean is_nontext;
@@ -11561,9 +12195,6 @@ ApplyOrgModColumnOrCell
CharPtr title;
CharPtr all_seq_fmt = "%s (all sequences)";
CharPtr one_seq_fmt = "%s (Seq_ID %s)";
- ValNode vn;
- DialoG org_dlg;
- DialoG strvalue_dlg;
Int4 num_sequences = 0;
SeqEntryPtr sep, nuc_sep;
Char id_txt[128];
@@ -11573,6 +12204,8 @@ ApplyOrgModColumnOrCell
ValNodePtr row_vnp = NULL, col_vnp;
Int4 row_num, col_num;
CharPtr mod_label;
+ Boolean done;
+ DialoG val_dlg;
if (StringHasNoText (mod_name) || row < -1)
{
@@ -11694,138 +12327,10 @@ ApplyOrgModColumnOrCell
h = HiddenGroup(w, -1, 0, NULL);
SetGroupSpacing (h, 10, 10);
- g = HiddenGroup (h, 1, 0, NULL);
-
- if (is_nontext)
- {
- nontext_popup = PopupList (g, TRUE, NULL);
- PopupItem (nontext_popup, "FALSE");
- PopupItem (nontext_popup, "TRUE");
- if (StringICmp (suggested_value, "TRUE") == 0)
- {
- SetValue (nontext_popup, 2);
- }
- else
- {
- SetValue (nontext_popup, 1);
- }
- instr_grp = MakeNontextInstructionGroup (h);
- }
- else if (mod_type == eModifierType_Location)
- {
- if (StringHasNoText (suggested_value))
- {
- vn.choice = 1;
- vn.data.ptrvalue = "genomic";
- }
- else
- {
- vn.choice = GetValForEnumName (biosource_genome_simple_alist, suggested_value);
- vn.data.ptrvalue = suggested_value;
- }
- vn.next = NULL;
- strvalue_dlg = EnumAssocSelectionDialog (g, biosource_genome_simple_alist,
- "location", FALSE, NULL, NULL);
- PointerToDialog (strvalue_dlg, &vn);
- instr_grp = MakeLocationInstructionGroup (h);
- }
- else if (mod_type == eModifierType_Organism)
- {
- org_dlg = OrganismSelectionDialog (g, suggested_value);
- instr_grp = MakeSourceInstructionGroup (h);
- }
- else if (mod_type == eModifierType_NucGeneticCode
- || mod_type == eModifierType_MitoGeneticCode
- || mod_type == eModifierType_GeneticCode)
- {
- gencodelist = GetGeneticCodeValNodeList ();
- if (StringHasNoText (suggested_value))
- {
- vn.choice = 0;
- }
- else if (isdigit (suggested_value[0]))
- {
- vn.choice = atoi (suggested_value);
- }
- else
- {
- vn.choice = GeneticCodeFromStringAndList (suggested_value, gencodelist);
- }
- vn.next = NULL;
- vn.data.ptrvalue = suggested_value;
- strvalue_dlg = ValNodeSelectionDialog (g, gencodelist, 6,
- ValNodeStringName,
- ValNodeSimpleDataFree,
- ValNodeStringCopy,
- ValNodeChoiceMatch,
- "genetic code",
- NULL, NULL, FALSE);
- PointerToDialog (strvalue_dlg, &vn);
- instr_grp = MakeGeneticCodeInstructionGroup (h);
- }
- else if (mod_type == eModifierType_MolType)
- {
- if (StringHasNoText (suggested_value))
- {
- if (PackageTypeIsSet (seqPackage) || seqPackage == SEQ_PKG_GENOMICCDNA)
- {
- vn.choice = 253;
- }
- else
- {
- vn.choice = 254;
- }
- }
- else if (isdigit (suggested_value[0]))
- {
- vn.choice = atoi (suggested_value);
- }
- else
- {
- vn.choice = MolTypeFromString (suggested_value);
- }
- vn.next = NULL;
- vn.data.ptrvalue = suggested_value;
- if (seqPackage == SEQ_PKG_GENOMICCDNA)
- {
- strvalue_dlg = EnumAssocSelectionDialog (g, biomol_nucGen_alist,
- "moltype", FALSE, NULL, NULL);
- }
- else
- {
- strvalue_dlg = EnumAssocSelectionDialog (g, biomol_nucX_alist,
- "moltype", FALSE, NULL, NULL);
- }
- PointerToDialog (strvalue_dlg, &vn);
- }
- else if (mod_type == eModifierType_Topology)
- {
- if (StringHasNoText (suggested_value))
- {
- vn.choice = 1;
- }
- else if (isdigit (suggested_value[0]))
- {
- vn.choice = atoi (suggested_value);
- }
- else
- {
- vn.choice = TopologyFromString (suggested_value);
- }
- vn.next = NULL;
- vn.data.ptrvalue = suggested_value;
- strvalue_dlg = EnumAssocSelectionDialog (g, topology_nuc_alist,
- "topology", FALSE, NULL, NULL);
- PointerToDialog (strvalue_dlg, &vn);
- }
- else
- {
- text_txt = DialogText (g, suggested_value, 20, NULL);
- if (mod_type == eModifierType_GeneticCodeComment)
- {
- instr_grp = MakeGeneticCodeCommentInstructionGroup (h);
- }
- }
+ instr_grp = MakeInstructionGroup (h, is_nontext, mod_type);
+
+ val_dlg = SingleModValDialog (h, is_nontext, mod_type, seqPackage);
+ PointerToDialog (val_dlg, suggested_value);
c = HiddenGroup (h, 2, 0, NULL);
b = PushButton (c, "Accept", ModalAcceptButton);
@@ -11835,127 +12340,103 @@ ApplyOrgModColumnOrCell
if (instr_grp == NULL)
{
- AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, (HANDLE) NULL);
+ AlignObjects (ALIGN_CENTER, (HANDLE) val_dlg, (HANDLE) c, (HANDLE) NULL);
}
else
{
- AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) instr_grp, (HANDLE) c, (HANDLE) NULL);
+ AlignObjects (ALIGN_CENTER, (HANDLE) val_dlg, (HANDLE) instr_grp, (HANDLE) c, (HANDLE) NULL);
}
mod_label = MemFree (mod_label);
Show (w);
Select (w);
- acd.accepted = FALSE;
- acd.cancelled = FALSE;
- while (!acd.accepted && ! acd.cancelled)
- {
- ProcessExternalEvent ();
- Update ();
- }
- ProcessAnEvent ();
- if (acd.cancelled)
- {
- Remove (w);
- return;
- }
- else
+
+ done = FALSE;
+ while (!done)
{
- if (is_nontext)
+ acd.accepted = FALSE;
+ acd.cancelled = FALSE;
+ while (!acd.accepted && ! acd.cancelled)
{
- if (GetValue (nontext_popup) == 2)
- {
- new_value = StringSave ("2");
- }
+ ProcessExternalEvent ();
+ Update ();
}
- else if (mod_type == eModifierType_Location
- || mod_type == eModifierType_NucGeneticCode
- || mod_type == eModifierType_MitoGeneticCode
- || mod_type == eModifierType_GeneticCode
- || mod_type == eModifierType_MolType
- || mod_type == eModifierType_Topology)
+ ProcessAnEvent ();
+ if (acd.cancelled)
{
- value_vnp = DialogToPointer (strvalue_dlg);
- new_value = value_vnp->data.ptrvalue;
- if (mod_type == eModifierType_Location)
- {
- StringToLower (new_value);
- }
- value_vnp = ValNodeFree (value_vnp);
- if (mod_type == eModifierType_MolType
- && StringICmp (new_value, "mRNA [cDNA]") == 0)
- {
- new_value = MemFree (new_value);
- new_value = StringSave ("mRNA");
- }
+ done = TRUE;
}
- else if (mod_type == eModifierType_Organism)
+ else if (row < 0 && ANS_NO == Message (MSG_YN, "Are you sure you want to apply this value to all of your sequences?"))
{
- new_value = DialogToPointer (org_dlg);
+ /* do nothing - they'll be able to cancel from the dialog if they want to */
}
else
{
- new_value = SaveStringFromText (text_txt);
- }
+ /* prepare value */
+ new_value = DialogToPointer (val_dlg);
- if (seq_list != NULL)
- {
- for (sep = seq_list, j = 0;
- sep != NULL;
- sep = sep->next, j++)
+ /* apply value to either seq_list, sap, or row_list */
+ if (seq_list != NULL)
{
- if (j == row || row == -1)
+ for (sep = seq_list, j = 0;
+ sep != NULL;
+ sep = sep->next, j++)
{
- ApplyOneModToSeqEntry (sep, mod_name, new_value);
+ if (j == row || row == -1)
+ {
+ ApplyOneModToSeqEntry (sep, mod_name, new_value);
+ }
}
- }
- if (mod_type == eModifierType_Organism
- || mod_type == eModifierType_Location
- || mod_type == eModifierType_GeneticCode)
- {
- UpdateGeneticCodesForSeqEntryList (seq_list);
- }
- }
- else if (sap != NULL)
- {
- for (j = 0; j < sap->num_deflines; j++)
- {
- if (j == row || row == -1)
+ if (mod_type == eModifierType_Organism
+ || mod_type == eModifierType_Location
+ || mod_type == eModifierType_GeneticCode)
{
- ReplaceValueInDefLines (sap, mod_name, new_value, j);
+ UpdateGeneticCodesForSeqEntryList (seq_list);
}
}
- if (mod_type == eModifierType_Organism
- || mod_type == eModifierType_Location
- || mod_type == eModifierType_GeneticCode)
+ else if (sap != NULL)
{
- UpdateGeneticCodesForSourceAssistant (sap);
- }
- }
- else if (row_list != NULL)
- {
- if (row < 0)
- {
- SetRowListColumn (row_list, row_list_column, new_value);
+ for (j = 0; j < sap->num_deflines; j++)
+ {
+ if (j == row || row == -1)
+ {
+ ReplaceValueInDefLines (sap, mod_name, new_value, j);
+ }
+ }
+ if (mod_type == eModifierType_Organism
+ || mod_type == eModifierType_Location
+ || mod_type == eModifierType_GeneticCode)
+ {
+ UpdateGeneticCodesForSourceAssistant (sap);
+ }
}
- else if (row_vnp != NULL)
+ else if (row_list != NULL)
{
- for (col_vnp = row_vnp->data.ptrvalue, col_num = 0;
- col_vnp != NULL && col_num < row_list_column;
- col_vnp = col_vnp->next, col_num++)
+ if (row < 0)
{
+ SetRowListColumn (row_list, row_list_column, new_value);
}
- if (col_vnp != NULL)
+ else if (row_vnp != NULL)
{
- col_vnp->data.ptrvalue = MemFree (col_vnp->data.ptrvalue);
- col_vnp->data.ptrvalue = StringSave (new_value);
+ for (col_vnp = row_vnp->data.ptrvalue, col_num = 0;
+ col_vnp != NULL && col_num < row_list_column;
+ col_vnp = col_vnp->next, col_num++)
+ {
+ }
+ if (col_vnp != NULL)
+ {
+ col_vnp->data.ptrvalue = MemFree (col_vnp->data.ptrvalue);
+ col_vnp->data.ptrvalue = StringSave (new_value);
+ }
}
}
- }
- new_value = MemFree (new_value);
- UpdateOrgModDlg (sap);
- Remove (w);
+ new_value = MemFree (new_value);
+ UpdateOrgModDlg (sap);
+ done = TRUE;
+ }
}
+ Remove (w);
}
static void
@@ -12136,7 +12617,7 @@ static void OrgModDblClick (PoinT cell_coord, CharPtr header_text, CharPtr cell_
static void SourceAssistant (ButtoN b)
{
SequencesFormPtr sqfp;
- SeqEntryPtr seq_list, cntr_sep;
+ SeqEntryPtr seq_list, cntr_sep, nsep;
SourceAssistantData sad;
CharPtr ttl;
BioseqPtr bsp;
@@ -12149,6 +12630,7 @@ static void SourceAssistant (ButtoN b)
FastaPagePtr fpp;
Int4 doc_width = stdCharWidth * 40;
ButtoN export_btn;
+ PrompT ppt1, ppt2;
sqfp = (SequencesFormPtr) GetObjectExtra (b);
if (sqfp == NULL) return;
@@ -12202,10 +12684,11 @@ static void SourceAssistant (ButtoN b)
cntr_sep = cntr_sep->next, i++)
{
ttl = NULL;
- SeqEntryExplore (cntr_sep, (Pointer) (&ttl), FindFirstTitle);
+ nsep = FindNucSeqEntry (cntr_sep);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
sad.defline_list[i] = StringSaveNoNull (ttl);
- bsp = FindNucBioseq (cntr_sep);
+ bsp = FindNucBioseq (nsep);
if (bsp != NULL)
{
sip = SeqIdFindWorst (bsp->id);
@@ -12260,9 +12743,12 @@ static void SourceAssistant (ButtoN b)
SetDocAutoAdjust (sad.mod_doc, TRUE);
sad.orgmod_dlg = TableDisplayDialog (h, doc_width, stdLineHeight * 16, 1, 1,
- OrgModDblClick, &sad);
+ OrgModDblClick, &sad,
+ OrganismMatchesAnotherRow, NULL);
UpdateOrgModDlg (&sad);
+ ppt1 = StaticPrompt (h, "Sequence IDs in red have source information", 0, 0, programFont, 'l');
+ ppt2 = StaticPrompt (h, "that matches at least one other sequence.", 0, 0, programFont, 'l');
export_btn = PushButton (h, "Export Source Modifier Table", SourceAssistantExport);
SetObjectExtra (export_btn, &sad, NULL);
@@ -12277,6 +12763,8 @@ static void SourceAssistant (ButtoN b)
(HANDLE) g,
(HANDLE) sad.mod_doc,
(HANDLE) sad.orgmod_dlg,
+ (HANDLE) ppt1,
+ (HANDLE) ppt2,
(HANDLE) export_btn,
(HANDLE) c,
NULL);
@@ -12298,9 +12786,10 @@ static void SourceAssistant (ButtoN b)
cntr_sep = cntr_sep->next, i++)
{
ttlvnp = NULL;
- SeqEntryExplore (cntr_sep, (Pointer) (&ttlvnp), FindFirstSeqDescrTitle);
+ nsep = FindNucSeqEntry (cntr_sep);
+ SeqEntryExplore (nsep, (Pointer) (&ttlvnp), FindFirstSeqDescrTitle);
if (ttlvnp == NULL) {
- ttlvnp = CreateNewDescriptor (cntr_sep, Seq_descr_title);
+ ttlvnp = CreateNewDescriptor (nsep, Seq_descr_title);
}
if (ttlvnp != NULL) {
ttlvnp->data.ptrvalue = MemFree (ttlvnp->data.ptrvalue);
@@ -12436,33 +12925,6 @@ static void ApplyModValuesAllBtn (ButtoN b)
Remove (w);
}
-static void ApplyOrganismValuesAllBtn (ButtoN b)
-{
- WindoW w;
-
- w = ParentWindow ((Nlm_GraphiC) b);
- ApplyOneValueToAllSequencesDialog (b, "organism");
- Remove (w);
-}
-
-static void ApplyLocationValuesAllBtn (ButtoN b)
-{
- WindoW w;
-
- w = ParentWindow ((Nlm_GraphiC) b);
- ApplyOneValueToAllSequencesDialog (b, "location");
- Remove (w);
-}
-
-static void ApplyGeneticCodeValuesAllBtn (ButtoN b)
-{
- WindoW w;
-
- w = ParentWindow ((Nlm_GraphiC) b);
- ApplyOneValueToAllSequencesDialog (b, "genetic_code");
- Remove (w);
-}
-
static void ApplyModValuesIndividuallyBtn (ButtoN b)
{
WindoW w;
@@ -12478,15 +12940,6 @@ static void ApplyModValuesIndividuallyBtn (ButtoN b)
Remove (w);
}
-static void ApplyOrgLocGcodeValuesIndividuallyBtn (ButtoN b)
-{
- WindoW w;
-
- w = ParentWindow ((Nlm_GraphiC) b);
- ApplyModValuesIndividually (b, "organism");
- Remove (w);
-}
-
static void SpecifyModValueButton (ButtoN b, CharPtr mod_name)
{
SequencesFormPtr sqfp;
@@ -12554,25 +13007,10 @@ static void SpecifyModValueButton (ButtoN b, CharPtr mod_name)
}
-static void SpecifyOrganisms (ButtoN b)
-{
- SpecifyModValueButton (b, "organism");
-}
-
-static void SpecifyLocations (ButtoN b)
-{
- SpecifyModValueButton (b, "location");
-}
-
static void SpecifyOrganismLocationGeneticCodeButton (ButtoN b)
{
SequencesFormPtr sqfp;
- WindoW w;
- GrouP h;
SeqEntryPtr seq_list;
- ButtoN apply_one_org_btn, apply_one_loc_btn, apply_one_gc_btn;
- ButtoN apply_all_btn = NULL;
- ButtoN cancel_btn;
sqfp = (SequencesFormPtr) GetObjectExtra (b);
if (sqfp == NULL)
@@ -12585,100 +13023,12 @@ static void SpecifyOrganismLocationGeneticCodeButton (ButtoN b)
{
Message (MSG_ERROR, "You must add sequences before you can add organisms, locations, or genetic codes!");
}
- else if (seq_list->next == NULL || sqfp->seqPackage == SEQ_PKG_SEGMENTED)
- {
- ApplyModValuesIndividually (b, "organism");
- }
- else
- {
- w = MovableModalWindow (-20, -13, -10, -10, "Edit Organisms, Locations, and Genetic Codes", NULL);
- h = HiddenGroup(w, -1, 0, NULL);
- SetGroupSpacing (h, 10, 10);
-
- apply_one_org_btn = PushButton (h, "Apply one organism name to all sequences", ApplyOrganismValuesAllBtn);
- SetObjectExtra (apply_one_org_btn, sqfp, NULL);
-
- apply_one_loc_btn = PushButton (h, "Apply one location to all sequences", ApplyLocationValuesAllBtn);
- SetObjectExtra (apply_one_loc_btn, sqfp, NULL);
-
- apply_one_gc_btn = PushButton (h, "Apply one genetic to all sequences", ApplyGeneticCodeValuesAllBtn);
- SetObjectExtra (apply_one_gc_btn, sqfp, NULL);
-
- apply_all_btn = PushButton (h, "Apply organism name, location, and genetic code to sequences individually", ApplyOrgLocGcodeValuesIndividuallyBtn);
- SetObjectExtra (apply_all_btn, sqfp, NULL);
-
- cancel_btn = PushButton (h, "Cancel", StdCancelButtonProc);
-
- if (apply_all_btn == NULL)
- {
- AlignObjects (ALIGN_CENTER, (HANDLE) apply_one_org_btn,
- (HANDLE) apply_one_loc_btn,
- (HANDLE) apply_one_gc_btn,
- (HANDLE) cancel_btn,
- NULL);
- }
- else
- {
- AlignObjects (ALIGN_CENTER, (HANDLE) apply_one_org_btn,
- (HANDLE) apply_one_loc_btn,
- (HANDLE) apply_one_gc_btn,
- (HANDLE) apply_all_btn,
- (HANDLE) cancel_btn,
- NULL);
- }
- Show(w);
- Select (w);
- }
-}
-
-static void ApplyOneGeneticCodeToAllSequencesDialog (ButtoN b, Boolean is_nuc)
-{
- WindoW w;
-
- w = ParentWindow ((Nlm_GraphiC) b);
- if (is_nuc)
- {
- ApplyOneValueToAllSequencesDialog (b, "gcode");
- }
- else
- {
- ApplyOneValueToAllSequencesDialog (b, "mgcode");
- }
- Remove (w);
-}
-
-static void ApplyOneNuclearGeneticCodeToAllSequencesDialog (ButtoN b)
-{
- ApplyOneGeneticCodeToAllSequencesDialog (b, TRUE);
-}
-
-static void ApplyOneMitochondrialGeneticCodeToAllSequencesDialog (ButtoN b)
-{
- ApplyOneGeneticCodeToAllSequencesDialog (b, FALSE);
-}
-
-static void ApplyGeneticCodeIndividually (ButtoN b, Boolean is_nuc)
-{
- if (is_nuc)
- {
- ApplyModValuesIndividually (b, "gcode");
- }
else
{
- ApplyModValuesIndividually (b, "mgcode");
+ ApplyModValuesIndividually (b, "organism");
}
}
-static void ApplyNuclearGeneticCodeIndividually (ButtoN b)
-{
- ApplyGeneticCodeIndividually (b, TRUE);
-}
-
-static void ApplyMitochondrialGeneticCodeIndividually (ButtoN b)
-{
- ApplyGeneticCodeIndividually (b, FALSE);
-}
-
static void SpecifyGeneticCode (ButtoN b)
{
SpecifyModValueButton (b, "genetic_code");
@@ -12687,7 +13037,7 @@ static void SpecifyGeneticCode (ButtoN b)
static void ClearAllSequenceModifiers (ButtoN b)
{
SequencesFormPtr sqfp;
- SeqEntryPtr seq_list, sep;
+ SeqEntryPtr seq_list, sep, nsep;
CharPtr ttl;
ValNodePtr found_modifiers = NULL, mod_vnp;
FastaPagePtr fpp;
@@ -12713,7 +13063,8 @@ static void ClearAllSequenceModifiers (ButtoN b)
for (sep = seq_list; sep != NULL; sep = sep->next)
{
ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
+ nsep = FindNucSeqEntry (sep);
+ SeqEntryExplore (nsep, (Pointer) (&ttl), FindFirstTitle);
found_modifiers = BuildModifierTypeList (found_modifiers, ttl);
for (mod_vnp = found_modifiers; mod_vnp != NULL; mod_vnp = mod_vnp->next)
{
@@ -12726,7 +13077,7 @@ static void ClearAllSequenceModifiers (ButtoN b)
&& mod_type != eModifierType_GeneticCodeComment
&& mod_type != eModifierType_Organism)
{
- ApplyOneModToSeqEntry (sep, mod_vnp->data.ptrvalue, NULL);
+ ApplyOneModToSeqEntry (nsep, mod_vnp->data.ptrvalue, NULL);
}
}
found_modifiers = ValNodeFreeData (found_modifiers);
@@ -12743,7 +13094,7 @@ static void ClearAllSequenceModifiers (ButtoN b)
static void SummaryDocOnClick (DoC d, PoinT pt)
{
SequencesFormPtr sqfp;
- SeqEntryPtr seq_list, sep;
+ SeqEntryPtr seq_list;
Int2 pos_item, pos_row, pos_col;
Int2 start_item = 0;
Int2 end_item = -1;
@@ -12771,16 +13122,53 @@ static void SummaryDocOnClick (DoC d, PoinT pt)
MapDocPoint (d, pt, &(pos_item), &(pos_row), &(pos_col), NULL);
/* get list of modifiers */
- ValNodeAddPointer (&found_modifiers, 0, "organism");
- for (sep = seq_list; sep != NULL; sep = sep->next)
+ found_modifiers = GetListOfCurrentModifiers (seq_list);
+
+ for (vnp = found_modifiers, mod_num = 1;
+ vnp != NULL && mod_num < pos_item;
+ vnp = vnp->next, mod_num++)
{
- ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
- found_modifiers = BuildModifierTypeList (found_modifiers, ttl);
+ }
+ if (vnp != NULL)
+ {
+ EditOrgModColumn (vnp->data.ptrvalue, NULL, seq_list, sqfp->seqPackage);
+ SeqEntryPtrToSourceTab (sqfp);
+ fpp = (FastaPagePtr) GetObjectExtra (sqfp->dnaseq);
+ if (fpp != NULL)
+ {
+ Reset (fpp->doc);
+ FormatFastaDoc (fpp);
+ }
+ }
+ ValNodeFreeData (found_modifiers);
+}
+
+static void SummaryDblClick (PoinT cell_coord, CharPtr header_text, CharPtr cell_text, Pointer userdata)
+{
+ ValNodePtr found_modifiers = NULL, vnp;
+ SequencesFormPtr sqfp;
+ SeqEntryPtr seq_list;
+ Int4 mod_num;
+ FastaPagePtr fpp;
+
+ if (cell_coord.y < 1 || userdata == NULL)
+ {
+ return;
}
+ sqfp = (SequencesFormPtr) userdata;
+
+ seq_list = GetSeqEntryFromSequencesForm (sqfp);
+ if (seq_list == NULL)
+ {
+ return;
+ }
+
+ /* get list of modifiers */
+ found_modifiers = GetListOfCurrentModifiers (seq_list);
+
for (vnp = found_modifiers, mod_num = 1;
- vnp != NULL && mod_num < pos_item;
+ vnp != NULL && mod_num < cell_coord.y;
vnp = vnp->next, mod_num++)
{
}
@@ -12795,6 +13183,7 @@ static void SummaryDocOnClick (DoC d, PoinT pt)
FormatFastaDoc (fpp);
}
}
+ ValNodeFreeData (found_modifiers);
}
static GrouP CreateSourceTab (GrouP h, SequencesFormPtr sqfp)
@@ -12816,11 +13205,14 @@ static GrouP CreateSourceTab (GrouP h, SequencesFormPtr sqfp)
sqfp->org_doc = DocumentPanel (mod_grp, stdCharWidth * 27, stdLineHeight * 2);
SetDocAutoAdjust (sqfp->org_doc, TRUE);
+ sqfp->ident_org_btn = PushButton (mod_grp, "Some Sequences Have Identical Organisms!", SourceAssistant);
+ SetObjectExtra (sqfp->ident_org_btn, sqfp, NULL);
+ Disable (sqfp->source_assist_btn);
- sqfp->summary_doc = DocumentPanel (mod_grp, stdCharWidth * 27, stdLineHeight * 12);
- SetObjectExtra (sqfp->summary_doc, sqfp, NULL);
- SetDocAutoAdjust (sqfp->summary_doc, TRUE);
- SetDocProcs (sqfp->summary_doc, SummaryDocOnClick, NULL, NULL, NULL);
+ sqfp->summary_dlg = TableDisplayDialog (mod_grp, stdCharWidth * 30, stdLineHeight * 12, 1, 1,
+ SummaryDblClick, sqfp,
+ NULL, NULL);
+
sqfp->specify_orgs_btn = PushButton (mod_grp,
"Add Organisms, Locations, and Genetic Codes",
@@ -12849,6 +13241,8 @@ static GrouP CreateSourceTab (GrouP h, SequencesFormPtr sqfp)
SeqEntryPtrToSourceTab (sqfp);
AlignObjects (ALIGN_CENTER, (HANDLE) sqfp->org_doc,
+ (HANDLE) sqfp->ident_org_btn,
+ (HANDLE) sqfp->summary_dlg,
(HANDLE) sqfp->specify_orgs_btn,
(HANDLE) k,
NULL);
@@ -12927,37 +13321,6 @@ static DialoG FastaSummaryDialog (GrouP parent)
return (DialoG) p;
}
-static void SetDefaultMolTypesAndTopologies (SeqEntryPtr seq_list, Int2 seqPackage)
-{
- SeqEntryPtr sep;
- CharPtr ttl = NULL;
- Char tmp[128];
-
- for (sep = seq_list; sep != NULL; sep = sep->next)
- {
- ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
-
- if (!LookForSearchString (ttl, "[moltype=", tmp, sizeof (tmp) - 1))
- {
- if (PackageTypeDefaultMolTypeIsDNA (seqPackage))
- {
- ApplyOneModToSeqEntry (sep, "moltype", "Genomic DNA");
- }
- else
- {
- ApplyOneModToSeqEntry (sep, "moltype", "Genomic RNA");
- }
- }
- ttl = NULL;
- SeqEntryExplore (sep, (Pointer) (&ttl), FindFirstTitle);
- if (!LookForSearchString (ttl, "[topology=", tmp, sizeof (tmp) - 1))
- {
- ApplyOneModToSeqEntry (sep, "topology", "Linear");
- }
- }
-}
-
/* The Sequence Assistant will allow users to paste in FASTA or create sequences one at a time.
* The list control for selecting a sequence to view and edit should be a DocPanel, so that we
* can add and remove sequences without needing to destroy and recreate the dialog.
@@ -12999,7 +13362,7 @@ static ValNodePtr PrepareSequenceAssistantTableData (SequenceAssistantPtr sap)
{
return NULL;
}
- SetDefaultMolTypesAndTopologies (sap->seq_list, sap->seqPackage);
+ SetDefaultMolTypesAndTopologies (sap->seq_list);
/* create header line for table */
/* store max column width in choice */
@@ -13058,14 +13421,7 @@ static ValNodePtr PrepareSequenceAssistantTableData (SequenceAssistantPtr sap)
header_vnp = header_vnp->next;
if (!LookForSearchString (ttl, "[moltype=", tmp, sizeof (tmp) - 1))
{
- if (PackageTypeDefaultMolTypeIsDNA (sap->seqPackage))
- {
- sprintf (tmp, "Genomic DNA");
- }
- else
- {
- sprintf (tmp, "Genomic RNA");
- }
+ sprintf (tmp, "Genomic DNA");
}
column_width = MAX (StringLen (tmp), header_vnp->choice);
column_width = MIN (column_width, max_column_width);
@@ -13202,184 +13558,252 @@ static Boolean
IsDuplicateID (SeqEntryPtr seq_list, BioseqPtr edit_bsp, SeqIdPtr sip);
static Uint2 idedit_types [] = {
- TAGLIST_PROMPT, TAGLIST_TEXT, TAGLIST_TEXT
+ TAGLIST_PROMPT, TAGLIST_PROMPT, TAGLIST_TEXT, TAGLIST_TEXT
};
static Uint2 idedit_widths [] = {
- 4, 10, 40,
+ 6, 5, 10, 40,
};
-typedef struct seqedittag
-{
- ValNodePtr current_list;
- ValNodePtr new_list;
-} SeqEditTagData, PNTR SeqEditTagPtr;
-
-static void
-AddSeqInfoToTagListData
-(SeqEntryPtr list,
- SeqEntryPtr current_list,
- SeqEntryPtr new_list,
- Int4Ptr pnum_sequences,
- ValNodePtr PNTR taglist_data)
+static Int4 CountSequencesAndSegments (SeqEntryPtr list)
{
- SeqEntryPtr sep;
- Char id_str [128];
- CharPtr title_txt;
- BioseqPtr bsp;
- BioseqSetPtr bssp;
- Int4 num_sequences = 0;
- SeqDescrPtr sdp;
- Boolean is_dup;
- CharPtr str;
- Int4 len;
-
- if (taglist_data == NULL)
- {
- return;
- }
+ Int4 num_seqs = 0;
+ BioseqSetPtr bssp;
- /* collect current IDs and titles */
- for (sep = list; sep != NULL; sep = sep->next)
+ while (list != NULL)
{
- if (sep->data.ptrvalue == NULL)
- {
- continue;
- }
- else if (IS_Bioseq (sep))
+ if (list->data.ptrvalue != NULL)
{
- bsp = (BioseqPtr) sep->data.ptrvalue;
- /* collect ID */
- SeqIdWrite (bsp->id, id_str, PRINTID_REPORT, sizeof (id_str) - 1);
- /* collect title */
- title_txt = NULL;
- sdp = bsp->descr;
- while (sdp != NULL && sdp->choice != Seq_descr_title)
- {
- sdp = sdp->next;
- }
- if (sdp != NULL)
+ if (IS_Bioseq (list))
{
- title_txt = sdp->data.ptrvalue;
+ num_seqs ++;
}
- /* determine whether this is a duplicate */
- is_dup = IsDuplicateID (current_list, NULL, bsp->id)
- || IsDuplicateID (new_list, bsp, bsp->id);
-
- len = StringLen (id_str) + StringLen (title_txt);
- str = MemNew (len + 9);
- if (str != NULL)
+ else if (IS_Bioseq_set (list))
{
- sprintf (str, "%s\t%s\t%s\n",
- is_dup ? "DUP" : "",
- id_str,
- title_txt == NULL ? "" : title_txt);
- ValNodeAddPointer (taglist_data, 0, str);
+ bssp = (BioseqSetPtr) list->data.ptrvalue;
+ num_seqs += CountSequencesAndSegments (bssp->seq_set);
}
- num_sequences ++;
- }
- else if (IS_Bioseq_set (sep))
- {
- bssp = (BioseqSetPtr) sep->data.ptrvalue;
- AddSeqInfoToTagListData (bssp->seq_set, current_list, new_list,
- &num_sequences, taglist_data);
}
+ list = list->next;
}
- if (pnum_sequences != NULL)
+ return num_seqs;
+}
+
+static BioseqPtr FindNthSequenceInSet (SeqEntryPtr seq_list, Int4 nth)
+{
+ Int4 pos = 0;
+ BioseqPtr bsp = NULL;
+ BioseqSetPtr bssp;
+ SeqEntryPtr sep;
+
+ while (seq_list != NULL && bsp == NULL)
{
- *pnum_sequences += num_sequences;
+ if (seq_list->data.ptrvalue != NULL)
+ {
+ if (IS_Bioseq (seq_list))
+ {
+ if (nth == pos)
+ {
+ bsp = seq_list->data.ptrvalue;
+ }
+ else
+ {
+ pos ++;
+ }
+ }
+ else if (IS_Bioseq_set (seq_list))
+ {
+ bssp = (BioseqSetPtr) seq_list->data.ptrvalue;
+ sep = bssp->seq_set;
+ while (sep != NULL && bsp == NULL)
+ {
+ bsp = FindNthSequenceInSet (sep, nth - pos);
+ if (bsp == NULL)
+ {
+ if (IS_Bioseq_set (sep))
+ {
+ bssp = (BioseqSetPtr) sep->data.ptrvalue;
+ pos += CountSequencesAndSegments (bssp->seq_set);
+ }
+ else if (IS_Bioseq (sep))
+ {
+ pos ++;
+ }
+ }
+ sep = sep->next;
+ }
+ }
+ }
+ seq_list = seq_list->next;
}
+ return bsp;
}
-static void SeqListToTagListDialog (DialoG d, Pointer userdata)
+static void
+SetSeqListInTagListDialog
+(DialoG d,
+ SeqEntryPtr new_list,
+ SeqEntryPtr current_list,
+ Boolean show_all)
{
TagListPtr tlp;
- SeqEditTagPtr setp;
- Int4 num_sequences = 0;
+ Int4 num_sequences = 0, total_sequences, seq_num;
ValNodePtr taglist_data = NULL;
+ Boolean is_dup;
+ BioseqPtr bsp;
+ Char id_str [128];
+ CharPtr title_txt;
+ SeqDescrPtr sdp;
+ CharPtr str;
+ Int4 len;
+ Int4 row_to_hide, row_to_show;
tlp = (TagListPtr) GetObjectExtra (d);
- setp = (SeqEditTagPtr) userdata;
- if (tlp == NULL || setp == NULL || setp->new_list == NULL)
+ if (tlp == NULL || new_list == NULL)
{
return;
}
/* collect current IDs and titles */
- AddSeqInfoToTagListData (setp->new_list, setp->current_list, setp->new_list,
- &num_sequences, &taglist_data);
+ total_sequences = CountSequencesAndSegments (new_list);
+ for (seq_num = 0; seq_num < total_sequences; seq_num++)
+ {
+ bsp = FindNthSequenceInSet (new_list, seq_num);
+ if (bsp == NULL)
+ {
+ continue;
+ }
+
+ /* determine whether this is a duplicate */
+ is_dup = IsDuplicateID (current_list, NULL, bsp->id)
+ || IsDuplicateID (new_list, bsp, bsp->id);
+ if (!is_dup && ! show_all)
+ {
+ continue;
+ }
+ /* collect ID */
+ SeqIdWrite (bsp->id, id_str, PRINTID_REPORT, sizeof (id_str) - 1);
+ /* collect title */
+ title_txt = NULL;
+ sdp = bsp->descr;
+ while (sdp != NULL && sdp->choice != Seq_descr_title)
+ {
+ sdp = sdp->next;
+ }
+ if (sdp != NULL)
+ {
+ title_txt = sdp->data.ptrvalue;
+ }
+ /* determine whether this is a duplicate */
+ is_dup = IsDuplicateID (current_list, NULL, bsp->id)
+ || IsDuplicateID (new_list, bsp, bsp->id);
+
+ len = StringLen (id_str) + StringLen (title_txt);
+ str = MemNew (len + 18);
+ if (str != NULL)
+ {
+ sprintf (str, "%s\t%d\t%s\t%s\n",
+ is_dup ? "Duplicate ID" : "",
+ seq_num + 1,
+ id_str,
+ title_txt == NULL ? "" : title_txt);
+ ValNodeAddPointer (&taglist_data, 0, StringSave (str));
+ }
+ num_sequences ++;
+ }
+
SendMessageToDialog (tlp->dialog, VIB_MSG_RESET);
tlp->vnp = taglist_data;
SendMessageToDialog (tlp->dialog, VIB_MSG_REDRAW);
tlp->max = MAX ((Int2) 0, (Int2) (num_sequences - tlp->rows));
CorrectBarMax (tlp->bar, tlp->max);
CorrectBarPage (tlp->bar, tlp->rows - 1, tlp->rows - 1);
+ for (row_to_show = 0; row_to_show < MIN (num_sequences, tlp->rows); row_to_show ++)
+ {
+ SafeShow (tlp->control [row_to_show * MAX_TAGLIST_COLS + 2]);
+ SafeShow (tlp->control [row_to_show * MAX_TAGLIST_COLS + 3]);
+ }
if (tlp->max > 0) {
SafeShow (tlp->bar);
} else {
SafeHide (tlp->bar);
+ for (row_to_hide = num_sequences; row_to_hide < tlp->rows; row_to_hide ++)
+ {
+ SafeHide (tlp->control [row_to_hide * MAX_TAGLIST_COLS + 2]);
+ SafeHide (tlp->control [row_to_hide * MAX_TAGLIST_COLS + 3]);
+ }
}
}
-static void CollectIdAndTitleFromDialog (TagListPtr tlp, SeqEntryPtr sep, Int4Ptr seq_num)
+static void CollectIdAndTitleFromDialog (TagListPtr tlp, SeqEntryPtr sep)
{
BioseqPtr bsp;
- BioseqSetPtr bssp;
CharPtr str;
SeqDescrPtr sdp;
SeqIdPtr new_sip;
+ Int4 num_rows, row_num, seq_pos;
- if (tlp == NULL || sep == NULL || seq_num == NULL)
+ if (tlp == NULL || sep == NULL)
{
return;
}
-
- if (sep->data.ptrvalue != NULL)
+
+ num_rows = ValNodeLen (tlp->vnp);
+ for (row_num = 0; row_num < num_rows; row_num++)
{
- if (IS_Bioseq (sep))
+ /* get position for this sequence */
+ str = GetTagListValueEx (tlp, row_num, 1);
+ seq_pos = atoi (str);
+ if (seq_pos < 1)
{
- bsp = (BioseqPtr) sep->data.ptrvalue;
- /* collect ID */
- str = GetTagListValueEx (tlp, *seq_num, 1);
- new_sip = MakeSeqID (str);
- str = MemFree (str);
- if (new_sip != NULL)
- {
- if (bsp->id != NULL)
- {
- new_sip->next = bsp->id->next;
- bsp->id->next = NULL;
- bsp->id = SeqIdFree (bsp->id);
- }
- bsp->id = new_sip;
- }
- /* collect title */
- str = GetTagListValueEx (tlp, *seq_num, 2);
- sdp = bsp->descr;
- while (sdp != NULL && sdp->choice != Seq_descr_title)
- {
- sdp = sdp->next;
- }
- if (sdp == NULL)
- {
- sdp = CreateNewDescriptor (sep, Seq_descr_title);
- sdp->data.ptrvalue = str;
- }
- else
+ continue;
+ }
+ seq_pos --;
+ bsp = FindNthSequenceInSet (sep, seq_pos);
+ if (bsp == NULL)
+ {
+ continue;
+ }
+ /* collect ID */
+ str = GetTagListValueEx (tlp, row_num, 2);
+ new_sip = MakeSeqID (str);
+ str = MemFree (str);
+ if (new_sip != NULL)
+ {
+ if (bsp->id != NULL)
{
- sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue);
- sdp->data.ptrvalue = str;
+ new_sip->next = bsp->id->next;
+ bsp->id->next = NULL;
+ bsp->id = SeqIdFree (bsp->id);
}
- (*seq_num)++;
+ bsp->id = new_sip;
+ SeqMgrReplaceInBioseqIndex(bsp);
}
- else if (IS_Bioseq_set (sep))
+ else
{
- bssp = (BioseqSetPtr) sep->data.ptrvalue;
- CollectIdAndTitleFromDialog (tlp, bssp->seq_set, seq_num);
+ bsp->id = SeqIdFree (bsp->id);
+ }
+
+ /* collect title */
+ str = GetTagListValueEx (tlp, row_num, 3);
+ sdp = bsp->descr;
+ while (sdp != NULL && sdp->choice != Seq_descr_title)
+ {
+ sdp = sdp->next;
+ }
+ if (sdp == NULL)
+ {
+ sdp = CreateNewDescriptor (sep, Seq_descr_title);
+ sdp->data.ptrvalue = str;
+ }
+ else
+ {
+ sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue);
+ sdp->data.ptrvalue = str;
}
}
- CollectIdAndTitleFromDialog (tlp, sep->next, seq_num);
+
}
@@ -13437,9 +13861,9 @@ static Boolean FixDefinitionLinesInAddSequence (SeqEntryPtr sep_list)
}
}
-static Boolean IDsNeedFix (SeqEntryPtr list, SeqEntryPtr current_list)
+static Boolean HasBlankIDs (SeqEntryPtr list)
{
- Boolean need_fix = FALSE;
+ Boolean has_blank = FALSE;
BioseqPtr bsp;
BioseqSetPtr bssp;
SeqEntryPtr sep;
@@ -13449,7 +13873,7 @@ static Boolean IDsNeedFix (SeqEntryPtr list, SeqEntryPtr current_list)
return FALSE;
}
/* check for unique IDs or missing IDs */
- for (sep = list; sep != NULL && ! need_fix; sep = sep->next)
+ for (sep = list; sep != NULL && ! has_blank; sep = sep->next)
{
if (sep->data.ptrvalue == NULL)
{
@@ -13458,55 +13882,495 @@ static Boolean IDsNeedFix (SeqEntryPtr list, SeqEntryPtr current_list)
else if (IS_Bioseq (sep))
{
bsp = (BioseqPtr) sep->data.ptrvalue;
- need_fix = bsp->id == NULL
- || IsDuplicateID (current_list, NULL, bsp->id)
- || IsDuplicateID (list, bsp, bsp->id);
+ if (bsp->id == NULL)
+ {
+ has_blank = TRUE;
+ }
}
else if (IS_Bioseq_set (sep))
{
bssp = (BioseqSetPtr) sep->data.ptrvalue;
- need_fix |= IDsNeedFix (bssp->seq_set, current_list);
+ has_blank |= HasBlankIDs (bssp->seq_set);
}
}
+ return has_blank;
+}
+
+static Boolean HasDuplicateIDs (SeqEntryPtr list, SeqEntryPtr current_list)
+{
+ Boolean has_dup = FALSE;
+ BioseqPtr bsp;
+ Int4 this_num, num_this_list;
+
+ if (list == NULL)
+ {
+ return FALSE;
+ }
+
+ /* check for unique IDs or missing IDs */
+
+ num_this_list = CountSequencesAndSegments (list);
+ for (this_num = 0; this_num < num_this_list && ! has_dup; this_num++)
+ {
+ bsp = FindNthSequenceInSet (list, this_num);
+ if (bsp != NULL)
+ {
+ has_dup |= IsDuplicateID (current_list, NULL, bsp->id)
+ || IsDuplicateID (list, bsp, bsp->id);
+ }
+ }
+ return has_dup;
+}
+
+static Boolean IDsNeedFix (SeqEntryPtr list, SeqEntryPtr current_list)
+{
+ Boolean need_fix = FALSE;
+ BioseqPtr bsp;
+ Int4 this_num, num_this_list;
+
+ if (list == NULL)
+ {
+ return FALSE;
+ }
+
+ /* check for unique IDs or missing IDs */
+
+ num_this_list = CountSequencesAndSegments (list);
+ for (this_num = 0; this_num < num_this_list && ! need_fix; this_num++)
+ {
+ bsp = FindNthSequenceInSet (list, this_num);
+ need_fix |= (bsp->id == NULL)
+ || IsDuplicateID (current_list, NULL, bsp->id)
+ || IsDuplicateID (list, bsp, bsp->id);
+ }
return need_fix;
}
-static Int4 CountSequencesAndSegments (SeqEntryPtr list)
+static void
+FindExtraTextForLocalIDs
+(SeqEntryPtr list,
+ ValNodePtr PNTR extended_ids,
+ ValNodePtr PNTR sep_for_ids)
{
- Int4 num_seqs = 0;
+ Boolean has_spaces = FALSE;
+ SeqEntryPtr sep;
+ BioseqPtr bsp;
BioseqSetPtr bssp;
+ SeqDescrPtr sdp;
+ CharPtr title, add_str;
+ Int4 len, add_str_len;
+ ObjectIdPtr oip;
+ SeqIdPtr new_sip;
- while (list != NULL)
+ if (list == NULL || extended_ids == NULL || sep_for_ids == NULL)
{
- if (list->data.ptrvalue != NULL)
+ return;
+ }
+ /* check for unique IDs or missing IDs */
+ for (sep = list; sep != NULL; sep = sep->next)
+ {
+ if (sep->data.ptrvalue == NULL)
{
- if (IS_Bioseq (list))
+ /* do nothing */
+ }
+ else if (IS_Bioseq (sep))
+ {
+ bsp = (BioseqPtr) sep->data.ptrvalue;
+ sdp = bsp->descr;
+ while (sdp != NULL
+ && (sdp->choice != Seq_descr_title
+ || StringHasNoText (sdp->data.ptrvalue)))
{
- num_seqs ++;
+ sdp = sdp->next;
}
- else if (IS_Bioseq_set (list))
+ title = NULL;
+ if (sdp != NULL)
{
- bssp = (BioseqSetPtr) list->data.ptrvalue;
- num_seqs += CountSequencesAndSegments (bssp->seq_set);
+ title = sdp->data.ptrvalue;
+ }
+ if (bsp->id != NULL
+ && IsDuplicateID (list, bsp, bsp->id)
+ && bsp->id->choice == SEQID_LOCAL
+ && (oip = bsp->id->data.ptrvalue) != NULL
+ && ! StringHasNoText (oip->str)
+ && title != NULL
+ && title [0] != '[')
+ {
+ len = StringCSpn (title, " \t[]");
+ if (len > 0)
+ {
+ add_str_len = len + StringLen (oip->str);
+ add_str = (CharPtr) MemNew ((add_str_len + 1) * sizeof (Char));
+ if (add_str != NULL)
+ {
+ StringCpy (add_str, oip->str);
+ StringNCat (add_str, title, len);
+ add_str [add_str_len] = 0;
+ new_sip = MakeSeqID (add_str);
+ ValNodeAddPointer (extended_ids, 0, new_sip);
+ ValNodeAddPointer (sep_for_ids, 0, sep);
+ add_str = MemFree (add_str);
+ }
+ }
}
}
- list = list->next;
+ else if (IS_Bioseq_set (sep))
+ {
+ bssp = (BioseqSetPtr) sep->data.ptrvalue;
+ FindExtraTextForLocalIDs (bssp->seq_set, extended_ids, sep_for_ids);
+ }
+ }
+}
+
+static ParData idParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0};
+static ColData idColFmt[] =
+ {
+ {0, 0, 40, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE},
+ {0, 0, 40, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}
+ };
+
+static void AddIDStatement (ValNodePtr id_vnp, ValNodePtr seq_vnp, DoC doc)
+{
+ CharPtr doc_txt;
+ CharPtr doc_txt_fmt = "%s\t%s %s\n";
+ ObjectIdPtr oip_old, oip_new;
+ SeqEntryPtr sep;
+ BioseqPtr bsp;
+ SeqDescrPtr sdp;
+ SeqIdPtr sip;
+ Int4 len;
+
+ if (id_vnp == NULL || id_vnp->data.ptrvalue == NULL
+ || seq_vnp == NULL || seq_vnp->data.ptrvalue == NULL)
+ {
+ return;
+ }
+
+ sip = (SeqIdPtr) id_vnp->data.ptrvalue;
+ if (sip->choice != SEQID_LOCAL || sip->data.ptrvalue == NULL)
+ {
+ return;
+ }
+ oip_new = (ObjectIdPtr) sip->data.ptrvalue;
+ if (StringHasNoText (oip_new->str))
+ {
+ return;
+ }
+
+ sep = (SeqEntryPtr) seq_vnp->data.ptrvalue;
+ if (!IS_Bioseq (sep))
+ {
+ return;
+ }
+
+ bsp = (BioseqPtr) sep->data.ptrvalue;
+
+ if (bsp->id == NULL || bsp->id->choice != SEQID_LOCAL || bsp->id->data.ptrvalue == NULL)
+ {
+ return;
+ }
+
+ oip_old = bsp->id->data.ptrvalue;
+ if (StringHasNoText (oip_old->str))
+ {
+ return;
+ }
+
+ len = StringLen (oip_old->str);
+ if (StringNCmp (oip_old->str, oip_new->str, len) != 0)
+ {
+ return;
+ }
+
+ sdp = bsp->descr;
+ while (sdp != NULL
+ && (sdp->choice != Seq_descr_title
+ || StringHasNoText (sdp->data.ptrvalue)))
+ {
+ sdp = sdp->next;
+ }
+ if (sdp == NULL)
+ {
+ return;
+ }
+
+ len = StringLen (doc_txt_fmt)
+ + StringLen (oip_new->str)
+ + StringLen (oip_old->str)
+ + StringLen (sdp->data.ptrvalue);
+ doc_txt = (CharPtr) MemNew (len * sizeof (Char));
+ if (doc_txt != NULL)
+ {
+ sprintf (doc_txt, doc_txt_fmt, oip_new->str, oip_old->str, sdp->data.ptrvalue);
+ AppendText (doc, doc_txt, &idParFmt, idColFmt, programFont);
+ doc_txt = MemFree (doc_txt);
+ }
+}
+
+
+static void FixOneSequenceIDWithSpaces (ValNodePtr id_vnp, ValNodePtr seq_vnp)
+{
+ ObjectIdPtr oip_old, oip_new;
+ SeqEntryPtr sep;
+ BioseqPtr bsp;
+ SeqDescrPtr sdp;
+ SeqIdPtr sip;
+ Int4 len_old, len_new, def_offset;
+ CharPtr defline, new_defline;
+
+ if (id_vnp == NULL || id_vnp->data.ptrvalue == NULL
+ || seq_vnp == NULL || seq_vnp->data.ptrvalue == NULL)
+ {
+ return;
+ }
+
+ sip = (SeqIdPtr) id_vnp->data.ptrvalue;
+ if (sip->choice != SEQID_LOCAL || sip->data.ptrvalue == NULL)
+ {
+ return;
+ }
+ oip_new = (ObjectIdPtr) sip->data.ptrvalue;
+ if (StringHasNoText (oip_new->str))
+ {
+ return;
+ }
+
+ sep = (SeqEntryPtr) seq_vnp->data.ptrvalue;
+ if (!IS_Bioseq (sep))
+ {
+ return;
+ }
+ bsp = (BioseqPtr) sep->data.ptrvalue;
+
+ if (bsp->id == NULL || bsp->id->choice != SEQID_LOCAL || bsp->id->data.ptrvalue == NULL)
+ {
+ return;
+ }
+
+ oip_old = bsp->id->data.ptrvalue;
+ if (StringHasNoText (oip_old->str))
+ {
+ return;
+ }
+
+ len_old = StringLen (oip_old->str);
+ if (StringNCmp (oip_old->str, oip_new->str, len_old) != 0)
+ {
+ return;
+ }
+
+ sdp = bsp->descr;
+ while (sdp != NULL
+ && (sdp->choice != Seq_descr_title
+ || StringHasNoText (sdp->data.ptrvalue)))
+ {
+ sdp = sdp->next;
+ }
+ if (sdp == NULL)
+ {
+ return;
+ }
+
+ defline = (CharPtr) sdp->data.ptrvalue;
+
+ len_new = StringLen (oip_new->str);
+ def_offset = len_new - len_old - 1;
+ if (def_offset > 0 && StringNCmp (oip_new->str + len_old + 1, defline, def_offset) == 0)
+ {
+ if (*(defline + def_offset) == 0)
+ {
+ new_defline = StringSave ("");
+ }
+ else
+ {
+ new_defline = StringSave (defline + def_offset + StringSpn (defline + def_offset, " \t"));
+ }
+ sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue);
+ sdp->data.ptrvalue = new_defline;
+ }
+
+ sip->next = bsp->id->next;
+ bsp->id->next = NULL;
+ /* put old ID in list to be freed later */
+ id_vnp->data.ptrvalue = bsp->id;
+ /* put new ID on Bioseq */
+ bsp->id = sip;
+}
+
+static void FixSpacesInLocalIDs (SeqEntryPtr list)
+{
+ ValNodePtr extended_ids = NULL, sep_for_ids = NULL;
+ WindoW w;
+ GrouP h, c;
+ ButtoN b;
+ DoC doc;
+ ModalAcceptCancelData acd;
+ ValNodePtr id_vnp, seq_vnp;
+ RecT r;
+
+ if (list == NULL)
+ {
+ return;
+ }
+
+ FindExtraTextForLocalIDs (list, &extended_ids, &sep_for_ids);
+
+ if (extended_ids != NULL && sep_for_ids != NULL)
+ {
+ w = MovableModalWindow (-20, -13, -10, -10, "Spaces in Sequence IDs", NULL);
+ h = HiddenGroup(w, -1, 0, NULL);
+ SetGroupSpacing (h, 10, 10);
+
+ doc = DocumentPanel (h, stdCharWidth * 27, stdLineHeight * 12);
+ SetDocAutoAdjust (doc, TRUE);
+ AppendText (doc, "Your sequence IDs are not unique. Did you try to put spaces in your sequence IDs? This is not allowed.\n\n", NULL, NULL, programFont);
+
+ ObjectRect (doc, &r);
+ InsetRect (&r, 4, 4);
+ idColFmt[0].pixWidth = (r.right - r.left) / 2;
+ idColFmt[1].pixWidth = (r.right - r.left) / 2;
+
+
+ AppendText (doc, "Corrected ID\tOriginal Description\n", &idParFmt, idColFmt, programFont);
+
+ for (id_vnp = extended_ids, seq_vnp = sep_for_ids;
+ id_vnp != NULL && seq_vnp != NULL;
+ id_vnp = id_vnp->next, seq_vnp = seq_vnp->next)
+ {
+ AddIDStatement (id_vnp, seq_vnp, doc);
+ }
+
+ c = HiddenGroup (h, 2, 0, NULL);
+ b = PushButton (c, "Make automatic corrections", ModalAcceptButton);
+ SetObjectExtra (b, &acd, NULL);
+ b = PushButton (c, "Allow manual corrections", ModalCancelButton);
+ SetObjectExtra (b, &acd, NULL);
+
+ AlignObjects (ALIGN_CENTER, (HANDLE) doc, (HANDLE) c, (HANDLE) NULL);
+
+ Show (w);
+ Select (w);
+
+ acd.cancelled = FALSE;
+ acd.accepted = FALSE;
+ while (!acd.accepted && ! acd.cancelled)
+ {
+ ProcessExternalEvent ();
+ Update ();
+ }
+ ProcessAnEvent ();
+ if (! acd.cancelled)
+ {
+ for (id_vnp = extended_ids, seq_vnp = sep_for_ids;
+ id_vnp != NULL && seq_vnp != NULL;
+ id_vnp = id_vnp->next, seq_vnp = seq_vnp->next)
+ {
+ FixOneSequenceIDWithSpaces (id_vnp, seq_vnp);
+ }
+ ResetSegSetIDLists (list);
+ }
+ Remove (w);
}
- return num_seqs;
+}
+
+typedef struct seqidedit
+{
+ SeqEntryPtr new_list;
+ SeqEntryPtr current_list;
+ DialoG dlg;
+ PrompT p_instr[3];
+} SeqIdEditData, PNTR SeqIdEditPtr;
+
+static void ShowErrorInstructions (Pointer userdata)
+{
+ Int4 i = 0;
+ SeqIdEditPtr siep;
+ TagListPtr tlp;
+
+ siep = (SeqIdEditPtr) userdata;
+ if (siep == NULL)
+ {
+ return;
+ }
+
+ tlp = (TagListPtr) GetObjectExtra (siep->dlg);
+ if (tlp != NULL)
+ {
+ CollectIdAndTitleFromDialog (tlp, siep->new_list);
+ }
+
+ if (HasBlankIDs (siep->new_list))
+ {
+ SetTitle (siep->p_instr [i++], "Some of your sequences lack sequence IDs.");
+ }
+
+ if (HasDuplicateIDs (siep->new_list, siep->current_list))
+ {
+ SetTitle (siep->p_instr [i++], "Some of your sequence IDs are duplicated.");
+ }
+
+ if (i == 0)
+ {
+ SetTitle (siep->p_instr [i++], "Sequence ID errors have been corrected.");
+ }
+ else
+ {
+ SetTitle (siep->p_instr [i++], "Please provide unique sequence IDs for every sequence.");
+ }
+ while (i < 3)
+ {
+ SetTitle (siep->p_instr [i++], "");
+ }
+}
+
+static void ShowAllSequences (ButtoN b)
+{
+ SeqIdEditPtr siep;
+ Boolean show_all;
+ TagListPtr tlp;
+
+ siep = (SeqIdEditPtr) GetObjectExtra (b);
+ if (siep == NULL || siep->dlg == NULL || siep->new_list == NULL)
+ {
+ return;
+ }
+
+ tlp = (TagListPtr) GetObjectExtra (siep->dlg);
+ if (tlp == NULL)
+ {
+ return;
+ }
+
+ show_all = HasBlankIDs (siep->new_list);
+ show_all |= GetStatus (b);
+
+ CollectIdAndTitleFromDialog (tlp, siep->new_list);
+ SetSeqListInTagListDialog (siep->dlg, siep->new_list, siep->current_list, show_all);
+ ShowErrorInstructions (siep);
}
static Boolean CollectIDsAndTitles (SeqEntryPtr new_list, SeqEntryPtr current_list)
{
WindoW w;
- GrouP h, ppt, c;
+ GrouP h, ppt, instr_grp, c;
ButtoN b;
- Int4 num_sequences = 0, seq_num;
+ Int4 num_sequences = 0;
BoolPtr is_dup_list = NULL;
Boolean need_fix = FALSE;
DialoG dlg;
TagListPtr tlp;
ModalAcceptCancelData acd;
- SeqEditTagData setd;
+ PrompT p1, p2, p3, p4;
+ Boolean show_all;
+ ButtoN force_all_btn;
+ SeqIdEditData sied;
+ TaglistCallback callback_list[4] =
+ { ShowErrorInstructions, ShowErrorInstructions, ShowErrorInstructions, ShowErrorInstructions };
+
+ ArrowCursor ();
+
+ /* look for spaces in local IDs */
+ FixSpacesInLocalIDs (new_list);
/* check for unique IDs - don't need to present dialog if they
* are all present and unique */
@@ -13519,33 +14383,61 @@ static Boolean CollectIDsAndTitles (SeqEntryPtr new_list, SeqEntryPtr current_li
}
num_sequences = CountSequencesAndSegments (new_list);
- setd.current_list = current_list;
- setd.new_list = new_list;
+ show_all = HasBlankIDs (new_list);
w = MovableModalWindow (-20, -13, -10, -10, "Provide Sequence IDs for your Sequences", NULL);
h = HiddenGroup(w, -1, 0, NULL);
SetGroupSpacing (h, 10, 10);
- ppt = HiddenGroup (h, 3, 0, NULL);
- StaticPrompt (ppt, "", 4 * stdCharWidth, 0, programFont, 'l');
- StaticPrompt (ppt, "Sequence ID", 10 * stdCharWidth, 0, programFont, 'l');
- StaticPrompt (ppt, "Description", 40 * stdCharWidth, 0, programFont, 'l');
+ instr_grp = HiddenGroup (h, -1, 0, NULL);
+ sied.p_instr [0] = StaticPrompt (instr_grp, "", 40 * stdCharWidth, 0, programFont, 'l');
+ sied.p_instr [1] = StaticPrompt (instr_grp, "", 40 * stdCharWidth, 0, programFont, 'l');
+ sied.p_instr [2] = StaticPrompt (instr_grp, "", 40 * stdCharWidth, 0, programFont, 'l');
- dlg = CreateTagListDialogEx (h, MIN (num_sequences, 8), 3, 2,
- idedit_types, idedit_widths,
- NULL, TRUE, TRUE, SeqListToTagListDialog, NULL);
- PointerToDialog (dlg, &setd);
+ ppt = HiddenGroup (h, 4, 0, NULL);
+ p1 = StaticPrompt (ppt, "", 6 * stdCharWidth, 0, programFont, 'l');
+ p2 = StaticPrompt (ppt, "Position", 5 * stdCharWidth, 0, programFont, 'l');
+ p3 = StaticPrompt (ppt, "Sequence ID", 10 * stdCharWidth, 0, programFont, 'l');
+ p4 = StaticPrompt (ppt, "Description", 40 * stdCharWidth, 0, programFont, 'l');
+ dlg = CreateTagListDialogExEx (h, MIN (num_sequences, 8), 4, 2,
+ idedit_types, idedit_widths,
+ NULL, TRUE, TRUE, NULL, NULL,
+ callback_list, &sied);
+
+
tlp = (TagListPtr) GetObjectExtra (dlg);
if (tlp == NULL) return;
+
+ sied.dlg = dlg;
+ sied.new_list = new_list;
+ sied.current_list = current_list;
+ SetSeqListInTagListDialog (dlg, new_list, current_list, show_all);
+ ShowErrorInstructions (&sied);
+
+ force_all_btn = CheckBox (h, "Show all sequences in set", ShowAllSequences);
+ SetObjectExtra (force_all_btn, &sied, NULL);
+ if (show_all)
+ {
+ Disable (force_all_btn);
+ }
+ else
+ {
+ Enable (force_all_btn);
+ }
+
c = HiddenGroup (h, 2, 0, NULL);
b = PushButton (c, "Accept", ModalAcceptButton);
SetObjectExtra (b, &acd, NULL);
b = PushButton (c, "Cancel", ModalCancelButton);
SetObjectExtra (b, &acd, NULL);
- AlignObjects (ALIGN_CENTER, (HANDLE) ppt, (HANDLE) dlg, (HANDLE) c, (HANDLE) NULL);
+ AlignObjects (ALIGN_CENTER, (HANDLE) instr_grp, (HANDLE) dlg, (HANDLE) force_all_btn, (HANDLE) c, NULL);
+ AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [0], (HANDLE) p1, NULL);
+ AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [1], (HANDLE) p2, NULL);
+ AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [2], (HANDLE) p3, NULL);
+ AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [3], (HANDLE) p4, NULL);
Show (w);
Select (w);
@@ -13562,15 +14454,25 @@ static Boolean CollectIDsAndTitles (SeqEntryPtr new_list, SeqEntryPtr current_li
ProcessAnEvent ();
if (! acd.cancelled)
{
- seq_num = 0;
- CollectIdAndTitleFromDialog (tlp, new_list, &seq_num);
+ CollectIdAndTitleFromDialog (tlp, new_list);
/* now check for unique IDs */
need_fix = IDsNeedFix (new_list, current_list);
if (need_fix)
{
Message (MSG_ERROR, "Blank or Duplicate IDs are not allowed!");
- PointerToDialog (dlg, &setd);
+ show_all = HasBlankIDs (new_list);
+ if (show_all)
+ {
+ Disable (force_all_btn);
+ }
+ else
+ {
+ Enable (force_all_btn);
+ show_all = GetStatus (force_all_btn);
+ }
+ SetSeqListInTagListDialog (dlg, new_list, current_list, show_all);
+ ShowErrorInstructions (&sied);
}
else if (! FixDefinitionLinesInAddSequence (new_list))
{
@@ -13579,7 +14481,18 @@ static Boolean CollectIDsAndTitles (SeqEntryPtr new_list, SeqEntryPtr current_li
if (need_fix)
{
- PointerToDialog (dlg, &setd);
+ show_all = HasBlankIDs (new_list);
+ if (show_all)
+ {
+ Disable (force_all_btn);
+ }
+ else
+ {
+ Enable (force_all_btn);
+ show_all = GetStatus (force_all_btn);
+ }
+ SetSeqListInTagListDialog (dlg, new_list, current_list, show_all);
+ ShowErrorInstructions (&sied);
}
}
}
@@ -13600,6 +14513,7 @@ static void ReplaceFakeIDWithIDFromTitle (BioseqPtr bsp)
SeqDescrPtr sdp;
CharPtr title_txt, new_id_str;
Int4 id_len;
+ Boolean remove_punct = FALSE;
if (bsp == NULL)
{
@@ -13618,7 +14532,38 @@ static void ReplaceFakeIDWithIDFromTitle (BioseqPtr bsp)
title_txt = sdp->data.ptrvalue;
/* skip any leading spaces */
title_txt += StringSpn (title_txt, " \t");
- id_len = StringCSpn (title_txt, " \t");
+ /* look for local IDs surrounded by quotes - the real way to have an ID with a space */
+ if (*title_txt == '\'')
+ {
+ title_txt ++;
+ id_len = StringCSpn (title_txt, "\'");
+ if (title_txt [id_len] == '\'')
+ {
+ remove_punct = TRUE;
+ }
+ else
+ {
+ id_len = 0;
+ }
+ }
+ else if (*title_txt == '\"')
+ {
+ title_txt ++;
+ id_len = StringCSpn (title_txt, "\"");
+ if (title_txt [id_len] == '\"')
+ {
+ remove_punct = TRUE;
+ }
+ else
+ {
+ id_len = 0;
+ }
+ }
+ else
+ {
+ id_len = StringCSpn (title_txt, " \t");
+ }
+
if (id_len > 0)
{
new_id_str = (CharPtr) MemNew ((id_len + 1) * sizeof (Char));
@@ -13630,6 +14575,10 @@ static void ReplaceFakeIDWithIDFromTitle (BioseqPtr bsp)
new_id_str = MemFree (new_id_str);
/* remove id from title */
title_txt += id_len;
+ if (remove_punct)
+ {
+ title_txt ++;
+ }
title_txt += StringSpn (title_txt, " \t");
title_txt = StringSave (title_txt);
sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue);
@@ -13668,7 +14617,8 @@ static SeqEntryPtr GetSequencesFromFile (CharPtr path, SeqEntryPtr current_list)
return NULL;
}
else if (!CollectIDsAndTitles (new_sep_list, current_list))
- {
+ {
+ new_sep = new_sep_list;
while (new_sep != NULL)
{
test_sep = new_sep->next;
@@ -13685,6 +14635,7 @@ static SeqEntryPtr GetSequencesFromFile (CharPtr path, SeqEntryPtr current_list)
if (cancelled)
{
+ new_sep = new_sep_list;
while (new_sep != NULL)
{
test_sep = new_sep->next;
@@ -14032,6 +14983,22 @@ static Boolean CheckBracketingInDefLine (CharPtr PNTR defline, CharPtr id_txt)
return !cancelled;
}
+static void PasteSequenceAssistant (IteM i)
+{
+ TexT txt;
+ CharPtr str;
+
+ txt = (TexT) GetObjectExtra (i);
+ if (txt == NULL)
+ {
+ return;
+ }
+
+ str = ClipboardToString ();
+ SetTitle (txt, str);
+ str = MemFree (str);
+}
+
static void SequenceAssistantAddSequence (SequenceAssistantPtr sap)
{
ModalAcceptCancelData acd;
@@ -14044,11 +15011,13 @@ static void SequenceAssistantAddSequence (SequenceAssistantPtr sap)
Char str [200];
ButtoN b;
SeqEntryPtr last_sep = NULL, new_sep;
- CharPtr errormsg = NULL;
- ValNodePtr err_list = NULL;
- Boolean done = FALSE;
+ CharPtr errormsg = NULL;
+ ValNodePtr err_list = NULL;
+ Boolean done = FALSE;
ByteStorePtr new_bs = NULL;
SeqIdPtr new_sip = NULL;
+ MenU edit_menu;
+ IteM local_item;
if (sap == NULL)
{
@@ -14084,6 +15053,11 @@ static void SequenceAssistantAddSequence (SequenceAssistantPtr sap)
(HANDLE) sequence_grp,
(HANDLE) c,
NULL);
+
+ /* Edit Menu */
+ edit_menu = PulldownMenu (w, "Edit");
+ local_item = CommandItem (edit_menu, "Paste", PasteSequenceAssistant);
+ SetObjectExtra (local_item, sequence_txt, NULL);
Show(w);
Select (w);
@@ -14145,6 +15119,8 @@ static void SequenceAssistantEditSequence (SequenceAssistantPtr sap, Int4 seq_nu
ByteStorePtr new_bs = NULL;
SeqIdPtr new_sip = NULL;
SeqDescrPtr sdp;
+ MenU edit_menu;
+ IteM local_item;
if (sap == NULL)
{
@@ -14173,7 +15149,7 @@ static void SequenceAssistantEditSequence (SequenceAssistantPtr sap, Int4 seq_nu
bsp = sep->data.ptrvalue;
if (bsp->repr == Seq_repr_delta)
{
- Message (MSG_ERROR, "Can't edit delta sequence!");
+ Message (MSG_ERROR, "Can't edit gapped sequence!");
return;
}
sip = SeqIdFindWorst (bsp->id);
@@ -14240,6 +15216,11 @@ static void SequenceAssistantEditSequence (SequenceAssistantPtr sap, Int4 seq_nu
AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, (HANDLE) sequence_grp,
(HANDLE) c, NULL);
}
+
+ /* Edit Menu */
+ edit_menu = PulldownMenu (w, "Edit");
+ local_item = CommandItem (edit_menu, "Paste", PasteSequenceAssistant);
+ SetObjectExtra (local_item, sequence_txt, NULL);
Show(w);
Select (w);
@@ -15025,7 +16006,7 @@ static void EditOneSequenceTitle (SequenceAssistantPtr sap, Int4 seq_num)
WindoW w;
CharPtr title = NULL;
BioseqPtr bsp = NULL;
- CharPtr title_fmt = "Title for %s";
+ CharPtr title_fmt = "Description for %s";
Char id_txt [128];
GrouP h, g, c;
ButtoN b;
@@ -15085,8 +16066,8 @@ static void EditOneSequenceTitle (SequenceAssistantPtr sap, Int4 seq_num)
SetGroupSpacing (h, 10, 10);
g = HiddenGroup (h, 2, 0, NULL);
- StaticPrompt (g, "Title", 0, popupMenuHeight, programFont, 'l');
- new_title_txt = DialogText (g, "", 20, NULL);
+ StaticPrompt (g, "Description", 0, popupMenuHeight, programFont, 'l');
+ new_title_txt = DialogText (g, "", 40, NULL);
if (sdp != NULL && !StringHasNoText (sdp->data.ptrvalue))
{
SetTitle (new_title_txt, sdp->data.ptrvalue);
@@ -15342,12 +16323,12 @@ static void EditSequenceTitleColumns (SequenceAssistantPtr sap)
}
rows_shown = MIN (rows_shown, 5);
- w = MovableModalWindow (-20, -13, -10, -10, "Sequence Titles", NULL);
+ w = MovableModalWindow (-20, -13, -10, -10, "Sequence Descriptions", NULL);
h = HiddenGroup(w, -1, 0, NULL);
SetGroupSpacing (h, 10, 10);
- ppt = StaticPrompt (h, "Title", 18 * stdCharWidth, 0, programFont, 'l');
+ ppt = StaticPrompt (h, "Description", 18 * stdCharWidth, 0, programFont, 'l');
dlg = CreateTagListDialogEx (h, rows_shown, 2, 2,
titleedit_types, titleedit_widths,
@@ -15583,7 +16564,8 @@ static void SequenceAssistant (ButtoN b)
sad.summary_dlg = FastaSummaryDialog (h);
sad.sequence_table = TableDisplayDialog (h, stdCharWidth * 27, stdLineHeight * 8, 1, 2,
- SequenceDblClick, &sad);
+ SequenceDblClick, &sad,
+ NULL, NULL);
c = HiddenGroup (h, 2, 0, NULL);
b = PushButton(c, "Done", SequenceAssistantOkButton);
@@ -18011,109 +18993,6 @@ extern void LoadHistoryAccessionNumbersFromFile (
LoadSecondaryAccessionNumbersPlusHistFromFile (i, TRUE);
}
-/* This section of code is used for managing lists of features.
- * Sometimes the features will be displayed alphabetically, sometimes
- * they will be displayed alphabetically with a list of the most used features
- * also appearing at the top of the list.
- */
-
-/* This is used to compare feature names with the special alphabetical order */
-static int CompareFeatureNames (CharPtr cp1, CharPtr cp2)
-{
- /* NULL name goes at the end */
- if (cp1 == NULL && cp2 == NULL) return 0;
- if (cp1 == NULL) return 1;
- if (cp2 == NULL) return -1;
-
- /* starts with a space goes at the beginning */
- if (cp1 [0] == ' ' && cp2 [0] == ' ') return 0;
- if (cp1 [0] == ' ') return -1;
- if (cp2 [0] == ' ') return 1;
-
- /* Is "All" or [ALL FEATURES] goes at the beginning */
- if ((StringCmp (cp1, "All") == 0
- || StringCmp (cp1, "[ALL FEATURES]") == 0)
- && (StringCmp (cp2, "All") == 0
- || StringCmp (cp2, "[ALL FEATURES]") == 0))
- {
- return 0;
- }
- if (StringCmp (cp1, "All") == 0
- || StringCmp (cp1, "[ALL FEATURES]") == 0)
- {
- return -1;
- }
- if (StringCmp (cp2, "All") == 0
- || StringCmp (cp2, "[ALL FEATURES]") == 0)
- {
- return 1;
- }
-
- /* starts with a number -> goes at the end */
- if (cp1 [0] >= '0' && cp1 [0] <= '9'
- && cp2 [0] >= '0' && cp2 [0] <= '9')
- {
- return StringICmp (cp1, cp2);
- }
- if (cp1 [0] >= '0' && cp1 [0] <= '9')
- {
- return 1;
- }
- if (cp2 [0] >= '0' && cp2 [0] <= '9')
- {
- return -1;
- }
-
- /* starts with a tilde or dash - sort with other tildes, put before numbers after alphas */
- if (cp1 [0] == '~' && cp2 [0] == '~')
- {
- return StringICmp (cp1 + 1, cp2 + 1);
- }
- if (cp1 [0] == '~') return 1;
- if (cp2 [0] == '~') return -1;
-
- if (cp1 [0] == '-' && cp2 [0] == '-')
- {
- return StringICmp (cp1 + 1, cp2 + 1);
- }
- if (cp1 [0] == '-') return 1;
- if (cp2 [0] == '-') return -1;
-
- return StringICmp (cp1, cp2);
-}
-
-extern int LIBCALLBACK CompareFeatureValNodeStrings (VoidPtr ptr1, VoidPtr ptr2)
-{
- ValNodePtr vnp1, vnp2;
-
- if (ptr1 == NULL || ptr2 == NULL) return 0;
-
- vnp1 = *((ValNodePtr PNTR) ptr1);
- vnp2 = *((ValNodePtr PNTR) ptr2);
-
- if (vnp1 == NULL || vnp2 == NULL) return 0;
-
- return CompareFeatureNames (vnp1->data.ptrvalue, vnp2->data.ptrvalue);
-}
-
-extern int LIBCALLBACK CompareImpFeatEnumFieldAssoc (VoidPtr ptr1, VoidPtr ptr2)
-{
- ValNodePtr vnp1, vnp2;
- EnumFieldAssocPtr ap1, ap2;
-
- if (ptr1 == NULL || ptr2 == NULL) return 0;
-
- vnp1 = *((ValNodePtr PNTR) ptr1);
- vnp2 = *((ValNodePtr PNTR) ptr2);
- if (vnp1 == NULL || vnp2 == NULL) return 0;
-
- ap1 = (EnumFieldAssocPtr) vnp1->data.ptrvalue;
- ap2 = (EnumFieldAssocPtr) vnp2->data.ptrvalue;
- if (ap1 == NULL || ap2 == NULL) return 0;
-
- return CompareFeatureNames (ap1->name, ap2->name);
-}
-
CharPtr MostUsedFeatureList[] = {
"CDS",
"exon",
@@ -18239,38 +19118,6 @@ extern EnumFieldAssocPtr InsertMostUsedFeatureEnumFieldAssoc (
}
-extern void SortEnumFieldAssocPtrArray (EnumFieldAssocPtr alist, CompareFunc compar)
-{
- ValNodePtr head, vnp;
- EnumFieldAssocPtr ap;
- Int4 index;
-
- /* first, create ValNode list so we can sort the data */
- head = NULL;
- for (ap = alist; ap != NULL && ap->name != NULL; ap++)
- {
- vnp = ValNodeNew (head);
- if (vnp == NULL) return;
- vnp->data.ptrvalue = MemNew (sizeof (EnumFieldAssoc));
- if (vnp->data.ptrvalue == NULL) return;
- MemCpy (vnp->data.ptrvalue, ap, sizeof (EnumFieldAssoc));
- if (head == NULL) head = vnp;
- }
-
- /* Now sort the ValNode list */
- head = SortValNode (head, compar);
-
- /* Now repopulate the EnumFieldAssoc list */
- index = 0;
- for (vnp = head; vnp != NULL; vnp = vnp->next)
- {
- MemCpy (alist + index++, vnp->data.ptrvalue, sizeof (EnumFieldAssoc));
- }
-
- /* And free the ValNode list */
- ValNodeFreeData (head);
-}
-
static Uint2 UnusualFeatureTypes [] = {
FEATDEF_ORG,
FEATDEF_mutation,
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-29 03:35:00 +0000