diff options
Diffstat (limited to 'desktop/macrodlg.c')
| -rwxr-xr-x | desktop/macrodlg.c | 3804 |
1 files changed, 1943 insertions, 1861 deletions
diff --git a/desktop/macrodlg.c b/desktop/macrodlg.c index 76d9c947..29546ba0 100755 --- a/desktop/macrodlg.c +++ b/desktop/macrodlg.c @@ -29,7 +29,7 @@ * * Version Creation Date: 11/23/2007 * -* $Revision: 1.157 $ +* $Revision: 1.185 $ * * File Description: * @@ -371,6 +371,7 @@ static void RunMacro (ButtoN b) Uint2 entityID; Int4 num_fields = 0, num_features = 0; Int4 tmp_fields, tmp_features; + LogInfoPtr lip; f = (MacroEditorFormPtr) GetObjectExtra (b); if (f == NULL) return; @@ -387,12 +388,13 @@ static void RunMacro (ButtoN b) } else { WatchCursor(); Update(); + lip = OpenLog ("Macro Actions"); for (vnp = sep_list; vnp != NULL; vnp = vnp->next) { sep = vnp->data.ptrvalue; entityID = ObjMgrGetEntityIDForChoice(sep); tmp_fields = 0; tmp_features = 0; - ApplyMacroToSeqEntry (sep, f->macro_list, &tmp_fields, &tmp_features); + lip->data_in_log |= ApplyMacroToSeqEntryEx (sep, f->macro_list, &tmp_fields, &tmp_features, lip->fp); num_fields += tmp_fields; num_features += tmp_features; ObjMgrSetDirtyFlag (entityID, TRUE); @@ -402,6 +404,12 @@ static void RunMacro (ButtoN b) ArrowCursor (); Update (); Message (MSG_OK, "Macro script affected %d fields and created %d features", num_fields, num_features); + if (!lip->data_in_log) { + fprintf (lip->fp, "Macro had no effect\n"); + lip->data_in_log = TRUE; + } + CloseLog (lip); + lip = FreeLog (lip); } } } @@ -800,19 +808,13 @@ static void DrawMacroDocControls (DoC d, RectPtr r, Int2 item, Int2 firstLine) } -NLM_EXTERN void LaunchMacroEditor (IteM i) +NLM_EXTERN void LaunchMacroEditorBaseForm (BaseFormPtr bfp) { - BaseFormPtr bfp; WindoW w; MacroEditorFormPtr f; GrouP h, c; MenU m; -#ifdef WIN_MAC - bfp = currentFormDataPtr; -#else - bfp = GetObjectExtra (i); -#endif if (bfp == NULL) return; f = (MacroEditorFormPtr) MemNew (sizeof (MacroEditorFormData)); @@ -862,6 +864,19 @@ NLM_EXTERN void LaunchMacroEditor (IteM i) } +NLM_EXTERN void LaunchMacroEditor (IteM i) +{ + BaseFormPtr bfp; + +#ifdef WIN_MAC + bfp = currentFormDataPtr; +#else + bfp = GetObjectExtra (i); +#endif + LaunchMacroEditorBaseForm (bfp); +} + + static void ClearDialogBtn (ButtoN b) { DialoG d; @@ -872,14 +887,198 @@ static void ClearDialogBtn (ButtoN b) } +typedef struct textmarkerdialog +{ + DIALOG_MESSAGE_BLOCK + + GrouP marker_choice; + TexT marker_text; + + Nlm_ChangeNotifyProc change_notify; + Pointer change_userdata; +} TextMarkerDialogData, PNTR TextMarkerDialogPtr; + + +static void ResetTextMarkerDialog (DialoG d) +{ + TextMarkerDialogPtr tp; + + tp = (TextMarkerDialogPtr) GetObjectExtra (d); + if (tp == NULL) { + return; + } + SetValue (tp->marker_choice, 1); + SetTitle (tp->marker_text, ""); + Enable (tp->marker_text); +} + + +static void TextMarkerToDialog(DialoG d, Pointer data) +{ + TextMarkerDialogPtr tp; + TextMarkerPtr tdata; + + tp = (TextMarkerDialogPtr) GetObjectExtra (d); + if (tp == NULL) { + return; + } + + tdata = (TextMarkerPtr) data; + + if (tdata == NULL) { + ResetTextMarkerDialog(d); + } else { + if (tdata->choice == TextMarker_free_text) { + SetValue (tp->marker_choice, 1); + SetTitle (tp->marker_text, tdata->data.ptrvalue == NULL ? "" : tdata->data.ptrvalue); + Enable (tp->marker_text); + } else if (tdata->choice == TextMarker_digits) { + SetValue (tp->marker_choice, 3); + SetTitle (tp->marker_text, ""); + Disable (tp->marker_text); + } else if (tdata->choice == TextMarker_letters) { + SetValue (tp->marker_choice, 4); + SetTitle (tp->marker_text, ""); + Disable (tp->marker_text); + } else { + SetValue (tp->marker_choice, 1); + SetTitle (tp->marker_text, ""); + Enable (tp->marker_text); + } + } +} + + +static Pointer DialogToTextMarker (DialoG d) +{ + TextMarkerDialogPtr tp; + Int2 val; + ValNodePtr tdata = NULL; + + tp = (TextMarkerDialogPtr) GetObjectExtra (d); + if (tp == NULL) { + return NULL; + } + + val = GetValue (tp->marker_choice); + if (val == 1) { + ValNodeAddPointer (&tdata, TextMarker_free_text, JustSaveStringFromText (tp->marker_text)); + } else if (val == 3) { + tdata = ValNodeNew (NULL); + tdata->choice = TextMarker_digits; + } else if (val == 4) { + tdata = ValNodeNew (NULL); + tdata->choice = TextMarker_letters; + } + + return tdata; +} + + +static void TextMarkerMessage (DialoG d, Int2 mssg) + +{ + TextMarkerDialogPtr tp; + + tp = (TextMarkerDialogPtr) GetObjectExtra (d); + if (tp != NULL) { + switch (mssg) { + case VIB_MSG_INIT : + ResetTextMarkerDialog (d); + break; + case VIB_MSG_ENTER : + Select (tp->marker_text); + break; + default : + break; + } + } +} + + +static void ChangeTextMarkerChoice (GrouP g) +{ + TextMarkerDialogPtr tp; + Int2 val; + + tp = (TextMarkerDialogPtr) GetObjectExtra (g); + if (tp == NULL) { + return; + } + + val = GetValue (tp->marker_choice); + if (val == 1) { + Enable (tp->marker_text); + } else { + Disable (tp->marker_text); + } + + if (tp->change_notify != NULL) { + (tp->change_notify) (tp->change_userdata); + } +} + + +static void ChangeTextMarkerText (TexT t) +{ + TextMarkerDialogPtr tp; + + tp = (TextMarkerDialogPtr) GetObjectExtra (t); + if (tp == NULL) { + return; + } + + if (tp->change_notify != NULL) { + (tp->change_notify) (tp->change_userdata); + } +} + + +static DialoG TextMarkerDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +{ + TextMarkerDialogPtr tp; + GrouP p; + + tp = (TextMarkerDialogPtr) MemNew (sizeof (TextMarkerDialogData)); + if (tp == NULL) + { + return NULL; + } + + p = HiddenGroup (h, -1, 0, NULL); + SetObjectExtra (p, tp, StdCleanupExtraProc); + + tp->dialog = (DialoG) p; + tp->todialog = TextMarkerToDialog; + tp->fromdialog = DialogToTextMarker; + tp->dialogmessage = TextMarkerMessage; + tp->testdialog = NULL; + + tp->change_notify = change_notify; + tp->change_userdata = change_userdata; + + tp->marker_choice = HiddenGroup (p, 4, 0, ChangeTextMarkerChoice); + SetObjectExtra (tp->marker_choice, tp, NULL); + SetGroupSpacing (tp->marker_choice, 10, 10); + + RadioButton (tp->marker_choice, "Text"); + tp->marker_text = DialogText (tp->marker_choice, "", 10, ChangeTextMarkerText); + RadioButton (tp->marker_choice, "Digits"); + RadioButton (tp->marker_choice, "Letters"); + SetValue (tp->marker_choice, 1); + + return (DialoG) p; +} + + typedef struct textportiondialog { DIALOG_MESSAGE_BLOCK GrouP start_choice; - TexT start_text; + DialoG start_marker; GrouP end_choice; - TexT end_text; + DialoG end_marker; ButtoN rem_before; ButtoN also_rem_before; ButtoN rem_after; @@ -902,22 +1101,22 @@ static void OutsideEnableDisable (TextPortionDialogPtr tp) } if (GetStatus (tp->rem_before)) { - Enable (tp->start_text); + Enable (tp->start_marker); Enable (tp->also_rem_before); } else { - Disable (tp->start_text); + Disable (tp->start_marker); Disable (tp->also_rem_before); } if (GetStatus (tp->rem_after)) { - Enable (tp->end_text); + Enable (tp->end_marker); Enable (tp->also_rem_after); } else { - Disable (tp->end_text); + Disable (tp->end_marker); Disable (tp->also_rem_after); } } @@ -940,8 +1139,8 @@ static void ResetTextPortionDialog (TextPortionDialogPtr tp) SetStatus (tp->rem_after, FALSE); SetStatus (tp->also_rem_after, FALSE); } - SetTitle (tp->start_text, ""); - SetTitle (tp->end_text, ""); + PointerToDialog (tp->start_marker, NULL); + PointerToDialog (tp->end_marker, NULL); SetStatus (tp->insensitive, FALSE); SetStatus (tp->whole_word, FALSE); OutsideEnableDisable (tp); @@ -971,18 +1170,13 @@ static void TextPortionToDialog (DialoG d, Pointer data) SetValue (tdlg->end_choice, 1); } } else { - SetStatus (tdlg->rem_before, StringHasNoText (tdata->left_text)); - SetStatus (tdlg->rem_after, StringHasNoText (tdata->right_text)); + SetStatus (tdlg->rem_before, !IsTextMarkerEmpty(tdata->left_marker)); + SetStatus (tdlg->rem_after, !IsTextMarkerEmpty(tdata->right_marker)); SetStatus (tdlg->also_rem_before, tdata->include_left); SetStatus (tdlg->also_rem_after, tdata->include_right); } - if (tdata->left_text != NULL) { - SetTitle (tdlg->start_text, tdata->left_text); - } - if (tdata->right_text != NULL) - { - SetTitle (tdlg->end_text, tdata->right_text); - } + PointerToDialog (tdlg->start_marker, tdata->left_marker); + PointerToDialog (tdlg->end_marker, tdata->right_marker); SetStatus (tdlg->insensitive, !tdata->case_sensitive); SetStatus (tdlg->whole_word, tdata->whole_word); } @@ -1007,24 +1201,24 @@ static Pointer DialogToTextPortion (DialoG d) } else { tdata->include_left = TRUE; } - tdata->left_text = JustSaveStringFromText (tdlg->start_text); + tdata->left_marker = DialogToPointer (tdlg->start_marker); if (GetValue (tdlg->end_choice) == 1) { tdata->include_right = FALSE; } else { tdata->include_right = TRUE; } - tdata->right_text = JustSaveStringFromText (tdlg->end_text); + tdata->right_marker = DialogToPointer (tdlg->end_marker); } else { if (GetStatus (tdlg->rem_before)) { - tdata->left_text = JustSaveStringFromText (tdlg->start_text); + tdata->left_marker = DialogToPointer (tdlg->start_marker); } else { - tdata->left_text = NULL; + tdata->left_marker = NULL; } if (GetStatus (tdlg->rem_after)) { - tdata->right_text = JustSaveStringFromText (tdlg->end_text); + tdata->right_marker = DialogToPointer (tdlg->end_marker); } else { - tdata->right_text = NULL; + tdata->right_marker = NULL; } tdata->include_left = GetStatus (tdlg->also_rem_before); @@ -1050,7 +1244,7 @@ static void TextPortionMessage (DialoG d, Int2 mssg) ResetTextPortionDialog (tp); break; case VIB_MSG_ENTER : - Select (tp->start_text); + Select (tp->start_marker); break; default : break; @@ -1140,7 +1334,7 @@ static GrouP GetTextPortionEndChoiceGroup (DialoG d) } -static DialoG TextPortionDialog (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +NLM_EXTERN DialoG TextPortionDialog (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) { TextPortionDialogPtr tp; GrouP p, g1, g2; @@ -1176,8 +1370,7 @@ static DialoG TextPortionDialog (GrouP h, Boolean inside, Nlm_ChangeNotifyProc c SetValue (tp->start_choice, 1); SetObjectExtra (tp->start_choice, tp, NULL); - tp->start_text = DialogText (g1, "", 10, ChangeTextPortionText); - SetObjectExtra (tp->start_text, tp, NULL); + tp->start_marker = TextMarkerDialog (g1, tp->change_notify, tp->change_userdata); StaticPrompt (g1, "And", 0, popupMenuHeight, programFont, 'r'); tp->end_choice = HiddenGroup (g1, 2, 0, ChangeTextPortionGroup); @@ -1186,21 +1379,18 @@ static DialoG TextPortionDialog (GrouP h, Boolean inside, Nlm_ChangeNotifyProc c SetValue (tp->end_choice, 1); SetObjectExtra (tp->end_choice, tp, NULL); - tp->end_text = DialogText (g1, "", 10, ChangeTextPortionText); - SetObjectExtra (tp->start_text, tp, NULL); + tp->end_marker = TextMarkerDialog (g1, tp->change_notify, tp->change_userdata); } else { tp->rem_before = CheckBox (g1, "Before", ChangeTextPortionBtn); SetObjectExtra (tp->rem_before, tp, NULL); - tp->start_text = DialogText (g1, "", 10, ChangeTextPortionText); - SetObjectExtra (tp->start_text, tp, NULL); + tp->start_marker = TextMarkerDialog (g1, tp->change_notify, tp->change_userdata); tp->also_rem_before = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionBtn); tp->rem_after = CheckBox (g1, "After", ChangeTextPortionBtn); SetObjectExtra (tp->rem_after, tp, NULL); - tp->end_text = DialogText (g1, "", 10, ChangeTextPortionText); - SetObjectExtra (tp->end_text, tp, NULL); + tp->end_marker = TextMarkerDialog (g1, tp->change_notify, tp->change_userdata); tp->also_rem_after = CheckBox (g1, "Also Remove Entered Text", ChangeTextPortionBtn); } @@ -1771,11 +1961,12 @@ NLM_EXTERN Uint2 TwoStepExistingText (Int4 num_found, Boolean non_text, Boolean ppt = StaticPrompt (h, "Separate new text and old text with", 0, dialogTextHeight, programFont, 'c'); - etdd.delim_grp = HiddenGroup (h, 0, 4, NULL); + etdd.delim_grp = HiddenGroup (h, 0, 5, NULL); SetGroupSpacing (etdd.delim_grp, 10, 10); RadioButton (etdd.delim_grp, "Semicolon"); RadioButton (etdd.delim_grp, "Space"); RadioButton (etdd.delim_grp, "Colon"); + RadioButton (etdd.delim_grp, "Comma"); RadioButton (etdd.delim_grp, "Do not separate"); SetValue (etdd.delim_grp, 1); @@ -1821,6 +2012,9 @@ NLM_EXTERN Uint2 TwoStepExistingText (Int4 num_found, Boolean non_text, Boolean existing_text = ExistingTextOption_append_colon; break; case 4: + existing_text = ExistingTextOption_append_comma; + break; + case 5: existing_text = ExistingTextOption_append_none; break; } @@ -1839,6 +2033,9 @@ NLM_EXTERN Uint2 TwoStepExistingText (Int4 num_found, Boolean non_text, Boolean existing_text = ExistingTextOption_prefix_colon; break; case 4: + existing_text = ExistingTextOption_prefix_comma; + break; + case 5: existing_text = ExistingTextOption_prefix_none; break; } @@ -2157,6 +2354,217 @@ NLM_EXTERN DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_ return (DialoG) p; } + +static Boolean IsAllDigits (CharPtr str) + +{ + CharPtr cp; + + if (StringHasNoText (str)) return FALSE; + + cp = str; + while (*cp != 0 && isdigit (*cp)) { + cp++; + } + if (*cp == 0) { + return TRUE; + } else { + return FALSE; + } +} + + +typedef struct enddistancedialog +{ + DIALOG_MESSAGE_BLOCK + PopuP dist_type; + TexT dist_val; + + Nlm_ChangeNotifyProc change_notify; + Pointer change_userdata; +} EndDistanceDialogData, PNTR EndDistanceDialogPtr; + + +static void ChangeEndDistanceDialogPopup (PopuP p) +{ + EndDistanceDialogPtr dlg; + Int2 val; + + dlg = (EndDistanceDialogPtr) GetObjectExtra (p); + if (dlg == NULL) { + return; + } + + val = GetValue (dlg->dist_type); + if (val == 2 || val == 3 || val == 4) { + Show (dlg->dist_val); + } else { + Hide (dlg->dist_val); + } + + if (dlg->change_notify != NULL) { + (dlg->change_notify) (dlg->change_userdata); + } +} + + +static void ChangeEndDistanceDialogTexT (TexT t) +{ + EndDistanceDialogPtr dlg; + + dlg = (EndDistanceDialogPtr) GetObjectExtra (t); + if (dlg != NULL && dlg->change_notify != NULL) { + (dlg->change_notify) (dlg->change_userdata); + } +} + + +static void EndDistanceToDialog (DialoG d, Pointer data) +{ + EndDistanceDialogPtr dlg; + ValNodePtr v; + Char buf[15]; + + dlg = (EndDistanceDialogPtr) GetObjectExtra (d); + if (dlg == NULL) return; + + v = (ValNodePtr) data; + if (v == NULL) { + SetValue (dlg->dist_type, 1); + SetTitle (dlg->dist_val, ""); + Hide (dlg->dist_val); + } else { + switch (v->choice) { + case LocationPosConstraint_dist_from_end: + SetValue (dlg->dist_type, 2); + sprintf (buf, "%d", v->data.intvalue); + SetTitle (dlg->dist_val, buf); + Show (dlg->dist_val); + break; + case LocationPosConstraint_max_dist_from_end: + SetValue (dlg->dist_type, 3); + sprintf (buf, "%d", v->data.intvalue); + SetTitle (dlg->dist_val, buf); + Show (dlg->dist_val); + break; + case LocationPosConstraint_min_dist_from_end: + SetValue (dlg->dist_type, 4); + sprintf (buf, "%d", v->data.intvalue); + SetTitle (dlg->dist_val, buf); + Show (dlg->dist_val); + break; + default: + SetValue (dlg->dist_type, 1); + SetTitle (dlg->dist_val, ""); + Hide (dlg->dist_val); + break; + } + } +} + + +static Pointer DialogToEndDistance (DialoG d) +{ + EndDistanceDialogPtr dlg; + Int2 val; + ValNodePtr v = NULL; + CharPtr str; + + dlg = (EndDistanceDialogPtr) GetObjectExtra (d); + if (dlg == NULL) return NULL; + + val = GetValue (dlg->dist_type); + if (val == 2 || val == 3 || val == 4 + && !TextHasNoText(dlg->dist_val)) + { + str = SaveStringFromText (dlg->dist_val); + if (IsAllDigits (str)) { + v = ValNodeNew (NULL); + switch (val) { + case 2: + v->choice = LocationPosConstraint_dist_from_end; + break; + case 3: + v->choice = LocationPosConstraint_max_dist_from_end; + break; + case 4: + v->choice = LocationPosConstraint_min_dist_from_end; + break; + } + str = SaveStringFromText (dlg->dist_val); + v->data.intvalue = atoi (str); + } + str = MemFree (str); + } + return v; +} + + +static ValNodePtr TestEndDistanceDialog (DialoG d) +{ + EndDistanceDialogPtr dlg; + Int2 val; + CharPtr str; + ValNodePtr err_list = NULL; + + dlg = (EndDistanceDialogPtr) GetObjectExtra (d); + if (dlg != NULL) { + val = GetValue (dlg->dist_type); + if (val == 2 || val == 3 || val == 4) { + if (TextHasNoText (dlg->dist_val)) { + ValNodeAddPointer (&err_list, 0, "No distance value"); + } else { + str = SaveStringFromText (dlg->dist_val); + if (!IsAllDigits (str)) { + ValNodeAddPointer (&err_list, 0, "Non-numeric value"); + } + } + } + } + + return err_list; +} + + +NLM_EXTERN DialoG EndDistanceDialog (GrouP h, CharPtr title, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) + +{ + EndDistanceDialogPtr dlg; + GrouP p; + + dlg = (EndDistanceDialogPtr) MemNew (sizeof (EndDistanceDialogData)); + if (dlg == NULL) + { + return NULL; + } + + p = HiddenGroup (h, 4, 0, NULL); + SetObjectExtra (p, dlg, StdCleanupExtraProc); + + dlg->dialog = (DialoG) p; + dlg->todialog = EndDistanceToDialog; + dlg->fromdialog = DialogToEndDistance; + dlg->testdialog = TestEndDistanceDialog; + dlg->change_notify = change_notify; + dlg->change_userdata = change_userdata; + + StaticPrompt (p, "Where end of sequence is ", 0, dialogTextHeight, systemFont, 'l'); + dlg->dist_type = PopupList (p, TRUE, ChangeEndDistanceDialogPopup); + SetObjectExtra (dlg->dist_type, dlg, NULL); + PopupItem (dlg->dist_type, "Any distance"); + PopupItem (dlg->dist_type, "Exactly"); + PopupItem (dlg->dist_type, "No more than"); + PopupItem (dlg->dist_type, "No less than"); + SetValue (dlg->dist_type, 1); + dlg->dist_val = DialogText (p, "", 5, ChangeEndDistanceDialogTexT); + SetObjectExtra (dlg->dist_val, dlg, NULL); + Hide (dlg->dist_val); + StaticPrompt (p, title, 0, dialogTextHeight, systemFont, 'l'); + + return (DialoG) p; +} + + typedef struct locationconstraintdialog { DIALOG_MESSAGE_BLOCK @@ -2164,6 +2572,9 @@ typedef struct locationconstraintdialog PopuP sequence_type; PopuP partial5; PopuP partial3; + PopuP location_type; + DialoG dist5; + DialoG dist3; Nlm_ChangeNotifyProc change_notify; Pointer change_userdata; @@ -2195,6 +2606,9 @@ static void LocationConstraintToDialog (DialoG d, Pointer data) SetValue (dlg->sequence_type, 1); SetValue (dlg->partial5, 1); SetValue (dlg->partial3, 1); + SetValue (dlg->location_type, 1); + PointerToDialog (dlg->dist5, NULL); + PointerToDialog (dlg->dist3, NULL); } else { switch (l->strand) { case Strand_constraint_any: @@ -2246,6 +2660,22 @@ static void LocationConstraintToDialog (DialoG d, Pointer data) SetValue (dlg->partial3, 3); break; } + switch (l->location_type) { + case Location_type_constraint_any: + SetValue (dlg->location_type, 1); + break; + case Location_type_constraint_single_interval: + SetValue (dlg->location_type, 2); + break; + case Location_type_constraint_joined: + SetValue (dlg->location_type, 3); + break; + case Location_type_constraint_ordered: + SetValue (dlg->location_type, 4); + break; + } + PointerToDialog (dlg->dist5, l->end5); + PointerToDialog (dlg->dist3, l->end3); } ChangeLocationConstraintDialogPopup (dlg->strand); } @@ -2310,6 +2740,22 @@ static Pointer DialogToLocationConstraint (DialoG d) l->partial3 = Partial_constraint_complete; break; } + switch (GetValue (dlg->location_type)) { + case 1: + l->location_type = Location_type_constraint_any; + break; + case 2: + l->location_type = Location_type_constraint_single_interval; + break; + case 3: + l->location_type = Location_type_constraint_joined; + break; + case 4: + l->location_type = Location_type_constraint_ordered; + break; + } + l->end5 = DialogToPointer (dlg->dist5); + l->end3 = DialogToPointer (dlg->dist3); } if (IsLocationConstraintEmpty (l)) { l = LocationConstraintFree (l); @@ -2322,23 +2768,27 @@ static ValNodePtr TestLocationConstraintDialog (DialoG d) { LocationConstraintDialogPtr dlg; ValNodePtr err_list = NULL; + LocationConstraintPtr lcp; dlg = (LocationConstraintDialogPtr) GetObjectExtra (d); if (dlg != NULL) { - if (GetValue (dlg->sequence_type) == 1 && GetValue (dlg->strand) == 1 - && GetValue (dlg->partial5) == 1 && GetValue (dlg->partial3) == 1) { - ValNodeAddPointer (&err_list, 0, "empty location constraint"); + lcp = DialogToPointer (d); + if (IsLocationConstraintEmpty (lcp)) { + ValNodeAddPointer (&err_list, 0, "location constraint empty"); } + lcp = LocationConstraintFree (lcp); + ValNodeLink (&err_list, TestDialog (dlg->dist5)); + ValNodeLink (&err_list, TestDialog (dlg->dist3)); } return err_list; } -extern DialoG LocationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +NLM_EXTERN DialoG LocationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) { LocationConstraintDialogPtr dlg; - GrouP p; + GrouP p, g1, g2; dlg = (LocationConstraintDialogPtr) MemNew (sizeof (LocationConstraintDialogData)); if (dlg == NULL) @@ -2346,7 +2796,8 @@ extern DialoG LocationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_not return NULL; } - p = HiddenGroup (h, 4, 0, NULL); + p = HiddenGroup (h, -1, 0, NULL); + SetGroupSpacing (p, 10, 10); SetObjectExtra (p, dlg, StdCleanupExtraProc); dlg->dialog = (DialoG) p; @@ -2356,38 +2807,56 @@ extern DialoG LocationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_not dlg->change_notify = change_notify; dlg->change_userdata = change_userdata; - StaticPrompt (p, "on", 0, dialogTextHeight, systemFont, 'l'); - dlg->strand = PopupList (p, TRUE, ChangeLocationConstraintDialogPopup); + g1 = HiddenGroup (p, 4, 0, NULL); + SetGroupSpacing (g1, 10, 10); + StaticPrompt (g1, "on", 0, dialogTextHeight, systemFont, 'l'); + dlg->strand = PopupList (g1, TRUE, ChangeLocationConstraintDialogPopup); SetObjectExtra (dlg->strand, dlg, NULL); PopupItem (dlg->strand, "Any strand"); PopupItem (dlg->strand, "Plus strand"); PopupItem (dlg->strand, "Minus strand"); SetValue (dlg->strand, 1); - StaticPrompt (p, "on", 0, dialogTextHeight, systemFont, 'l'); - dlg->sequence_type = PopupList (p, TRUE, ChangeLocationConstraintDialogPopup); + StaticPrompt (g1, "on", 0, dialogTextHeight, systemFont, 'l'); + dlg->sequence_type = PopupList (g1, TRUE, ChangeLocationConstraintDialogPopup); SetObjectExtra (dlg->sequence_type, dlg, NULL); PopupItem (dlg->sequence_type, "nucleotide and protein sequences"); PopupItem (dlg->sequence_type, "nucleotide sequences only"); PopupItem (dlg->sequence_type, "protein sequences only"); SetValue (dlg->sequence_type, 1); - StaticPrompt (p, "5' end", 0, dialogTextHeight, systemFont, 'l'); - dlg->partial5 = PopupList (p, TRUE, ChangeLocationConstraintDialogPopup); + StaticPrompt (g1, "5' end", 0, dialogTextHeight, systemFont, 'l'); + dlg->partial5 = PopupList (g1, TRUE, ChangeLocationConstraintDialogPopup); SetObjectExtra (dlg->partial5, dlg, NULL); PopupItem (dlg->partial5, "Partial or Complete"); PopupItem (dlg->partial5, "Partial"); PopupItem (dlg->partial5, "Complete"); SetValue (dlg->partial5, 1); - StaticPrompt (p, "3' end", 0, dialogTextHeight, systemFont, 'l'); - dlg->partial3 = PopupList (p, TRUE, ChangeLocationConstraintDialogPopup); + StaticPrompt (g1, "3' end", 0, dialogTextHeight, systemFont, 'l'); + dlg->partial3 = PopupList (g1, TRUE, ChangeLocationConstraintDialogPopup); SetObjectExtra (dlg->partial3, dlg, NULL); PopupItem (dlg->partial3, "Partial or Complete"); PopupItem (dlg->partial3, "Partial"); PopupItem (dlg->partial3, "Complete"); SetValue (dlg->partial3, 1); + StaticPrompt (g1, "location type", 0, dialogTextHeight, systemFont, 'l'); + dlg->location_type = PopupList (g1, TRUE, ChangeLocationConstraintDialogPopup); + SetObjectExtra (dlg->location_type, dlg, NULL); + PopupItem (dlg->location_type, "Any"); + PopupItem (dlg->location_type, "Single Interval"); + PopupItem (dlg->location_type, "Joined"); + PopupItem (dlg->location_type, "Ordered"); + SetValue (dlg->location_type, 1); + + g2 = HiddenGroup (p, 0, 2, NULL); + SetGroupSpacing (g2, 10, 10); + dlg->dist5 = EndDistanceDialog (g2, "from 5' end of feature", dlg->change_notify, dlg->change_userdata); + dlg->dist3 = EndDistanceDialog (g2, "from 3' end of feature", dlg->change_notify, dlg->change_userdata); + + AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL); + return (DialoG) p; } @@ -4178,10 +4647,10 @@ static DialoG MolInfoBlockListDialog (GrouP h, CharPtr any_name, Nlm_ChangeNotif vnp->next = val_list; val_list = vnp; } - dlg->technique = ValNodeSelectionDialog (p, val_list, SHORT_SELECTION_LIST, ValNodeStringName, + dlg->technique = ValNodeSelectionDialogExEx (p, val_list, SHORT_SELECTION_LIST, ValNodeStringName, ValNodeSimpleDataFree, ValNodeStringCopy, ValNodeChoiceMatch, "location", - change_notify, change_userdata, FALSE); + change_notify, change_userdata, FALSE, FALSE, TRUE, NULL); /* completedness */ StaticPrompt (p, molinfo_block_labels[2], wid, popupMenuHeight, programFont, 'l'); @@ -4300,8 +4769,7 @@ static Pointer MolInfoBlockFromDialog (DialoG d) return (Pointer) mib; } - -static void ChangeComplexConstraintFieldType (DialoG d, Uint2 qual_type, ValNodePtr rna_type, Int2 feat_type); + NLM_EXTERN DialoG MolInfoBlockDialog (GrouP h, Boolean edit, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) { @@ -4353,12 +4821,17 @@ static DialoG PubFieldDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Point } + + typedef struct PublicationConstraintdlg { DIALOG_MESSAGE_BLOCK PopuP pub_type; DialoG field_type; DialoG string_constraint; + DialoG special_field; + PopuP special_field_type; + Nlm_ChangeNotifyProc change_notify; Pointer change_userdata; } PublicationConstraintDialogData, PNTR PublicationConstraintDialogPtr; @@ -4419,6 +4892,29 @@ static Pointer DialogToPublicationConstraint (DialoG d) } vnp = ValNodeFree (vnp); string_constraint = StringConstraintFree (string_constraint); + + vnp = DialogToPointer (dlg->special_field); + if (vnp != NULL) { + val = GetValue (dlg->special_field_type); + if (val > 1 && val <= k_NumSpecialPubFieldWords + 1) { + constraint->special_field = PubFieldSpecialConstraintNew (); + constraint->special_field->field = vnp->choice; + constraint->special_field->constraint = ValNodeNew (NULL); + switch (val) { + case 2: + constraint->special_field->constraint->choice = PubFieldSpecialConstraintType_is_present; + break; + case 3: + constraint->special_field->constraint->choice = PubFieldSpecialConstraintType_is_not_present; + break; + case 4: + constraint->special_field->constraint->choice = PubFieldSpecialConstraintType_is_all_caps; + break; + } + } + vnp = ValNodeFree (vnp); + } + return (Pointer) constraint; } @@ -4437,6 +4933,8 @@ static void PublicationConstraintToDialog (DialoG d, Pointer data) SetValue (dlg->pub_type, 1); PointerToDialog (dlg->field_type, NULL); PointerToDialog (dlg->string_constraint, NULL); + PointerToDialog (dlg->special_field, NULL); + SetValue (dlg->special_field_type, 1); } else { switch (constraint->type) { case Pub_type_published: @@ -4466,6 +4964,33 @@ static void PublicationConstraintToDialog (DialoG d, Pointer data) PointerToDialog (dlg->field_type, &vn); PointerToDialog (dlg->string_constraint, constraint->field->constraint); } + if (constraint->special_field == NULL) { + PointerToDialog (dlg->special_field, NULL); + SetValue (dlg->special_field_type, 1); + } else { + vn.choice = constraint->special_field->field; + vn.data.ptrvalue = NULL; + vn.next = NULL; + PointerToDialog (dlg->special_field, &vn); + if (constraint->special_field->constraint == NULL) { + SetValue (dlg->special_field_type, 1); + } else { + switch (constraint->special_field->constraint->choice) { + case PubFieldSpecialConstraintType_is_present: + SetValue (dlg->special_field_type, 2); + break; + case PubFieldSpecialConstraintType_is_not_present: + SetValue (dlg->special_field_type, 3); + break; + case PubFieldSpecialConstraintType_is_all_caps: + SetValue (dlg->special_field_type, 4); + break; + default: + SetValue (dlg->special_field_type, 1); + break; + } + } + } } } @@ -4483,7 +5008,7 @@ static ValNodePtr TestPublicationConstraintDialog (DialoG d) } -static void ChangePublicationConstraintPubType (PopuP p) +static void ChangePublicationConstraintPopup (PopuP p) { PublicationConstraintDialogPtr dlg; @@ -4497,7 +5022,8 @@ static void ChangePublicationConstraintPubType (PopuP p) static DialoG PublicationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) { PublicationConstraintDialogPtr dlg; - GrouP p, g1, g2; + GrouP p, g1, g2; + Int4 i; dlg = (PublicationConstraintDialogPtr) MemNew (sizeof (PublicationConstraintDialogData)); if (dlg == NULL) @@ -4518,7 +5044,7 @@ static DialoG PublicationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_ g1 = HiddenGroup (p, 2, 0, NULL); StaticPrompt (g1, "Publication Status", 0, dialogTextHeight, programFont, 'r'); - dlg->pub_type = PopupList (g1, TRUE, ChangePublicationConstraintPubType); + dlg->pub_type = PopupList (g1, TRUE, ChangePublicationConstraintPopup); SetObjectExtra (dlg->pub_type, dlg, NULL); PopupItem (dlg->pub_type, "Any"); PopupItem (dlg->pub_type, "Published"); @@ -4531,12 +5057,210 @@ static DialoG PublicationConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_ dlg->field_type = PubFieldDialog (g2, change_notify, change_userdata); dlg->string_constraint = StringConstraintDialog (g2, NULL, FALSE, change_notify, change_userdata); + dlg->special_field = PubFieldDialog (g2, change_notify, change_userdata); + dlg->special_field_type = PopupList (g2, TRUE, ChangePublicationConstraintPopup); + SetObjectExtra (dlg->special_field_type, dlg, NULL); + PopupItem (dlg->special_field_type, "Any"); + for (i = 0; i < k_NumSpecialPubFieldWords; i++) { + PopupItem (dlg->special_field_type, s_SpecialPubFieldWords[i]); + } + SetValue (dlg->special_field_type, 1); + AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, NULL); return (DialoG) p; } + +typedef struct quantityconstraintdlg { + DIALOG_MESSAGE_BLOCK + PopuP quantity_type; + TexT quantity; + + Nlm_ChangeNotifyProc change_notify; + Pointer change_userdata; +} QuantityConstraintDlgDaga, PNTR QuantityConstraintDlgPtr; + + +static void QuantityConstraintToDialog (DialoG d, Pointer data) +{ + QuantityConstraintDlgPtr dlg; + ValNodePtr vnp; + Char buf[15]; + + dlg = (QuantityConstraintDlgPtr) GetObjectExtra (d); + + if (dlg == NULL) { + return; + } + + vnp = (ValNodePtr) data; + if (vnp == NULL) { + SetValue (dlg->quantity_type, 1); + Hide (dlg->quantity); + } else if (vnp->choice == QuantityConstraint_equals) { + SetValue (dlg->quantity_type, 2); + sprintf (buf, "%d", vnp->data.intvalue); + SetTitle (dlg->quantity, buf); + Show (dlg->quantity); + } else if (vnp->choice == QuantityConstraint_greater_than) { + SetValue (dlg->quantity_type, 3); + sprintf (buf, "%d", vnp->data.intvalue); + SetTitle (dlg->quantity, buf); + Show (dlg->quantity); + } else if (vnp->choice == QuantityConstraint_less_than) { + SetValue (dlg->quantity_type, 4); + sprintf (buf, "%d", vnp->data.intvalue); + SetTitle (dlg->quantity, buf); + Show (dlg->quantity); + } else { + SetValue (dlg->quantity_type, 1); + Hide (dlg->quantity); + } +} + + +static Pointer DialogToQuantityConstraint (DialoG d) +{ + QuantityConstraintDlgPtr dlg; + ValNodePtr vnp = NULL; + Int2 val; + CharPtr num_text; + + dlg = (QuantityConstraintDlgPtr) GetObjectExtra (d); + + if (dlg == NULL) { + return NULL; + } + + if (!TextHasNoText (dlg->quantity)) { + num_text = SaveStringFromText (dlg->quantity); + if (IsAllDigits(num_text)) { + val = GetValue (dlg->quantity_type); + switch (val) { + case 2: + vnp = ValNodeNew (NULL); + vnp->choice = QuantityConstraint_equals; + vnp->data.intvalue = atoi (num_text); + break; + case 3: + vnp = ValNodeNew (NULL); + vnp->choice = QuantityConstraint_greater_than; + vnp->data.intvalue = atoi (num_text); + break; + case 4: + vnp = ValNodeNew (NULL); + vnp->choice = QuantityConstraint_less_than; + vnp->data.intvalue = atoi (num_text); + break; + } + } + num_text = MemFree (num_text); + } + return vnp; +} + + +static ValNodePtr TestQuantityConstraintDialog (DialoG d) +{ + QuantityConstraintDlgPtr dlg; + Int2 val; + CharPtr num_text; + ValNodePtr err_list = NULL; + + dlg = (QuantityConstraintDlgPtr) GetObjectExtra (d); + if (dlg != NULL) { + val = GetValue (dlg->quantity_type); + if (val > 1 && val <= k_NumQuantityWords + 1) { + if (TextHasNoText (dlg->quantity)) { + ValNodeAddPointer (&err_list, 0, "missing value"); + } else { + num_text = SaveStringFromText (dlg->quantity); + if (!IsAllDigits (num_text)) { + ValNodeAddPointer (&err_list, 0, "bad value"); + } + num_text = MemFree (num_text); + } + } + } + return err_list; +} + + +static void ChangeQuantityConstraintQuantityType (PopuP p) +{ + QuantityConstraintDlgPtr dlg; + Int2 val; + + dlg = (QuantityConstraintDlgPtr) GetObjectExtra (p); + if (dlg == NULL) { + return; + } + val = GetValue (dlg->quantity_type); + + if (val < 2 || val > k_NumQuantityWords + 1) { + Hide (dlg->quantity); + } else { + Show (dlg->quantity); + } + if (dlg->change_notify != NULL) { + (dlg->change_notify)(dlg->change_userdata); + } +} + + +static void ChangeQuantityConstraintQuantity (TexT t) +{ + QuantityConstraintDlgPtr dlg; + + dlg = (QuantityConstraintDlgPtr) GetObjectExtra (t); + if (dlg != NULL && dlg->change_notify != NULL) { + (dlg->change_notify)(dlg->change_userdata); + } +} + + +static DialoG QuantityConstraintDialog (GrouP h, CharPtr title, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +{ + QuantityConstraintDlgPtr dlg; + GrouP p; + Int4 i; + + dlg = (QuantityConstraintDlgPtr) MemNew (sizeof (QuantityConstraintDlgDaga)); + if (dlg == NULL) + { + return NULL; + } + + p = HiddenGroup (h, 3, 0, NULL); + SetGroupSpacing (p, 10, 10); + SetObjectExtra (p, dlg, StdCleanupExtraProc); + + dlg->dialog = (DialoG) p; + dlg->todialog = QuantityConstraintToDialog; + dlg->fromdialog = DialogToQuantityConstraint; + dlg->testdialog = TestQuantityConstraintDialog; + + dlg->change_notify = change_notify; + dlg->change_userdata = change_userdata; + + StaticPrompt (p, title, 0, dialogTextHeight, programFont, 'r'); + dlg->quantity_type = PopupList (p, TRUE, ChangeQuantityConstraintQuantityType); + SetObjectExtra (dlg->quantity_type, dlg, NULL); + PopupItem (dlg->quantity_type, "Any"); + for (i = 0; i < k_NumQuantityWords; i++) { + PopupItem (dlg->quantity_type, s_QuantityWords[i]); + } + SetValue (dlg->quantity_type, 1); + dlg->quantity = DialogText (p, "1", 5, ChangeQuantityConstraintQuantity); + SetObjectExtra (dlg->quantity, dlg, NULL); + Hide (dlg->quantity); + + return (DialoG) p; +} + + typedef struct sequenceconstraintdlg { DIALOG_MESSAGE_BLOCK GrouP seqtype; @@ -4544,6 +5268,7 @@ typedef struct sequenceconstraintdlg { DialoG rna_subtype; ButtoN feat_present; DialoG feature_type; + DialoG num_features; DialoG id; Nlm_ChangeNotifyProc change_notify; @@ -4605,6 +5330,7 @@ static void SequenceConstraintToDialog (DialoG d, Pointer data) SetStatus (dlg->feat_present, FALSE); PointerToDialog (dlg->feature_type, NULL); PointerToDialog (dlg->id, NULL); + PointerToDialog (dlg->num_features, NULL); } else { if (constraint->seqtype == NULL) { SetValue (dlg->seqtype, 2); @@ -4655,6 +5381,7 @@ static void SequenceConstraintToDialog (DialoG d, Pointer data) } PointerToDialog (dlg->id, constraint->id); + PointerToDialog (dlg->num_features, constraint->num_features); } ChangeSequenceConstraintButton (dlg->feat_present); } @@ -4716,6 +5443,7 @@ static Pointer SequenceConstraintFromDialog (DialoG d) if (IsStringConstraintEmpty (constraint->id)) { constraint->id = StringConstraintFree (constraint->id); } + constraint->num_features = DialogToPointer (dlg->num_features); return constraint; } @@ -4757,6 +5485,7 @@ static ValNodePtr TestSequenceConstraintDialog (DialoG d) if (IsSequenceConstraintEmpty (constraint)) { ValNodeAddPointer (&err_list, 0, "empty constraint"); } + ValNodeLink (&err_list, TestDialog (dlg->num_features)); constraint = SequenceConstraintFree (constraint); } return err_list; @@ -4803,9 +5532,16 @@ static DialoG SequenceConstraintDialog (GrouP h, Nlm_ChangeNotifyProc change_not SetObjectExtra (dlg->feat_present, dlg, NULL); dlg->feature_type = FeatureTypeDialog (g, change_notify, change_userdata); + dlg->num_features = QuantityConstraintDialog (g, "Number of features present (any type)", change_notify, change_userdata); + dlg->id = StringConstraintDialog (p, "Where sequence ID", FALSE, change_notify, change_userdata); - AlignObjects (ALIGN_CENTER, (HANDLE) dlg->seqtype, (HANDLE) dlg->rna_subtype_grp, (HANDLE) dlg->id, (HANDLE) g, NULL); + AlignObjects (ALIGN_CENTER, (HANDLE) dlg->seqtype, + (HANDLE) dlg->rna_subtype_grp, + (HANDLE) dlg->num_features, + (HANDLE) dlg->id, + (HANDLE) g, + NULL); return (DialoG) p; } @@ -5177,8 +5913,6 @@ static Boolean EditConstraint (ValNodePtr constraint) } -static CharPtr SummarizeConstraint (ValNodePtr constraint); - typedef struct constraintsetdlg { DIALOG_MESSAGE_BLOCK DoC constraint_doc; @@ -5481,7 +6215,7 @@ static void AddConstraintBtn (ButtoN b) } -static DialoG ConstraintSetDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +NLM_EXTERN DialoG ConstraintSetDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) { ConstraintSetDlgPtr dlg; GrouP p, g; @@ -6620,7 +7354,7 @@ static ValNodePtr DefaultFeatureFieldConstraint (Int2 feat_type) } -static void ChangeComplexConstraintFieldType (DialoG d, Uint2 qual_type, ValNodePtr rna_type, Int2 feat_type) +NLM_EXTERN void ChangeComplexConstraintFieldType (DialoG d, Uint2 qual_type, ValNodePtr rna_type, Int2 feat_type) { ComplexConstraintDlgPtr dlg; ValNodePtr default_constraint; @@ -7453,10 +8187,10 @@ static void ChangeStructureCommentFieldChoice (PopuP p) val = GetValue (dlg->field_type); switch (val) { - case 1: + case 2: Hide (dlg->field_name); break; - case 2: + case 1: Show (dlg->field_name); break; case 3: @@ -7486,10 +8220,10 @@ static void StructuredCommentFieldToDialog (DialoG d, Pointer data) } else { switch (field->choice) { case StructuredCommentField_database: - SetValue (dlg->field_type, 1); + SetValue (dlg->field_type, 2); break; case StructuredCommentField_named: - SetValue (dlg->field_type, 2); + SetValue (dlg->field_type, 1); SetTitle (dlg->field_name, field->data.ptrvalue); break; case StructuredCommentField_field_name: @@ -7517,10 +8251,10 @@ static Pointer StructuredCommentFieldFromDialog (DialoG d) val = GetValue (dlg->field_type); switch (val) { - case 1: + case 2: field->choice = StructuredCommentField_database; break; - case 2: + case 1: field->choice = StructuredCommentField_named; field->data.ptrvalue = SaveStringFromText (dlg->field_name); if (StringHasNoText (field->data.ptrvalue)) { @@ -7590,8 +8324,8 @@ static DialoG StructuredCommentFieldDialog (GrouP h, Nlm_ChangeNotifyProc change dlg->field_type = PopupList (p, TRUE, ChangeStructureCommentFieldChoice); SetObjectExtra (dlg->field_type, dlg, NULL); - PopupItem (dlg->field_type, "Database Name"); PopupItem (dlg->field_type, "Field"); + PopupItem (dlg->field_type, "Database Name"); PopupItem (dlg->field_type, "Field Name"); SetValue (dlg->field_type, 1); @@ -8330,43 +9064,6 @@ static DialoG FieldPairTypeDialog (GrouP h, Boolean for_convert, Nlm_ChangeNotif } -static Boolean IsFieldTypeNonText (ValNodePtr field_type) -{ - ValNodePtr vnp; - FeatureFieldPtr ffp; - Boolean rval = FALSE; - - if (field_type == NULL) { - return FALSE; - } - switch (field_type->choice) { - case FieldType_source_qual : - vnp = (ValNodePtr) field_type->data.ptrvalue; - if (vnp != NULL) { - if (vnp->choice == SourceQualChoice_location || vnp->choice == SourceQualChoice_origin) { - rval = TRUE; - } else if (vnp->choice == SourceQualChoice_textqual) { - if (IsNonTextSourceQual (vnp->data.intvalue)) { - rval = TRUE; - } - } - } - break; - case FieldType_feature_field : - ffp = (FeatureFieldPtr) field_type->data.ptrvalue; - if (ffp != NULL && ffp->field != NULL && ffp->field->choice == FeatQualChoice_legal_qual - && ffp->field->data.intvalue == Feat_qual_legal_pseudo) { - rval = TRUE; - } - break; - case FieldType_molinfo_field : - rval = TRUE; - break; - } - return rval; -} - - #define AECR_DLG_BLOCK \ DIALOG_MESSAGE_BLOCK \ DialoG qual_type_dlg; \ @@ -8521,7 +9218,6 @@ typedef struct applyactiondlg { static Pointer DialogToApplyAction (DialoG d) { ApplyActionDlgPtr dlg; - Uint1 qual_type = FieldType_source_qual; ApplyActionPtr apply; dlg = (ApplyActionDlgPtr) GetObjectExtra (d); @@ -8848,6 +9544,7 @@ typedef struct convertactiondlg { ButtoN strip_name; ButtoN keep_original; + DialoG capitalization; DialoG existing_text; } ConvertActionDlgData, PNTR ConvertActionDlgPtr; @@ -8866,11 +9563,13 @@ static void PointerToConvertActionDlg (DialoG d, Pointer data) FieldPairToAECRActionDlg (d, NULL); SetStatus (dlg->strip_name, FALSE); SetStatus (dlg->keep_original, FALSE); + PointerToDialog (dlg->capitalization, NULL); PointerToDialog (dlg->existing_text, NULL); } else { FieldPairToAECRActionDlg (d, convert->fields); SetStatus (dlg->strip_name, convert->strip_name); SetStatus (dlg->keep_original, convert->keep_original); + PointerToDialog (dlg->capitalization, (Pointer) convert->capitalization); PointerToDialog (dlg->existing_text, (Pointer) convert->existing_text); } } @@ -8888,6 +9587,7 @@ static Pointer DialogToConvertAction (DialoG d) convert->fields = DialogToPointer (dlg->field_dlg); convert->strip_name = GetStatus (dlg->strip_name); convert->keep_original = GetStatus (dlg->keep_original); + convert->capitalization = (Uint2) DialogToPointer (dlg->capitalization); convert->existing_text = (Uint2) DialogToPointer (dlg->existing_text); return convert; } @@ -8912,6 +9612,7 @@ static ValNodePtr TestConvertActionDialog (DialoG d) } ValNodeLink (&err_list, TestDialog (dlg->field_dlg)); + ValNodeLink (&err_list, TestDialog (dlg->capitalization)); ValNodeLink (&err_list, TestDialog (dlg->existing_text)); field_pair = DialogToPointer (dlg->field_dlg); @@ -8960,13 +9661,15 @@ ConvertActionDialog dlg->keep_original = CheckBox (g, "Leave on original", NULL); dlg->strip_name = CheckBox (g, "Strip name from text", NULL); + dlg->capitalization = CapChangeDialog(p, change_notify, change_userdata); + if (show_existing_text) { dlg->existing_text = ExistingTextDialog (p, change_notify, change_userdata); } else { dlg->existing_text = NULL; } - AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) dlg->existing_text, NULL); + AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) dlg->capitalization, (HANDLE) dlg->existing_text, NULL); return (DialoG) p; } @@ -9810,20 +10513,112 @@ EditAECRActionDialog } -typedef struct applyfeatureactiondlg { +static SeqFeatPtr CreateFeatureWithImportFeatureQuals (Uint1 featdef_type, ValNodePtr fields) +{ + SeqFeatPtr sfp; + ValNodePtr vnp; + FeatQualLegalValPtr q; + GBQualPtr gbq; + CharPtr qualname, cp; + + sfp = SeqFeatNew(); + sfp->idx.subtype = featdef_type; + sfp->data.choice = FindFeatFromFeatDefType (sfp->idx.subtype); + + for (vnp = fields; vnp != NULL; vnp = vnp->next) { + q = (FeatQualLegalValPtr) vnp->data.ptrvalue; + if (q != NULL && q->qual != Feat_qual_legal_gene && q->qual != Feat_qual_legal_gene_description && q->qual != Feat_qual_legal_note) { + gbq = GBQualNew (); + qualname = StringSave (GetFeatQualName(q->qual)); + cp = StringChr (qualname, '-'); + while (cp != NULL) { + *cp = '_'; + cp = StringChr (cp + 1, '-'); + } + gbq->qual = qualname; + gbq->val = StringSave (q->val); + gbq->next = sfp->qual; + sfp->qual = gbq; + } + } + return sfp; +} + + +static CharPtr FindFeatQualValue (ValNodePtr vnp, Int4 featqual) +{ + FeatQualLegalValPtr q; + CharPtr str = NULL; + while (vnp != NULL && str == NULL) { + q = (FeatQualLegalValPtr) vnp->data.ptrvalue; + if (q != NULL && q->qual == featqual) { + str = q->val; + } + vnp = vnp->next; + } + if (str == NULL) { + str = ""; + } + return str; +} + + +static void SetFeatQualValue (ValNodePtr PNTR fields, Int4 featqual, CharPtr val) +{ + FeatQualLegalValPtr q; + + q = FeatQualLegalValNew (); + q->qual = featqual; + q->val = StringSave (val); + ValNodeAddPointer (fields, 1, q); +} + + +static void AddGBQualsToActionFields (GBQualPtr gbq, ValNodePtr PNTR fields) +{ + Int4 qualtype; + + if (fields == NULL) return; + + while (gbq != NULL) { + qualtype = GetFeatQualByName (gbq->qual); + if (qualtype > -1) { + SetFeatQualValue (fields, qualtype, gbq->val); + } + gbq = gbq->next; + } +} + + +NLM_EXTERN ApplyFeatureDetailsPtr ApplyFeatureDetailsNew (ApplyFeatureActionPtr action) +{ + ApplyFeatureDetailsPtr details; + + details = (ApplyFeatureDetailsPtr) MemNew (sizeof (ApplyFeatureDetailsData)); + + if (action != NULL) { + details->add_mrna = action->add_mrna; + details->fields = AsnIoMemCopy (action->fields, (AsnReadFunc) FeatQualLegalSetAsnRead, (AsnWriteFunc) FeatQualLegalSetAsnWrite); + details->src_fields = AsnIoMemCopy(action->src_fields, (AsnReadFunc) SourceQualValSetAsnRead, (AsnWriteFunc) SourceQualValSetAsnWrite); + } + return details; +} + + +NLM_EXTERN ApplyFeatureDetailsPtr ApplyFeatureDetailsFree (ApplyFeatureDetailsPtr details) +{ + if (details != NULL) { + details->fields = FeatQualLegalSetFree (details->fields); + details->src_fields = SourceQualValSetFree (details->src_fields); + details = MemFree (details); + } + return details; +} + + +typedef struct applyfeaturedetailsdlg { DIALOG_MESSAGE_BLOCK - DialoG feature_type_dlg; - ButtoN apply_to_parts; - TexT only_this_part; - ButtoN partial5; - ButtoN partial3; - GrouP strand_group; - GrouP use_whole_interval; - TexT left_end; - TexT right_end; - GrouP all_or_some_group; - TexT accession_list_txt; - ButtoN add_redundant; + /* for CDS */ ButtoN add_mrna; PopuP reading_frame; @@ -9845,6 +10640,351 @@ typedef struct applyfeatureactiondlg { TexT gene_description; TexT comment; + Uint2 featdef_type; + Nlm_ChangeNotifyProc change_notify; + Pointer change_userdata; +} ApplyFeatureDetailsDlgData, PNTR ApplyFeatureDetailsDlgPtr; + + +static void ApplyFeatureDetailsToDialog (DialoG d, Pointer data) +{ + ApplyFeatureDetailsDlgPtr dlg; + ApplyFeatureDetailsPtr details; + CharPtr txt; + BioSourcePtr biop; + + dlg = (ApplyFeatureDetailsDlgPtr) GetObjectExtra (d); + if (dlg == NULL) { + return; + } + details = (ApplyFeatureDetailsPtr) data; + + if (data == NULL) { + /* for CDS */ + SafeSetStatus (dlg->add_mrna, FALSE); + SafeSetValue (dlg->reading_frame, 4); + SafeSetTitle (dlg->protein_name, ""); + SafeSetTitle (dlg->protein_description, ""); + + /* for RNA */ + PointerToDialog (dlg->ncrna_class, NULL); + SafeSetTitle (dlg->rna_name, ""); + + /* for import features */ + PointerToDialog (dlg->quals, NULL); + + /* for source features */ + PointerToDialog (dlg->src_quals, NULL); + + /* for all */ + SafeSetTitle (dlg->gene_locus, ""); + SafeSetTitle (dlg->gene_description, ""); + SafeSetTitle (dlg->comment, ""); + } else { + /* for CDS */ + SafeSetStatus (dlg->add_mrna, details->add_mrna); + txt = FindFeatQualValue (details->fields, Feat_qual_legal_codon_start); + if (StringICmp (txt, "best") == 0) { + SafeSetValue (dlg->reading_frame, 4); + } else { + SafeSetValue (dlg->reading_frame, atoi (txt)); + } + + SafeSetTitle (dlg->protein_name, FindFeatQualValue (details->fields, Feat_qual_legal_product)); + SafeSetTitle (dlg->protein_description, FindFeatQualValue (details->fields, Feat_qual_legal_description)); + + /* for source feature */ + biop = BioSourceFromSourceQualVals (details->src_fields); + PointerToDialog (dlg->src_quals, biop); + biop = BioSourceFree (biop); + + /* for RNA */ + PointerToDialog (dlg->ncrna_class, FindFeatQualValue (details->fields, Feat_qual_legal_ncRNA_class)); + SafeSetTitle (dlg->rna_name, FindFeatQualValue (details->fields, Feat_qual_legal_product)); + + /* for all */ + SafeSetTitle (dlg->gene_locus, FindFeatQualValue (details->fields, Feat_qual_legal_gene)); + SafeSetTitle (dlg->gene_description, FindFeatQualValue (details->fields, Feat_qual_legal_gene_description)); + SafeSetTitle (dlg->comment, FindFeatQualValue (details->fields, Feat_qual_legal_note)); + } + + if (dlg->change_notify != NULL) { + (dlg->change_notify) (dlg->change_userdata); + } +} + +static Pointer DialogToApplyFeatureDetails (DialoG d) +{ + ApplyFeatureDetailsDlgPtr dlg; + ApplyFeatureDetailsPtr details; + CharPtr txt; + Char num[15]; + Int4 frame; + GBQualPtr gbq; + BioSourcePtr biop; + + dlg = (ApplyFeatureDetailsDlgPtr) GetObjectExtra (d); + if (dlg == NULL) { + return NULL; + } + + details = ApplyFeatureDetailsNew (NULL); + + /* for CDS */ + if (dlg->add_mrna != NULL && GetStatus (dlg->add_mrna)) { + details->add_mrna = TRUE; + } else { + details->add_mrna = FALSE; + } + + if (dlg->reading_frame != NULL) { + frame = GetValue (dlg->reading_frame); + if (frame > 0 && frame < 4) { + sprintf (num, "%d", frame); + SetFeatQualValue (&(details->fields), Feat_qual_legal_codon_start, num); + } else { + SetFeatQualValue (&(details->fields), Feat_qual_legal_codon_start, "best"); + } + } + + if (dlg->protein_name != NULL && !TextHasNoText (dlg->protein_name)) { + txt = SaveStringFromText (dlg->protein_name); + SetFeatQualValue (&(details->fields), Feat_qual_legal_product, txt); + txt = MemFree (txt); + } + if (dlg->protein_name != NULL && !TextHasNoText (dlg->protein_description)) { + txt = SaveStringFromText (dlg->protein_description); + SetFeatQualValue (&(details->fields), Feat_qual_legal_description, txt); + txt = MemFree (txt); + } + + /* for RNA */ + if (dlg->ncrna_class != NULL) { + txt = DialogToPointer (dlg->ncrna_class); + if (!StringHasNoText (txt)) { + SetFeatQualValue (&(details->fields), Feat_qual_legal_ncRNA_class, txt); + } + txt = MemFree (txt); + } + if (dlg->rna_name != NULL && !TextHasNoText (dlg->rna_name)) { + txt = SaveStringFromText (dlg->rna_name); + SetFeatQualValue (&(details->fields), Feat_qual_legal_product, txt); + txt = MemFree (txt); + } + + /* for source features */ + if (dlg->src_quals != NULL) { + biop = DialogToPointer (dlg->src_quals); + details->src_fields = SourceQualValsFromBioSourcePtr (biop); + biop = BioSourceFree (biop); + } + + /* for import features */ + if (dlg->quals != NULL) { + gbq = DialogToPointer (dlg->quals); + AddGBQualsToActionFields (gbq, &(details->fields)); + gbq = GBQualFree (gbq); + } + + /* for all */ + if (dlg->gene_locus != NULL && !TextHasNoText (dlg->gene_locus)) { + txt = SaveStringFromText (dlg->gene_locus); + SetFeatQualValue (&(details->fields), Feat_qual_legal_gene, txt); + txt = MemFree (txt); + } + if (dlg->gene_description != NULL && !TextHasNoText (dlg->gene_description)) { + txt = SaveStringFromText (dlg->gene_description); + SetFeatQualValue (&(details->fields), Feat_qual_legal_gene_description, txt); + txt = MemFree (txt); + } + if (dlg->comment != NULL && !TextHasNoText (dlg->comment)) { + txt = SaveStringFromText (dlg->comment); + SetFeatQualValue (&(details->fields), Feat_qual_legal_note, txt); + txt = MemFree (txt); + } + + return (Pointer) details; +} + +static void AddTextToComment (ButtoN b, CharPtr text) +{ + ApplyFeatureDetailsDlgPtr dlg; + CharPtr orig_comment; + CharPtr new_comment; + + dlg = (ApplyFeatureDetailsDlgPtr) GetObjectExtra (b); + if (dlg == NULL || StringHasNoText (text)) + { + return; + } + + orig_comment = SaveStringFromText (dlg->comment); + if (StringHasNoText (orig_comment)) + { + SetTitle (dlg->comment, text); + } + else + { + new_comment = (CharPtr) MemNew ((StringLen (orig_comment) + StringLen (text) + 3) * sizeof (Char)); + if (new_comment != NULL) + { + StringCpy (new_comment, orig_comment); + StringCat (new_comment, "; "); + StringCat (new_comment, text); + SetTitle (dlg->comment, new_comment); + new_comment = MemFree (new_comment); + } + } + orig_comment = MemFree (orig_comment); +} + + +static void Add18SITS28SToComment (ButtoN b) +{ + AddTextToComment (b, "contains 18S ribosomal RNA, internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed spacer 2, and 28S ribosomal RNA"); +} + + +static void Add16SIGS23SToComment (ButtoN b) +{ + AddTextToComment (b, "contains 16S ribosomal RNA, 16S-23S ribosomal RNA intergenic spacer, and 23S ribosomal RNA"); +} + + +static void ChangeApplyFeatureDetailsBtn (ButtoN b) +{ + ApplyFeatureDetailsDlgPtr dlg; + + dlg = (ApplyFeatureDetailsDlgPtr) GetObjectExtra (b); + if (dlg == NULL) { + return; + } + + if (dlg->change_notify != NULL) { + (dlg->change_notify) (dlg->change_userdata); + } +} + + +NLM_EXTERN DialoG ApplyFeatureDetailsDialog (GrouP h, Uint1 featdef_type, ApplyFeatureDetailsPtr details, Boolean indexer_version, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +{ + ApplyFeatureDetailsDlgPtr dlg; + GrouP p; + GrouP r, frame_grp = NULL, comment_btns_grp = NULL; + ButtoN comment_btn; + Int4 seqfeattype; + SeqFeatPtr sfp; + + dlg = (ApplyFeatureDetailsDlgPtr) MemNew (sizeof (ApplyFeatureDetailsDlgData)); + p = HiddenGroup (h, -1, 0, NULL); + SetGroupSpacing (p, 10, 10); + SetObjectExtra (p, dlg, StdCleanupExtraProc); + + dlg->dialog = (DialoG) p; + dlg->todialog = ApplyFeatureDetailsToDialog; + dlg->fromdialog = DialogToApplyFeatureDetails; + dlg->dialogmessage = NULL; + dlg->change_notify = change_notify; + dlg->change_userdata = change_userdata; + + dlg->featdef_type = featdef_type; + + seqfeattype = FindFeatFromFeatDefType (featdef_type); + + if (featdef_type == FEATDEF_CDS) { + if (indexer_version) { + dlg->add_mrna = CheckBox (p, "Also add mRNA", ChangeApplyFeatureDetailsBtn); + SetObjectExtra (dlg->add_mrna, dlg, NULL); + } + + frame_grp = HiddenGroup (p, 2, 0, NULL); + StaticPrompt (frame_grp, "Reading Frame", 0, dialogTextHeight, programFont, 'l'); + dlg->reading_frame = PopupList (frame_grp, TRUE, NULL); + PopupItem (dlg->reading_frame, "1"); + PopupItem (dlg->reading_frame, "2"); + PopupItem (dlg->reading_frame, "3"); + PopupItem (dlg->reading_frame, "Best"); + SetValue (dlg->reading_frame, 4); + } else if (featdef_type == FEATDEF_source) { + dlg->src_quals = BioSourceDialog (p); + } + + r = HiddenGroup (p, 2, 0, NULL); + if (featdef_type == FEATDEF_CDS) { + + StaticPrompt (r, "Protein Name", 0, dialogTextHeight, programFont, 'l'); + dlg->protein_name = DialogText (r, "", 20, NULL); + StaticPrompt (r, "Protein Description", 0, dialogTextHeight, programFont, 'l'); + dlg->protein_description = DialogText (r, "", 20, NULL); + } else if (seqfeattype == SEQFEAT_RNA) { + /* RNA name */ + StaticPrompt (r, "RNA Name", 0, dialogTextHeight, programFont, 'l'); + dlg->rna_name = DialogText (r, "", 20, NULL); + /* ncRNA class */ + if (featdef_type == FEATDEF_ncRNA) { + StaticPrompt (r, "ncRNA Class", 0, dialogTextHeight, programFont, 'l'); + dlg->ncrna_class = CreatencRNAClassDialog (r, FALSE, NULL, NULL); + } + } else if (featdef_type != FEATDEF_GENE && featdef_type != FEATDEF_source) { + StaticPrompt (r, "Qualifiers", 0, dialogTextHeight, programFont, 'l'); + sfp = CreateFeatureWithImportFeatureQuals (featdef_type, details == NULL ? NULL : details->fields); + dlg->quals = NewCreateImportFields (r, GetFeatureNameFromFeatureType (GetFeatureTypeFromFeatdef(featdef_type)), sfp, FALSE); + sfp = SeqFeatFree (sfp); + } + + /* gene qualifiers ( for all ) */ + StaticPrompt (r, "Gene Locus", 0, dialogTextHeight, programFont, 'l'); + dlg->gene_locus = DialogText (r, "", 20, NULL); + StaticPrompt (r, "Gene Description", 0, dialogTextHeight, programFont, 'l'); + dlg->gene_description = DialogText (r, "", 20, NULL); + StaticPrompt (r, "Comment", 0, dialogTextHeight, programFont, 'l'); + dlg->comment = DialogText (r, "", 20, NULL); + if ((featdef_type == FEATDEF_otherRNA || featdef_type == FEATDEF_misc_RNA) && indexer_version) { + comment_btns_grp = HiddenGroup (p, 2, 0, NULL); + comment_btn = PushButton (comment_btns_grp, "Add '18S-ITS-5.8S-ITS-28S' to comment", Add18SITS28SToComment); + SetObjectExtra (comment_btn, dlg, NULL); + comment_btn = PushButton (comment_btns_grp, "Add '16S-IGS-23S' to comment", Add16SIGS23SToComment); + SetObjectExtra (comment_btn, dlg, NULL); + } + + if (frame_grp != NULL) { + AlignObjects (ALIGN_CENTER, (HANDLE) r, + (HANDLE) frame_grp, + (HANDLE) dlg->add_mrna, + NULL); + } else if (comment_btns_grp != NULL) { + AlignObjects (ALIGN_CENTER, (HANDLE) r, + (HANDLE) comment_btns_grp, + NULL); + } else if (dlg->src_quals != NULL) { + AlignObjects (ALIGN_CENTER, (HANDLE) r, + (HANDLE) dlg->src_quals, + NULL); + } else { + AlignObjects (ALIGN_CENTER, (HANDLE) r, + NULL); + } + return (DialoG) p; +} + + +typedef struct applyfeatureactiondlg { + DIALOG_MESSAGE_BLOCK + DialoG feature_type_dlg; + ButtoN apply_to_parts; + TexT only_this_part; + ButtoN partial5; + ButtoN partial3; + GrouP strand_group; + GrouP use_whole_interval; + TexT left_end; + TexT right_end; + GrouP all_or_some_group; + TexT accession_list_txt; + ButtoN add_redundant; + + DialoG details; + Nlm_ChangeNotifyProc change_notify; Pointer change_userdata; @@ -9949,83 +11089,6 @@ static ValNodePtr SequenceListCollect (CharPtr txt) } -static CharPtr FindFeatQualValue (ValNodePtr vnp, Int4 featqual) -{ - FeatQualLegalValPtr q; - CharPtr str = NULL; - while (vnp != NULL && str == NULL) { - q = (FeatQualLegalValPtr) vnp->data.ptrvalue; - if (q != NULL && q->qual == featqual) { - str = q->val; - } - vnp = vnp->next; - } - if (str == NULL) { - str = ""; - } - return str; -} - - -static void SetFeatQualValue (ValNodePtr PNTR fields, Int4 featqual, CharPtr val) -{ - FeatQualLegalValPtr q; - - q = FeatQualLegalValNew (); - q->qual = featqual; - q->val = StringSave (val); - ValNodeAddPointer (fields, 1, q); -} - - -static SeqFeatPtr CreateFeatureWithImportFeatureQuals (ApplyFeatureActionPtr action) -{ - SeqFeatPtr sfp; - ValNodePtr vnp; - FeatQualLegalValPtr q; - GBQualPtr gbq; - CharPtr qualname, cp; - - sfp = SeqFeatNew(); - sfp->idx.subtype = GetFeatdefFromFeatureType (action->type); - sfp->data.choice = FindFeatFromFeatDefType (sfp->idx.subtype); - - for (vnp = action->fields; vnp != NULL; vnp = vnp->next) { - q = (FeatQualLegalValPtr) vnp->data.ptrvalue; - if (q != NULL && q->qual != Feat_qual_legal_gene && q->qual != Feat_qual_legal_gene_description && q->qual != Feat_qual_legal_note) { - gbq = GBQualNew (); - qualname = StringSave (GetFeatQualName(q->qual)); - cp = StringChr (qualname, '-'); - while (cp != NULL) { - *cp = '_'; - cp = StringChr (cp + 1, '-'); - } - gbq->qual = qualname; - gbq->val = StringSave (q->val); - gbq->next = sfp->qual; - sfp->qual = gbq; - } - } - return sfp; -} - - -static void AddGBQualsToActionFields (GBQualPtr gbq, ApplyFeatureActionPtr action) -{ - Int4 qualtype; - - if (action == NULL) return; - - while (gbq != NULL) { - qualtype = GetFeatQualByName (gbq->qual); - if (qualtype > -1) { - SetFeatQualValue (&(action->fields), qualtype, gbq->val); - } - gbq = gbq->next; - } -} - - static void ApplyFeatureActionToDialog (DialoG d, Pointer data) { ApplyFeatureActionDlgPtr dlg; @@ -10034,7 +11097,7 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data) LocationIntervalPtr lint; CharPtr txt; ValNode vn; - BioSourcePtr biop; + ApplyFeatureDetailsPtr details; dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d); if (dlg == NULL) { @@ -10057,26 +11120,6 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data) SetTitle (dlg->accession_list_txt, ""); SetStatus (dlg->add_redundant, FALSE); - /* for CDS */ - SafeSetStatus (dlg->add_mrna, FALSE); - SafeSetValue (dlg->reading_frame, 4); - SafeSetTitle (dlg->protein_name, ""); - SafeSetTitle (dlg->protein_description, ""); - - /* for RNA */ - PointerToDialog (dlg->ncrna_class, NULL); - SafeSetTitle (dlg->rna_name, ""); - - /* for import features */ - PointerToDialog (dlg->quals, NULL); - - /* for source features */ - PointerToDialog (dlg->src_quals, NULL); - - /* for all */ - SafeSetTitle (dlg->gene_locus, ""); - SafeSetTitle (dlg->gene_description, ""); - SafeSetTitle (dlg->comment, ""); } else { vn.choice = (Uint1) action->type; vn.next = NULL; @@ -10103,15 +11146,25 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data) SetTitle (dlg->right_end, ""); } else { SetValue (dlg->use_whole_interval, 2); - lint = (LocationIntervalPtr) action->location->data.ptrvalue; - if (lint == NULL) { - SetTitle (dlg->left_end, ""); - SetTitle (dlg->right_end, ""); - } else { - sprintf (num, "%d", lint->from); + if (action->location->choice == LocationChoice_interval) { + lint = (LocationIntervalPtr) action->location->data.ptrvalue; + if (lint == NULL) { + SetTitle (dlg->left_end, ""); + SetTitle (dlg->right_end, ""); + } else { + sprintf (num, "%d", lint->from); + SetTitle (dlg->left_end, num); + sprintf (num, "%d", lint->to); + SetTitle (dlg->right_end, num); + } + } else if (action->location->choice == LocationChoice_point) { + sprintf (num, "%d^", action->location->data.intvalue); SetTitle (dlg->left_end, num); - sprintf (num, "%d", lint->to); + sprintf (num, "%d", action->location->data.intvalue + 1); SetTitle (dlg->right_end, num); + } else { + SetTitle (dlg->left_end, ""); + SetTitle (dlg->right_end, ""); } } @@ -10126,34 +11179,11 @@ static void ApplyFeatureActionToDialog (DialoG d, Pointer data) } SetStatus (dlg->add_redundant, action->add_redundant); - - /* for CDS */ - SafeSetStatus (dlg->add_mrna, action->add_mrna); - txt = FindFeatQualValue (action->fields, Feat_qual_legal_codon_start); - if (StringICmp (txt, "best") == 0) { - SafeSetValue (dlg->reading_frame, 4); - } else { - SafeSetValue (dlg->reading_frame, atoi (txt)); - } - - SafeSetTitle (dlg->protein_name, FindFeatQualValue (action->fields, Feat_qual_legal_product)); - SafeSetTitle (dlg->protein_description, FindFeatQualValue (action->fields, Feat_qual_legal_description)); - - /* for source feature */ - biop = BioSourceFromSourceQualVals (action->src_fields); - PointerToDialog (dlg->src_quals, biop); - biop = BioSourceFree (biop); - - /* for RNA */ - PointerToDialog (dlg->ncrna_class, FindFeatQualValue (action->fields, Feat_qual_legal_ncRNA_class)); - SafeSetTitle (dlg->rna_name, FindFeatQualValue (action->fields, Feat_qual_legal_product)); - - /* for all */ - SafeSetTitle (dlg->gene_locus, FindFeatQualValue (action->fields, Feat_qual_legal_gene)); - SafeSetTitle (dlg->gene_description, FindFeatQualValue (action->fields, Feat_qual_legal_gene_description)); - SafeSetTitle (dlg->comment, FindFeatQualValue (action->fields, Feat_qual_legal_note)); } + details = ApplyFeatureDetailsNew (action); + PointerToDialog (dlg->details, details); + details = ApplyFeatureDetailsFree (details); ChangeApplyFeatureActionDlg (dlg); if (dlg->change_notify != NULL) { (dlg->change_notify) (dlg->change_userdata); @@ -10165,13 +11195,10 @@ static Pointer DialogToApplyFeatureAction (DialoG d) { ApplyFeatureActionDlgPtr dlg; ApplyFeatureActionPtr action; - CharPtr num_txt, txt; - Char num[15]; + CharPtr num_txt; LocationIntervalPtr lint; - Int4 frame; - GBQualPtr gbq; ValNodePtr vnp; - BioSourcePtr biop; + ApplyFeatureDetailsPtr details; dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (d); if (dlg == NULL) { @@ -10207,18 +11234,35 @@ static Pointer DialogToApplyFeatureAction (DialoG d) action->location = ValNodeNew(NULL); action->location->choice = LocationChoice_whole_sequence; } else { - lint = LocationIntervalNew (); num_txt = SaveStringFromText (dlg->left_end); - lint->from = atoi (num_txt); - num_txt = MemFree (num_txt); - num_txt = SaveStringFromText (dlg->right_end); - lint->to = atoi (num_txt); - num_txt = MemFree (num_txt); - action->location = ValNodeNew(NULL); - action->location->choice = LocationChoice_interval; - action->location->data.ptrvalue = lint; + if (num_txt != NULL && num_txt[StringLen(num_txt) - 1] == '^') { + action->location = ValNodeNew(NULL); + action->location->choice = LocationChoice_point; + action->location->data.intvalue = atoi (num_txt); + num_txt = MemFree (num_txt); + } else { + num_txt = MemFree (num_txt); + num_txt = SaveStringFromText (dlg->right_end); + if (num_txt != NULL && num_txt[0] == '^') { + action->location = ValNodeNew(NULL); + action->location->choice = LocationChoice_point; + action->location->data.intvalue = atoi (num_txt + 1) - 1; + num_txt = MemFree (num_txt); + } else { + num_txt = MemFree (num_txt); + lint = LocationIntervalNew (); + num_txt = SaveStringFromText (dlg->left_end); + lint->from = atoi (num_txt); + num_txt = MemFree (num_txt); + num_txt = SaveStringFromText (dlg->right_end); + lint->to = atoi (num_txt); + num_txt = MemFree (num_txt); + action->location = ValNodeNew(NULL); + action->location->choice = LocationChoice_interval; + action->location->data.ptrvalue = lint; + } + } } - if (GetValue (dlg->all_or_some_group) == 1) { action->seq_list = ValNodeNew(NULL); action->seq_list->choice = SequenceListChoice_all; @@ -10232,128 +11276,18 @@ static Pointer DialogToApplyFeatureAction (DialoG d) action->add_redundant = GetStatus (dlg->add_redundant); - /* for CDS */ - if (dlg->add_mrna != NULL && GetStatus (dlg->add_mrna)) { - action->add_mrna = TRUE; - } else { - action->add_mrna = FALSE; - } - - if (dlg->reading_frame != NULL) { - frame = GetValue (dlg->reading_frame); - if (frame > 0 && frame < 4) { - sprintf (num, "%d", frame); - SetFeatQualValue (&(action->fields), Feat_qual_legal_codon_start, num); - } else { - SetFeatQualValue (&(action->fields), Feat_qual_legal_codon_start, "best"); - } - } - - if (dlg->protein_name != NULL && !TextHasNoText (dlg->protein_name)) { - txt = SaveStringFromText (dlg->protein_name); - SetFeatQualValue (&(action->fields), Feat_qual_legal_product, txt); - txt = MemFree (txt); - } - if (dlg->protein_name != NULL && !TextHasNoText (dlg->protein_description)) { - txt = SaveStringFromText (dlg->protein_description); - SetFeatQualValue (&(action->fields), Feat_qual_legal_description, txt); - txt = MemFree (txt); - } - - /* for RNA */ - if (dlg->ncrna_class != NULL) { - txt = DialogToPointer (dlg->ncrna_class); - if (!StringHasNoText (txt)) { - SetFeatQualValue (&(action->fields), Feat_qual_legal_ncRNA_class, txt); - } - txt = MemFree (txt); - } - if (dlg->rna_name != NULL && !TextHasNoText (dlg->rna_name)) { - txt = SaveStringFromText (dlg->rna_name); - SetFeatQualValue (&(action->fields), Feat_qual_legal_product, txt); - txt = MemFree (txt); - } - - /* for source features */ - if (dlg->src_quals != NULL) { - biop = DialogToPointer (dlg->src_quals); - action->src_fields = SourceQualValsFromBioSourcePtr (biop); - biop = BioSourceFree (biop); - } - - /* for import features */ - if (dlg->quals != NULL) { - gbq = DialogToPointer (dlg->quals); - AddGBQualsToActionFields (gbq, action); - gbq = GBQualFree (gbq); - } - - /* for all */ - if (dlg->gene_locus != NULL && !TextHasNoText (dlg->gene_locus)) { - txt = SaveStringFromText (dlg->gene_locus); - SetFeatQualValue (&(action->fields), Feat_qual_legal_gene, txt); - txt = MemFree (txt); - } - if (dlg->gene_description != NULL && !TextHasNoText (dlg->gene_description)) { - txt = SaveStringFromText (dlg->gene_description); - SetFeatQualValue (&(action->fields), Feat_qual_legal_gene_description, txt); - txt = MemFree (txt); - } - if (dlg->comment != NULL && !TextHasNoText (dlg->comment)) { - txt = SaveStringFromText (dlg->comment); - SetFeatQualValue (&(action->fields), Feat_qual_legal_note, txt); - txt = MemFree (txt); - } + details = DialogToPointer (dlg->details); + action->add_mrna = details->add_mrna; + action->fields = details->fields; + details->fields = NULL; + action->src_fields = details->src_fields; + details->src_fields = NULL; + details = ApplyFeatureDetailsFree (details); return action; } -static void AddTextToComment (ButtoN b, CharPtr text) -{ - ApplyFeatureActionDlgPtr dlg; - CharPtr orig_comment; - CharPtr new_comment; - - dlg = (ApplyFeatureActionDlgPtr) GetObjectExtra (b); - if (dlg == NULL || StringHasNoText (text)) - { - return; - } - - orig_comment = SaveStringFromText (dlg->comment); - if (StringHasNoText (orig_comment)) - { - SetTitle (dlg->comment, text); - } - else - { - new_comment = (CharPtr) MemNew ((StringLen (orig_comment) + StringLen (text) + 3) * sizeof (Char)); - if (new_comment != NULL) - { - StringCpy (new_comment, orig_comment); - StringCat (new_comment, "; "); - StringCat (new_comment, text); - SetTitle (dlg->comment, new_comment); - new_comment = MemFree (new_comment); - } - } - orig_comment = MemFree (orig_comment); -} - - -static void Add18SITS28SToComment (ButtoN b) -{ - AddTextToComment (b, "contains 18S ribosomal RNA, internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed spacer 2, and 28S ribosomal RNA"); -} - - -static void Add16SIGS23SToComment (ButtoN b) -{ - AddTextToComment (b, "contains 16S ribosomal RNA, 16S-23S ribosomal RNA intergenic spacer, and 23S ribosomal RNA"); -} - - static void ChangeApplyFeatureActionDlgBtn (ButtoN b) { ApplyFeatureActionDlgPtr dlg; @@ -10386,11 +11320,9 @@ ApplyFeatureActionDialog { ApplyFeatureActionDlgPtr dlg; GrouP p, g, parts_group, x, indexer_only_group; - GrouP r, r2, r3, r4, frame_grp = NULL, comment_btns_grp = NULL; - ButtoN comment_btn; + GrouP r2, r3, r4; ValNodePtr feature_type_list = NULL; - SeqFeatPtr sfp; - BioSourcePtr biop; + ApplyFeatureDetailsPtr details; dlg = (ApplyFeatureActionDlgPtr) MemNew (sizeof (ApplyFeatureActionDlgData)); p = HiddenGroup (h, -1, 0, NULL); @@ -10472,112 +11404,22 @@ ApplyFeatureActionDialog dlg->add_redundant = CheckBox (indexer_only_group, "Add even if feature of same type already present", ChangeApplyFeatureActionDlgBtn); SetObjectExtra (dlg->add_redundant, dlg, NULL); - if (action != NULL && action->type == Feature_type_cds) { - dlg->add_mrna = CheckBox (indexer_only_group, "Also add mRNA", ChangeApplyFeatureActionDlgBtn); - SetObjectExtra (dlg->add_mrna, dlg, NULL); - } - AlignObjects (ALIGN_CENTER, (HANDLE) r2, (HANDLE) dlg->all_or_some_group, (HANDLE) dlg->add_redundant, (HANDLE) dlg->add_mrna, NULL); + AlignObjects (ALIGN_CENTER, (HANDLE) r2, (HANDLE) dlg->all_or_some_group, (HANDLE) dlg->add_redundant, NULL); } - if (action != NULL && action->type == Feature_type_cds) { - frame_grp = HiddenGroup (p, 2, 0, NULL); - StaticPrompt (frame_grp, "Reading Frame", 0, dialogTextHeight, programFont, 'l'); - dlg->reading_frame = PopupList (frame_grp, TRUE, NULL); - PopupItem (dlg->reading_frame, "1"); - PopupItem (dlg->reading_frame, "2"); - PopupItem (dlg->reading_frame, "3"); - PopupItem (dlg->reading_frame, "Best"); - SetValue (dlg->reading_frame, 4); - } else if (action != NULL && action->type == Feature_type_source) { - dlg->src_quals = BioSourceDialog (p); - biop = BioSourceFromSourceQualVals (action->src_fields); - PointerToDialog (dlg->src_quals, biop); - biop = BioSourceFree (biop); - } - - r = HiddenGroup (p, 2, 0, NULL); - if (action != NULL && action->type == Feature_type_cds) { - - StaticPrompt (r, "Protein Name", 0, dialogTextHeight, programFont, 'l'); - dlg->protein_name = DialogText (r, "", 20, NULL); - StaticPrompt (r, "Protein Description", 0, dialogTextHeight, programFont, 'l'); - dlg->protein_description = DialogText (r, "", 20, NULL); - } else if (action != NULL && (action->type == Feature_type_preRNA - || action->type == Feature_type_mRNA - || action->type == Feature_type_tRNA - || action->type == Feature_type_rRNA - || action->type == Feature_type_snRNA - || action->type == Feature_type_scRNA - || action->type == Feature_type_otherRNA - || action->type == Feature_type_tmRNA - || action->type == Feature_type_ncRNA)) { - /* RNA name */ - StaticPrompt (r, "RNA Name", 0, dialogTextHeight, programFont, 'l'); - dlg->rna_name = DialogText (r, "", 20, NULL); - /* ncRNA class */ - if (action->type == Feature_type_ncRNA) { - StaticPrompt (r, "ncRNA Class", 0, dialogTextHeight, programFont, 'l'); - dlg->ncrna_class = CreatencRNAClassDialog (r, FALSE, NULL, NULL); - } - } else if (action != NULL && action->type != Feature_type_gene && action->type != Feature_type_source) { - StaticPrompt (r, "Qualifiers", 0, dialogTextHeight, programFont, 'l'); - sfp = CreateFeatureWithImportFeatureQuals (action); - dlg->quals = NewCreateImportFields (r, GetFeatureNameFromFeatureType (action->type), sfp, FALSE); - sfp = SeqFeatFree (sfp); - } - - /* gene qualifiers ( for all ) */ - StaticPrompt (r, "Gene Locus", 0, dialogTextHeight, programFont, 'l'); - dlg->gene_locus = DialogText (r, "", 20, NULL); - StaticPrompt (r, "Gene Description", 0, dialogTextHeight, programFont, 'l'); - dlg->gene_description = DialogText (r, "", 20, NULL); - StaticPrompt (r, "Comment", 0, dialogTextHeight, programFont, 'l'); - dlg->comment = DialogText (r, "", 20, NULL); - if (action != NULL && action->type == Feature_type_otherRNA && indexer_version) { - comment_btns_grp = HiddenGroup (p, 2, 0, NULL); - comment_btn = PushButton (comment_btns_grp, "Add '18S-ITS-5.8S-ITS-28S' to comment", Add18SITS28SToComment); - SetObjectExtra (comment_btn, dlg, NULL); - comment_btn = PushButton (comment_btns_grp, "Add '16S-IGS-23S' to comment", Add16SIGS23SToComment); - SetObjectExtra (comment_btn, dlg, NULL); - } - - if (frame_grp != NULL) { - AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg, - (HANDLE) parts_group, - (HANDLE) g, - (HANDLE) dlg->strand_group, - (HANDLE) indexer_only_group, - (HANDLE) r, - (HANDLE) frame_grp, - NULL); - } else if (comment_btns_grp != NULL) { - AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg, - (HANDLE) parts_group, - (HANDLE) g, - (HANDLE) dlg->strand_group, - (HANDLE) indexer_only_group, - (HANDLE) r, - (HANDLE) comment_btns_grp, - NULL); - } else if (dlg->src_quals != NULL) { - AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg, - (HANDLE) parts_group, - (HANDLE) g, - (HANDLE) dlg->strand_group, - (HANDLE) indexer_only_group, - (HANDLE) r, - (HANDLE) dlg->src_quals, - NULL); - } else { - AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg, - (HANDLE) parts_group, - (HANDLE) g, - (HANDLE) dlg->strand_group, - (HANDLE) indexer_only_group, - (HANDLE) r, - NULL); - } + details = ApplyFeatureDetailsNew (action); + dlg->details = ApplyFeatureDetailsDialog (p, action == NULL ? FEATDEF_CDS : GetFeatdefFromFeatureType(action->type), + details, indexer_version, change_notify, change_userdata); + details = ApplyFeatureDetailsFree (details); + + AlignObjects (ALIGN_CENTER, (HANDLE) dlg->feature_type_dlg, + (HANDLE) parts_group, + (HANDLE) g, + (HANDLE) dlg->strand_group, + (HANDLE) indexer_only_group, + (HANDLE) dlg->details, + NULL); return (DialoG) p; } @@ -11363,6 +12205,7 @@ static DialoG AutodefActionDialog ValNodeAddPointer (&src_quals, 0, StringSave ("clone")); ValNodeAddPointer (&src_quals, 0, StringSave ("cultivar")); + ValNodeAddPointer (&src_quals, 0, StringSave ("culture-collection")); ValNodeAddPointer (&src_quals, 0, StringSave ("haplogroup")); ValNodeAddPointer (&src_quals, 0, StringSave ("isolate")); ValNodeAddPointer (&src_quals, 0, StringSave ("strain")); @@ -11395,6 +12238,139 @@ static DialoG AutodefActionDialog } +typedef struct fixpubcapsdlg { + DIALOG_MESSAGE_BLOCK + + ButtoN fix_title; + ButtoN fix_author; + ButtoN fix_affil; + DialoG constraint; + + Nlm_ChangeNotifyProc change_notify; + Pointer change_userdata; +} FixPubCapsDlgData, PNTR FixPubCapsDlgPtr; + + +static void FixPubCapsActionToDialog (DialoG d, Pointer data) +{ + FixPubCapsDlgPtr dlg; + FixPubCapsActionPtr action; + + dlg = (FixPubCapsDlgPtr) GetObjectExtra (d); + if (dlg == NULL) { + return; + } + + action = (FixPubCapsActionPtr) data; + if (action == NULL) { + SetStatus (dlg->fix_title, FALSE); + SetStatus (dlg->fix_author, FALSE); + SetStatus (dlg->fix_affil, FALSE); + PointerToDialog (dlg->constraint, NULL); + } else { + SetStatus (dlg->fix_title, action->title); + SetStatus (dlg->fix_author, action->authors); + SetStatus (dlg->fix_affil, action->affiliation); + PointerToDialog (dlg->constraint, action->constraint); + } + +} + + +static Pointer DialogToFixPubCapsAction (DialoG d) +{ + FixPubCapsDlgPtr dlg; + FixPubCapsActionPtr action = NULL; + + dlg = (FixPubCapsDlgPtr) GetObjectExtra (d); + if (dlg == NULL) { + return NULL; + } + + action = FixPubCapsActionNew (); + action->title = GetStatus (dlg->fix_title); + action->authors = GetStatus (dlg->fix_author); + action->affiliation = GetStatus (dlg->fix_affil); + if (IsFixPubCapsActionEmpty(action)) { + action = FixPubCapsActionFree (action); + } else { + action->constraint = DialogToPointer (dlg->constraint); + } + return action; +} + + +static void ChangeFixPubCapsActionBtn (ButtoN b) +{ + FixPubCapsDlgPtr dlg; + + dlg = (FixPubCapsDlgPtr) GetObjectExtra (b); + if (dlg == NULL) { + return; + } + + if (dlg->change_notify != NULL) { + (dlg->change_notify) (dlg->change_userdata); + } +} + + +static ValNodePtr TestFixPubCapsActionDialog (DialoG d) +{ + FixPubCapsDlgPtr dlg; + FixPubCapsActionPtr a; + ValNodePtr err_list = NULL; + + dlg = (FixPubCapsDlgPtr) GetObjectExtra (d); + if (dlg == NULL) return NULL; + a = (FixPubCapsActionPtr) DialogToPointer (d); + if (a == NULL) { + ValNodeAddPointer (&err_list, 0, "bad action"); + } + return err_list; +} + + +static DialoG FixPubCapsDialog +(GrouP h, + Boolean indexer_version, + Nlm_ChangeNotifyProc change_notify, + Pointer change_userdata) +{ + FixPubCapsDlgPtr dlg; + GrouP p, g1; + + dlg = (FixPubCapsDlgPtr) MemNew (sizeof (FixPubCapsDlgData)); + p = HiddenGroup (h, -1, 0, NULL); + SetGroupSpacing (p, 10, 10); + SetObjectExtra (p, dlg, StdCleanupExtraProc); + + dlg->dialog = (DialoG) p; + dlg->todialog = FixPubCapsActionToDialog; + dlg->fromdialog = DialogToFixPubCapsAction; + dlg->dialogmessage = NULL; + dlg->testdialog = TestFixPubCapsActionDialog; + dlg->change_notify = change_notify; + dlg->change_userdata = change_userdata; + + g1 = HiddenGroup (p, 0, 3, NULL); + SetGroupSpacing (g1, 10, 10); + dlg->fix_title = CheckBox (g1, "Fix title", ChangeFixPubCapsActionBtn); + SetObjectExtra (dlg->fix_title, dlg, NULL); + dlg->fix_author = CheckBox (g1, "Fix authors", ChangeFixPubCapsActionBtn); + SetObjectExtra (dlg->fix_author, dlg, NULL); + dlg->fix_affil = CheckBox (g1, "Fix affiliation", ChangeFixPubCapsActionBtn); + SetObjectExtra (dlg->fix_affil, dlg, NULL); + + dlg->constraint = ConstraintSetDialog (p, change_notify, change_userdata); + + AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) dlg->constraint, NULL); + + return (DialoG) p; +} + + + typedef struct editfeaturelocationactiondlg { DIALOG_MESSAGE_BLOCK DialoG feature_type_dlg; @@ -11647,6 +12623,12 @@ static void EditFeatureLocationActionToDialog (DialoG d, Pointer data) break; } break; + case LocationEditType_extend_5: + SetValue (dlg->feature_edit_type, 7); + break; + case LocationEditType_extend_3: + SetValue (dlg->feature_edit_type, 8); + break; default: ResetFeatureLocationActionEditType (dlg); break; @@ -11837,6 +12819,14 @@ static Pointer DialogToEditFeatureLocationAction (DialoG d) break; } break; + case 7: + action->action = ValNodeNew (NULL); + action->action->choice = LocationEditType_extend_5; + break; + case 8: + action->action = ValNodeNew (NULL); + action->action->choice = LocationEditType_extend_3; + break; default: action = EditFeatureLocationActionFree (action); break; @@ -11921,6 +12911,8 @@ EditFeatureLocationActionDialog PopupItem (dlg->feature_edit_type, "Set 3' Partial"); PopupItem (dlg->feature_edit_type, "Clear 3' Partial"); PopupItem (dlg->feature_edit_type, "Convert location"); + PopupItem (dlg->feature_edit_type, "Extend 5' end to end of sequence"); + PopupItem (dlg->feature_edit_type, "Extend 3' end to end of sequence"); SetValue (dlg->feature_edit_type, 1); g = HiddenGroup (p, 0, 0, NULL); @@ -12023,8 +13015,6 @@ typedef struct parsesrcdlg { } ParseSrcDlgData, PNTR ParseSrcDlgPtr; -const CharPtr kTaxnameAfterBinomialString = "Taxname after binomial"; - static void ChangeParseSrcDialogPopup (PopuP p) { ParseSrcDlgPtr dlg; @@ -12554,10 +13544,10 @@ static void ParseDstToDialog (DialoG d, Pointer data) SetValue (dlg->feat_or_desc, 1); break; case Object_type_constraint_feature: - SetValue (dlg->feat_or_desc, 2); + SetValue (dlg->feat_or_desc, 3); break; case Object_type_constraint_descriptor: - SetValue (dlg->feat_or_desc, 3); + SetValue (dlg->feat_or_desc, 2); break; default: SetValue (dlg->feat_or_desc, 1); @@ -12646,10 +13636,10 @@ static Pointer DialogToParseDst (DialoG d) case 1: org->type = Object_type_constraint_any; break; - case 2: + case 3: org->type = Object_type_constraint_feature; break; - case 3: + case 2: org->type = Object_type_constraint_descriptor; break; default: @@ -12684,10 +13674,10 @@ static Pointer DialogToParseDst (DialoG d) case 1: org->type = Object_type_constraint_any; break; - case 2: + case 3: org->type = Object_type_constraint_feature; break; - case 3: + case 2: org->type = Object_type_constraint_descriptor; break; default: @@ -12938,7 +13928,7 @@ static ValNodePtr TestParseDstDialog (DialoG d) } -static DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) +NLM_EXTERN DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata) { ParseDstDlgPtr dlg; GrouP p, g, g2; @@ -13045,12 +14035,143 @@ static DialoG ParseDstDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Point } +typedef struct capchangedlg { + DIALOG_MESSAGE_BLOCK + GrouP cap_change; + Nlm_ChangeNotifyProc change_notify; + Pointer change_userdata; +} CapChangeDlgData, PNTR CapChangeDlgPtr; + + +static void CapChangeToDialog (DialoG d, Pointer data) +{ + CapChangeDlgPtr dlg; + Int4 cap_change; + + dlg = (CapChangeDlgPtr) GetObjectExtra (d); + if (dlg == NULL) { + return; + } + cap_change = (Int4) data; + switch (cap_change) { + case Cap_change_none: + SetValue (dlg->cap_change, 1); + break; + case Cap_change_tolower: + SetValue (dlg->cap_change, 2); + break; + case Cap_change_toupper: + SetValue (dlg->cap_change, 3); + break; + case Cap_change_firstcap: + SetValue (dlg->cap_change, 4); + break; + case Cap_change_firstcaprestnochange: + SetValue (dlg->cap_change, 5); + break; + default: + SetValue (dlg->cap_change, 1); + break; + } + if (dlg->change_notify != NULL) { + (dlg->change_notify) (dlg->change_userdata); + } +} + + +static Pointer DialogToCapChange (DialoG d) +{ + CapChangeDlgPtr dlg; + Int4 cap_change = Cap_change_none; + + dlg = (CapChangeDlgPtr) GetObjectExtra (d); + if (dlg == NULL) return NULL; + + switch (GetValue (dlg->cap_change)) { + case 1: + cap_change = Cap_change_none; + break; + case 2: + cap_change = Cap_change_tolower; + break; + case 3: + cap_change = Cap_change_toupper; + break; + case 4: + cap_change = Cap_change_firstcap; + break; + case 5: + cap_change = Cap_change_firstcaprestnochange; + break; + default: + cap_change = Cap_change_none; + break; + } + return (Pointer) cap_change; +} + + +static ValNodePtr TestCapChangeDialog (DialoG d) +{ + CapChangeDlgPtr dlg; + ValNodePtr err_list = NULL; + Int2 val; + + dlg = (CapChangeDlgPtr) GetObjectExtra (d); + if (dlg == NULL) return NULL; + + val = GetValue (dlg->cap_change); + if (val < 1 || val > 5) { + ValNodeAddPointer (&err_list, 0, "cap change"); + } + return err_list; +} + + +NLM_EXTERN DialoG +CapChangeDialog +(GrouP h, + Nlm_ChangeNotifyProc change_notify, + Pointer change_userdata) +{ + CapChangeDlgPtr dlg; + GrouP p; + + dlg = (CapChangeDlgPtr) MemNew (sizeof (CapChangeDlgData)); + p = NormalGroup (h, 5, 0, "Capitalization", programFont, NULL); + SetGroupSpacing (p, 10, 10); + SetObjectExtra (p, dlg, StdCleanupExtraProc); + + dlg->dialog = (DialoG) p; + dlg->todialog = CapChangeToDialog; + dlg->fromdialog = DialogToCapChange; + dlg->dialogmessage = NULL; + dlg->testdialog = TestCapChangeDialog; + dlg->change_notify = change_notify; + dlg->change_userdata = change_userdata; + + dlg->cap_change = p; + SetGroupSpacing (dlg->cap_change, 10, 10); + + RadioButton (dlg->cap_change, "No change"); + RadioButton (dlg->cap_change, "To lower"); + RadioButton (dlg->cap_change, "To upper"); + RadioButton (dlg->cap_change, "First cap, rest lower"); + RadioButton (dlg->cap_change, "First cap, rest no change"); + SetValue (dlg->cap_change, 1); + + return (DialoG) p; +} + + + + typedef struct parseactiondlg { DIALOG_MESSAGE_BLOCK DialoG text_portion; DialoG src; DialoG dst; - GrouP cap_change; + DialoG cap_change; ButtoN remove_from_parsed; DialoG existing_text; Nlm_ChangeNotifyProc change_notify; @@ -13073,30 +14194,14 @@ static void ParseActionToDialog (DialoG d, Pointer data) PointerToDialog (dlg->text_portion, NULL); PointerToDialog (dlg->src, NULL); PointerToDialog (dlg->dst, NULL); - SetValue (dlg->cap_change, 1); + PointerToDialog (dlg->cap_change, NULL); SetStatus (dlg->remove_from_parsed, FALSE); PointerToDialog (dlg->existing_text, NULL); } else { PointerToDialog (dlg->text_portion, action->portion); PointerToDialog (dlg->src, action->src); PointerToDialog (dlg->dst, action->dest); - switch (action->capitalization) { - case Cap_change_none: - SetValue (dlg->cap_change, 1); - break; - case Cap_change_tolower: - SetValue (dlg->cap_change, 2); - break; - case Cap_change_toupper: - SetValue (dlg->cap_change, 3); - break; - case Cap_change_firstcap: - SetValue (dlg->cap_change, 4); - break; - default: - SetValue (dlg->cap_change, 1); - break; - } + PointerToDialog (dlg->cap_change, (Pointer) action->capitalization); SetStatus (dlg->remove_from_parsed, action->remove_from_parsed); PointerToDialog (dlg->existing_text, (Pointer) action->existing_text); } @@ -13116,23 +14221,7 @@ static Pointer DialogToParseAction (DialoG d) action->src = DialogToPointer (dlg->src); action->dest = DialogToPointer (dlg->dst); action->remove_from_parsed = GetStatus (dlg->remove_from_parsed); - switch (GetValue (dlg->cap_change)) { - case 1: - action->capitalization = Cap_change_none; - break; - case 2: - action->capitalization = Cap_change_tolower; - break; - case 3: - action->capitalization = Cap_change_toupper; - break; - case 4: - action->capitalization = Cap_change_firstcap; - break; - default: - action->capitalization = Cap_change_none; - break; - } + action->capitalization = (Int4) DialogToPointer (dlg->cap_change); action->existing_text = (Uint2) DialogToPointer (dlg->existing_text); return action; } @@ -13142,7 +14231,6 @@ static ValNodePtr TestParseActionDialog (DialoG d) { ParseActionDlgPtr dlg; ValNodePtr err_list = NULL; - Int2 val; dlg = (ParseActionDlgPtr) GetObjectExtra (d); if (dlg == NULL) return NULL; @@ -13151,10 +14239,7 @@ static ValNodePtr TestParseActionDialog (DialoG d) ValNodeLink (&err_list, TestDialog (dlg->src)); ValNodeLink (&err_list, TestDialog (dlg->dst)); ValNodeLink (&err_list, TestDialog (dlg->existing_text)); - val = GetValue (dlg->cap_change); - if (val < 1 || val > 4) { - ValNodeAddPointer (&err_list, 0, "cap change"); - } + ValNodeLink (&err_list, TestDialog (dlg->cap_change)); return err_list; } @@ -13168,7 +14253,7 @@ ParseActionDialogEx Pointer change_userdata) { ParseActionDlgPtr dlg; - GrouP p, g; + GrouP p, g1, g2, g3; dlg = (ParseActionDlgPtr) MemNew (sizeof (ParseActionDlgData)); p = HiddenGroup (h, -1, 0, NULL); @@ -13183,21 +14268,17 @@ ParseActionDialogEx dlg->change_notify = change_notify; dlg->change_userdata = change_userdata; - dlg->text_portion = TextPortionDialog (p, TRUE, change_notify, change_userdata); - - g = HiddenGroup (p, 2, 0, NULL); - StaticPrompt (g, "From", 0, popupMenuHeight, programFont, 'r'); - dlg->src = ParseSrcDialog (g, change_notify, change_userdata); - StaticPrompt (g, "And place in", 0, popupMenuHeight, programFont, 'r'); - dlg->dst = ParseDstDialog (g, change_notify, change_userdata); - dlg->cap_change = NormalGroup (p, 4, 0, "Capitalization", programFont, NULL); - SetGroupSpacing (dlg->cap_change, 10, 10); + g3 =HiddenGroup (p, 2, 0, NULL); + StaticPrompt (g3, "Select text", 0, dialogTextHeight, systemFont, 'l'); + dlg->text_portion = TextPortionDialog (g3, TRUE, change_notify, change_userdata); - RadioButton (dlg->cap_change, "No change"); - RadioButton (dlg->cap_change, "To lower"); - RadioButton (dlg->cap_change, "To upper"); - RadioButton (dlg->cap_change, "First cap, rest lower"); - SetValue (dlg->cap_change, 1); + g1 = HiddenGroup (p, 2, 0, NULL); + StaticPrompt (g1, "From", 0, dialogTextHeight, systemFont, 'r'); + dlg->src = ParseSrcDialog (g1, change_notify, change_userdata); + g2 = HiddenGroup (p, 2, 0, NULL); + StaticPrompt (g2, "And place in", 0, dialogTextHeight, systemFont, 'r'); + dlg->dst = ParseDstDialog (g2, change_notify, change_userdata); + dlg->cap_change = CapChangeDialog (p, NULL, NULL); dlg->remove_from_parsed = CheckBox (p, "Remove from parsed field", NULL); @@ -13207,8 +14288,8 @@ ParseActionDialogEx AlignObjects (ALIGN_CENTER, (HANDLE) dlg->cap_change, (HANDLE) dlg->remove_from_parsed, - (HANDLE) dlg->text_portion, - (HANDLE) g, + (HANDLE) g3, + (HANDLE) g1, (HANDLE) g2, (HANDLE) dlg->existing_text, NULL); @@ -13292,6 +14373,7 @@ static void RunMacroInEditor (ButtoN b) Uint2 entityID; Int4 num_fields = 0, num_features = 0; Int4 tmp_fields, tmp_features; + LogInfoPtr lip; e = (EditMacroActionPtr) GetObjectExtra (b); if (e == NULL) return; @@ -13336,6 +14418,31 @@ static void RunMacroInEditor (ButtoN b) action->choice = MacroActionChoice_autodef; action->data.ptrvalue = DialogToPointer (e->action_dlg); break; + case 15: + action->choice = MacroActionChoice_removesets; + action->data.ptrvalue = DialogToPointer (e->action_dlg); + break; + case 16: + action->choice = MacroActionChoice_trim_junk_from_primer_seq; + break; + case 17: + action->choice = MacroActionChoice_fix_usa_and_states; + break; + case 18: + action->choice = MacroActionChoice_trim_stop_from_complete_cds; + break; + case 19: + action->choice = MacroActionChoice_synchronize_cds_partials; + break; + case 20: + action->choice = MacroActionChoice_adjust_for_consensus_splice; + break; + case 21: + action->choice = MacroActionChoice_fix_pub_caps; + break; + case 22: + action->choice = MacroActionChoice_remove_seg_gaps; + break; } sep_list = GetViewedSeqEntryList (); @@ -13347,12 +14454,13 @@ static void RunMacroInEditor (ButtoN b) } else { WatchCursor(); Update(); + lip = OpenLog ("Macro Actions"); for (vnp = sep_list; vnp != NULL; vnp = vnp->next) { sep = vnp->data.ptrvalue; entityID = ObjMgrGetEntityIDForChoice(sep); tmp_fields = 0; tmp_features = 0; - ApplyMacroToSeqEntry (sep, action, &tmp_fields, &tmp_features); + lip->data_in_log |= ApplyMacroToSeqEntryEx (sep, action, &tmp_fields, &tmp_features, lip->fp); num_fields += tmp_fields; num_features += tmp_features; ObjMgrSetDirtyFlag (entityID, TRUE); @@ -13362,6 +14470,12 @@ static void RunMacroInEditor (ButtoN b) ArrowCursor (); Update (); Message (MSG_OK, "Macro action affected %d fields and created %d features", num_fields, num_features); + if (!lip->data_in_log) { + fprintf (lip->fp, "Macro had no effect\n"); + lip->data_in_log = TRUE; + } + CloseLog (lip); + lip = FreeLog (lip); } action = MacroActionChoiceFree (action); @@ -13479,6 +14593,7 @@ BuildEditMacroActionWindow ParseActionPtr parse = NULL; RemoveDescriptorActionPtr remove_desc = NULL; AutodefActionPtr autodef = NULL; + FixPubCapsActionPtr fix_pubs = NULL; WindoW w; GrouP h, c; ButtoN b; @@ -13508,6 +14623,14 @@ BuildEditMacroActionWindow PopupItem (d->action_type, "Convert Feature"); PopupItem (d->action_type, "Remove Descriptor"); PopupItem (d->action_type, "Autodef"); + PopupItem (d->action_type, "Remove Duplicate Nested Sets"); + PopupItem (d->action_type, "Trim Junk in Primer Seqs"); + PopupItem (d->action_type, "Fix USA and state abbreviations in publications"); + PopupItem (d->action_type, "Remove trailing * from Coding Regions"); + PopupItem (d->action_type, "Synchronize Coding Region Partials"); + PopupItem (d->action_type, "Adjust coding regions for consensus splice sites"); + PopupItem (d->action_type, "Fix publication capitalization"); + PopupItem (d->action_type, "Remove Seg-gaps"); if (d->action_copy == NULL) { SetValue (d->action_type, 1); @@ -13574,6 +14697,31 @@ BuildEditMacroActionWindow SetValue (d->action_type, 14); autodef = (AutodefActionPtr) d->action_copy->data.ptrvalue; break; + case MacroActionChoice_removesets: + SetValue (d->action_type, 15); + break; + case MacroActionChoice_trim_junk_from_primer_seq: + SetValue (d->action_type, 16); + break; + case MacroActionChoice_fix_usa_and_states: + SetValue (d->action_type, 17); + break; + case MacroActionChoice_trim_stop_from_complete_cds: + SetValue (d->action_type, 18); + break; + case MacroActionChoice_synchronize_cds_partials: + SetValue (d->action_type, 19); + break; + case MacroActionChoice_adjust_for_consensus_splice: + SetValue (d->action_type, 20); + break; + case MacroActionChoice_fix_pub_caps: + SetValue (d->action_type, 21); + fix_pubs = (FixPubCapsActionPtr) d->action_copy->data.ptrvalue; + break; + case MacroActionChoice_remove_seg_gaps: + SetValue (d->action_type, 22); + break; default: SetValue (d->action_type, 1); break; @@ -13621,7 +14769,12 @@ BuildEditMacroActionWindow case 14: d->action_dlg = AutodefActionDialog (h, d->indexer_version, EnableEditMacroActionAccept, d); break; + case 21: + d->action_dlg = FixPubCapsDialog (h, d->indexer_version, EnableEditMacroActionAccept, d); + PointerToDialog (d->action_dlg, fix_pubs); + break; } + c = HiddenGroup (h, 4, 0, NULL); SetGroupSpacing (c, 10, 10); d->accept_btn = PushButton (c, "Accept", ModalAcceptButton); @@ -13731,6 +14884,31 @@ static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version) d.action_copy = ValNodeNew (NULL); d.action_copy->choice = MacroActionChoice_autodef; d.action_copy->data.ptrvalue = BuildDefaultAutodefAction (); + } else if (action_type == 15) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_removesets; + } else if (action_type == 16) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_trim_junk_from_primer_seq; + } else if (action_type == 17) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_fix_usa_and_states; + } else if (action_type == 18) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_trim_stop_from_complete_cds; + } else if (action_type == 19) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_synchronize_cds_partials; + } else if (action_type == 20) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_adjust_for_consensus_splice; + } else if (action_type == 21) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_fix_pub_caps; + d.action_copy->data.ptrvalue = FixPubCapsActionNew(); + } else if (action_type == 22) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_remove_seg_gaps; } } @@ -13773,6 +14951,30 @@ static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version) case MacroActionChoice_autodef: action->data.ptrvalue = AutodefActionFree (action->data.ptrvalue); break; + case MacroActionChoice_removesets: + action->data.ptrvalue = NULL; + break; + case MacroActionChoice_trim_junk_from_primer_seq: + action->data.ptrvalue = NULL; + break; + case MacroActionChoice_fix_usa_and_states: + action->data.ptrvalue = NULL; + break; + case MacroActionChoice_trim_stop_from_complete_cds: + action->data.ptrvalue = NULL; + break; + case MacroActionChoice_synchronize_cds_partials: + action->data.ptrvalue = NULL; + break; + case MacroActionChoice_adjust_for_consensus_splice: + action->data.ptrvalue = NULL; + break; + case MacroActionChoice_fix_pub_caps: + action->data.ptrvalue = FixPubCapsActionFree(action->data.ptrvalue); + break; + case MacroActionChoice_remove_seg_gaps: + action->data.ptrvalue = NULL; + break; } switch (GetValue (d.action_type)) { case 1: @@ -13813,6 +15015,38 @@ static Boolean EditMacroAction (ValNodePtr action, Boolean indexer_version) action->choice = MacroActionChoice_autodef; action->data.ptrvalue = DialogToPointer (d.action_dlg); break; + case 15: + action->choice = MacroActionChoice_removesets; + action->data.ptrvalue = NULL; + break; + case 16: + action->choice = MacroActionChoice_trim_junk_from_primer_seq; + action->data.ptrvalue = NULL; + break; + case 17: + action->choice = MacroActionChoice_fix_usa_and_states; + action->data.ptrvalue = NULL; + break; + case 18: + action->choice = MacroActionChoice_trim_stop_from_complete_cds; + action->data.ptrvalue = NULL; + break; + case 19: + action->choice = MacroActionChoice_synchronize_cds_partials; + action->data.ptrvalue = NULL; + break; + case 20: + action->choice = MacroActionChoice_adjust_for_consensus_splice; + action->data.ptrvalue = NULL; + break; + case 21: + action->choice = MacroActionChoice_fix_pub_caps; + action->data.ptrvalue = DialogToPointer (d.action_dlg); + break; + case 22: + action->choice = MacroActionChoice_remove_seg_gaps; + action->data.ptrvalue = NULL; + break; } } Remove (w); @@ -13914,6 +15148,38 @@ static void AddMacroActions (MacroEditorFormPtr f, Int2 item) d.action_copy = ValNodeNew (NULL); d.action_copy->choice = MacroActionChoice_autodef; d.action_copy->data.ptrvalue = BuildDefaultAutodefAction(); + } else if (action_type == 15) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_removesets; + d.action_copy->data.ptrvalue = NULL; + } else if (action_type == 16) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_trim_junk_from_primer_seq; + d.action_copy->data.ptrvalue = NULL; + } else if (action_type == 17) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_fix_usa_and_states; + d.action_copy->data.ptrvalue = NULL; + } else if (action_type == 18) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_trim_stop_from_complete_cds; + d.action_copy->data.ptrvalue = NULL; + } else if (action_type == 19) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_synchronize_cds_partials; + d.action_copy->data.ptrvalue = NULL; + } else if (action_type == 20) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_adjust_for_consensus_splice; + d.action_copy->data.ptrvalue = NULL; + } else if (action_type == 21) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_fix_pub_caps; + d.action_copy->data.ptrvalue = FixPubCapsActionNew(); + } else if (action_type == 22) { + d.action_copy = ValNodeNew (NULL); + d.action_copy->choice = MacroActionChoice_remove_seg_gaps; + d.action_copy->data.ptrvalue = NULL; } } @@ -13985,6 +15251,38 @@ static void AddMacroActions (MacroEditorFormPtr f, Int2 item) new_action->choice = MacroActionChoice_autodef; new_action->data.ptrvalue = DialogToPointer (d.action_dlg); break; + case 15: + new_action->choice = MacroActionChoice_removesets; + new_action->data.ptrvalue = NULL; + break; + case 16: + new_action->choice = MacroActionChoice_trim_junk_from_primer_seq; + new_action->data.ptrvalue = NULL; + break; + case 17: + new_action->choice = MacroActionChoice_fix_usa_and_states; + new_action->data.ptrvalue = NULL; + break; + case 18: + new_action->choice = MacroActionChoice_trim_stop_from_complete_cds; + new_action->data.ptrvalue = NULL; + break; + case 19: + new_action->choice = MacroActionChoice_synchronize_cds_partials; + new_action->data.ptrvalue = NULL; + break; + case 20: + new_action->choice = MacroActionChoice_adjust_for_consensus_splice; + new_action->data.ptrvalue = NULL; + break; + case 21: + new_action->choice = MacroActionChoice_fix_pub_caps; + new_action->data.ptrvalue = DialogToPointer (d.action_dlg); + break; + case 22: + new_action->choice = MacroActionChoice_remove_seg_gaps; + new_action->data.ptrvalue = NULL; + break; } /* add action to macro list */ if (prev_action == NULL) { @@ -15130,7 +16428,6 @@ static void ChangeSingleMacroActionPopup (PopuP p) OneMacroActionPtr d; Int2 val; Int4 i; - ValNodePtr rna_type = NULL; d = (OneMacroActionPtr) GetObjectExtra (p); if (d == NULL || d->no_callback) return; @@ -15848,9 +17145,9 @@ SingleMacroAction (Uint2 entityID, Boolean indexer_version) g5 = HiddenGroup (h, 0, 0, NULL); /* temporarily shut off callbacks */ frm->no_callback = TRUE; - frm->action_dlgs[0] = ApplyActionDialog (g5, frm->indexer_version, FALSE, AutopopulateSingleMacroDialog, frm, EnableSingleMacroActionAccept, frm, EnableSingleMacroActionAccept, frm); + frm->action_dlgs[0] = ApplyActionDialog (g5, frm->indexer_version, FALSE, (Nlm_ChangeNotifyProc) AutopopulateSingleMacroDialog, frm, EnableSingleMacroActionAccept, frm, EnableSingleMacroActionAccept, frm); SetAECRActionDlgFieldTypeDialogs (frm->action_dlgs[0], frm->single_qual_type_dlg, frm->single_field); - frm->action_dlgs[1] = EditActionDialog (g5, frm->indexer_version, AutopopulateSingleMacroDialog, frm, EnableSingleMacroActionAccept, frm, EnableSingleMacroActionAccept, frm); + frm->action_dlgs[1] = EditActionDialog (g5, frm->indexer_version, (Nlm_ChangeNotifyProc) AutopopulateSingleMacroDialog, frm, EnableSingleMacroActionAccept, frm, EnableSingleMacroActionAccept, frm); SetAECRActionDlgFieldTypeDialogs (frm->action_dlgs[1], frm->single_qual_type_dlg, frm->single_field); frm->action_dlgs[2] = ConvertActionDialog (g5, frm->indexer_version, FALSE, EnableSingleMacroActionAccept, frm, EnableSingleMacroActionAccept, frm); SetAECRActionDlgFieldTypeDialogs (frm->action_dlgs[2], frm->pair_qual_type_dlg, frm->field_pair_convert); @@ -16029,8 +17326,8 @@ static void ClearTextSingleParseAction (ButtoN b) parse = DialogToPointer (frm->dlg); if (parse != NULL && parse->portion != NULL) { - parse->portion->left_text = MemFree (parse->portion->left_text); - parse->portion->right_text = MemFree (parse->portion->right_text); + parse->portion->left_marker = TextMarkerFree (parse->portion->left_marker); + parse->portion->right_marker = TextMarkerFree (parse->portion->right_marker); PointerToDialog (frm->dlg, parse); parse = ParseActionFree (parse); ChangeSingleParseAction (frm); @@ -16168,1202 +17465,6 @@ NLM_EXTERN ForM SingleParseAction (Uint2 entityID) /* Functions for summarizing macro actions for display */ -static CharPtr SummarizeExistingText (Uint2 existing_text) -{ - CharPtr str = NULL; - - switch (existing_text) { - case ExistingTextOption_append_semi : - str = "append separated by semicolon"; - break; - case ExistingTextOption_append_space : - str = "append separated by space"; - break; - case ExistingTextOption_append_colon : - str = "append separated by colon"; - break; - case ExistingTextOption_append_none : - str = "append (no separator)"; - break; - case ExistingTextOption_prefix_semi : - str = "prefix separated by semicolon"; - break; - case ExistingTextOption_prefix_space : - str = "prefix separated by space"; - break; - case ExistingTextOption_prefix_colon : - str = "prefix separated by colon"; - break; - case ExistingTextOption_prefix_none : - str = "prefix (no separator)"; - break; - case ExistingTextOption_leave_old : - str = "ignore new text when existing text is present"; - break; - case ExistingTextOption_replace_old : - str = "overwrite existing text"; - break; - case ExistingTextOption_add_qual : - str = "add new qual"; - break; - default: - str = "invalid existing_text option"; - break; - } - return str; -} - - -static CharPtr GetStringLocationPhrase (Uint2 match_location, Boolean not_present) -{ - CharPtr location_word = NULL; - - switch (match_location) { - case String_location_contains : - if (not_present) { - location_word = "does not contain"; - } else { - location_word = "contains"; - } - break; - case String_location_equals : - if (not_present) { - location_word = "does not equal"; - } else { - location_word = "equals"; - } - break; - case String_location_starts : - if (not_present) { - location_word = "does not start with"; - } else { - location_word = "starts with"; - } - break; - case String_location_ends : - if (not_present) { - location_word = "does not end with"; - } else { - location_word = "ends with"; - } - break; - case String_location_inlist : - if (not_present) { - location_word = "is not one of"; - } else { - location_word = "is one of"; - } - break; - } - return location_word; -} - - -/* summarizing constraints */ -static CharPtr SummarizeStringConstraint (StringConstraintPtr constraint) -{ - CharPtr location_word = NULL; - CharPtr case_sensitive = "case-sensitive"; - CharPtr whole_word = "whole word"; - CharPtr str = NULL; - Int4 len; - CharPtr fmt = "%s '%s'"; - - if (constraint == NULL || constraint->match_text == NULL) return NULL; - - location_word = GetStringLocationPhrase (constraint->match_location, constraint->not_present); - if (location_word == NULL) return NULL; - len = StringLen (location_word) + StringLen (constraint->match_text) + StringLen (fmt); - if (constraint->case_sensitive) { - len += StringLen (case_sensitive) + 3; - } - if (constraint->whole_word) { - len += StringLen (whole_word) + 3; - } - str = (CharPtr) MemNew (sizeof (Char) * len); - sprintf (str, fmt, location_word, constraint->match_text); - if (constraint->case_sensitive || constraint->whole_word) { - StringCat (str, " ("); - } - if (constraint->case_sensitive) { - StringCat (str, case_sensitive); - if (constraint->whole_word) { - StringCat (str, ", "); - } - } - if (constraint->whole_word) { - StringCat (str, whole_word); - } - if (constraint->case_sensitive || constraint->whole_word) { - StringCat (str, ")"); - } - - return str; -} - - -static CharPtr SummarizePartialnessForLocationConstraint (LocationConstraintPtr constraint) -{ - if (constraint == NULL - || (constraint->partial5 == Partial_constraint_either - && constraint->partial3 == Partial_constraint_either)) { - return NULL; - } - if (constraint->partial5 == Partial_constraint_either) { - if (constraint->partial3 == Partial_constraint_partial) { - return "that are 3' partial"; - } else { - return "that are 3' complete"; - } - } else if (constraint->partial3 == Partial_constraint_either) { - if (constraint->partial5 == Partial_constraint_partial) { - return "that are 5' partial"; - } else { - return "that are 5' complete"; - } - } else if (constraint->partial5 == Partial_constraint_partial - && constraint->partial3 == Partial_constraint_partial) { - return "that are partial on both ends"; - } else if (constraint->partial5 == Partial_constraint_complete - && constraint->partial3 == Partial_constraint_complete) { - return "that are complete on both ends"; - } else if (constraint->partial5 == Partial_constraint_complete - && constraint->partial3 == Partial_constraint_partial) { - return "that are 5' complete and 3' partial"; - } else if (constraint->partial5 == Partial_constraint_partial - && constraint->partial3 == Partial_constraint_complete) { - return "that are 5' partial and 3' complete"; - } else { - return NULL; - } -} - -static CharPtr SummarizeLocationConstraint (LocationConstraintPtr constraint) -{ - CharPtr str = NULL; - CharPtr strand_word = NULL, seq_word = NULL; - CharPtr fmt = "only objects"; - CharPtr partial; - Int4 len = 0; - - if (IsLocationConstraintEmpty (constraint)) { - return NULL; - } - - partial = SummarizePartialnessForLocationConstraint (constraint); - - if (constraint->seq_type == Seqtype_constraint_nuc) { - seq_word = "nucleotide sequences"; - } else if (constraint->seq_type == Seqtype_constraint_prot) { - seq_word = "protein sequences"; - } - - if (constraint->strand == Strand_constraint_plus) { - strand_word = " on plus strands"; - } else if (constraint->strand == Strand_constraint_minus) { - strand_word = " on minus strands"; - } - - len = StringLen (fmt) + 1; - if (strand_word != NULL) { - len += StringLen (strand_word); - } - if (seq_word != NULL) { - len += StringLen (seq_word) + 4; - } - if (partial != NULL) { - len += StringLen (partial) + 2; - } - str = (CharPtr) MemNew (sizeof (Char) * len); - sprintf (str, fmt); - if (strand_word == NULL && seq_word != NULL) { - StringCat (str, " on "); - StringCat (str, seq_word); - } else if (strand_word != NULL) { - StringCat (str, strand_word); - if (seq_word != NULL) { - StringCat (str, " of "); - StringCat (str, seq_word); - } - } - if (partial != NULL) { - StringCat (str, " "); - StringCat (str, partial); - } - return str; -} - - -static CharPtr SummarizeSourceConstraint (SourceConstraintPtr constraint) -{ - CharPtr string, intro = NULL, field1, field2; - CharPtr match_fmt = "%s %s matches %s"; - CharPtr present_fmt = "%s %s is present"; - CharPtr text_fmt = "%s text %s"; - CharPtr two_match_fmt = "%s %s matches %s and %s %s"; - CharPtr one_match_fmt = "%s %s %s"; - CharPtr summ = NULL; - - if (constraint == NULL) return NULL; - - string = SummarizeStringConstraint (constraint->constraint); - field1 = SummarizeSourceQual (constraint->field1); - field2 = SummarizeSourceQual (constraint->field2); - - if (constraint->field1 == NULL && constraint->field2 == NULL && string == NULL) { - if (constraint->type_constraint == Object_type_constraint_feature) { - summ = StringSave ("where source is a feature"); - } else if (constraint->type_constraint == Object_type_constraint_descriptor) { - summ = StringSave ("where source is a descriptor"); - } - } else { - if (constraint->type_constraint == Object_type_constraint_any) { - intro = "where source"; - } else if (constraint->type_constraint == Object_type_constraint_feature) { - intro = "where source feature"; - } else if (constraint->type_constraint == Object_type_constraint_descriptor) { - intro = "where source descriptor"; - } else { - string = MemFree (string); - field1 = MemFree (field1); - field2 = MemFree (field2); - return NULL; - } - - if (string == NULL) { - if (field1 == NULL && field2 == NULL) { - if (constraint->type_constraint == Object_type_constraint_feature) { - summ = StringSave ("where source is a feature"); - } else if (constraint->type_constraint == Object_type_constraint_descriptor) { - summ = StringSave ("where source is a descriptor"); - } - } else if (field1 != NULL && field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (match_fmt) + StringLen (intro) + StringLen (field1) + StringLen (field2))); - sprintf (summ, match_fmt, intro, field1, field2); - } else if (field1 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (intro) + StringLen (field1))); - sprintf (summ, present_fmt, intro, field1); - } else if (field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (intro) + StringLen (field2))); - sprintf (summ, present_fmt, intro, field2); - } - } else { - if (field1 == NULL && field2 == NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (text_fmt) + StringLen (intro) + StringLen (string))); - sprintf (summ, text_fmt, intro, string); - } else if (field1 != NULL && field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (two_match_fmt) + StringLen (intro) - + 2 * StringLen (field1) + StringLen (field2) + StringLen (string))); - sprintf (summ, two_match_fmt, intro, field1, field2, field1, string); - } else if (field1 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (intro) + StringLen (field1) + StringLen (string))); - sprintf (summ, one_match_fmt, intro, field1, string); - } else if (field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (intro) + StringLen (field2) + StringLen (string))); - sprintf (summ, one_match_fmt, intro, field2, string); - } - } - } - string = MemFree (string); - field1 = MemFree (field1); - field2 = MemFree (field2); - return summ; -} - - - -static CharPtr SummarizeCDSGeneProtPseudoConstraint (CDSGeneProtPseudoConstraintPtr constraint) -{ - CharPtr summ = NULL, pseudo_feat; - CharPtr is_pseudo_fmt = "where %s is pseudo"; - CharPtr not_pseudo_fmt = "where %s is not pseudo"; - - if (constraint != NULL) { - pseudo_feat = CDSGeneProtFeatureNameFromFeatureType (constraint->feature); - if (pseudo_feat != NULL) { - if (constraint->is_pseudo) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (is_pseudo_fmt) + StringLen (pseudo_feat))); - sprintf (summ, is_pseudo_fmt, pseudo_feat); - } else { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (not_pseudo_fmt) + StringLen (pseudo_feat))); - sprintf (summ, not_pseudo_fmt, pseudo_feat); - } - } - } - - return summ; -} - - -static CharPtr SummarizeCDSGeneProtQualConstraint (CDSGeneProtQualConstraintPtr constraint) -{ - CharPtr string, field1 = NULL, field2 = NULL; - CharPtr match_fmt = "where %s matches %s"; - CharPtr present_fmt = "where %s is present"; - CharPtr text_fmt = "where CDS-gene-prot text %s"; - CharPtr two_match_fmt = "where %s matches %s and %s %s"; - CharPtr one_match_fmt = "where %s %s"; - CharPtr summ = NULL; - - if (constraint == NULL) return NULL; - - string = SummarizeStringConstraint (constraint->constraint); - if (constraint->field1 != NULL && constraint->field1->choice == CDSGeneProtConstraintField_field) { - field1 = CDSGeneProtNameFromField (constraint->field1->data.intvalue); - } - if (constraint->field2 != NULL && constraint->field2->choice == CDSGeneProtConstraintField_field) { - field2 = CDSGeneProtNameFromField (constraint->field2->data.intvalue); - } - - if (string == NULL) { - if (field1 != NULL && field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (match_fmt) + StringLen (field1) + StringLen (field2))); - sprintf (summ, match_fmt, field1, field2); - } else if (field1 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (field1))); - sprintf (summ, present_fmt, field1); - } else if (field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (present_fmt) + StringLen (field2))); - sprintf (summ, present_fmt, field2); - } - } else { - if (field1 == NULL && field2 == NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (text_fmt) + StringLen (string))); - sprintf (summ, text_fmt, string); - } else if (field1 != NULL && field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (two_match_fmt) - + 2 * StringLen (field1) + StringLen (field2) + StringLen (string))); - sprintf (summ, two_match_fmt, field1, field2, field1, string); - } else if (field1 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (field1) + StringLen (string))); - sprintf (summ, one_match_fmt, field1, string); - } else if (field2 != NULL) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (one_match_fmt) + StringLen (field2) + StringLen (string))); - sprintf (summ, one_match_fmt, field2, string); - } - } - - string = MemFree (string); - /* note - field1 and field2 aren't allocated, so we don't need to free them */ - - return summ; -} - - -static CharPtr SummarizeSequenceConstraint (SequenceConstraintPtr constraint) -{ - CharPtr summ = NULL; - CharPtr seq_word = NULL, featpresent = NULL, id = NULL; - Int4 len = 0; - CharPtr seq_word_intro = "where sequence type is "; - CharPtr feat_after = " is present"; - CharPtr id_intro = "sequence ID "; - - if (IsSequenceConstraintEmpty (constraint)) { - summ = StringSave ("Missing sequence constraint"); - } else { - if (constraint->seqtype != NULL && constraint->seqtype->choice != SequenceConstraintMolTypeConstraint_any) { - switch (constraint->seqtype->choice) { - case SequenceConstraintMolTypeConstraint_nucleotide: - seq_word = "nucleotide"; - break; - case SequenceConstraintMolTypeConstraint_dna: - seq_word = "DNA"; - break; - case SequenceConstraintMolTypeConstraint_rna: - if (constraint->seqtype->data.intvalue == Sequence_constraint_rnamol_any) { - seq_word = "RNA"; - } else { - seq_word = GetBiomolNameForRnaType (constraint->seqtype->data.intvalue); - } - break; - case SequenceConstraintMolTypeConstraint_protein: - seq_word = "protein"; - break; - } - } - - if (constraint->feature != Feature_type_any) { - featpresent = GetFeatureNameFromFeatureType (constraint->feature); - } - - if (!IsStringConstraintEmpty (constraint->id)) { - id = SummarizeStringConstraint (constraint->id); - } - - if (seq_word != NULL) { - len += StringLen (seq_word) + StringLen (seq_word_intro); - } - - if (featpresent != NULL) { - if (len == 0) { - len += 6; - } else { - len += 5; - } - len += StringLen (featpresent); - len += StringLen (feat_after); - } - - if (id != NULL) { - if (len == 0) { - len += 6; - } else { - len += 5; - } - len += StringLen (id_intro); - len += StringLen (id); - } - - if (len == 0) { - summ = StringSave ("missing sequence constraint"); - } else { - len++; - summ = (CharPtr) MemNew (sizeof (Char) * len); - summ[0] = 0; - if (seq_word != NULL) { - StringCat (summ, seq_word_intro); - StringCat (summ, seq_word); - } - if (featpresent != NULL) { - if (seq_word == NULL) { - StringCat (summ, "where "); - } else { - StringCat (summ, " and "); - } - StringCat (summ, featpresent); - StringCat (summ, feat_after); - } - if (id != NULL) { - if (seq_word == NULL && featpresent == NULL) { - StringCat (summ, "where "); - } else { - StringCat (summ, " and "); - } - StringCat (summ, id_intro); - StringCat (summ, id); - } - } - id = MemFree (id); - } - return summ; -} - -static CharPtr SummarizePublicationConstraint (PublicationConstraintPtr constraint) -{ - CharPtr rval = NULL; - CharPtr type = NULL, string = NULL, label = NULL; - CharPtr type_and_field_fmt = "%s and %s %s"; - CharPtr fmt = "where %s %s"; - - if (IsPublicationConstraintEmpty (constraint)) return NULL; - - switch (constraint->type) { - case Pub_type_published: - type = "where pub is published"; - break; - case Pub_type_unpublished: - type = "where pub is unpublished"; - break; - case Pub_type_in_press: - type = "where pub is in press"; - break; - case Pub_type_submitter_block: - type = "where pub is submitter block"; - break; - } - if (constraint->field != NULL) { - string = SummarizeStringConstraint (constraint->field->constraint); - label = GetPubFieldLabel (constraint->field->field); - } - - if (type != NULL && string != NULL && label != NULL) { - rval = (CharPtr) MemNew (sizeof (Char) * (StringLen (type_and_field_fmt) + StringLen (type) + StringLen (label) + StringLen (string))); - sprintf (rval, fmt, label, string); - } else if (string != NULL && label != NULL) { - rval = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (label) + StringLen (string))); - sprintf (rval, fmt, label, string); - } else if (type != NULL) { - rval = StringSave (type); - } - string = MemFree (string); - - return rval; -} - - -static CharPtr SummarizeFieldConstraint (FieldConstraintPtr constraint) -{ - CharPtr rval = NULL; - CharPtr string = NULL, label = NULL; - CharPtr fmt = "where %s %s"; - - if (IsFieldConstraintEmpty (constraint)) return NULL; - - string = SummarizeStringConstraint (constraint->string_constraint); - label = SummarizeFieldType (constraint->field); - - if (string != NULL && label != NULL) { - rval = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (label) + StringLen (string))); - sprintf (rval, fmt, label, string); - } - string = MemFree (string); - label = MemFree (label); - - return rval; -} - - -static CharPtr SummarizeConstraint (ValNodePtr constraint) -{ - CharPtr phrase = NULL, tmp; - CharPtr fmt = "where object text %s"; - - if (constraint == NULL) return NULL; - switch (constraint->choice) { - case ConstraintChoice_string: - tmp = SummarizeStringConstraint (constraint->data.ptrvalue); - if (tmp != NULL) { - phrase = (CharPtr) MemNew (sizeof (Char) * (StringLen (tmp) + StringLen (fmt))); - sprintf (phrase, fmt, tmp); - tmp = MemFree (tmp); - } - break; - case ConstraintChoice_location: - phrase = SummarizeLocationConstraint (constraint->data.ptrvalue); - break; - case ConstraintChoice_source: - phrase = SummarizeSourceConstraint (constraint->data.ptrvalue); - break; - case ConstraintChoice_cdsgeneprot_qual: - phrase = SummarizeCDSGeneProtQualConstraint (constraint->data.ptrvalue); - break; - case ConstraintChoice_cdsgeneprot_pseudo: - phrase = SummarizeCDSGeneProtPseudoConstraint (constraint->data.ptrvalue); - break; - case ConstraintChoice_sequence: - phrase = SummarizeSequenceConstraint (constraint->data.ptrvalue); - break; - case ConstraintChoice_pub: - phrase = SummarizePublicationConstraint (constraint->data.ptrvalue); - break; - case ConstraintChoice_field: - phrase = SummarizeFieldConstraint (constraint->data.ptrvalue); - break; - } - return phrase; -} - - -static CharPtr SummarizeConstraintSet (ValNodePtr constraint_set) -{ - ValNodePtr phrases = NULL, vnp; - Int4 len = 0; - CharPtr phrase, str = NULL; - - while (constraint_set != NULL) { - phrase = SummarizeConstraint (constraint_set); - if (phrase != NULL) { - ValNodeAddPointer (&phrases, 0, phrase); - if (len > 0) { - len += 5; /* for " and " */ - } else { - len += 1; /* for terminal NULL */ - } - len += StringLen (phrase); - } - constraint_set = constraint_set->next; - } - if (len > 0) { - str = (CharPtr) MemNew (sizeof (Char) * len); - for (vnp = phrases; vnp != NULL; vnp = vnp->next) { - StringCat (str, vnp->data.ptrvalue); - if (vnp->next != NULL) { - StringCat (str, " and "); - } - } - } - return str; -} - -/* summarizing AECR actions */ -static CharPtr SummarizeFieldPairType (ValNodePtr vnp, CharPtr connect_word) -{ - FeatureFieldPairPtr ffp; - CDSGeneProtFieldPairPtr cgp; - SourceQualPairPtr quals; - MolinfoFieldPairPtr m_fields; - RnaQualPairPtr rna_quals; - CharPtr str = NULL; - CharPtr from_label = NULL, to_label = NULL; - CharPtr label_fmt = "%s %s %s"; - CharPtr type_label_fmt = "%s %s %s %s"; - CharPtr label = NULL; - - if (connect_word == NULL) { - connect_word = "to"; - } - if (vnp == NULL) { - str = StringSave ("missing field"); - } else { - switch (vnp->choice) { - case FieldPairType_source_qual: - if (vnp->data.ptrvalue != NULL) { - quals = (SourceQualPairPtr) vnp->data.ptrvalue; - from_label = GetSourceQualName (quals->field_from); - to_label = GetSourceQualName (quals->field_to); - } - if (from_label != NULL && to_label != NULL) { - str = (CharPtr) MemNew (sizeof (Char) * - (StringLen (from_label) + StringLen (connect_word) + StringLen (to_label) - + 3)); - sprintf (str, "%s %s %s", from_label, connect_word, to_label); - } else { - str = StringSave ("missing field"); - } - break; - case FieldPairType_feature_field: - ffp = (FeatureFieldPairPtr) vnp->data.ptrvalue; - if (ffp == NULL || ffp->field_from == NULL || ffp->field_to == NULL) { - str = StringSave ("missing field"); - } else { - label = GetFeatureNameFromFeatureType (ffp->type); - from_label = FeatureFieldLabel (label, ffp->field_from); - to_label = FeatureFieldLabel (label, ffp->field_to); - str = (CharPtr) MemNew (sizeof (Char) * - (StringLen (label_fmt) - + StringLen (from_label) + StringLen (to_label) - + StringLen (connect_word))); - sprintf (str, label_fmt, from_label, connect_word, to_label); - from_label = MemFree (from_label); - to_label = MemFree (to_label); - } - break; - case FieldPairType_cds_gene_prot: - cgp = (CDSGeneProtFieldPairPtr) vnp->data.ptrvalue; - from_label = CDSGeneProtNameFromField (cgp->field_from); - to_label = CDSGeneProtNameFromField (cgp->field_to); - str = (CharPtr) MemNew (sizeof (Char) * - StringLen (from_label) + StringLen (connect_word) + StringLen (to_label) - + 3); - sprintf (str, "%s %s %s", from_label, connect_word, to_label); - break; - case FieldPairType_molinfo_field: - m_fields = (MolinfoFieldPairPtr) vnp->data.ptrvalue; - from_label = NULL; - to_label = NULL; - label = NULL; - switch (m_fields->choice) { - case MolinfoFieldPair_molecule: - from_label = BiomolNameFromBiomol (BiomolFromMoleculeType (((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->from)); - to_label = BiomolNameFromBiomol (BiomolFromMoleculeType (((MolinfoMoleculePairPtr) m_fields->data.ptrvalue)->to)); - label = "molecule"; - break; - case MolinfoFieldPair_technique: - from_label = TechNameFromTech (TechFromTechniqueType (((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->from)); - to_label = TechNameFromTech (TechFromTechniqueType (((MolinfoTechniquePairPtr) m_fields->data.ptrvalue)->to)); - label = "technique"; - break; - case MolinfoFieldPair_completedness: - from_label = CompletenessNameFromCompleteness (CompletenessFromCompletednessType (((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->from)); - to_label = CompletenessNameFromCompleteness (CompletenessFromCompletednessType (((MolinfoCompletednessPairPtr) m_fields->data.ptrvalue)->to)); - label = "completeness"; - break; - case MolinfoFieldPair_mol_class: - from_label = MolNameFromMol (MolFromMoleculeClassType (((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->from)); - to_label = MolNameFromMol (MolFromMoleculeClassType (((MolinfoMolClassPairPtr) m_fields->data.ptrvalue)->to)); - label = "class"; - break; - case MolinfoFieldPair_topology: - from_label = TopologyNameFromTopology (TopologyFromTopologyType (((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->from)); - to_label = TopologyNameFromTopology (TopologyFromTopologyType (((MolinfoTopologyPairPtr) m_fields->data.ptrvalue)->to)); - label = "topology"; - break; - case MolinfoFieldPair_strand: - from_label = StrandNameFromStrand (StrandFromStrandType (((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->from)); - to_label = StrandNameFromStrand (StrandFromStrandType (((MolinfoStrandPairPtr) m_fields->data.ptrvalue)->to)); - label = "strand"; - break; - } - if (from_label == NULL) { - from_label = "Unknown value"; - } - if (to_label == NULL) { - to_label = "Unknown value"; - } - if (label == NULL) { - label = "Unknown molinfo field"; - } - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (type_label_fmt) - + StringLen (label) - + StringLen (from_label) - + StringLen (to_label) - + StringLen (connect_word))); - sprintf (str, type_label_fmt, label, from_label, connect_word, to_label); - break; - case FieldPairType_rna_field: - if (vnp->data.ptrvalue != NULL) { - rna_quals = (RnaQualPairPtr) vnp->data.ptrvalue; - label = SummarizeRnaType (rna_quals->type); - from_label = GetNameForRnaField (rna_quals->field_from); - to_label = GetNameForRnaField (rna_quals->field_to); - } - if (from_label != NULL && to_label != NULL && label != NULL) { - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (type_label_fmt) - + StringLen (label) - + StringLen (from_label) + StringLen (connect_word) + StringLen (to_label))); - sprintf (str, type_label_fmt, label, from_label, connect_word, to_label); - } else { - str = StringSave ("missing field"); - } - label = MemFree (label); - break; - - default: - str = StringSave ("Invalid field type"); - break; - } - } - return str; -} - - -static CharPtr SummarizeTextPortion (TextPortionPtr text_portion) -{ - CharPtr summ = NULL; - CharPtr left_fmt = NULL, right_fmt = NULL; - Int4 len = 6; - - if (text_portion == NULL - || ((text_portion->left_text == NULL || text_portion->left_text[0] == 0) - && (text_portion->right_text == NULL || text_portion->right_text[0] == 0))) { - summ = StringSave ("entire text"); - } else if (text_portion->inside) { - if (text_portion->left_text != NULL && text_portion->left_text[0] != 0) { - if (text_portion->include_left) { - left_fmt = "starting with "; - } else { - left_fmt = "just after "; - } - len += StringLen (left_fmt) + StringLen (text_portion->left_text) + 3; - } - if (text_portion->right_text != NULL && text_portion->right_text[0] != 0) { - if (text_portion->include_right) { - right_fmt = "up to and including "; - } else { - right_fmt = "up to "; - } - len += StringLen (right_fmt) + StringLen (text_portion->right_text) + 3; - if (left_fmt != NULL) { - len += 2; - } - } - if (left_fmt == NULL && right_fmt == NULL) { - summ = StringSave ("entire text"); - } else { - summ = (CharPtr) MemNew (sizeof (Char) * len); - StringCat (summ, "text "); - if (left_fmt != NULL) { - StringCat (summ, left_fmt); - StringCat (summ, "'"); - StringCat (summ, text_portion->left_text); - StringCat (summ, "'"); - if (right_fmt != NULL) { - StringCat (summ, ", "); - } - } - if (right_fmt != NULL) { - StringCat (summ, right_fmt); - StringCat (summ, "'"); - StringCat (summ, text_portion->right_text); - StringCat (summ, "'"); - } - } - } else { - if (text_portion->right_text != NULL && text_portion->right_text[0] != 0) { - if (text_portion->include_right) { - right_fmt = "starting with "; - } else { - right_fmt = "after "; - } - len += StringLen (right_fmt) + StringLen (text_portion->right_text) + 3; - } - if (text_portion->left_text != NULL && text_portion->left_text[0] != 0) { - if (text_portion->include_left) { - left_fmt = "up to and including "; - } else { - left_fmt = "before "; - } - len += StringLen (left_fmt) + StringLen (text_portion->left_text) + 3; - if (right_fmt != NULL) { - len += 5; - } - } - - if (left_fmt == NULL && right_fmt == NULL) { - summ = StringSave ("entire text"); - } else { - summ = (CharPtr) MemNew (sizeof (Char) * len); - StringCat (summ, "text "); - if (right_fmt != NULL) { - StringCat (summ, right_fmt); - StringCat (summ, "'"); - StringCat (summ, text_portion->right_text); - StringCat (summ, "'"); - if (left_fmt != NULL) { - StringCat (summ, " and "); - } - } - if (left_fmt != NULL) { - StringCat (summ, left_fmt); - StringCat (summ, "'"); - StringCat (summ, text_portion->left_text); - StringCat (summ, "'"); - } - } - } - return summ; -} - - -static CharPtr SummarizeApplyAction (ApplyActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Apply %s to %s (%s)"; - CharPtr nontextqual_fmt = "Apply %s (%s)"; - CharPtr field, existing_text; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->value == NULL || a->field == NULL) { - str = StringSave ("Invalid action"); - } else { - field = SummarizeFieldType (a->field); - existing_text = SummarizeExistingText (a->existing_text); - if (IsFieldTypeNonText (a->field)) { - str = (CharPtr) MemNew (sizeof (Char) * StringLen (nontextqual_fmt) + StringLen (field) + StringLen (existing_text)); - sprintf (str, nontextqual_fmt, field, existing_text); - } else { - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (a->value) + StringLen (field) + StringLen (existing_text))); - sprintf (str, fmt, a->value, field, existing_text); - } - field = MemFree (field); - } - return str; -} - - -static CharPtr SummarizeEditAction (EditActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Edit %s replace '%s' with '%s'"; - CharPtr field; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->field == NULL || a->field == NULL || a->edit == NULL || a->edit->find_txt == NULL) { - str = StringSave ("Invalid action"); - } else { - field = SummarizeFieldType (a->field); - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (field) + StringLen (a->edit->find_txt) + StringLen (a->edit->repl_txt))); - sprintf (str, fmt, field, a->edit->find_txt, a->edit->repl_txt == NULL ? "" : a->edit->repl_txt); - field = MemFree (field); - } - return str; -} - - -static CharPtr SummarizeConvertAction (ConvertActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Convert %s (%s)"; - CharPtr fields, existing_text; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->fields == NULL || a->fields == NULL) { - str = StringSave ("Invalid action"); - } else { - fields = SummarizeFieldPairType (a->fields, "to"); - existing_text = SummarizeExistingText (a->existing_text); - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fields) + StringLen (existing_text))); - sprintf (str, fmt, fields, existing_text); - fields = MemFree (fields); - } - return str; -} - - -static CharPtr SummarizeCopyAction (CopyActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Copy %s (%s)"; - CharPtr fields, existing_text; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->fields == NULL) { - str = StringSave ("Invalid action"); - } else { - fields = SummarizeFieldPairType (a->fields, "to"); - existing_text = SummarizeExistingText (a->existing_text); - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fields) + StringLen (existing_text))); - sprintf (str, fmt, fields, existing_text); - fields = MemFree (fields); - } - return str; -} - - -static CharPtr SummarizeSwapAction (SwapActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Swap %s"; - CharPtr fields; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->fields == NULL) { - str = StringSave ("Invalid action"); - } else { - fields = SummarizeFieldPairType (a->fields, "with"); - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (fields))); - sprintf (str, fmt, fields); - fields = MemFree (fields); - } - return str; -} - - -static CharPtr SummarizeAECRParseAction (AECRParseActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Parse %s from %s (%s)"; - CharPtr fields, existing_text, text_portion; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->fields == NULL) { - str = StringSave ("Invalid action"); - } else { - fields = SummarizeFieldPairType (a->fields, "to"); - existing_text = SummarizeExistingText (a->existing_text); - text_portion = SummarizeTextPortion (a->portion); - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (text_portion) + StringLen (fields) + StringLen (existing_text))); - sprintf (str, fmt, text_portion, fields, existing_text); - fields = MemFree (fields); - text_portion = MemFree (text_portion); - } - return str; -} - - -static CharPtr SummarizeRemoveAction (RemoveActionPtr a) -{ - CharPtr str = NULL; - CharPtr fmt = "Remove %s"; - CharPtr field; - - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->field == NULL || a->field == NULL) { - str = StringSave ("Invalid action"); - } else { - field = SummarizeFieldType (a->field); - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (field))); - sprintf (str, fmt, field); - field = MemFree (field); - } - return str; -} - - -static CharPtr SummarizeAECRAction (AECRActionPtr a) -{ - CharPtr str = NULL, act = NULL, constraint = NULL; - if (a == NULL) { - str = StringSave ("No action"); - } else if (a->action == NULL) { - str = StringSave ("Invalid command"); - } else { - switch (a->action->choice) { - case ActionChoice_apply: - act = SummarizeApplyAction (a->action->data.ptrvalue); - break; - case ActionChoice_edit: - act = SummarizeEditAction (a->action->data.ptrvalue); - break; - case ActionChoice_convert: - act = SummarizeConvertAction (a->action->data.ptrvalue); - break; - case ActionChoice_copy: - act = SummarizeCopyAction (a->action->data.ptrvalue); - break; - case ActionChoice_swap: - act = SummarizeSwapAction (a->action->data.ptrvalue); - break; - case ActionChoice_remove: - act = SummarizeRemoveAction (a->action->data.ptrvalue); - break; - case ActionChoice_parse: - act = SummarizeAECRParseAction (a->action->data.ptrvalue); - break; - } - if (act == NULL) { - str = StringSave ("Invalid action"); - } else { - constraint = SummarizeConstraintSet (a->constraint); - if (constraint == NULL) { - str = act; - } else { - str = (CharPtr) MemNew (sizeof (Char) * (StringLen(act) + 2 + StringLen (constraint))); - sprintf (str, "%s %s", act, constraint); - act = MemFree (act); - constraint = MemFree (constraint); - } - } - } - return str; -} - - -static CharPtr SummarizeParseSrc (ValNodePtr src) -{ - CharPtr summ = NULL; - CharPtr fmt = "structured comment field %s"; - ParseSrcOrgPtr src_org; - Boolean need_to_save = TRUE; - - if (src != NULL) { - switch (src->choice) { - case ParseSrc_defline: - summ = "defline"; - break; - case ParseSrc_flatfile: - summ = "flat file"; - break; - case ParseSrc_local_id: - summ = "local ID"; - break; - case ParseSrc_org: - src_org = (ParseSrcOrgPtr) src->data.ptrvalue; - if (src_org != NULL) { - if (src_org->field != NULL) { - if (src_org->field->choice == ParseSrcOrgChoice_taxname_after_binomial) { - summ = kTaxnameAfterBinomialString; - } else if (src_org->field->choice == ParseSrcOrgChoice_source_qual) { - summ = GetSourceQualName (src_org->field->data.intvalue); - } - } - } - break; - case ParseSrc_comment: - summ = "comment"; - break; - case ParseSrc_bankit_comment: - summ = "BankIT comment"; - break; - case ParseSrc_structured_comment: - if (!StringHasNoText (src->data.ptrvalue)) { - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (src->data.ptrvalue) + StringLen (fmt))); - sprintf (summ, fmt, src->data.ptrvalue); - need_to_save = FALSE; - } - break; - case ParseSrc_file_id: - summ = "file ID"; - break; - } - } - if (summ == NULL) { - summ = StringSave ("missing field"); - } else if (need_to_save) { - summ = StringSave (summ); - } - return summ; -} - - -static CharPtr SummarizeParseDst (ValNodePtr dst) -{ - CharPtr summ = NULL; - CharPtr fmt = "%s %s"; - CharPtr feature, field; - ParseDstOrgPtr dst_org; - Boolean need_to_save = TRUE; - FeatureFieldLegalPtr ffp; - - if (dst != NULL) { - switch (dst->choice) { - case ParseDest_defline: - summ = "defline"; - break; - case ParseDest_org: - dst_org = (ParseDstOrgPtr) dst->data.ptrvalue; - if (dst_org != NULL) { - if (dst_org->field != NULL) { - switch (dst_org->field->choice) { - case SourceQualChoice_textqual: - summ = GetSourceQualName (dst_org->field->data.intvalue); - break; - case SourceQualChoice_location: - summ = "location"; - break; - case SourceQualChoice_origin: - summ = "origin"; - break; - } - } - } - break; - case ParseDest_featqual: - ffp = (FeatureFieldLegalPtr) dst->data.ptrvalue; - if (ffp != NULL) { - feature = GetFeatureNameFromFeatureType (ffp->type); - field = GetFeatQualName (ffp->field); - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (feature) + StringLen (field))); - sprintf (summ, fmt, feature, field); - need_to_save = FALSE; - } - break; - case ParseDest_dbxref: - summ = "dbxref"; - break; - } - } - if (summ == NULL) { - summ = StringSave ("missing field"); - } else if (need_to_save) { - summ = StringSave (summ); - } - return summ; -} - - -static CharPtr SummarizeParseAction (ParseActionPtr p) -{ - CharPtr field_from = NULL, field_to = NULL; - CharPtr existing_text = NULL, text_portion = NULL; - CharPtr summ = NULL; - CharPtr fmt = "Parse %s from %s to %s (%s)"; - - if (p == NULL) { - summ = StringSave ("No action"); - } else { - field_from = SummarizeParseSrc (p->src); - field_to = SummarizeParseDst (p->dest); - existing_text = SummarizeExistingText (p->existing_text); - text_portion = SummarizeTextPortion (p->portion); - summ = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (text_portion) + StringLen (field_from) + StringLen (field_to) + StringLen (existing_text))); - sprintf (summ, fmt, text_portion, field_from, field_to, existing_text); - text_portion = MemFree (text_portion); - field_from = MemFree (field_from); - field_to = MemFree (field_to); - } - return summ; -} - - static CharPtr SummarizeApplyFeatureAction (ApplyFeatureActionPtr a) { CharPtr label = NULL; @@ -17407,98 +17508,6 @@ static CharPtr SummarizeRemoveFeatureAction (RemoveFeatureActionPtr a) } -static CharPtr SummarizeRemoveDescriptorAction (RemoveDescriptorActionPtr a) -{ - CharPtr label = NULL; - CharPtr constraint, str; - CharPtr fmt = "Remove %s"; - CharPtr constraint_fmt = "Remove %s descriptors %s"; - - if (a == NULL) { - str = StringSave ("No action"); - } else { - label = GetDescriptorNameFromDescriptorType (a->type); - constraint = SummarizeConstraintSet (a->constraint); - if (constraint == NULL) { - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (label))); - sprintf (str, fmt, label); - } else { - str = (CharPtr) MemNew (sizeof (Char) * (StringLen (constraint_fmt) + StringLen (label) + StringLen (constraint))); - sprintf (str, constraint_fmt, label, constraint); - constraint = MemFree (constraint); - } - } - - return str; -} - - -static CharPtr SummarizeAutodefClauseListType (Uint2 clause_list_type) -{ - CharPtr str = "complete sequence"; - - switch (clause_list_type) { - case Autodef_list_type_feature_list: - str = "list fFeatures"; - break; - case Autodef_list_type_complete_sequence: - str = "complete sequence"; - break; - case Autodef_list_type_complete_genome: - str = "complete genome"; - break; - } - return str; -} - - -static CharPtr SummarizeAutodefAction (AutodefActionPtr autodef) -{ - CharPtr label = NULL, mod_name; - CharPtr str = NULL; - CharPtr fmt = "Autodef %s"; - CharPtr modifiers_fmt = " with modifier"; - Int4 len; - ValNodePtr mod_names = NULL, vnp; - - if (autodef == NULL) { - str = StringSave ("No action"); - } else { - label = SummarizeAutodefClauseListType (autodef->clause_list_type); - len = StringLen (fmt) + StringLen (label); - if (autodef->modifiers != NULL) { - len += StringLen (modifiers_fmt) + 2; - for (vnp = autodef->modifiers; vnp != NULL; vnp = vnp->next) { - mod_name = GetSourceQualName (vnp->data.intvalue); - len += StringLen (mod_name) + 3; - ValNodeAddPointer (&mod_names, 0, mod_name); - } - } - - str = (CharPtr) MemNew (sizeof (Char) * (len + 1)); - sprintf (str, fmt, label); - - if (autodef->modifiers != NULL) { - StringCat (str, modifiers_fmt); - if (autodef->modifiers->next != NULL) { - StringCat (str, "s"); - } - for (vnp = mod_names; vnp != NULL; vnp = vnp->next) { - StringCat (str, " "); - StringCat (str, vnp->data.ptrvalue); - if (vnp->next != NULL) { - StringCat (str, ","); - } - } - } - - mod_names = ValNodeFree (mod_names); - } - - return str; -} - - static CharPtr SummarizeConvertSourceOptions (ValNodePtr vnp) { ConvertFromCDSOptionsPtr options; @@ -17815,6 +17824,12 @@ static CharPtr SummarizeEditFeatureLocationAction (EditFeatureLocationActionPtr case LocationEditType_convert: action_label = SummarizeConvertLoc (a->action->data.intvalue); break; + case LocationEditType_extend_5: + action_label = StringSave ("Extend 5' end of feature to end of sequence"); + break; + case LocationEditType_extend_3: + action_label = StringSave ("Extend 3' end of feature to end of sequence"); + break; } if (action_label == NULL) { str = StringSave ("Invalid action"); @@ -17835,7 +17850,6 @@ static CharPtr SummarizeEditFeatureLocationAction (EditFeatureLocationActionPtr } - static CharPtr SummarizeMacroAction (ValNodePtr vnp) { CharPtr str = NULL; @@ -17868,6 +17882,30 @@ static CharPtr SummarizeMacroAction (ValNodePtr vnp) case MacroActionChoice_autodef: str = SummarizeAutodefAction (vnp->data.ptrvalue); break; + case MacroActionChoice_removesets: + str = StringSave ("Remove duplicate nested sets"); + break; + case MacroActionChoice_trim_junk_from_primer_seq: + str = StringSave ("Trim junk from primer seqs"); + break; + case MacroActionChoice_fix_usa_and_states: + str = StringSave ("Fix USA and state abbreviations in publications"); + break; + case MacroActionChoice_trim_stop_from_complete_cds: + str = StringSave ("Remove trailing * from complete coding regions"); + break; + case MacroActionChoice_synchronize_cds_partials: + str = StringSave ("Synchronize coding region partials"); + break; + case MacroActionChoice_adjust_for_consensus_splice: + str = StringSave ("Adjust coding regions for consensus splice sites"); + break; + case MacroActionChoice_fix_pub_caps: + str = SummarizeFixPubCapsAction(vnp->data.ptrvalue); + break; + case MacroActionChoice_remove_seg_gaps: + str = StringSave ("Remove seg-gaps"); + break; default: str = StringSave ("Invalid action"); break; @@ -17893,6 +17931,7 @@ typedef struct tabcolumnconfigdlg { DialoG cdsgeneprot; DialoG pub_field; DialoG molinfo_field; + DialoG struccomm_field; ButtoN change_mrna; GrouP apply_options; @@ -17923,7 +17962,8 @@ typedef enum { eTabColumnConfig_Apply_CommentDescriptor, eTabColumnConfig_Apply_Defline, eTabColumnConfig_Apply_Keyword, - eTabColumnConfig_Apply_Molinfo + eTabColumnConfig_Apply_Molinfo, + eTabColumnConfig_Apply_StructuredCommentField } ETabColumnConfig; typedef enum { @@ -18136,8 +18176,13 @@ static Pointer TabColumnConfigDialogToChoice (DialoG d) f->field = ValNodeNew (NULL); f->field->choice = FieldType_molinfo_field; f->field->data.ptrvalue = DialogToPointer (dlg->molinfo_field); + } else if (val == eTabColumnConfig_Apply_StructuredCommentField) { + f->field = ValNodeNew (NULL); + f->field->choice = FieldType_struc_comment_field; + f->field->data.ptrvalue = DialogToPointer (dlg->struccomm_field); } + if (dlg->erase_when_blank == NULL) { f->skip_blank = TRUE; } else { @@ -18203,6 +18248,7 @@ static void TabColumnActionChange (PopuP p) Hide (dlg->cdsgeneprot); Hide (dlg->pub_field); Hide (dlg->molinfo_field); + Hide (dlg->struccomm_field); Disable (dlg->change_mrna); Enable (dlg->apply_options); Hide (dlg->match_grp); @@ -18216,6 +18262,7 @@ static void TabColumnActionChange (PopuP p) Hide (dlg->cdsgeneprot); Hide (dlg->pub_field); Hide (dlg->molinfo_field); + Hide (dlg->struccomm_field); config = DialogToPointer (dlg->dialog); if (config == NULL || !IsFieldTypeCDSProduct (config->field)) { SafeDisable (dlg->change_mrna); @@ -18235,6 +18282,7 @@ static void TabColumnActionChange (PopuP p) Show (dlg->cdsgeneprot); Hide (dlg->pub_field); Hide (dlg->molinfo_field); + Hide (dlg->struccomm_field); config = DialogToPointer (dlg->dialog); if (config == NULL || !IsFieldTypeCDSProduct (config->field)) { SafeDisable (dlg->change_mrna); @@ -18253,6 +18301,7 @@ static void TabColumnActionChange (PopuP p) Hide (dlg->cdsgeneprot); Show (dlg->pub_field); Hide (dlg->molinfo_field); + Hide (dlg->struccomm_field); Enable (dlg->apply_options); Hide (dlg->match_grp); EnableNonTextOptions (dlg->existing_text); @@ -18266,6 +18315,7 @@ static void TabColumnActionChange (PopuP p) Hide (dlg->cdsgeneprot); Hide (dlg->pub_field); Hide (dlg->molinfo_field); + Hide (dlg->struccomm_field); Enable (dlg->apply_options); Hide (dlg->match_grp); Disable (dlg->change_mrna); @@ -18279,6 +18329,7 @@ static void TabColumnActionChange (PopuP p) Hide (dlg->cdsgeneprot); Hide (dlg->pub_field); Hide (dlg->molinfo_field); + Hide (dlg->struccomm_field); Enable (dlg->apply_options); Hide (dlg->match_grp); Disable (dlg->change_mrna); @@ -18292,12 +18343,27 @@ static void TabColumnActionChange (PopuP p) Hide (dlg->cdsgeneprot); Hide (dlg->pub_field); Show (dlg->molinfo_field); + Hide (dlg->struccomm_field); Enable (dlg->apply_options); Hide (dlg->match_grp); Disable (dlg->change_mrna); DisableMultiOptions (dlg->existing_text); DisableNonTextOptions (dlg->existing_text); break; + case eTabColumnConfig_Apply_StructuredCommentField: + Show (dlg->qual_grp); + Hide (dlg->src_qual); + Hide (dlg->feature_field_grp); + Hide (dlg->cdsgeneprot); + Hide (dlg->pub_field); + Hide (dlg->molinfo_field); + Show (dlg->struccomm_field); + Enable (dlg->apply_options); + Hide (dlg->match_grp); + Disable (dlg->change_mrna); + DisableMultiOptions (dlg->existing_text); + EnableNonTextOptions (dlg->existing_text); + break; } if (dlg != NULL && dlg->change_notify != NULL) { (dlg->change_notify) (dlg->change_userdata); @@ -18417,6 +18483,9 @@ static void TabColumnConfigToDialog (DialoG d, Pointer data) } else if (f->field->choice == FieldType_molinfo_field) { SetValue (dlg->column_action, eTabColumnConfig_Apply_Molinfo); PointerToDialog (dlg->molinfo_field, f->field->data.ptrvalue); + } else if (f->field->choice == FieldType_struc_comment_field) { + SetValue (dlg->column_action, eTabColumnConfig_Apply_StructuredCommentField); + PointerToDialog (dlg->struccomm_field, f->field->data.ptrvalue); } SafeSetStatus (dlg->change_mrna, f->match_mrna); @@ -18531,6 +18600,7 @@ NLM_EXTERN DialoG TabColumnConfigDialog PopupItem (dlg->column_action, "Apply to Definition Line"); PopupItem (dlg->column_action, "Apply to Keyword"); PopupItem (dlg->column_action, "Apply to Molinfo"); + PopupItem (dlg->column_action, "Apply to Structured Comment Field"); SetValue (dlg->column_action, 1); k = HiddenGroup (p, 0, 0, NULL); @@ -18553,6 +18623,7 @@ NLM_EXTERN DialoG TabColumnConfigDialog dlg->cdsgeneprot = CDSGeneProtFieldDialog (dlg->qual_grp, TabColumnConfigFieldChange, dlg); dlg->pub_field = PubFieldDialog (dlg->qual_grp, TabColumnConfigFieldChange, dlg); dlg->molinfo_field = MolinfoFieldChoiceDialog (dlg->qual_grp, TabColumnConfigFieldChange, dlg); + dlg->struccomm_field = StructuredCommentFieldDialog (dlg->qual_grp, TabColumnConfigFieldChange, dlg); AlignObjects (ALIGN_CENTER, (HANDLE) dlg->match_grp, (HANDLE) dlg->qual_grp, NULL); dlg->change_mrna = CheckBox (p, "Also change mRNA product name", TabColumnConfigButtonChange); @@ -18798,10 +18869,18 @@ static void PopulateTabConfigListColumnListDoc (DialoG d) {0, 0, 1, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, FALSE}, /* action */ {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE} /* first value */ }; + Int4 scroll_pos = 0; + BaR sb_vert; + dlg = (TabColumnConfigListDlgPtr) GetObjectExtra (d); if (dlg == NULL) return; + sb_vert = GetSlateVScrollBar ((SlatE) dlg->column_list_doc); + if (sb_vert) { + scroll_pos = GetBarValue (sb_vert); + } + Reset (dlg->column_list_doc); ObjectRect (dlg->column_list_doc, &r); @@ -18824,6 +18903,9 @@ static void PopulateTabConfigListColumnListDoc (DialoG d) tmp = MemFree (tmp); } UpdateDocument (dlg->column_list_doc, 0, 0); + if (scroll_pos > 0) { + CorrectBarValue (sb_vert, scroll_pos); + } } |