libvibrant6-dev 6.1.20120620-7 / usr / include / ncbi / dlogutil.h

/*   dlogutil.h
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*            National Center for Biotechnology Information (NCBI)
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government do not place any restriction on its use or reproduction.
*  We would, however, appreciate having the NCBI and the author cited in
*  any work or product based on this material
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
* ===========================================================================
*
* File Name:  dlogutil.h
*
* Author:  Jonathan Kans
*
* Version Creation Date:   1/22/95
*
* $Revision: 6.119 $
*
* File Description: 
*
* Modifications:  
* --------------------------------------------------------------------------
* Date     Name        Description of modification
* -------  ----------  -----------------------------------------------------
*
*
* ==========================================================================
*/

#ifndef _DLOGUTIL_
#define _DLOGUTIL_

#include <vibrant.h>
#include <document.h>
#include <sqnutils.h>
#include <prtutil.h>
#include <asn.h>
#include <objall.h>
#include <objfeat.h>
#include <objfdef.h>
#include <sequtil.h>


#ifdef __cplusplus
extern "C" {
#endif

#define CHANGE_VIEW_NOTABS        0
#define CHANGE_VIEW_FOLDERTABS    1
#define CHANGE_VIEW_TEXTTABS      2
#define CHANGE_VIEW_RADIOBUTTONS  3
#define CHANGE_VIEW_POPUP         4

extern StdPrintOptionsPtr  spop;

extern Boolean SetupPrintOptions (void);
extern void FreePrintOptions (void);

extern EnumFieldAssoc  months_alist [];
extern EnumFieldAssoc  new_pseudogene_alist [];

extern void DatePtrToVibrant (DatePtr dp, PopuP dateMonth, TexT dateDay, TexT dateYear);
extern DatePtr VibrantToDatePtr (PopuP dateMonth, TexT dateDay, TexT dateYear);

extern ValNodePtr AddStringToValNodeChain (ValNodePtr head, CharPtr str, Uint1 choice);

#define DESCRIPTOR_FORM_BLOCK       \
  FORM_MESSAGE_BLOCK                \
  DialoG          data;


#define FEATURE_FORM_BLOCK            \
  DESCRIPTOR_FORM_BLOCK               \
  DialoG            commonRadio;      \
  GrouP             commonSubGrp [8]; \
  Int2              commonPage;       \
  ButtoN            partial;          \
  ButtoN            exception;        \
  ButtoN            pseudo;           \
  PopuP             pseudogene;       \
  EnumFieldAssocPtr pseudoalist;      \
  DialoG            experiment;       \
  DialoG            inference;        \
  TexT              comment;          \
  TexT              title;            \
  TexT              exceptText;       \
  PopuP             evidence;         \
  Handle            gene;             \
  PopuP             genePopup;        \
  LisT              geneList;         \
  ValNodePtr        geneNames;        \
  GrouP             useGeneXref;      \
  GrouP             newGeneGrp;       \
  TexT              geneSymbol;       \
  TexT              geneAllele;       \
  TexT              geneDesc;         \
  TexT              locusTag;         \
  TexT              geneSynonym;      \
  ButtoN            editGeneBtn;      \
  TexT              protXrefName;     \
  TexT              protXrefDesc;     \
  DialoG            location;         \
  DialoG            product;          \
  DialoG            featcits;         \
  DialoG            dbxrefs;          \
  DialoG            gbquals;          \
  DialoG            usrobjext;        \
  TexT              featid;           \
  TexT              fidxref;          \
  ButtoN            leave_dlg_up;     \
  UserObjectPtr     goTermUserObj;    \
  Int2              badInfAttempts;   \
  Boolean           acceptBadInf;

typedef struct descform {
  DESCRIPTOR_FORM_BLOCK
} DescriptorForm, PNTR DescriptorFormPtr;

typedef struct featform {
  FEATURE_FORM_BLOCK
} FeatureForm, PNTR FeatureFormPtr;

extern Int2 LIBCALLBACK DescriptorPropagate (Pointer data);
extern Boolean DescFormReplaceWithoutUpdateProc (ForM f);
extern Boolean DescFormReplaceWithoutUpdateProcEx (ForM f, Boolean feature_or_molinfo_change);
extern void StdDescFormActnProc (ForM f);
extern void StdDescFormActnProcNoFeatureChangeNoMolInfoChange (ForM f);

extern void StdDescFormCleanupProc (GraphiC g, VoidPtr data);

extern Boolean FeatFormReplaceWithoutUpdateProc (ForM f);
extern void StdFeatFormActnProc (ForM f);

extern void StdSeqFeatPtrToFeatFormProc (ForM f, Pointer data);
extern void StdInitFeatFormProc (ForM f);
extern void StdFeatFormCleanupProc (GraphiC g, VoidPtr data);
extern void StdFeatFormAcceptButtonProc (ButtoN b);

extern void InferenceDialogToGBQuals (DialoG d, SeqFeatPtr sfp, Boolean convertBadToNote);
extern void GBQualsToInferenceDialog (DialoG d, SeqFeatPtr sfp);

/*
extern void ExtendGeneFeatIfOnMRNA (Uint2 entityID, SeqEntryPtr sep);
*/

extern OMUserDataPtr ItemAlreadyHasEditor (Uint2 entityID, Uint4 itemID, Uint2 itemtype, Uint2 procid);
extern Uint2 GetProcIdForItemEditor (Uint2 entityID, Uint2 itemID, Uint1 itemtype, Uint2 subinputtype);
extern OMUserDataPtr EntityAlreadyHasViewer (Uint2 entityID);
extern Boolean MakeViewerIndependent (Uint2 entityID, OMUserDataPtr omudp);

extern Int2 LIBCALLBACK StdVibrantEditorMsgFunc (OMMsgStructPtr ommsp);

extern Boolean TestInference (FeatureFormPtr ffp, CharPtr badInfQual, size_t len, CharPtr badInfMssg);

extern void InitPseudogenePopup (FeatureFormPtr ffp, PopuP p, Boolean ispseudo, CharPtr pseudogene, Boolean indexerVersion);

/*****************************************************************************
*
*   Various specific spreadsheet or editor dialogs.
*
*****************************************************************************/

extern DialoG CreateAuthorDialog (GrouP prnt, Uint2 rows, Int2 spacing);

extern DialoG CreateDateDialogEx (GrouP prnt, CharPtr title, Int4 start_year, Int4 num_years);
extern DialoG CreateDateDialog (GrouP prnt, CharPtr title);

extern DialoG CreateAffilDialog (GrouP prnt, CharPtr title);
extern DialoG CreatePublisherAffilDialog (GrouP prnt, CharPtr title);
extern DialoG CreateProceedingsDialog (GrouP prnt, CharPtr title);

/* The Ext versions split the affil dialogs into two superimposed pages,
   both of which are initially hidden, that can go in separate folder tabs */

extern DialoG CreateExtAffilDialog (GrouP prnt, CharPtr title,
                                    GrouP PNTR grp1, GrouP PNTR grp2);
extern DialoG CreateExtPublisherAffilDialog (GrouP prnt, CharPtr title,
                                             GrouP PNTR grp1, GrouP PNTR grp2);
extern DialoG CreateExtProceedingsDialog (GrouP prnt, CharPtr title,
                                          GrouP PNTR grp1, GrouP PNTR grp2);

extern GrouP CreateCommonFeatureGroup (GrouP h, FeatureFormPtr ffp,
                                       SeqFeatPtr sfp, Boolean hasGeneControl,
                                       Boolean hasCitationTab);
extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp,
                                         SeqFeatPtr sfp, Boolean hasGeneControl,
                                         Boolean hasCitationTab, Boolean hasGeneSuppress);
extern void UpdateGeneLocation (SeqFeatPtr gene, SeqLocPtr old_feat_loc,
                                SeqLocPtr new_feat_loc, Uint2 entityID);
extern void PopulateGenePopup (FeatureFormPtr ffp);
extern void SeqFeatPtrToCommon (FeatureFormPtr ffp, SeqFeatPtr sfp);
extern void SetNewFeatureDefaultInterval (FeatureFormPtr ffp);
extern DialoG CreateImportFields (GrouP h, CharPtr name, SeqFeatPtr sfp, Boolean allowProductGBQual);
extern DialoG NewCreateImportFields (GrouP h, CharPtr name, SeqFeatPtr sfp, Boolean allowProductGBQual);


extern DialoG CreateIntervalEditorDialog (GrouP h, CharPtr title, Uint2 rows,
                                          Int2 spacing, SeqEntryPtr sep,
                                          Boolean nucsOK, Boolean protsOK);

typedef void (*IntEdPartialProc) (FeatureFormPtr ffp, Boolean partial5, Boolean partial3, Boolean order);

extern DialoG CreateIntervalEditorDialogEx (GrouP h, CharPtr title, Uint2 rows,
                                            Int2 spacing, SeqEntryPtr sep,
                                            Boolean nucsOK, Boolean protsOK,
                                            Boolean useBar, Boolean showPartials,
                                            Boolean allowGaps, FeatureFormPtr ffp,
                                            IntEdPartialProc proc);
                                            
extern DialoG CreateIntervalEditorDialogExEx (GrouP h, CharPtr title, Uint2 rows,
                                              Int2 spacing, SeqEntryPtr sep,
                                              Boolean nucsOK, Boolean protsOK,
                                              Boolean useBar, Boolean showPartials,
                                              Boolean allowGaps, FeatureFormPtr ffp,
                                              IntEdPartialProc proc, 
                                              Boolean use_aln, Boolean show_seqid,
                                              TaglistCallback tlp_callback, 
                                              Pointer callback_data,
                                              Boolean allow_nulls_in_list);

extern void DisplayErrorMessages (CharPtr title, ValNodePtr err_list);

extern Boolean AdjustFromForGap (Int4Ptr p_from, SeqAlignPtr salp, Int4 aln_len, Int4 aln_row);
extern Boolean AdjustToForGap (Int4Ptr p_to, SeqAlignPtr salp, Int4 aln_row);
                                            
extern void SetSequenceAndStrandForIntervalPage (DialoG d);                                            
extern void StdFeatIntEdPartialCallback (FeatureFormPtr ffp, Boolean partial5, Boolean partial3, Boolean order);

extern DialoG CreateVisibleStringDialog (GrouP h, Uint2 rows,
                                         Int2 spacing, Int2 width);

extern DialoG CreateDbtagDialog (GrouP h, Uint2 rows, Int2 spacing,
                                 Int2 width1, Int2 width2);

/*****************************************************************************
*
*   Miscellaneous functions.
*
*****************************************************************************/

/*
*  The TextViewProcsPtr may be registered with a call to SetAppProperty
*  e.g., SetAppProperty ("TextDisplayForm", &viewprocs), where viewprocs
*  is a persistent structure filled with callback function pointers specific
*  for a given application.
*/

typedef struct textviewprocs {
  WndActnProc      activateForm;
  WndActnProc      closeForm;
  WndActnProc      createMenus;

  FormMessageFunc  handleMessages;

  Int2             minPixelWidth;
  Int2             minPixelHeight;
  Boolean          useScrollText;

  FonT             displayFont;

  Char             screenMode;

} TextViewProcs, PNTR TextViewProcsPtr;

typedef CharPtr (*Nlm_RepopulateViewer) PROTO ((Pointer userdata));
typedef Pointer (*Nlm_RepopulateDataFree) PROTO ((Pointer userdata));

extern void LaunchGeneralTextViewer (CharPtr path, CharPtr title);
extern void LaunchAsnTextViewer (Pointer from, AsnWriteFunc writefunc, CharPtr title);
extern void LaunchGeneralTextViewerWithRepopulate 
         (CharPtr path, CharPtr title, 
         Nlm_RepopulateViewer repopulate_func, Pointer repopulate_data,
         Nlm_RepopulateDataFree free_data_func);

extern Boolean FileToScrollText (TexT t, CharPtr path);
extern void ScrollTextToFile (TexT t, CharPtr path);

extern void FileToClipboard (CharPtr path);

/*
*  The StdEditorProcsPtr may be registered with a call to SetAppProperty
*  e.g., SetAppProperty ("StdEditorForm", &viewprocs), where viewprocs
*  is a persistent structure filled with callback function pointers specific
*  for a given application.
*/

typedef struct stdeditorprocs {
  WndActnProc      activateForm;
  FormMessageFunc  handleMessages;

  Boolean          duplicateExisting;

  Char             screenMode;

} StdEditorProcs, PNTR StdEditorProcsPtr;

#ifndef WIN_MAC
extern void CreateStdEditorFormMenus (WindoW w);
#endif

/*
*  When duplicating instead of editing, the editors call the following
*  function to change the baseFormPtr itemID and itemtype to the closest
*  Bioseq or BioseqSet, thus adding the new item to that parent.
*/

extern Boolean SetClosestParentIfDuplicating (BaseFormPtr bfp);

/*
*  The HelpMessageFunc may be registered with a call to SetAppProperty
*  e.g., SetAppProperty ("HelpMessageProc", helpproc), where helpproc
*  is an application-supplied callback function that takes character
*  strings for the heading and section.
*/

typedef void (*HelpMessageFunc) (CharPtr, CharPtr);

/*****************************************************************************
*
*   Miscellaneous functions.
*
*****************************************************************************/

extern CharPtr SaveStringFromTextAndStripNewlines (TexT t);
extern CharPtr StripNewlines (CharPtr str);
extern void NewlinesToTildes (CharPtr str);

/* GetRidOfEmptyFeatsDescStrings takes either an entityID or a SeqEntryPtr */

extern void GetRidOfEmptyFeatsDescStrings (Uint2 entityID, SeqEntryPtr sep);

/*****************************************************************************
*
*   LaunchEntrezURL constructs a web-Entrez URL query.  Parameter choices are:
*
*     Database      Report Formats
*
*      PubMed        DocSum, Brief, Abstract, Citation, MEDLINE, ASN.1, ExternalLink
*      Nucleotide    DocSum, Brief, GenBank, ASN.1, FASTA, ExternalLink
*      Protein       DocSum, Brief, GenPept, ASN.1, FASTA, ExternalLink
*      Genome        DocSum, Brief, ASN.1, ExternalLink
*      Popset        DocSum, Brief, ASN.1, FASTA, ExternalLink
*      Structure     DocSum, Brief
*      OMIM          DocSum, Text, Synopsis, Variants, MiniMIM, ASN.1, ExternalLink
*      Taxonomy      DocSum, Brief, TxInfo, TxTree, ExternalLink
*
*****************************************************************************/

NLM_EXTERN void LaunchEntrezURL (CharPtr database, Int4 uid, CharPtr format);

/* this function creates a dialog for selecting publications in a record */
extern DialoG FeatCitEditDialog (GrouP parent, Uint2 entityID);

/* This structure and the functions after it are used for
 * modal dialogs with two choices.
 */
typedef struct modalacceptcancel
{
  Boolean accepted;
  Boolean cancelled; 
  Boolean third_option; 
} ModalAcceptCancelData, PNTR ModalAcceptCancelPtr;

extern void ModalAcceptButton (ButtoN b);
extern void ModalCancelButton (ButtoN b);
extern void ModalThirdOptionButton (ButtoN b);
NLM_EXTERN Int4 ThreeOptionsDlg (CharPtr title_txt, CharPtr explain_txt, CharPtr opt1, CharPtr opt2, CharPtr opt3);

typedef void (*TableDisplayDblClick) PROTO((PoinT, CharPtr, CharPtr, Pointer));
typedef Boolean (*TableDisplayLeftInRed) PROTO ((Int4, ValNodePtr, Pointer));
extern DialoG TableDisplayDialog (GrouP parent, Int4 width, Int4 height,
                                  Int4 frozen_header, Int4 frozen_left,
                                  TableDisplayDblClick dbl_click,
                                  Pointer dbl_click_data,
                                  TableDisplayLeftInRed,
                                  Pointer left_in_red_data);
extern DialoG EditableTableDisplayDialog (GrouP parent, Int4 width, Int4 height,
                                  Int4 frozen_header, Int4 frozen_left,
                                  TableDisplayDblClick dbl_click,
                                  Pointer dbl_click_data,
                                  TableDisplayLeftInRed left_in_red,
                                  Pointer left_in_red_data);
extern ValNodePtr FreeTableDisplayRowList (ValNodePtr row_list);
extern void PrintTableDisplayRowListToFile (ValNodePtr row_list, FILE *fp);
extern ValNodePtr CopyTableDisplayRowList (ValNodePtr row_list);
extern CharPtr GetRowListCellText (ValNodePtr row_list, Int4 row, Int4 column);
extern FonT GetTableDisplayDefaultFont (void);


#define TALL_SELECTION_LIST 6
#define SHORT_SELECTION_LIST 4
/* err_msg is the message to put in the results from TestDialog if nothing is selected */
/* choice_list should be a valnode list of strings to use for the names of the choices. */
/* All is automatically included as a choice if allow_multi is true. */
/* The ValNodeList returned is a list of integers indicating the position of the item
 * in the list: 1 is the first item, 2 is the second item, etc. */
extern DialoG SelectionDialog 
(GrouP h,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 CharPtr                  err_msg,
 ValNodePtr               choice_list,
 Int2                     list_height);

extern DialoG SelectionDialogEx 
(GrouP h,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 CharPtr                  err_msg,
 ValNodePtr               choice_list,
 Int2                     list_height,
 Boolean                  force_list);

extern DialoG SelectionDialogExEx 
(GrouP h,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 CharPtr                  err_msg,
 ValNodePtr               choice_list,
 Int2                     list_height,
 Boolean                  force_list,
 Boolean                  force_popup);


/* This function should free just the data associated with the ValNode */
typedef void (*FreeValNodeProc) PROTO ((ValNodePtr));
/* This function should copy just this ValNode, not the chain */
typedef ValNodePtr (*CopyValNodeDataProc) PROTO ((ValNodePtr));
typedef ValNodePtr (*RemapValNodeProc) PROTO ((ValNodePtr));
typedef Boolean (*MatchValNodeProc) PROTO ((ValNodePtr, ValNodePtr));
typedef CharPtr (*NameFromValNodeProc) PROTO ((ValNodePtr));

extern DialoG ValNodeSelectionDialogExEx
(GrouP h,
 ValNodePtr               choice_list,
 Int2                     list_height,
 NameFromValNodeProc      name_proc,
 FreeValNodeProc          free_vn_proc,
 CopyValNodeDataProc      copy_vn_proc,
 MatchValNodeProc         match_vn_proc,
 CharPtr                  err_name,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 Boolean                  force_list,
 Boolean                  force_popup,
 RemapValNodeProc         remap_vn_proc);
extern DialoG ValNodeSelectionDialogEx
(GrouP h,
 ValNodePtr               choice_list,
 Int2                     list_height,
 NameFromValNodeProc      name_proc,
 FreeValNodeProc          free_vn_proc,
 CopyValNodeDataProc      copy_vn_proc,
 MatchValNodeProc         match_vn_proc,
 CharPtr                  err_name,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 Boolean                  force_list, 
 RemapValNodeProc         remap_vn_proc);
extern DialoG ValNodeSelectionDialog
(GrouP h,
 ValNodePtr               choice_list,
 Int2                     list_height,
 NameFromValNodeProc      name_proc,
 FreeValNodeProc          free_vn_proc,
 CopyValNodeDataProc      copy_vn_proc,
 MatchValNodeProc         match_vn_proc,
 CharPtr                  err_name,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi);

extern DialoG EnumAssocSelectionDialog 
(GrouP                 h,
 Nlm_EnumFieldAssocPtr eap,
 CharPtr               err_name,
 Boolean               allow_multi,
 Nlm_ChangeNotifyProc  change_notify,
 Pointer               change_userdata);

extern CharPtr ValNodeStringName (ValNodePtr vnp);
extern void ValNodeSimpleDataFree (ValNodePtr vnp);
extern ValNodePtr ValNodeStringCopy (ValNodePtr vnp);
extern Boolean ValNodeChoiceMatch (ValNodePtr vnp1, ValNodePtr vnp2);
extern Boolean ValNodeStringMatch (ValNodePtr vnp1, ValNodePtr vnp2);

/* choice list is a list of strings */
extern DialoG StringComboDialog
(GrouP h,
 ValNodePtr               choice_list,
 Int2                     list_height,
 Int2                     list_width,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata);

extern DialoG SequenceSelectionDialog 
(GrouP h,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 Boolean                  show_nucs,
 Boolean                  show_prots,
 Uint2                    entityID);

extern DialoG SequenceSelectionDialogEx 
(GrouP h,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 Boolean                  allow_none,
 Boolean                  show_nucs,
 Boolean                  show_prots,
 Uint2                    entityID,
 Int4                     list_height);

extern DialoG SubSourceTypeDialog 
(GrouP                    h,
 Int2                     list_height,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 Boolean                  force_list,
 Boolean                  include_note);

extern DialoG OrgModTypeDialog 
(GrouP                    h,
 Int2                     list_height,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata,
 Boolean                  allow_multi,
 Boolean                  force_list,
 Boolean                  include_note);


typedef CharPtr (*GetClickableItemText) (ValNodePtr item_list);

extern DialoG 
CreateClickableListDialog 
(GrouP h, 
 CharPtr label1, 
 CharPtr label2,
 ClickableCallback item_single_click_callback,
 ClickableCallback item_double_click_callback,
 Pointer         item_click_callback_data,
 GetClickableItemText get_item_text);

extern DialoG 
CreateClickableListDialogEx 
(GrouP h, 
 CharPtr label1, 
 CharPtr label2,
 CharPtr help1,
 CharPtr help2,
 ClickableCallback item_single_click_callback,
 ClickableCallback item_double_click_callback,
 Pointer         item_click_callback_data,
 GetClickableItemText get_item_text,
 Int4            left_width,
 Int4            right_width,
 Boolean         horizontal,
 Boolean         show_find);

extern DialoG 
CreateClickableListDialogExEx 
(GrouP h, 
 CharPtr label1, 
 CharPtr label2,
 CharPtr help1,
 CharPtr help2,
 ClickableCallback item_single_click_callback,
 ClickableCallback item_double_click_callback,
 Pointer         item_click_callback_data,
 GetClickableItemText get_item_text,
 Int4            left_width,
 Int4            right_width,
 Boolean         horizontal,
 Boolean         show_find,
 Boolean         display_chosen);

extern DialoG 
CreateClickableListDialogExExEx 
(GrouP h, 
 CharPtr label1, 
 CharPtr label2,
 CharPtr help1,
 CharPtr help2,
 ClickableCallback item_single_click_callback,
 ClickableCallback item_double_click_callback,
 Pointer         item_click_callback_data,
 GetClickableItemText get_item_text,
 Int4            num_item_text_columns,
 Int4            left_width,
 Int4            right_width,
 Boolean         horizontal,
 Boolean         show_find,
 Boolean         display_chosen);

extern void SetClickableListDialogTitles (DialoG d, CharPtr title1, CharPtr title2, CharPtr help1, CharPtr help2);
extern void SetClickableListDisplayChosen (DialoG d, Boolean set);

extern void ScrollToNextClickableTextDescription (CharPtr txt, DialoG d);
extern void ScrollToPreviousClickableTextDescription (CharPtr txt, DialoG d);

extern CharPtr GetSelectedClickableListText (DialoG d);

extern void GetAlignmentsInSeqEntryCallback (SeqAnnotPtr sap, Pointer userdata);
extern void CreateSeqAlignLabel (SeqAlignPtr salp, CharPtr buf, Int4 buf_size);


typedef struct existingtext
{
  Int4    existing_text_choice;
} ExistingTextData, PNTR ExistingTextPtr;

typedef enum {
  eExistingTextChoiceReplaceOld = 1,
  eExistingTextChoiceAppendSemi,
  eExistingTextChoiceAppendSpace,
  eExistingTextChoiceAppendColon,
  eExistingTextChoiceAppendNone,
  eExistingTextChoicePrefixSemi,
  eExistingTextChoicePrefixSpace,
  eExistingTextChoicePrefixColon,
  eExistingTextChoicePrefixNone,
  eExistingTextChoiceLeaveOld,
  eExistingTextChoiceCancel } EExistingTextChoice;

extern CharPtr 
HandleExistingText 
(CharPtr existing_text,
 CharPtr new_text, 
 ExistingTextPtr etp);

extern ExistingTextPtr GetExistingTextHandlerInfo (Int4 num_found, Boolean non_text);

typedef enum {
  EditApplyFindLocation_anywhere = 1,
  EditApplyFindLocation_beginning,
  EditApplyFindLocation_end
} EditApplyFindLocation;

typedef struct applyvalue 
{
  ValNodePtr        field_list;
  ExistingTextPtr   etp;
  CharPtr           new_text;
  CharPtr           text_to_replace;
  EditApplyFindLocation where_to_replace;

} ApplyValueData, PNTR ApplyValuePtr;


typedef struct editapply
{
  CharPtr               find_txt;
  EditApplyFindLocation find_location;
  CharPtr               repl_txt;
  CharPtr               apply_txt;  
} EditApplyData, PNTR EditApplyPtr;

extern EditApplyPtr EditApplyFree (EditApplyPtr eap);
extern EditApplyPtr EditApplyNew (void);

typedef enum {
  eEditApplyChoice_Apply = 0,
  eEditApplyChoice_Edit } EEditApplyChoice;

extern DialoG EditApplyDialog 
(GrouP                    h,
 Int4                     action_choice, 
 CharPtr                  apply_label,
 ValNodePtr               choice_list,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata);

/* For the global inference editor */
typedef struct inferenceparsedata
{
  CharPtr category;
  CharPtr type;
  Boolean same_species;
  CharPtr first_field;
  CharPtr second_field;
} InferenceParseData, PNTR InferenceParsePtr;

extern InferenceParsePtr ParseInferenceText (CharPtr inference);
extern CharPtr InferenceTextFromStruct (InferenceParsePtr ipp);

typedef struct inferencefieldedit
{
  CharPtr field_type;
  Int4 field_choice;
  EditApplyPtr edit_apply;
} InferenceFieldEditData, PNTR InferenceFieldEditPtr;

extern InferenceFieldEditPtr InferenceFieldEditFree (InferenceFieldEditPtr ifep);

typedef enum {
  eInferenceRemove = 0,
  eInferenceEditCategory,
  eInferenceEditType,
  eInferenceApplyTypeFields,
  eInferenceEditTypeFields,
  eNumInferenceEditActions } EInferenceEditAction;


typedef struct inferenceedit {
  EInferenceEditAction action;
  CharPtr category_from;
  CharPtr category_to;
  CharPtr type_from;
  CharPtr type_to;

  InferenceFieldEditPtr field_edit;
} InferenceEditData, PNTR InferenceEditPtr;

extern InferenceEditPtr InferenceEditFree (InferenceEditPtr iep);

extern DialoG CreateInferenceEditDialog 
(GrouP                    h,
 Nlm_ChangeNotifyProc     change_notify,
 Pointer                  change_userdata);

typedef enum {
 eValueEditSimpleText = 0,
 eValueEditTrueFalse,
 eValueEditLatLon,
 eValueEditSpecimenVoucher,
 eNumValueEditors
} EValueEdit;

/* In name_vnp, choice is type of editor, ptrvalue is string with choice name */
typedef struct namevaluepair {
  ValNodePtr name_vnp;
  CharPtr    value;
} NameValuePairData, PNTR NameValuePairPtr;

extern NameValuePairPtr NameValuePairFree (NameValuePairPtr nvp);
extern NameValuePairPtr NameValuePairCopy (NameValuePairPtr nvp);
extern ValNodePtr NameValuePairListFree (ValNodePtr vnp);

#define VALUE_LIST_PARENT_FIELDS \
  DIALOG_MESSAGE_BLOCK \
  TexT note;


typedef struct valuelistparent {
  VALUE_LIST_PARENT_FIELDS
} ValueListParentData, PNTR ValueListParentPtr;


extern DialoG 
ValueListDialog 
(GrouP           h,
 Uint2           num_rows,
 Int2            width,
 ValNodePtr      choice_list,
 ValueListParentPtr parent,
 TaglistCallback change_notify,
 Pointer         change_userdata);

extern DialoG CreateSubSourceDialog (GrouP h, EnumFieldAssocPtr al);
extern DialoG CreateOrgModDialog (GrouP h, EnumFieldAssocPtr al, TexT taxname);

extern Boolean IsNonTextModifier (CharPtr mod_name);


typedef Boolean (*ParseOK) PROTO ((CharPtr));

extern Boolean ParseCollectionDateOk (CharPtr txt);
extern DialoG CollectionDateDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
                               TaglistCallback tlp_callback,
                               Pointer callback_data);

extern DialoG CreateRptUnitRangeDialog (GrouP h, SeqEntryPtr sep, CharPtr name,
                                         TaglistCallback tlp_callback,
                                         Pointer callback_data);

extern void CreateStandardEditMenu (WindoW w);

extern void CleanupEvidenceGBQuals (GBQualPtr PNTR prevgbq);
extern void VisStringDialogToGbquals (SeqFeatPtr sfp, DialoG d, CharPtr qual);

extern void RememberSqnTempFile (CharPtr file);
extern void FreeSqnTempFiles (void);

/* For fixing special characters */
NLM_EXTERN Boolean FixSpecialCharacters (Uint2 entityID);
extern Boolean FixSpecialCharactersForStringsInList (ValNodePtr find_list, CharPtr exp_text, Boolean force_fix);
NLM_EXTERN Boolean FixSpecialCharactersForObject (Uint2 datatype, Pointer objdata, CharPtr msg, Boolean force_fix, BoolPtr changed);

/* for functions that act on all open records */
NLM_EXTERN ValNodePtr GetBaseFormList (void);
NLM_EXTERN ValNodePtr GetViewedSeqEntryList (void);
NLM_EXTERN SeqEntryPtr RestoreFromFileEx (CharPtr path, Boolean convert_seqsubmit_to_pub);
NLM_EXTERN SeqEntryPtr RestoreFromFile (CharPtr path);
NLM_EXTERN Uint2 RestoreEntityIDFromFileEx (CharPtr path, Uint2 entityID, Boolean convert_seqsubmit_to_pub);
NLM_EXTERN Uint2 RestoreEntityIDFromFile (CharPtr path, Uint2 entityID);


NLM_EXTERN Int2 PanelOffsetFromCharOffsetEx (DoC doc, FonT font, Int2 item, Int2 col, Int2 char_offset);
NLM_EXTERN Int2 GetTextSelectCharOffsetEx (PoinT pt, DoC doc, FonT font, Int2 item, Int2 row, Int2 col);
NLM_EXTERN CharPtr GetSelectedDocText (DoC doc, Int2 item_start, Int2 row_start, Int2 col_start, Int2 char_start,
                                       Int2 item_stop, Int2 row_stop, Int2 col_stop, Int2 char_stop,
                                       Int2Ptr only_these_columns, Int2 num_col);


/* for feature replace */
NLM_EXTERN ValNodePtr FeatureReplaceListFree (ValNodePtr vnp);
NLM_EXTERN void ActOnFeatureReplaceList (ValNodePtr list);
NLM_EXTERN DialoG FeatureReplaceListDialog (GrouP h, Int4 width, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
NLM_EXTERN Boolean AddFeaturesToReplaceList (DialoG d, ValNodePtr feature_list);
NLM_EXTERN ValNodePtr RemoveFeaturesFromReplaceList (DialoG d);
NLM_EXTERN ValNodePtr FeatureReplaceListFromSeqAnnot (SeqAnnotPtr sap);
NLM_EXTERN DialoG FeatureSelectListDialog (GrouP h, Int4 width);
NLM_EXTERN ValNodePtr RemoveSelectedFeaturesFromList (DialoG d);
NLM_EXTERN void AddFeaturesToList (DialoG d, ValNodePtr features);
NLM_EXTERN void SortSeqFeatInAnnot (SeqAnnotPtr sap);
NLM_EXTERN SeqFeatPtr GetSelectedNewFeature (DialoG d);
NLM_EXTERN void ScrollToMatchingFeatures (DialoG d, SeqFeatPtr sfp);
NLM_EXTERN Boolean AutomatchFeatures (DialoG d, ValNodePtr PNTR existing_features);

NLM_EXTERN void CloseLog (LogInfoPtr lip);

NLM_EXTERN void TextToFeatID (TexT t, ChoicePtr cp);
NLM_EXTERN void TextToFeatXref (TexT t, SeqFeatPtr sfp);

NLM_EXTERN DialoG DescriptorStreamEditor (GrouP h,  Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
NLM_EXTERN void SetDescriptorStreamEditorIdList (DialoG d, SeqIdPtr sip_list);

#ifdef __cplusplus
}
#endif

#endif /* ndef _DLOGUTIL_ */