xmenu.c

经典生物信息学多序列比对工具clustalw

/***********************************************************************************************
 *
 *
 *
 *   History 
 *
 *   27.3.2002   - color parameter chooser can browse filenames like load sequences - Jose
 *   16.1.2002   - remove the 'cut sequences' dialog box, not needed - Jise
 *   17.1.2002   - 'Remove positions that contain gaps in all sequences ?'  removed, no need for confirmation - Toby
 *
 *
 *
*/

#include <stdarg.h>
#include <string.h>

#include <vibrant.h>
#include <document.h>

/* #include <ncbi.h>   ramu   for time funs */

#include "clustalw.h"
#include "xmenu.h"


static void RemoveWin(WindoW w);
static void QuitWinW(WindoW w);
static void QuitWinI(IteM i);
static void QuitHelpW(WindoW w);
static void QuitHelpB(ButtoN b);
static void SearchStrWin (IteM item);
static void SavePSSeqWin (IteM item);
static void SavePSPrf1Win (IteM item);
static void SavePSPrf2Win (IteM item);
static void SaveSeqFileWin (IteM item);
static void SavePrf1FileWin (IteM item);
static void SavePrf2FileWin (IteM item);
static void OpenColorParWin (IteM item);
static void SearchStr(ButtoN but);
static void SavePSSeqFile(ButtoN but);
static void SavePSPrf1File(ButtoN but);
static void SavePSPrf2File(ButtoN but);
static void SaveSeqFile(ButtoN but);
static void SavePrf1File(ButtoN but);
static void SavePrf2File(ButtoN but);
static void SaveScoresWin (IteM item);
static void SaveScores(ButtoN but);
static void OpenColorPar(ButtoN but);
static void CancelWin(ButtoN but);
static void SaveTreeWin (IteM item);
static void CAlignWin (IteM item);
static void RealignSeqsWin (IteM item);
static void RealignSeqRangeWin (IteM item);
static void DrawTreeWin (IteM item);
static void AlignFromTreeWin(IteM item);
static void PrfPrfAlignWin(IteM item);
static void PrfPrfTreeAlignWin(IteM item);
static void SeqPrfAlignWin(IteM item);
static void SeqPrfTreeAlignWin(IteM item);
static void BootstrapTreeWin (IteM item);
static void CreateAlignTree(ButtoN but);
static void CompleteAlign(ButtoN but);
static void RealignSeqs(ButtoN but);
static void RealignSeqRange(ButtoN but);
static void DrawTree(ButtoN but);
static void AlignFromTree(ButtoN but);
static void PrfPrfAlign(ButtoN but);
static void PrfPrfTreeAlign(ButtoN but);
static void SeqPrfAlign(ButtoN but);
static void SeqPrfTreeAlign(ButtoN but);
static void BootstrapTree(ButtoN but);
static void OpenSeqFile (IteM item);
static void AppendSeqFile (IteM item);
static void OpenPrf1File (IteM item);
static void OpenPrf2File (IteM item);
static void ScoreWin(IteM item);
static void SegmentWin(IteM item);
static void ScoreSegments(ButtoN but);
static void PWParameters(IteM item);
static void MultiParameters(IteM item);
static void GapParameters(IteM item);
static void SSParameters(IteM item);
static void OutputParameters(IteM item);
static void OutputTreeParameters(IteM item);
static void HelpProc(IteM item);
static void DefColorPar(IteM item);
static void BlackandWhite(IteM item);
static void set_reset_new_gaps(IteM i);
static void set_reset_all_gaps(IteM i);
static void SearchStringAgain(ButtoN but);

static PopuP make_toggle(GrouP g,CharPtr title,CharPtr true_text, CharPtr false_text,
				 Boolean *value,PupActnProc SetProc);
static PrompT make_scale(GrouP g,CharPtr title,int length,int value,int max,BarScrlProc SetProc);
static PrompT make_prompt(GrouP g,CharPtr title);

static void CutSequences(IteM item);
static void PasteSequences(IteM item);
static void RemoveGaps(IteM item);
static void RemoveGapPos(IteM item);

static void SelectSeqs(IteM item);
static void SelectPrf1(IteM item);
static void SelectPrf2(IteM item);
static void MergeProfiles(IteM item);
static void ClearSeqs(IteM item);
 
static void cut_multiplem(void);
static void cut_profile1(void);
static void cut_profile2(void);
static void ssave(int j);
static void sscpy(int i,int j);
static void sload(int i);
static void clear_seqrange(spanel p);
static void select_seqs(spanel p,Boolean flag);
static void clear_seg_exceptions(spanel p);

static void make_menu_headers(WindoW w);
static void make_help_menu(void);
static void make_score_menu(void);
static void make_file_menu(void);
static void make_edit_menu(void);
static void make_align_menu(void);
static void make_tree_menu(void);
static void make_color_menu(void);

static void save_aln_window(int prf_no,char *title,char *prompt,void save_proc(ButtoN but));
static void save_ps_window(int prf_no,char *prompt,void save_proc(ButtoN but));
static void read_file_window(char *title,char *prompt,char *filename,void read_proc(ButtoN but));
static void do_align_window(WindoW *alignw,TexT *treetext,Boolean treestatus,char *title,void align_proc(ButtoN but));
static void do_palign_window(WindoW *alignw,TexT *tree1text,TexT *tree2test,Boolean treestatus,char *title,void align_proc(ButtoN but));
static Boolean open_aln_files(void);
static void write_file(int fseq,int lseq,int fres,int lres);


Boolean x_menus=FALSE;

int    mheader = 2; /* maximum header lines */
int    mfooter = 1; /* maximum footer lines */
int max_mlines = 20;      /*   multiple align display length */
int min_mlines = 10;      /*   multiple align display length */
int max_plines = 8;     /*   profile align display length */
int min_plines1 = 5;     /*   profile align display length */
int min_plines2 = 3;     /*   profile align display length */

Boolean aln_mode = MULTIPLEM;
Boolean window_displayed = FALSE;

int    save_format = CLUSTAL;
Boolean fixed_prf_scroll = FALSE;
int loffset,boffset,toffset;
int roffset;
int poffset;

int score_cutoff=5;    /* cutoff for residue exceptions */
int score_hwin=5;    /* half window for summing alignment column scores */
int score_scale=5;
int segment_dnascale=5;
int length_cutoff=1;    /* length cutoff for segment exceptions */
Boolean residue_exceptions=FALSE;
Boolean segment_exceptions=FALSE;
int score_matnum=4;
char score_mtrxname[FILENAMELEN];
int segment_matnum=3;
char segment_mtrxname[FILENAMELEN];
int score_dnamatnum=1;
char score_dnamtrxname[FILENAMELEN];
int segment_dnamatnum=1;
char segment_dnamtrxname[FILENAMELEN];

Boolean output_ss;
Boolean output_gp;

extern char     revision_level[];
extern Boolean interactive;

extern char seqname[];
extern char     outfile_name[];
extern char    profile1_name[];
extern char    profile2_name[];
extern char     usermtrxname[], pw_usermtrxname[];
extern char     dnausermtrxname[], pw_dnausermtrxname[];

extern Boolean usemenu;
extern Boolean use_tree_file;
extern Boolean use_tree1_file,use_tree2_file;
extern Boolean  dnaflag;
extern sint     nseqs;
extern sint    profile1_nseqs;
extern sint profile_no;
extern sint     max_aa;
extern sint     *seqlen_array;
extern char     **seq_array;
extern char     **names, **titles;
extern Boolean empty;
extern Boolean profile1_empty, profile2_empty;
extern sint     gap_pos1, gap_pos2;
extern Boolean use_ambiguities;


extern float    gap_open,      gap_extend;
extern float    dna_gap_open,  dna_gap_extend;
extern float    prot_gap_open, prot_gap_extend;
extern float    pw_go_penalty,      pw_ge_penalty;
extern float    dna_pw_go_penalty,  dna_pw_ge_penalty;
extern float    prot_pw_go_penalty, prot_pw_ge_penalty;
extern sint    wind_gap,ktup,window,signif;
extern sint    dna_wind_gap, dna_ktup, dna_window, dna_signif;
extern sint    prot_wind_gap,prot_ktup,prot_window,prot_signif;
extern sint        helix_penalty;
extern sint        strand_penalty;
extern sint        loop_penalty;
extern sint        helix_end_minus;
extern sint        helix_end_plus;
extern sint        strand_end_minus;
extern sint        strand_end_plus;
extern sint        helix_end_penalty;
extern sint        strand_end_penalty;
extern sint     divergence_cutoff;
extern sint     gap_dist;
extern sint boot_ntrials;               /* number of bootstrap trials */
extern unsigned sint boot_ran_seed;     /* random number generator seed */

extern sint        matnum,pw_matnum;
extern char     mtrxname[], pw_mtrxname[];
extern sint        dnamatnum,pw_dnamatnum;
extern char     dnamtrxname[], pw_dnamtrxname[];

extern MatMenu matrix_menu;
extern MatMenu pw_matrix_menu;
extern MatMenu dnamatrix_menu;

extern Boolean  quick_pairalign;
extern sint        matnum,pw_matnum;
extern Boolean  neg_matrix;
extern float    transition_weight;
extern char     hyd_residues[];
extern Boolean  no_var_penalties, no_hyd_penalties, no_pref_penalties;
extern Boolean         use_endgaps;
extern Boolean         endgappenalties;
extern Boolean  output_clustal, output_nbrf, output_phylip, output_gcg, output_gde, output_nexus;
extern Boolean output_fasta; /* Ramu */

extern Boolean  save_parameters;
extern Boolean  output_tree_clustal, output_tree_phylip, output_tree_distances, output_tree_nexus, output_pim;
extern Boolean  lowercase; /* Flag for GDE output - set on comm. line*/
extern Boolean  cl_seq_numbers;

extern Boolean  seqRange;

extern sint     output_order;
extern sint     *output_index;
extern Boolean  reset_alignments_new;               /* DES */
extern Boolean  reset_alignments_all;               /* DES */

extern FILE     *clustal_outfile, *gcg_outfile, *nbrf_outfile, *phylip_outfile;
extern FILE     *gde_outfile, *nexus_outfile;
extern FILE     *fasta_outfile;

extern sint     max_aln_length;

extern Boolean tossgaps;  /* Ignore places in align. where ANY seq. has a gap*/
extern Boolean kimura;    /* Use correction for multiple substitutions */
extern sint    bootstrap_format;      /* bootstrap file format */

extern sint output_struct_penalties;
extern Boolean use_ss1, use_ss2;
extern char *res_cat1[];
extern char *res_cat2[];

extern char     *amino_acid_codes;

PrompT   message;           /* used in temporary message window */

static Char filename[FILENAMELEN]; /* used in temporary file selection window */

Boolean mess_output=TRUE;
Boolean save_log=FALSE;
FILE *save_log_fd=NULL;
static char save_log_filename[FILENAMELEN];
static IteM save_item1,save_item2,exc_item;

spanel  seq_panel;        /* data for multiple alignment area */
spanel  prf_panel[2];       /* data for profile alignment areas */
spanel  active_panel;       /* 'in-use' panel -scrolling,clicking etc. */
static range selected_seqs;           /* sequences selected by clicking on names */
static range selected_res;           /* residues selected by clicking on seqs */
int firstres, lastres;	/* range of alignment for saving as ... */
 
/* data for Search function */

char find_string[MAXFINDSTR]="";
aln_pos find_pos;

/* arrays for storing clustalw data for cut-and-paste sequences */
static sint     *saveseqlen_array=NULL;
static char     **saveseq_array=NULL;
static char     **savenames=NULL, **savetitles=NULL;
sint     ncutseqs=0;

FonT datafont,helpfont;
WindoW mainw=NULL;
WindoW messagew=NULL;
WindoW readfilew=NULL;
WindoW savealnw=NULL;
WindoW savescoresw=NULL;
WindoW savepsw=NULL;
WindoW findw=NULL;
WindoW calignw=NULL;
WindoW ralignw=NULL;
WindoW rralignw=NULL;
WindoW talignw=NULL;
WindoW palignw=NULL;
WindoW salignw=NULL;
WindoW scorew=NULL;
WindoW exceptionw=NULL;
TexT savealntext;
TexT savescorestext;
TexT savepstext;
TexT findtext;
TexT pspartext;
TexT ctreetext;
TexT rtreetext;
TexT rrtreetext;
TexT ttreetext;
TexT ptree1text,ptree2text;
TexT streetext;
TexT readfiletext;
WindoW savetreew=NULL;
TexT savetreetext;
WindoW drawtreew=NULL;
TexT drawnjtreetext;
TexT drawphtreetext;
TexT drawdsttreetext;
TexT drawnxstreetext;

TexT drawpimtext;

WindoW boottreew=NULL;
TexT bootnjtreetext;
TexT bootphtreetext;
TexT bootnxstreetext;
TexT blocklentext;
PrompT mattext,pwmattext,dnamattext,pwdnamattext,scoremattext,segmentmattext;
PrompT scorednamattext,segmentdnamattext;
GrouP seg_matrix_list,score_matrix_list;
GrouP seg_dnamatrix_list,score_dnamatrix_list;
GrouP matrix_list,pw_matrix_list,dnamatrix_list,pw_dnamatrix_list;

TexT cl_outtext,pir_outtext,msf_outtext,phylip_outtext,gde_outtext,nexus_outtext;
TexT fasta_outtext; /* Ramu */

GrouP slow_para,fast_para;
GrouP  seq_display,prf1_display,prf2_display;

MenU   filem,alignm,editm,treem,colorm;
menu_item file_item,align_item,edit_item,tree_item,color_item;
MenU   scorem,helpmenu;
menu_item score_item,help_item;
IteM segment_item;
IteM bw_item,defcol_item,usercol_item;
IteM new_gaps_item,all_gaps_item;
WindoW helpw[MAXHELPW];
int numhelp=0;

PopuP modetext,flisttext;
ButtoN pscrolltext;

ButtoN selFonts;

PopuP show_seg_toggle;
PrompT residue_cutofftext;
PrompT length_cutofftext;
PrompT scorescaletext;
PrompT segmentdnascaletext;

#define MAXFONTS 6
int nfonts=6;   /*shoud be MAXFONTS ................ ramu */
int av_font[MAXFONTS]={8,10,12,14,18,24};
int font_size=1;

int ncolors=0;
int ncolor_pars=0;
color color_lut[MAXCOLORS+1];
char def_protpar_file[]="colprot.par";
char def_dnapar_file[]="coldna.par";
char *explicit_par_file = NULL;
char *par_file = NULL;
int    inverted = TRUE;
int usebw=FALSE,usedefcolors=TRUE,useusercolors=FALSE;

char ps_par_file[FILENAMELEN]="colprint.par";
int pagesize=A4;
int orientation=LANDSCAPE;
Boolean ps_header=TRUE;
Boolean ps_ruler=TRUE;
Boolean resize=TRUE;
int first_printres=0,last_printres=0,blocklen;
Boolean ps_curve=TRUE;
Boolean ps_resno=TRUE;
PoinT display_pos;
int namewidth,seqwidth; /* fixed widths of sequence display areas */

Boolean         realign_endgappenalties=TRUE;
Boolean         align_endgappenalties=FALSE;

char helptext[MAXHELPLENGTH];




/* ramu  */

#include <time.h>
#include <math.h>
#include <unistd.h>
#include <pwd.h>
#include <sys/times.h>

float cputime(float *seconds);  /*  Ramu ,   need's reset function */

float cputime(float *seconds)
{
  struct tms buf;
  static time_t last=0, first;
  static int calls=0;
  int hertz=sysconf(_SC_CLK_TCK);
  time_t this;

  /* get the current number of user and system cpu ticks */

  times(&buf);
  this = buf.tms_utime + buf.tms_stime;

  /* if this is the first call then this is time zero */

  if ( !calls ) {
    first = this;
    calls = -1; 
  }
  else
      this = this - first;
  if(seconds)
      *seconds = ((float)(this - last))/(float)hertz;
  last = this;
  return ((float)this)/(float)hertz;
}

/*  Ramu   */


/* main subroutine called from clustalx.c, initialises windows and enters a
   forever loop monitoring user input */

void x_menu(void)
{
	int i,n;
	char font[30];
	char tstr[30];
	int height;
	PrompT   fsize;
	RecT wr,r,r1;
 

/*  make the pulldown menu bar  */

#ifdef WIN_MAC
	MenU   m;

        m=AppleMenu (NULL);
        DeskAccGroup (m);
	make_menu_headers(NULL);
#endif
#ifndef UNIX
	ProcessUpdatesFirst(FALSE);
#endif

	sprintf(tstr,"Clustal%s",revision_level);
/*#ifdef WIN_MSWIN
	mainw = FixedWindow (-50,-33,-10,-10,tstr,QuitWinW);
#else*/
	mainw = DocumentWindow (-50,-33,-10,-10,tstr,QuitWinW,ResizeWindowProc);
/*#endif*/	SetGroupSpacing(mainw,0,10);
	SetGroupSpacing(mainw,0,10);
 
	x_menus=TRUE;

#ifndef WIN_MAC
	make_menu_headers(mainw);
#endif
/* decide if we're starting in profile or sequence mode */
	if (!profile1_empty) aln_mode=PROFILEM;
	else aln_mode=MULTIPLEM;

	make_file_menu();
	make_edit_menu();
	make_align_menu();
	make_tree_menu();
	make_color_menu();
	make_score_menu();
	make_help_menu();

/*  add a button to switch between multiple and profile alignment modes */

	modetext=PopupList(mainw,TRUE,set_aln_mode);
	PopupItem(modetext,"Multiple Alignment Mode");
	PopupItem(modetext,"Profile Alignment Mode");
	if(aln_mode==MULTIPLEM)
		SetValue(modetext,1);
	else
		SetValue(modetext,2);

	sprintf(font, "%s,%d,%c", "courier", av_font[font_size], 'm');
        datafont=ParseFont(font);

	sprintf(font, "%s,%d,%c", "courier", 10, 'm');
        helpfont=ParseFont(font);

	Advance(mainw);
	shift(mainw,20,0);

/*  add a button to select font size */
	fsize=StaticPrompt(mainw,"Font Size:",0,dialogTextHeight,systemFont,'r');
	Advance(mainw);
	flisttext=PopupList(mainw,TRUE,set_font_size);
	for(i=0;i<nfonts;i++)
	{
		sprintf(tstr,"%d",av_font[i]);
		PopupItem(flisttext,tstr);