/*********************************************************************************************** * * * *   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 6int 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);