xmenu.c

是有关基因比对的经典算法的实现。这对于初学计算生物学的人是非常重要的算法。

        SelectFont(programFont);
	Break(savealnw);
	savealntext=DialogText(savealnw, "", 35, NULL);
	Break(savealnw);
	savegr=HiddenGroup(savealnw, 2, 0, NULL);
	shift(savegr, 60, 20);
	save_ok=PushButton(savegr, "  OK  ", save_proc);
	shift(savegr, 20,0);
	save_can=PushButton(savegr, "CANCEL", CancelWin);

	SetTitle(savealntext, path);
	Show(savealnw);
}

static void read_file_window(char *title,char *prompt,char *filename,void read_proc(ButtoN but))
{
	GrouP readgr;
	ButtoN read_ok, read_can;
	GrouP maing;

	SelectFont(systemFont);
	stdCharWidth=CharWidth('A');
	stdLineHeight=LineHeight();
	readfilew=FixedWindow(-50, -33, -10, -10, title,RemoveWin);

	maing=HiddenGroup(readfilew,2,0,NULL);
	SetGroupSpacing(maing,0,10);

	shift(readfilew, 0, 20);
	make_prompt(readfilew, prompt);
        stdLineHeight=18;
        SelectFont(programFont);
	Break(readfilew);
	readfiletext=DialogText(readfilew, "", 35, NULL);
	if (filename != NULL) SetTitle(readfiletext, filename);
	Break(readfilew);
	readgr=HiddenGroup(readfilew, 2, 0, NULL);
	shift(readgr, 60, 20);
	read_ok=PushButton(readgr, "  OK  ", read_proc);
	shift(readgr, 20,0);
	read_can=PushButton(readgr, "CANCEL", CancelWin);

	Show(readfilew);
}

static void CancelWin (ButtoN but)
{
	Remove(ParentWindow(but));
}

static void SearchStr(ButtoN but)
{

/* reset the current position */

	find_pos.seq=0;
	find_pos.res=-1;

/* find the next occurrence of the string */
	SearchStringAgain(but);


}

static void SearchStringAgain(ButtoN but)
{
	int i,j,ix,length;
	int seq,res,start_res;
	Boolean in_string,found;
	panel_data ndata,sdata;

	GetTitle(findtext, filename, FILENAMELEN);
	stripspace(filename);

	strncpy(find_string,filename,MAXFINDSTR);
	length=strlen(find_string);
	if(length==0) return;
	for(i=0;i<length;i++)
		find_string[i]=toupper(find_string[i]);

        GetPanelExtra(active_panel.names,&ndata);
        GetPanelExtra(active_panel.seqs,&sdata);

	in_string=FALSE;
	found=FALSE;
	start_res=0;
	ix=0;
	seq=find_pos.seq;
	res=find_pos.res+1;
        while (seq<ndata.nseqs)
	{
                if(ndata.selected[seq]==TRUE)
                {
        		while (res<sdata.ncols)
			{
				if(sdata.lines[seq][res]==find_string[ix])
				{
					if(in_string==FALSE) 
						start_res=res;
					ix++;
					in_string=TRUE;
				}
				else if(in_string==TRUE)
				{
					res=start_res;
					ix=0;
					in_string=FALSE;
				}
				if(ix==length)
				{
					find_pos.seq=seq;
					find_pos.res=start_res;
					found=TRUE;
					break;
				}
				res++;
				while(res<sdata.ncols && sdata.lines[seq][res]=='-')
					res++;
			}
                }
		if(found) break;
		seq++;
		res=0;
	}


	if(found==FALSE)
		info("String %s not found",find_string);
	else
	{
		info("String %s in sequence %s, column %d",find_string,names[find_pos.seq+1],find_pos.res+1);
	}
}

static void SavePSSeqFile(ButtoN but)
{
	char *ps_file;

	GetTitle(savepstext, filename, FILENAMELEN);
	stripspace(filename);

        ps_file=(char *)ckalloc(FILENAMELEN*sizeof(char));
	strcpy(ps_file,filename); 

	GetTitle(pspartext, filename, FILENAMELEN);
	stripspace(filename);

	strcpy(ps_par_file,filename); 

	write_ps_file(seq_panel,ps_file,ps_par_file,pagesize,orientation,
		ps_header,ps_ruler,ps_resno,
		resize,first_printres,last_printres,blocklen,ps_curve);

	info("Postscript file %s written",ps_file);
	ckfree(ps_file);

}

static void SavePSPrf1File(ButtoN but)
{
	char *ps_file;
	char *ps_par_file;

	GetTitle(savepstext, filename, FILENAMELEN);
	stripspace(filename);

        ps_file=(char *)ckalloc(FILENAMELEN*sizeof(char));
	strcpy(ps_file,filename); 

	GetTitle(pspartext, filename, FILENAMELEN);
	stripspace(filename);

        ps_par_file=(char *)ckalloc(FILENAMELEN*sizeof(char));
	strcpy(ps_par_file,filename); 

	write_ps_file(prf_panel[0],ps_file,ps_par_file,pagesize,orientation,
		ps_header,ps_ruler,ps_resno,
		resize,first_printres,last_printres,blocklen,ps_curve);

	info("Postscript file %s written",ps_file);
	ckfree(ps_file);

}

static void SavePSPrf2File(ButtoN but)
{
	char *ps_file;
	char *ps_par_file;

	GetTitle(savepstext, filename, FILENAMELEN);
	stripspace(filename);

        ps_file=(char *)ckalloc(FILENAMELEN*sizeof(char));
	strcpy(ps_file,filename); 

	GetTitle(pspartext, filename, FILENAMELEN);
	stripspace(filename);

        ps_par_file=(char *)ckalloc(FILENAMELEN*sizeof(char));
	strcpy(ps_par_file,filename); 

	write_ps_file(prf_panel[1],ps_file,ps_par_file,pagesize,orientation,
		ps_header,ps_ruler,ps_resno,
		resize,first_printres,last_printres,blocklen,ps_curve);

	info("Postscript file %s written",ps_file);
	ckfree(ps_file);

}

static void SaveSeqFile(ButtoN but)
{
	write_file(1,nseqs,firstres,lastres);
	seq_panel.modified=FALSE;
	info("File %s saved",filename);
}

static void SavePrf1File(ButtoN but)
{
	write_file(1,profile1_nseqs,firstres,lastres);
	prf_panel[0].modified=FALSE;
	info("File %s saved",filename);
}

static void SavePrf2File(ButtoN but)
{
	write_file(profile1_nseqs+1,nseqs,firstres,lastres);
	prf_panel[1].modified=FALSE;
	info("File %s saved",filename);
}

/* this is equivalent to open_alignment_output(), but uses the window
interface to input file names */

static Boolean open_aln_files(void)
{
	char path[FILENAMELEN];

	if(!output_clustal && !output_nbrf && !output_gcg &&
		 !output_phylip && !output_gde && !output_nexus) {
                error("You must select an alignment output format");
                return FALSE;
        }

	if(output_clustal) {
		GetTitle(cl_outtext,filename,FILENAMELEN);
		stripspace(filename);
		if((clustal_outfile = open_explicit_file(
			filename))==NULL) return FALSE;
	}
	if(output_nbrf) {
		GetTitle(pir_outtext,filename,FILENAMELEN);
		stripspace(filename);
		if((nbrf_outfile = open_explicit_file(
			filename))==NULL) return FALSE;
	}
	if(output_gcg) {
		GetTitle(msf_outtext,filename,FILENAMELEN);
		stripspace(filename);
		if((gcg_outfile = open_explicit_file(
			filename))==NULL) return FALSE;
	}
	if(output_phylip) {
		GetTitle(phylip_outtext,filename,FILENAMELEN);
		stripspace(filename);
		if((phylip_outfile = open_explicit_file(
			filename))==NULL) return FALSE;
	}
	if(output_gde) {
		GetTitle(gde_outtext,filename,FILENAMELEN);
		stripspace(filename);
		if((gde_outfile = open_explicit_file(
			filename))==NULL) return FALSE;
	}
	if(output_nexus) {
		GetTitle(nexus_outtext,filename,FILENAMELEN);
		stripspace(filename);
		if((nexus_outfile = open_explicit_file(
			filename))==NULL) return FALSE;
	}

	if(save_log)
	{
        	get_path(seqname,path);
        	strcpy(save_log_filename,path);
        	strcat(save_log_filename,"log");
		if ((save_log_fd=fopen(save_log_filename,"a"))==NULL)
			error("Cannot open log file %s",save_log_filename);
	}

	return TRUE;
}

static void write_file(int fseq, int lseq, int fres, int lres)
{
	int i,length=0;
	FILE *outfile;

	GetTitle(savealntext, filename, FILENAMELEN);
	stripspace(filename);

	outfile=open_explicit_file(filename); 

        for (i=fseq;i<=lseq;i++)
           if (length < seqlen_array[i]) length = seqlen_array[i];

	if(fres<1) fres=1;
	if(lres<1) lres=length;
	length=lres-fres+1;
 
        if(save_format==CLUSTAL) {
                clustal_out(outfile, fres, length, fseq, lseq);
                fclose(outfile);
                info("CLUSTAL format file created  [%s]",filename);
        }
        else if(save_format==PIR)  {
                nbrf_out(outfile, fres, length, fseq, lseq);
                fclose(outfile);
                info("NBRF/PIR format file created  [%s]",filename);
        }
        else if(save_format==MSF)  {
                gcg_out(outfile, fres, length, fseq, lseq);
                fclose(outfile);
                info("GCG/MSF format file created  [%s]",filename);
        }
        else if(save_format==PHYLIP)  {
                phylip_out(outfile, fres, length, fseq, lseq);
                fclose(outfile);
                info("PHYLIP format file created  [%s]",filename);
        }
        else if(save_format==GDE)  {
                gde_out(outfile, fres, length, fseq, lseq);
                fclose(outfile);
                info("GDE format file created  [%s]",filename);
        }
        else if(save_format==NEXUS)  {
                nexus_out(outfile, fres, length, fseq, lseq);
                fclose(outfile);
                info("NEXUS format file created  [%s]",filename);
        }


	if (Visible(savealnw))
	{
		Remove(savealnw);
		savealnw=NULL;
	}


}

static void SaveTreeWin (IteM item)
{
	GrouP savegr;
	ButtoN save_ok, save_can;
	char path[FILENAMELEN];

	if (empty)
	{
		error("No file loaded");
		return;
	}
        if (nseqs < 2)
	{
                error("Alignment has only %d sequences",nseqs);
                return;
        }

	SelectFont(systemFont);
	stdCharWidth=CharWidth('A');
	stdLineHeight=LineHeight();
	savetreew=FixedWindow(-50, -33, -10, -10, "CREATE TREE",RemoveWin);
	shift(savetreew, 0, 20);
	make_prompt(savetreew, "SAVE TREE AS :");
	Advance(savetreew);
	shift(savetreew, 0, -10);
	stdLineHeight=18;
	SelectFont(programFont);
	savetreetext=DialogText(savetreew, "", 35, NULL);
	SelectFont(systemFont);
	stdLineHeight=15;
	Break(savetreew);
	savegr=HiddenGroup(savetreew, 2, 0, NULL);
	shift(savegr, 140, 20);
	save_ok=PushButton(savegr, "  OK  ", CreateAlignTree);
	shift(savegr, 20, 0);
	save_can=PushButton(savegr, "CANCEL", CancelWin);

	get_path(seqname,path);
	strcat(path,"dnd");
  
	SetTitle(savetreetext, path);
	Show(savetreew);
}

static void DrawTreeWin (IteM item)
{
	GrouP drawgr;
	GrouP output_list;
	ButtoN draw_ok, draw_can;
	char path[FILENAMELEN];
	char name[FILENAMELEN];

	if (empty)
	{
		error("No file loaded");
		return;
	}
        if (nseqs < 2)
	{
                error("Alignment has only %d sequences",nseqs);
                return;
        }

	get_path(seqname,path);

	SelectFont(systemFont);
	stdCharWidth=CharWidth('A');
	stdLineHeight=LineHeight();
	drawtreew=FixedWindow(-50, -33, -10, -10, "DRAW TREE",RemoveWin);
	output_list=HiddenGroup(drawtreew, 2, 0, NULL);
	if (output_tree_clustal)
	{
		make_prompt(output_list, "SAVE CLUSTAL TREE AS :");
		drawnjtreetext=DialogText(output_list, "", 35, NULL);
		strcpy(name,path);
        	strcat(name,"nj");
		SetTitle(drawnjtreetext, name);
		Break(output_list);
	}
	if (output_tree_phylip)
	{
		make_prompt(output_list, "SAVE PHYLIP TREE AS :");
		drawphtreetext=DialogText(output_list, "", 35, NULL);
		strcpy(name,path);
        	strcat(name,"ph");
		SetTitle(drawphtreetext, name);
		Break(output_list);
	}
	if (output_tree_distances)
	{
		make_prompt(output_list, "SAVE DISTANCE MATRIX AS :");
		drawdsttreetext=DialogText(output_list, "", 35, NULL);
		strcpy(name,path);
        	strcat(name,"dst");
		SetTitle(drawdsttreetext, name);
		Break(output_list);
	}
	if (output_tree_nexus)
	{
		make_prompt(output_list, "SAVE NEXUS TREE AS :");
		drawnxstreetext=DialogText(output_list, "", 35, NULL);
		strcpy(name,path);
        	strcat(name,"tre");
		SetTitle(drawnxstreetext, name);
		Break(output_list);
	}
	SelectFont(systemFont);
	stdLineHeight=15;
	Break(drawtreew);
	drawgr=HiddenGroup(drawtreew, 2, 0, NULL);
	shift(drawgr, 140, 20);
	draw_ok=PushButton(drawgr, "  OK  ", DrawTree);
	shift(drawgr, 20, 0);
	draw_can=PushButton(drawgr, "CANCEL", CancelWin);


	Show(drawtreew);
}

static void BootstrapTreeWin (IteM item)
{
	GrouP bootgr;
	ButtoN boot_ok, boot_can;
	TexT seed,ntrials;
	char name[FILENAMELEN];
	char path[FILENAMELEN];
	char str[FILENAMELEN];
	GrouP output_list;

	if (empty)
	{
		error("No file loaded");
		return;
	}
        if (nseqs < 2)
	{
                error("Alignment has only %d sequences",nseqs);
                return;
        }

	get_path(seqname,path);

	SelectFont(systemFont);
	stdCharWidth=CharWidth('A');
	stdLineHeight=LineHeight();
	boottreew=FixedWindow(-50, -33, -10, -10, "BOOTSTRAP TREE",RemoveWin);
        make_prompt(boottreew, "Random number generator seed [1-1000] :");
	Advance(boottreew);
	sprintf(str,"%4d",boot_ran_seed);
        seed=DialogText(boottreew, str, 4,set_ran_seed);
	Break(boottreew);
        make_prompt(boottreew, "Number of bootstrap trials [1-10000] :");
	Advance(boottreew);
	sprintf(str,"%5d",boot_ntrials);
        ntrials=DialogText(boottreew, str, 5,set_ntrials);
	Break(boottreew);

	output_list=HiddenGroup(boottreew, 2, 0, NULL);