if (par_file != NULL)    ckfree(par_file);  par_file=(char *)ckalloc(FILENAMELEN*sizeof(char));  if (!GetInputFileName (par_file,FILENAMELEN,"par","")) return;       /* GetTitle(readfiletext, filename, FILENAMELEN); */  /*  stripspace(filename); */   if (explicit_par_file != NULL)    ckfree(explicit_par_file);  explicit_par_file=(char *)ckalloc(FILENAMELEN*sizeof(char));  /*  if (par_file != NULL)    ckfree(par_file);    par_file=(char *)ckalloc(FILENAMELEN*sizeof(char));     strcpy(explicit_par_file,filename); */  strcpy(explicit_par_file,par_file);  /*strcpy(par_file,filename); */  info("Loading color file: %s\n",par_file);  init_color_parameters(par_file);  if (Visible(readfilew))    {      Remove(readfilew);      readfilew=NULL;    }  if (aln_mode == MULTIPLEM)    color_seqs();  else    {      color_prf1();      color_prf2();    }  usebw=FALSE;  usedefcolors=FALSE;  useusercolors=TRUE;  SetStatus(bw_item,usebw);  SetStatus(defcol_item,usedefcolors);  SetStatus(usercol_item,useusercolors);  info("Done.");}static void RemoveGapPos(IteM item){	int i,j,sl;	Boolean sel=FALSE;	if (nseqs==0)	{		Message(MSG_OK,"No file loaded.");		return;	}	/*  no need for a confirmation!  Ramu	if (Message(MSG_YN,"Remove positions that contain gaps in all sequences ?")==ANS_NO)		return;	*/	if(aln_mode==MULTIPLEM)	{		remove_gap_pos(1,nseqs,0);		load_aln(seq_panel,0,nseqs-1,FALSE);	}	else	{		remove_gap_pos(1,profile1_nseqs,1);		load_aln(prf_panel[0],0,profile1_nseqs-1,FALSE);		remove_gap_pos(profile1_nseqs+1,nseqs,2);		load_aln(prf_panel[1],profile1_nseqs,nseqs-1,FALSE);	}	/*	info("Gap positions removed.");*/	info("All the columns that contains only the gaps, are removed!");}static void RemoveGaps(IteM item){	int i,j,sl;	panel_data data;	Boolean sel=FALSE;	if (nseqs==0)	{		Message(MSG_OK,"No file loaded.");		return;	}	GetPanelExtra(active_panel.names,&data);	for (i=0;i<data.nseqs;i++)		if(data.selected[i]==TRUE)		{			sel=TRUE;			break;		}	if(sel==FALSE)	{		Message(MSG_OK,"Select sequences by clicking on the names.");		return;	}	if (Message(MSG_YN,"Remove gaps from selected sequences ?")==ANS_NO)		return;	for (i=data.firstseq+1;i<=data.firstseq+data.nseqs;i++)		if(data.selected[i-data.firstseq-1]==TRUE)		{                	sl=0;                	for(j=1;j<=seqlen_array[i];++j) {                        	if((seq_array[i][j] == gap_pos1) ||                        	   (seq_array[i][j] == gap_pos2)) continue;                        	++sl;                        	seq_array[i][sl]=seq_array[i][j];                	}                        seq_array[i][sl+1]=-3;                	seqlen_array[i]=sl;		}	load_aln(active_panel,data.firstseq,data.firstseq+data.nseqs-1,FALSE);	active_panel.modified=TRUE;	info("Gaps in selected sequences removed.");}static void CutSequences(IteM item){	int i,pos;	Boolean sel=FALSE;	panel_data data;	if (nseqs==0)	{		Message(MSG_OK,"No file loaded.");		return;	}	GetPanelExtra(active_panel.names,&data);	for (i=0;i<data.nseqs;i++)		if(data.selected[i]==TRUE)		{			sel=TRUE;			pos=i;			break;		}	if(sel==FALSE)	{		Message(MSG_OK,"Select sequences to be cut by clicking on the names.");		return;	}	/*	if(ncutseqs>0)	{		if (Message(MSG_YN,"The previously cut sequences will be lost.\nDo you want to continue?")==ANS_NO) return;	}	*/	if (saveseqlen_array!=NULL) ckfree(saveseqlen_array);	if (saveseq_array!=NULL)	{		for(i=0;i<ncutseqs;i++)		{			if (saveseq_array[i]!=NULL) ckfree(saveseq_array[i]);		}		ckfree(saveseq_array);	}	if (savetitles!=NULL)	{		for(i=0;i<ncutseqs;i++)		{			if (savetitles[i]!=NULL) ckfree(savetitles[i]);		}		ckfree(savetitles);	}	if (savenames!=NULL)	{		for(i=0;i<ncutseqs;i++)		{			if (savenames[i]!=NULL) ckfree(savenames[i]);		}		ckfree(savenames);	}	ncutseqs=0;	savenames=(char **)ckalloc((data.nseqs+1) * sizeof(char *));	savetitles=(char **)ckalloc((data.nseqs+1) * sizeof(char *));	saveseq_array=(char **)ckalloc((data.nseqs+1) * sizeof(char *));	saveseqlen_array=(sint *)ckalloc((data.nseqs+1) * sizeof(sint));	for(i=0;i<data.nseqs;i++)	{		savenames[i]=NULL;		savetitles[i]=NULL;		saveseq_array[i]=NULL;	}	if (data.prf_no == 0)		cut_multiplem();	else if (data.prf_no == 1)		cut_profile1();	else if (data.prf_no == 2)		cut_profile2();	GetPanelExtra(active_panel.names,&data);	if(pos>=data.nseqs) pos=data.nseqs-1;	if(data.nseqs>0)		data.selected[pos]=TRUE;	SetPanelExtra(active_panel.names,&data);	DrawPanel(active_panel.names);	active_panel.modified=TRUE;	info("Cut %d sequences.",ncutseqs);}static void cut_multiplem(void){	int i,j;	panel_data data;        GetPanelExtra(active_panel.names,&data);	for (i=data.nseqs;i>0;i--)	{		if(data.selected[i-1]==TRUE)		{			ssave(i);			for(j=i;j<data.nseqs;j++)				sscpy(j,j+1);		}	}        nseqs-=ncutseqs;        if (nseqs<=0) empty=TRUE;	if (ncutseqs>0)		if(nseqs<=data.vseqs)			load_aln(active_panel,0,nseqs-1,TRUE);		else			load_aln(active_panel,0,nseqs-1,FALSE);}static void cut_profile1(void){	int i,j;	panel_data data;        GetPanelExtra(active_panel.names,&data);	for (i=data.nseqs;i>0;i--)	{		if(data.selected[i-1]==TRUE)		{			ssave(i);			for(j=i;j<nseqs;j++)				sscpy(j,j+1);		}	}        profile1_nseqs-=ncutseqs;	nseqs-=ncutseqs;        if (profile1_nseqs<=0) profile1_empty=TRUE;        if (nseqs<=0) empty=TRUE;	if (ncutseqs>0)	{		if(profile1_nseqs<=data.vseqs)			load_aln(active_panel,0,profile1_nseqs-1,TRUE);		else			load_aln(active_panel,0,profile1_nseqs-1,FALSE);		if (!profile2_empty)			load_aln(prf_panel[1],profile1_nseqs,nseqs-1,FALSE);	}}static void cut_profile2(void){	int i,j;	panel_data data;        GetPanelExtra(active_panel.names,&data);	for (i=data.nseqs;i>0;i--)	{		if(data.selected[i-1]==TRUE)		{			ssave(i+profile1_nseqs);			for(j=i+profile1_nseqs;j<nseqs;j++)				sscpy(j,j+1);		}	}        nseqs-=ncutseqs;        if (nseqs-profile1_nseqs<=0) profile2_empty=TRUE;        if (nseqs<=0) empty=TRUE;	if (ncutseqs>0)		if(nseqs-profile1_nseqs<=data.vseqs)			load_aln(active_panel,profile1_nseqs,nseqs-1,FALSE);		else			load_aln(active_panel,profile1_nseqs,nseqs-1,TRUE);}static void PasteSequences(IteM item){	int insert;	int i,n;	panel_data data;	if (ncutseqs<=0)	{		Message(MSG_OK,"No sequences available for pasting.\n"                  " Cut selected sequences first.");		 return;	}	GetPanelExtra(active_panel.names,&data);	n=ncutseqs;	insert=-1;        if (data.nseqs>0)        {                for(i=data.nseqs-1;i>=0;i--)                        if(data.selected[i]==TRUE)                        {                                insert=i;                                break;                        }                if (insert==-1)                {                        Message(MSG_OK,"Select a sequence by clicking on the name.\n"                        " Cut sequences will be pasted after this one.");			return;                }        }	if (data.prf_no == 2)	{		insert += profile1_nseqs;		for(i=profile1_nseqs+data.nseqs;i>insert+1;i--)			sscpy(i+ncutseqs,i);		for(i=1;ncutseqs>0;i++)			sload(insert+i+1);	}       	else	{		for(i=nseqs;i>insert+1;i--)			sscpy(i+ncutseqs,i);		for(i=1;ncutseqs>0;i++)			sload(insert+i+1);	}        if(data.prf_no==0)        {                nseqs=data.nseqs+n;                if (nseqs>0) empty=FALSE;		load_aln(seq_panel,0,nseqs-1,FALSE);        }        else if(data.prf_no==1)        {                profile1_nseqs=data.nseqs+n;                nseqs+=n;                if (profile1_nseqs>0) profile1_empty=FALSE;		load_aln(active_panel,0,profile1_nseqs-1,FALSE);		if (!profile2_empty)			load_aln(prf_panel[1],profile1_nseqs,nseqs-1,FALSE);        }        else if(data.prf_no==2)        {                nseqs=profile1_nseqs+data.nseqs+n;                if (profile1_nseqs<nseqs)		{			profile2_empty=FALSE;			empty=FALSE;		}/*		load_aln(prf_panel[0],0,profile1_nseqs-1,FALSE);*/		load_aln(prf_panel[1],profile1_nseqs,nseqs-1,FALSE);        }	active_panel.modified=TRUE;	info("Pasted %d sequences.",n);}/* copies a sequence from clustal arrays position j to temp arrays */static void ssave(int j){	int k;	if (saveseq_array[ncutseqs] != NULL) ckfree(saveseq_array[ncutseqs]);	if (savenames[ncutseqs] != NULL) ckfree(savenames[ncutseqs]);	if (savetitles[ncutseqs] != NULL) ckfree(savetitles[ncutseqs]);	savenames[ncutseqs]=(char *)ckalloc((MAXNAMES+2)*sizeof(char));	savetitles[ncutseqs]=(char *)ckalloc((MAXTITLES+2)*sizeof(char));	strcpy(savenames[ncutseqs],names[j]);	strcpy(savetitles[ncutseqs],titles[j]);	saveseqlen_array[ncutseqs]=seqlen_array[j];	saveseq_array[ncutseqs]=(char *)ckalloc((seqlen_array[j]+2)*sizeof(char));	for(k=1;k<=seqlen_array[j];k++)		saveseq_array[ncutseqs][k]=seq_array[j][k];	saveseq_array[ncutseqs][k]= -3;	ncutseqs++;}/* copies a sequence from clustal arrays position i to position j */static void sscpy(int i,int j){	int k;	strcpy(names[i],names[j]);	strcpy(titles[i],titles[j]);	seqlen_array[i]=seqlen_array[j];	realloc_seq(i,seqlen_array[i]);	for(k=1;k<=seqlen_array[j];k++)		seq_array[i][k]=seq_array[j][k];	seq_array[i][k]= -3;}/* copies last sequence in temp arrays to clustal arrays after entry i */static void sload(int i){	int k;	if (ncutseqs<1) return;	ncutseqs--;	strcpy(names[i],savenames[ncutseqs]);	strcpy(titles[i],savetitles[ncutseqs]);	seqlen_array[i]=saveseqlen_array[ncutseqs];	realloc_seq(i,seqlen_array[i]);	for(k=1;k<=seqlen_array[i];k++)		seq_array[i][k]=saveseq_array[ncutseqs][k];	seq_array[i][k]= -3;}static void SelectSeqs(IteM item){	select_seqs(seq_panel,TRUE);}static void SelectPrf1(IteM item){	select_seqs(prf_panel[0],TRUE);}static void SelectPrf2(IteM item){	select_seqs(prf_panel[1],TRUE);}static void MergeProfiles(IteM item){        if (profile2_empty)        {                error("Profile 2 not loaded");                return;        }	profile_no=1;	profile1_nseqs=nseqs;	profile2_empty=TRUE;	load_aln(prf_panel[0],0,profile1_nseqs-1,FALSE);	load_aln(prf_panel[1],profile1_nseqs,nseqs-1,FALSE);	active_panel=prf_panel[0];	info("Added Profile 2 to Profile 1.");}static void ClearSeqRange(IteM item){	if(aln_mode==MULTIPLEM)		clear_seqrange(seq_panel);	else	{		clear_seqrange(prf_panel[1]);		clear_seqrange(prf_panel[0]);	}}static void ClearSeqs(IteM item){	if(aln_mode==MULTIPLEM)		select_seqs(seq_panel,FALSE);	else	{		select_seqs(prf_panel[1],FALSE);		select_seqs(prf_panel[0],FALSE);	}}static void clear_seqrange(spanel p){	int f,l;	panel_data data;	GetPanelExtra(p.seqs,&data);	f=data.firstsel;	l=data.lastsel;	data.firstsel=data.lastsel=-1;	SetPanelExtra(p.seqs,&data);	highlight_seqrange(p.seqs,f,l,NORMAL);}static void select_seqs(spanel p,Boolean flag){	int i;	panel_data data;	GetPanelExtra(p.names,&data);	if (data.nseqs == 0) return;	for (i=0;i<data.nseqs;i++)		data.selected[i]=flag;	SetPanelExtra(p.names,&data);	draw_names(p.names);	if(flag==TRUE) active_panel=p;}static void CAlignWin (IteM item){        if (empty)        {                error("No sequences loaded");                return;        }        if (nseqs <= 1)	{                error("Alignment has only %d sequences",nseqs);                return;        }	do_align_window(&calignw,&ctreetext,NEW,"Complete Alignment",CompleteAlign);}void CompleteAlign(ButtoN but){	char phylip_name[FILENAMELEN];    float et