diff --git a/CORE/.GDEmenus b/CORE/.GDEmenus
index 77486c8..76ae008 100644
--- a/CORE/.GDEmenus
+++ b/CORE/.GDEmenus
@@ -744,21 +744,3 @@ informat:genbank
 inmask:
 insave:
 
-
-#Online menu  
-menu:On-Line Res.
-
-item:GDE for Linux resources at Bioafrica.net
-itemmethod:netscape http://www.bioafrica.net &
-
-item:-------------------------
-item:add a new website
-itemmethod:xterm -e /usr/local/bio/GDE/newURL.pl $name $url
-
-arg:name
-argtype:text
-arglabel:Enter the site name
-
-arg:url
-argtype:text
-arglabel:Enter the URL (including http://)
diff --git a/CORE/FileIO.c b/CORE/FileIO.c
index dd0226d..118f8d5 100755
--- a/CORE/FileIO.c
+++ b/CORE/FileIO.c
@@ -1,10 +1,11 @@
-#include <stdio.h>
 #include <malloc.h>
-#include <xview/xview.h>
+#include <stdio.h>
 #include <xview/notice.h>
 #include <xview/panel.h>
-#include "menudefs.h"
+#include <xview/xview.h>
+
 #include "defines.h"
+#include "menudefs.h"
 
 /*
 LoadData():
@@ -20,57 +21,51 @@ All rights reserved.
 
 */
 
-LoadData(filename)
-char *filename;
+LoadData(filename) char *filename;
 {
 	extern NA_Alignment *DataSet;
-	extern int DataType,FileFormat,Default_DNA_Trans[],Default_RNA_Trans[];
-	extern int Default_NA_RTrans[],Default_PROColor_LKUP[],Default_NAColor_LKUP[];
+	extern int DataType, FileFormat, Default_DNA_Trans[],
+	    Default_RNA_Trans[];
+	extern int Default_NA_RTrans[], Default_PROColor_LKUP[],
+	    Default_NAColor_LKUP[];
 
 	extern Frame frame;
-	extern Canvas EditCan,EditNameCan;
+	extern Canvas EditCan, EditNameCan;
 	extern char FileName[];
 	FILE *file;
 	NA_Alignment *DataNaAln;
 	char temp[1024];
-/*
-*	Get file name, determine the file type, and away we go..
-*/
-	if(Find2(filename,"gde")!=0)
-		strcpy(FileName,filename);
-	if( (file=fopen(filename,"r"))!=0 )
-	{
-		FindType(filename,&DataType,&FileFormat);
-		switch(DataType)
-		{
-		case NASEQ_ALIGN:
-			if(DataSet == NULL)
-			{
-				DataSet = (NA_Alignment*)Calloc(1,
-				    sizeof(NA_Alignment));
-				DataNaAln =(NA_Alignment*)DataSet;
-				DataSet->rel_offset = 0;
-			}
-			else
-				DataNaAln = (NA_Alignment*)DataSet;
+	/*
+	 *	Get file name, determine the file type, and away we go..
+	 */
+	if (Find2(filename, "gde") != 0) strcpy(FileName, filename);
+	if ((file = fopen(filename, "r")) != 0) {
+		FindType(filename, &DataType, &FileFormat);
+		switch (DataType) {
+			case NASEQ_ALIGN:
+				if (DataSet == NULL) {
+					DataSet = (NA_Alignment *)Calloc(
+					    1, sizeof(NA_Alignment));
+					DataNaAln = (NA_Alignment *)DataSet;
+					DataSet->rel_offset = 0;
+				}
+				else
+					DataNaAln = (NA_Alignment *)DataSet;
 
-			LoadFile(filename,DataNaAln,
-			    DataType,FileFormat);
+				LoadFile(filename, DataNaAln, DataType,
+					 FileFormat);
 
-			break;
-		default:
-			break;
+				break;
+			default:
+				break;
 		}
 	}
 	fclose(file);
-	sprintf(temp,"Genetic Data Environment 2.2 for HIV research(%s)",FileName);
-	xv_set(frame,
-	    FRAME_LABEL, temp,
-	    0);
+	sprintf(temp, "Genetic Data Environment 2.2");
+	xv_set(frame, FRAME_LABEL, temp, 0);
 	return;
 }
 
-
 /*
 LoadFile():
 	Load the given filename into the given dataset.  Handle any
@@ -86,79 +81,72 @@ Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
 All rights reserved.
 */
 
-LoadFile(filename,dataset,type,format)
-char *filename;
+LoadFile(filename, dataset, type, format) char *filename;
 char *dataset;
-int type,format;
+int type, format;
 {
 	extern int DataType;
 
 	if (DataType != type)
-		fprintf(stderr,"Warning, datatypes do not match.\n");
-/*
-Handle the overwrite/create/merge dialog here.
-*/
-	switch(format)
-	{
-	case NA_FLAT:
-		ReadNA_Flat(filename,dataset,type);
-		((NA_Alignment*)dataset)->format = GDE;
-		break;
+		fprintf(stderr, "Warning, datatypes do not match.\n");
+	/*
+	Handle the overwrite/create/merge dialog here.
+	*/
+	switch (format) {
+		case NA_FLAT:
+			ReadNA_Flat(filename, dataset, type);
+			((NA_Alignment *)dataset)->format = GDE;
+			break;
 
-	case GENBANK:
-		ReadGen(filename,dataset,type);
-		((NA_Alignment*)dataset)->format = GENBANK;
-		break;
+		case GENBANK:
+			ReadGen(filename, dataset, type);
+			((NA_Alignment *)dataset)->format = GENBANK;
+			break;
 
-	case GDE:
-		ReadGDE(filename,dataset,type);
-		((NA_Alignment*)dataset)->format = GDE;
-		break;
-	case COLORMASK:
-		ReadCMask(filename);
+		case GDE:
+			ReadGDE(filename, dataset, type);
+			((NA_Alignment *)dataset)->format = GDE;
+			break;
+		case COLORMASK:
+			ReadCMask(filename);
 
-	default:
-		break;
+		default:
+			break;
 	}
 	return;
 }
 
-
-
 /*
-*	Print error message, and die
-*/
-ErrorOut(code,string)
-int code;
+ *	Print error message, and die
+ */
+ErrorOut(code, string) int code;
 char *string;
 {
-	if (code == 0)
-	{
-		fprintf(stderr,"Error:%s\n",string);
+	if (code == 0) {
+		fprintf(stderr, "Error:%s\n", string);
 		exit(1);
 	}
 	return;
 }
 
-
 /*
-*	More robust memory management routines
-*/
-char *Calloc(count,size)
-int count,size;
+ *	More robust memory management routines
+ */
+char *Calloc(count, size)
+int count, size;
 {
 	char *temp;
 #ifdef SeeAlloc
 	extern int TotalCalloc;
-	TotalCalloc += count*size;
-	fprintf(stderr,"Calloc %d %d\n",count*size,TotalCalloc);
+	TotalCalloc += count * size;
+	fprintf(stderr, "Calloc %d %d\n", count * size, TotalCalloc);
 #endif
-	temp = calloc(count,size);
-	ErrorOut(temp,"Cannot allocate memory");
-	return(temp);
+	temp = calloc(count, size);
+	ErrorOut(temp, "Cannot allocate memory");
+	return (temp);
 }
 
-char *Realloc(block,size)
+char *Realloc(block, size)
 char *block;
 int size;
 {
@@ -166,343 +154,340 @@ int size;
 #ifdef SeeAlloc
 	extern int TotalRealloc;
 	TotalRealloc += size;
-	fprintf(stderr,"Realloc %d\n",TotalRealloc);
+	fprintf(stderr, "Realloc %d\n", TotalRealloc);
 #endif
-	temp=realloc(block,size);
-	ErrorOut(temp,"Cannot change memory size");
-	return(temp);
+	temp = realloc(block, size);
+	ErrorOut(temp, "Cannot change memory size");
+	return (temp);
 }
 
-Cfree(block)
-char* block;
+Cfree(block) char *block;
 {
-	if (block)
-	{
-	    /* rtm 18.III.98 
-	       FileIO.c: In function `Cfree':
-	       FileIO.c:181: void value not ignored as it ought to be
+	if (block) {
+		/* rtm 18.III.98
+		   FileIO.c: In function `Cfree':
+		   FileIO.c:181: void value not ignored as it ought to be
 
-		if(free(block) == 0)
-			Warning("Error in Cfree...");
-			*/
-	    free(block);
+		    if(free(block) == 0)
+			    Warning("Error in Cfree...");
+			    */
+		free(block);
 	}
 	else
 		Warning("Error in Cfree, NULL block");
 	return;
 }
 
-
-
 /*
-*	same as strdup
-*/
+ *	same as strdup
+ */
 char *String(string)
 char *string;
 {
 	char *temp;
 
-	temp = Calloc(strlen(string)+1,sizeof(char));
-	strcpy(temp,string);
-	return(temp);
+	temp = Calloc(strlen(string) + 1, sizeof(char));
+	strcpy(temp, string);
+	return (temp);
 }
 
-
-FindType(name,dtype,ftype)
-char *name;
-int *dtype,*ftype;
+FindType(name, dtype, ftype) char *name;
+int *dtype, *ftype;
 {
 	FILE *file;
 	char Inline[GBUFSIZ];
 
-	file = fopen(name,"r");
-	*dtype=0;
-	*ftype=0;
+	file = fopen(name, "r");
+	*dtype = 0;
+	*ftype = 0;
 
-	if (file == NULL)
-		return(1);
+	if (file == NULL) return (1);
 
 	/*
-*	Is this a flat file?
-*	Get the first non blank line, see if a type marker shows up.
-*/
-	fgets(Inline,GBUFSIZ,file);
-	for(;strlen(Inline)<2 && fgets(Inline,GBUFSIZ,file) != NULL;);
-	if(Inline[0] == '#' || Inline[0] == '%' ||
-	    Inline[0] == '"' || Inline[0] == '@' )
-	{
-		*dtype=NASEQ_ALIGN;
-		*ftype=NA_FLAT;
+	 *	Is this a flat file?
+	 *	Get the first non blank line, see if a type marker shows up.
+	 */
+	fgets(Inline, GBUFSIZ, file);
+	for (; strlen(Inline) < 2 && fgets(Inline, GBUFSIZ, file) != NULL;)
+		;
+	if (Inline[0] == '#' || Inline[0] == '%' || Inline[0] == '"' ||
+	    Inline[0] == '@') {
+		*dtype = NASEQ_ALIGN;
+		*ftype = NA_FLAT;
 	}
 
 	/*
-*	Else, try genbank
-*/
-	else
-	{
+	 *	Else, try genbank
+	 */
+	else {
 		fclose(file);
-		file = fopen(name,"r");
-		*dtype=0;
-		*ftype=0;
+		file = fopen(name, "r");
+		*dtype = 0;
+		*ftype = 0;
 
-		if (file == NULL)
-			return(1);
+		if (file == NULL) return (1);
 
-		for(;fgets(Inline,GBUFSIZ,file) != NULL;)
-			if(Find(Inline,"LOCUS"))
-			{
-				*dtype=NASEQ_ALIGN;
-				*ftype=GENBANK;
+		for (; fgets(Inline, GBUFSIZ, file) != NULL;)
+			if (Find(Inline, "LOCUS")) {
+				*dtype = NASEQ_ALIGN;
+				*ftype = GENBANK;
 				fclose(file);
-				return(0);
+				return (0);
 			}
-		/*
-*	and last, try GDE
-*/
-			else if(Find(Inline,"sequence"))
-			{
+			/*
+			 *	and last, try GDE
+			 */
+			else if (Find(Inline, "sequence")) {
 				*dtype = NASEQ_ALIGN;
 				*ftype = GDE;
 				fclose(file);
-				return(0);
+				return (0);
 			}
-			else if(Find(Inline,"start:"))
-			{
+			else if (Find(Inline, "start:")) {
 				*dtype = NASEQ_ALIGN;
 				*ftype = COLORMASK;
 				fclose(file);
-				return(0);
+				return (0);
 			}
 	}
 
 	fclose(file);
-	return(0);
+	return (0);
 }
 
-AppendNA(buffer,len,seq)
-NA_Base *buffer;
+AppendNA(buffer, len, seq) NA_Base *buffer;
 int len;
 NA_Sequence *seq;
 {
-	int curlen=0,j;
+	int curlen = 0, j;
 	NA_Base *temp;
 
-	if(seq->seqlen+len >= seq->seqmaxlen)
-	{
-		if(seq->seqlen>0)
-			seq->sequence = (NA_Base*)Realloc(seq->sequence,
-			    (seq->seqlen + len+GBUFSIZ) * sizeof(NA_Base));
+	if (seq->seqlen + len >= seq->seqmaxlen) {
+		if (seq->seqlen > 0)
+			seq->sequence = (NA_Base *)Realloc(
+			    seq->sequence,
+			    (seq->seqlen + len + GBUFSIZ) * sizeof(NA_Base));
 		else
-			seq->sequence = (NA_Base*)Calloc(1,(seq->seqlen +
-			    len+GBUFSIZ) * sizeof(NA_Base));
-		seq->seqmaxlen = seq->seqlen + len+GBUFSIZ;
+			seq->sequence = (NA_Base *)Calloc(
+			    1, (seq->seqlen + len + GBUFSIZ) * sizeof(NA_Base));
+		seq->seqmaxlen = seq->seqlen + len + GBUFSIZ;
 	}
 	/*
-*	seqlen is the length, and the index of the next free
-*	base
-*/
+	 *	seqlen is the length, and the index of the next free
+	 *	base
+	 */
 	curlen = seq->seqlen + seq->offset;
-	for(j=0;j<len;j++)
-		putelem(seq,j+curlen,buffer[j]);
+	for (j = 0; j < len; j++) putelem(seq, j + curlen, buffer[j]);
 
 	seq->seqlen += len;
 	return;
 }
 
-Ascii2NA(buffer,len,matrix)
-char *buffer;
+Ascii2NA(buffer, len, matrix) char *buffer;
 int len;
 int matrix[16];
 {
 	/*
-*	if the translation matrix exists, use it to
-*	encode the buffer.
-*/
+	 *	if the translation matrix exists, use it to
+	 *	encode the buffer.
+	 */
 	register i;
-	if(matrix != NULL)
-		for(i=0;i<len;i++)
-			buffer[i] = matrix[buffer[i]];
+	if (matrix != NULL)
+		for (i = 0; i < len; i++) buffer[i] = matrix[buffer[i]];
 	return;
 }
 
-WriteNA_Flat(aln,filename,method,maskable)
-NA_Alignment *aln;
+WriteNA_Flat(aln, filename, method, maskable) NA_Alignment *aln;
 char *filename;
-int method,maskable;
+int method, maskable;
 {
-	int j,kk,mask = -1,k,offset,min_offset= -999999;
-	char offset_str[100],buf[100];
+	int j, kk, mask = -1, k, offset, min_offset = -999999;
+	char offset_str[100], buf[100];
 	NA_Sequence *seqs;
 	FILE *file;
-	if(aln == (NA_Alignment *) NULL)
-		return;
-	if(aln->numelements == (int) NULL)
-		return;
+	if (aln == (NA_Alignment *)NULL) return;
+	if (aln->numelements == (int)NULL) return;
 	seqs = aln->element;
 
-	file = fopen(filename,"w");
-	if(file == NULL)
-	{
+	file = fopen(filename, "w");
+	if (file == NULL) {
 		Warning("Cannot open file for output");
-		return(1);
+		return (1);
 	}
-	if(maskable && (method != SELECT_REGION))
-	{
-		for(j=0;j<aln->numelements;j++)
-			if(seqs[j].elementtype == MASK && 
-			    seqs[j].selected)
+	if (maskable && (method != SELECT_REGION)) {
+		for (j = 0; j < aln->numelements; j++)
+			if (seqs[j].elementtype == MASK && seqs[j].selected)
 				mask = j;
 	}
-	for(j=0;j<aln->numelements;j++)
-	{
+	for (j = 0; j < aln->numelements; j++) {
 		SeqNorm(&(seqs[j]));
 	}
 
-	for(j=0;j<aln->numelements;j++)
-	{
-		if(method != SELECT_REGION)
+	for (j = 0; j < aln->numelements; j++) {
+		if (method != SELECT_REGION)
 			offset = seqs[j].offset;
 		else
-			for(offset=seqs[j].offset;
-			aln->selection_mask[offset] == '0';
-			offset++);
+			for (offset = seqs[j].offset;
+			     aln->selection_mask[offset] == '0'; offset++)
+				;
 
-		if(offset+aln->rel_offset != 0)
-			sprintf(offset_str,"(%d)",offset+aln->rel_offset);
+		if (offset + aln->rel_offset != 0)
+			sprintf(offset_str, "(%d)", offset + aln->rel_offset);
 		else
 			offset_str[0] = '\0';
-		
-		if(((j!=mask) && (seqs[j].selected) && method != SELECT_REGION) 
-		|| (method == SELECT_REGION && seqs[j].subselected)
-		|| method == ALL)
-		{
-			fprintf(file,"%c%s%s\n",
-			    seqs[j].elementtype == DNA?'#':
-			    seqs[j].elementtype == RNA?'#':
-			    seqs[j].elementtype == PROTEIN?'%':
-			    seqs[j].elementtype == TEXT?'"':
-			    seqs[j].elementtype == MASK?'@':'"',
+
+		if (((j != mask) && (seqs[j].selected) &&
+		     method != SELECT_REGION) ||
+		    (method == SELECT_REGION && seqs[j].subselected) ||
+		    method == ALL) {
+			fprintf(
+			    file, "%c%s%s\n",
+			    seqs[j].elementtype == DNA	     ? '#'
+			    : seqs[j].elementtype == RNA     ? '#'
+			    : seqs[j].elementtype == PROTEIN ? '%'
+			    : seqs[j].elementtype == TEXT    ? '"'
+			    : seqs[j].elementtype == MASK    ? '@'
+							     : '"',
 			    seqs[j].short_name,
-			    (offset+aln->rel_offset  == 0)? "":offset_str);
-			if(seqs[j].tmatrix)
-			{
-				if(mask == -1)
-					for(k=0,kk=0;kk<seqs[j].seqlen;kk++)
-					{
-						if((k)%60 == 0 && k>0)
-						{
+			    (offset + aln->rel_offset == 0) ? "" : offset_str);
+			if (seqs[j].tmatrix) {
+				if (mask == -1)
+					for (k = 0, kk = 0; kk < seqs[j].seqlen;
+					     kk++) {
+						if ((k) % 60 == 0 && k > 0) {
 							buf[60] = '\0';
-							fputs(buf,file);
-							putc('\n',file);
+							fputs(buf, file);
+							putc('\n', file);
 						}
-						if(method == SELECT_REGION)
-						{
-							if(aln->selection_mask[kk+offset]=='1')
-							{
-								buf[k%60] =((char)seqs[j].tmatrix[
-								(int)getelem( &(seqs[j]),kk+offset) ]);
+						if (method == SELECT_REGION) {
+							if (aln->selection_mask
+								[kk + offset] ==
+							    '1') {
+								buf[k % 60] =
+								    ((char)seqs[j]
+									 .tmatrix[(int)getelem(
+									     &(seqs[j]),
+									     kk +
+										 offset)]);
 								k++;
 							}
 						}
-						else
-						{
-							buf[k%60] =((char)seqs[j].tmatrix[
-							(int)getelem( &(seqs[j]),kk+offset) ]);
+						else {
+							buf[k % 60] =
+							    ((char)seqs[j].tmatrix
+								 [(int)getelem(
+								     &(seqs[j]),
+								     kk +
+									 offset)]);
 							k++;
 						}
 					}
 				else
-					for(k=0,kk=0;kk<seqs[j].seqlen;kk++)
-					{
-						if(getelem(&(seqs[mask]),kk+seqs[mask].offset) != '0'
-						    && (getelem(&(seqs[mask]),kk+seqs[mask].offset)
-						    != '-'))
-						{
-							if((k++)%60 == 0 && k>1)
-							{
+					for (k = 0, kk = 0; kk < seqs[j].seqlen;
+					     kk++) {
+						if (getelem(&(seqs[mask]),
+							    kk + seqs[mask]
+								     .offset) !=
+							'0' &&
+						    (getelem(
+							 &(seqs[mask]),
+							 kk + seqs[mask]
+								  .offset) !=
+						     '-')) {
+							if ((k++) % 60 == 0 &&
+							    k > 1) {
 								buf[60] = '\0';
-								fputs(buf,file);
-								putc('\n',file);
+								fputs(buf,
+								      file);
+								putc('\n',
+								     file);
 							}
-							buf[k%60] = ((char)seqs[j].tmatrix
-							    [getelem(&(seqs[j]),kk+offset)]);
+							buf[k % 60] =
+							    ((char)seqs[j].tmatrix
+								 [getelem(
+								     &(seqs[j]),
+								     kk +
+									 offset)]);
 						}
 					}
 			}
-			else
-			{
-				if(mask == -1)
-					for(k=0,kk=0;kk<seqs[j].seqlen;kk++)
-					{
-						if((k)%60 == 0 && k>0)
-						{
+			else {
+				if (mask == -1)
+					for (k = 0, kk = 0; kk < seqs[j].seqlen;
+					     kk++) {
+						if ((k) % 60 == 0 && k > 0) {
 							buf[60] = '\0';
-							fputs(buf,file);
-							putc('\n',file);
+							fputs(buf, file);
+							putc('\n', file);
 						}
-						if(method == SELECT_REGION)
-						{
-							if(aln->selection_mask[kk+offset]=='1')
-							{
-								buf[k%60] =(getelem( &(seqs[j]),kk+offset));
+						if (method == SELECT_REGION) {
+							if (aln->selection_mask
+								[kk + offset] ==
+							    '1') {
+								buf[k % 60] = (getelem(
+								    &(seqs[j]),
+								    kk +
+									offset));
 								k++;
 							}
 						}
-						else
-						{
-							buf[k%60] =( getelem( &(seqs[j]),kk+offset) );
+						else {
+							buf[k % 60] = (getelem(
+							    &(seqs[j]),
+							    kk + offset));
 							k++;
 						}
 					}
 				else
-					for(k=0,kk=0;kk<seqs[j].seqlen;kk++)
-					{
-						if(getelem(&(seqs[mask]),kk+offset) == '1')
-						{
-							if((k++)%60 == 0 && k>1)
-							{
+					for (k = 0, kk = 0; kk < seqs[j].seqlen;
+					     kk++) {
+						if (getelem(&(seqs[mask]),
+							    kk + offset) ==
+						    '1') {
+							if ((k++) % 60 == 0 &&
+							    k > 1) {
 								buf[60] = '\0';
-								fputs(buf,file);
-								putc('\n',file);
+								fputs(buf,
+								      file);
+								putc('\n',
+								     file);
 							}
-							buf[k%60] =((char)getelem(&(seqs[j]),
-							    kk+offset));
+							buf[k % 60] =
+							    ((char)getelem(
+								&(seqs[j]),
+								kk + offset));
 						}
 					}
 			}
-			buf[(k%60)>0 ? (k%60):60] = '\0';
-			fputs(buf,file);
-			putc('\n',file);
+			buf[(k % 60) > 0 ? (k % 60) : 60] = '\0';
+			fputs(buf, file);
+			putc('\n', file);
 		}
 	}
 	fclose(file);
-	return(0);
+	return (0);
 }
 
-
-Warning(s)
-char *s;
+Warning(s) char *s;
 {
 	extern Frame frame;
-	extern Panel_item left_foot,right_foot;
+	extern Panel_item left_foot, right_foot;
 	Beep();
-	xv_set(frame,FRAME_RIGHT_FOOTER,s,0);
-	xv_set(right_foot,PANEL_LABEL_STRING,s,0);
+	xv_set(frame, FRAME_RIGHT_FOOTER, s, 0);
+	xv_set(right_foot, PANEL_LABEL_STRING, s, 0);
 }
 
-
-InitNASeq(seq,type)
-NA_Sequence *seq;
+InitNASeq(seq, type) NA_Sequence *seq;
 int type;
 {
-	extern int Default_RNA_Trans[];  /* rtm 18.III.98 */
-	extern int Default_DNA_Trans[],Default_NA_RTrans[];
-	extern int
-		Default_NA_RTrans[],Default_PROColor_LKUP[],Default_NAColor_LKUP[];
+	extern int Default_RNA_Trans[]; /* rtm 18.III.98 */
+	extern int Default_DNA_Trans[], Default_NA_RTrans[];
+	extern int Default_NA_RTrans[], Default_PROColor_LKUP[],
+	    Default_NAColor_LKUP[];
 
 	SetTime(&(seq->t_stamp.origin));
 	SetTime(&(seq->t_stamp.modify));
-	strncpy(seq->id,uniqueID(),79);
+	strncpy(seq->id, uniqueID(), 79);
 	seq->seq_name[0] = '\0';
 	seq->barcode[0] = '\0';
 	seq->contig[0] = '\0';
@@ -535,370 +520,348 @@ int type;
 	seq->selected = 0;
 	seq->subselected = 0;
 
-	switch (type)
-	{
-	case DNA:
-		seq->tmatrix = Default_DNA_Trans;
-		seq->rmatrix = Default_NA_RTrans;
-		seq->col_lut = Default_NAColor_LKUP;
-		break;
-	case RNA:
-		seq->tmatrix = Default_RNA_Trans;
-		seq->rmatrix = Default_NA_RTrans;
-		seq->col_lut = Default_NAColor_LKUP;
-		break;
-	case PROTEIN:
-		seq->tmatrix = NULL;
-		seq->rmatrix = NULL;
-		seq->col_lut = Default_PROColor_LKUP;
-		break;
-	case MASK:
-	case TEXT:
-	default:
-		seq->tmatrix = NULL;
-		seq->rmatrix = NULL;
-		seq->col_lut = NULL;
-		break;
+	switch (type) {
+		case DNA:
+			seq->tmatrix = Default_DNA_Trans;
+			seq->rmatrix = Default_NA_RTrans;
+			seq->col_lut = Default_NAColor_LKUP;
+			break;
+		case RNA:
+			seq->tmatrix = Default_RNA_Trans;
+			seq->rmatrix = Default_NA_RTrans;
+			seq->col_lut = Default_NAColor_LKUP;
+			break;
+		case PROTEIN:
+			seq->tmatrix = NULL;
+			seq->rmatrix = NULL;
+			seq->col_lut = Default_PROColor_LKUP;
+			break;
+		case MASK:
+		case TEXT:
+		default:
+			seq->tmatrix = NULL;
+			seq->rmatrix = NULL;
+			seq->col_lut = NULL;
+			break;
 	}
 	return;
 }
 
-
-ReadCMask(filename)
-char *filename;
+ReadCMask(filename) char *filename;
 {
 	extern Frame frame;
 	extern NA_Alignment *DataSet;
 
-	char Inline[GBUFSIZ],head[GBUFSIZ],curname[GBUFSIZ],
-	temp[GBUFSIZ];
-	int IGNORE_DASH = FALSE,offset;
+	char Inline[GBUFSIZ], head[GBUFSIZ], curname[GBUFSIZ], temp[GBUFSIZ];
+	int IGNORE_DASH = FALSE, offset;
 	NA_DisplayData *NAdd;
 	NA_Alignment *aln;
 
-	int i,j,k,curlen = 0,*colors,orig_ctype,jj,indx = 0;
+	int i, j, k, curlen = 0, *colors, orig_ctype, jj, indx = 0;
 	FILE *file;
 
-	if(DataSet == NULL) return;
+	if (DataSet == NULL) return;
 
-	NAdd = (NA_DisplayData*)((NA_Alignment*)DataSet)->na_ddata;
+	NAdd = (NA_DisplayData *)((NA_Alignment *)DataSet)->na_ddata;
 
-	if(NAdd == NULL)
-		return;
+	if (NAdd == NULL) return;
 
-	aln = (NA_Alignment*)DataSet;
+	aln = (NA_Alignment *)DataSet;
 
 	curname[0] = '\0';
 	orig_ctype = NAdd->color_type;
-	file = fopen(filename,"r");
-	if(file == NULL)
-	{
+	file = fopen(filename, "r");
+	if (file == NULL) {
 		Warning("File not found");
 		Warning(filename);
 		return;
 	}
 
 	NAdd->color_type = COLOR_ALN_MASK;
-	for(;fgets(Inline,GBUFSIZ,file) !=0;)
-	{
-		if(Find(Inline,"offset:"))
-		{
-			crop(Inline,head,temp);
-			sscanf(temp,"%d",&(aln->cmask_offset));
+	for (; fgets(Inline, GBUFSIZ, file) != 0;) {
+		if (Find(Inline, "offset:")) {
+			crop(Inline, head, temp);
+			sscanf(temp, "%d", &(aln->cmask_offset));
 		}
-		else if(Find(Inline,"nodash:"))
+		else if (Find(Inline, "nodash:"))
 			IGNORE_DASH = TRUE;
-		else if(Find(Inline,"dash:"))
+		else if (Find(Inline, "dash:"))
 			IGNORE_DASH = TRUE;
-		else if(Find(Inline,"name:"))
-		{
-			crop(Inline,head,curname);
-			curname[strlen(curname)-1] = '\0';
-			for(j=0;j<strlen(curname);j++)
-				if(curname[j] == '(')
-					curname[j] = '\0';
+		else if (Find(Inline, "name:")) {
+			crop(Inline, head, curname);
+			curname[strlen(curname) - 1] = '\0';
+			for (j = 0; j < strlen(curname); j++)
+				if (curname[j] == '(') curname[j] = '\0';
 		}
-		else if(Find(Inline,"length:"))
-		{
-			crop(Inline,head,temp);
-			sscanf(temp,"%d",&curlen);
+		else if (Find(Inline, "length:")) {
+			crop(Inline, head, temp);
+			sscanf(temp, "%d", &curlen);
 		}
-		else if(Find(Inline,"start:"))
-		{
+		else if (Find(Inline, "start:")) {
 			indx = -1;
-			if(curlen == 0)
-			{
+			if (curlen == 0) {
 				Warning("illegal format in colormask");
 				NAdd->color_type = orig_ctype;
 				return;
 			}
-			if(strlen(curname) != 0)
-			{
+			if (strlen(curname) != 0) {
 				indx = -1;
-				for(j=0;j<aln->numelements;j++)
-					if(Find(aln->element[j].short_name,curname)
-					    || Find(aln->element[j].id,curname))
-					{
-						if(aln->element[j].cmask != NULL)
-							Cfree(aln -> element[j].cmask);
-						colors=(int*)Calloc(aln->element[j]
-						    .seqmaxlen+1+aln->element[j].offset
-						    ,sizeof(int));
+				for (j = 0; j < aln->numelements; j++)
+					if (Find(aln->element[j].short_name,
+						 curname) ||
+					    Find(aln->element[j].id, curname)) {
+						if (aln->element[j].cmask !=
+						    NULL)
+							Cfree(aln->element[j]
+								  .cmask);
+						colors = (int *)Calloc(
+						    aln->element[j].seqmaxlen +
+							1 +
+							aln->element[j].offset,
+						    sizeof(int));
 						aln->element[j].cmask = colors;
-						NAdd->color_type = COLOR_SEQ_MASK;
+						NAdd->color_type =
+						    COLOR_SEQ_MASK;
 						indx = j;
 						j = aln->numelements;
 					}
-				if(indx == -1)
-					colors=NULL;
+				if (indx == -1) colors = NULL;
 			}
-			else
-			{
-				if(aln->cmask != NULL) Cfree(aln->cmask);
-				colors=(int*)Calloc(curlen,sizeof(int));
+			else {
+				if (aln->cmask != NULL) Cfree(aln->cmask);
+				colors = (int *)Calloc(curlen, sizeof(int));
 				aln->cmask = colors;
 				aln->cmask_len = curlen;
 				NAdd->color_type = COLOR_ALN_MASK;
-				for(j=0;j<curlen;j++)
-					colors[j] = 12;
+				for (j = 0; j < curlen; j++) colors[j] = 12;
 			}
 
-			if(IGNORE_DASH && (indx != -1))
-			{
-				for(jj=0,j=0;(j<curlen) && 
-				    (jj<aln->element[indx].seqlen);j++,jj++)
-				{
+			if (IGNORE_DASH && (indx != -1)) {
+				for (jj = 0, j = 0;
+				     (j < curlen) &&
+				     (jj < aln->element[indx].seqlen);
+				     j++, jj++) {
 					offset = aln->element[indx].offset;
-					if(fgets(Inline,GBUFSIZ,file)==NULL)
-					{
-						Warning
-						    ("illegal format in colormask");
+					if (fgets(Inline, GBUFSIZ, file) ==
+					    NULL) {
+						Warning(
+						    "illegal format in "
+						    "colormask");
 						NAdd->color_type = orig_ctype;
 						return;
 					}
-/*
-*	Fixed so that the keyword nodash causes the colormask to be mapped
-*	to the sequence, not the alignment.
-*
-*	The allocated space is equal the seqlen of the matched sequence.
-*	
-*/
-					if(aln->element[indx].tmatrix)
-						for(;(getelem(&(aln->element[indx]),jj
-						    +offset)
-						    ==(aln->element[indx].tmatrix['-'])
-						    || (getelem(&(aln->element[indx]),jj
-						    +offset)
-						    ==aln->element[indx].tmatrix['~']))
-						    && jj < aln->element[indx].seqlen;)
+					/*
+					 *	Fixed so that the keyword nodash
+					 *causes the colormask to be mapped to
+					 *the sequence, not the alignment.
+					 *
+					 *	The allocated space is equal the
+					 *seqlen of the matched sequence.
+					 *
+					 */
+					if (aln->element[indx].tmatrix)
+						for (;
+						     (getelem(
+							  &(aln->element[indx]),
+							  jj + offset) ==
+							  (aln->element[indx]
+							       .tmatrix['-']) ||
+						      (getelem(&(aln->element
+								     [indx]),
+							       jj + offset) ==
+						       aln->element[indx]
+							   .tmatrix['~'])) &&
+						     jj < aln->element[indx]
+							      .seqlen;)
 							colors[jj++] = 12;
 					else
-						for(;getelem(&(aln->element[indx]),jj
-						    +offset)
-						    =='-' && jj < aln->element[indx].seqlen;)
+						for (;
+						     getelem(
+							 &(aln->element[indx]),
+							 jj + offset) == '-' &&
+						     jj < aln->element[indx]
+							      .seqlen;)
 							colors[jj++] = 12;
 
-					sscanf(Inline,"%d",&(colors[jj]));
+					sscanf(Inline, "%d", &(colors[jj]));
 				}
 			}
-			else if((indx == -1)  && (strlen(curname) != 0))
-				for(j=0;j<curlen;j++)
-					fgets(Inline,GBUFSIZ,file);
+			else if ((indx == -1) && (strlen(curname) != 0))
+				for (j = 0; j < curlen; j++)
+					fgets(Inline, GBUFSIZ, file);
 			else
-				for(j=0;j<curlen;j++)
-				{
-					if(fgets(Inline,GBUFSIZ,file)==NULL)
-					{
-						Warning
-						    ("illegal format in colormask");
+				for (j = 0; j < curlen; j++) {
+					if (fgets(Inline, GBUFSIZ, file) ==
+					    NULL) {
+						Warning(
+						    "illegal format in "
+						    "colormask");
 						NAdd->color_type = orig_ctype;
 						return;
 					}
-					sscanf(Inline,"%d",&(colors[j]));
+					sscanf(Inline, "%d", &(colors[j]));
 				}
 			IGNORE_DASH = FALSE;
 			curname[0] = '\0';
 		}
-
 	}
 	RepaintAll(TRUE);
 	return;
 }
 
-
-ReadNA_Flat(filename,dataset,type)
-char *filename;
+ReadNA_Flat(filename, dataset, type) char *filename;
 char *dataset;
 int type;
 {
-	int i, j, jj, c, curelem,offset;
+	int i, j, jj, c, curelem, offset;
 	char name[GBUFSIZ];
 	char buffer[GBUFSIZ];
-	char origin[GBUFSIZ],ref[GBUFSIZ];
-	char Inline[GBUFSIZ],head[GBUFSIZ],tail[GBUFSIZ],temp[GBUFSIZ];
+	char origin[GBUFSIZ], ref[GBUFSIZ];
+	char Inline[GBUFSIZ], head[GBUFSIZ], tail[GBUFSIZ], temp[GBUFSIZ];
 	char curname[GBUFSIZ];
 
 	NA_Sequence *this_elem;
 	NA_Alignment *data;
-	extern int Default_DNA_Trans[],Default_RNA_Trans[],Default_NA_RTrans[];
+	extern int Default_DNA_Trans[], Default_RNA_Trans[],
+	    Default_NA_RTrans[];
 
 	FILE *file;
 
 	curname[0] = '\0';
-	data = (NA_Alignment*)dataset;
+	data = (NA_Alignment *)dataset;
 
-	file = fopen(filename,"r");
-	if(file == NULL)
-	{
-		fprintf(stderr,"Cannot open %s.\n",filename);
+	file = fopen(filename, "r");
+	if (file == NULL) {
+		fprintf(stderr, "Cannot open %s.\n", filename);
 		return;
 	}
-	for(;fgets(Inline,GBUFSIZ,file) !=0;)
-	{
-		if(
-			Inline[0] == '#' ||
-		    Inline[0] == '%' ||
-		    Inline[0] == '"' ||
-		    Inline[0] == '@'
-		    )
-		{
+	for (; fgets(Inline, GBUFSIZ, file) != 0;) {
+		if (Inline[0] == '#' || Inline[0] == '%' || Inline[0] == '"' ||
+		    Inline[0] == '@') {
 			offset = 0;
-			for(j=0;j<strlen(Inline);j++)
-			{
-				if(Inline[j] == '(')
-				{
-					sscanf((char*)
-					    &(Inline[j+1]),"%d",&offset);
+			for (j = 0; j < strlen(Inline); j++) {
+				if (Inline[j] == '(') {
+					sscanf((char *)&(Inline[j + 1]), "%d",
+					       &offset);
 					Inline[j] = '\0';
 				}
 			}
 
 			curelem = data->numelements++;
-			if( curelem == 0 )
-			{
-				data->element=(NA_Sequence*)
-				    Calloc(5,sizeof(NA_Sequence));
+			if (curelem == 0) {
+				data->element = (NA_Sequence *)Calloc(
+				    5, sizeof(NA_Sequence));
 				data->maxnumelements = 5;
 			}
-			else if (curelem==data->maxnumelements)
-			{
+			else if (curelem == data->maxnumelements) {
 				(data->maxnumelements) *= 2;
-				data->element=
-				    (NA_Sequence*)Realloc(data->element
-				    ,data->maxnumelements*sizeof(NA_Sequence));
+				data->element = (NA_Sequence *)Realloc(
+				    data->element,
+				    data->maxnumelements * sizeof(NA_Sequence));
 			}
 
 			InitNASeq(&(data->element[curelem]),
-			    Inline[0] == '#'?DNA:
-			    Inline[0] == '%'?PROTEIN:
-			    Inline[0] == '"'?TEXT:
-			    Inline[0] == '@'?MASK:TEXT);
-			this_elem= &(data->element[curelem]);
-			if(Inline[strlen(Inline)-1] == '\n')
-				Inline[strlen(Inline)-1] = '\0';
-			strncpy(this_elem->short_name,(char*)&(Inline[1]),31);
+				  Inline[0] == '#'   ? DNA
+				  : Inline[0] == '%' ? PROTEIN
+				  : Inline[0] == '"' ? TEXT
+				  : Inline[0] == '@' ? MASK
+						     : TEXT);
+			this_elem = &(data->element[curelem]);
+			if (Inline[strlen(Inline) - 1] == '\n')
+				Inline[strlen(Inline) - 1] = '\0';
+			strncpy(this_elem->short_name, (char *)&(Inline[1]),
+				31);
 			this_elem->offset = offset;
 		}
-		else if(Inline[0] != '\n')
-		{
-			for(j=0,jj=0;j<strlen(Inline);j++)
-				if(Inline[j] != ' ' && Inline[j] != '\n' &&
+		else if (Inline[0] != '\n') {
+			for (j = 0, jj = 0; j < strlen(Inline); j++)
+				if (Inline[j] != ' ' && Inline[j] != '\n' &&
 				    Inline[j] != '\t')
 					buffer[jj++] = Inline[j];
 
-			if(data->element[curelem].rmatrix)
-				Ascii2NA(buffer,jj,data->element[curelem]
-				    .rmatrix);
-			AppendNA(buffer,jj,&(data->element[curelem]));
+			if (data->element[curelem].rmatrix)
+				Ascii2NA(buffer, jj,
+					 data->element[curelem].rmatrix);
+			AppendNA(buffer, jj, &(data->element[curelem]));
 		}
 	}
 
-	for(j=0;j<data->numelements;j++)
-		data->maxlen = MAX(data->maxlen,data->element[j].seqlen +
-		    data->element[j].offset);
+	for (j = 0; j < data->numelements; j++)
+		data->maxlen = MAX(data->maxlen, data->element[j].seqlen +
+						     data->element[j].offset);
 
-	for(j=0;j<data->numelements;j++)
-		if(data->element[j].seqlen==0)
+	for (j = 0; j < data->numelements; j++)
+		if (data->element[j].seqlen == 0)
 			data->element[j].protect =
-			    PROT_BASE_CHANGES+ PROT_GREY_SPACE+
-			    PROT_WHITE_SPACE+ PROT_TRANSLATION;
+			    PROT_BASE_CHANGES + PROT_GREY_SPACE +
+			    PROT_WHITE_SPACE + PROT_TRANSLATION;
 
 	NormalizeOffset(data);
 	Regroup(data);
 	return;
 }
 
-
-WriteStatus(aln,filename,method)
-NA_Alignment *aln;
+WriteStatus(aln, filename, method) NA_Alignment *aln;
 char *filename;
 int method;
 {
-	extern int EditMode,FileFormat;
+	extern int EditMode, FileFormat;
 	extern NA_Alignment *DataSet;
 	NA_DisplayData *NAdd;
 	NA_Sequence *this_seq;
 	int j;
 	FILE *file;
 
-	if(DataSet == NULL)
-		return;
+	if (DataSet == NULL) return;
 
-	NAdd = (NA_DisplayData*)((NA_Alignment*)DataSet)->na_ddata;
-	if(NAdd == NULL)
-		return;
+	NAdd = (NA_DisplayData *)((NA_Alignment *)DataSet)->na_ddata;
+	if (NAdd == NULL) return;
 
-	file = fopen(filename,"w");
-	if (file == NULL)
-	{
+	file = fopen(filename, "w");
+	if (file == NULL) {
 		Warning("Cannot open status file.");
-		return(1);
+		return (1);
 	}
-	fprintf(file,"File_format: %s\n",FileFormat==GENBANK?"genbank":"flat");
+	fprintf(file, "File_format: %s\n",
+		FileFormat == GENBANK ? "genbank" : "flat");
 	/*
 	fprintf(file,"EditMode: %s\n",EditMode==INSERT?"insert":
 					"check");
 */
 
 	this_seq = &(aln->element[NAdd->cursor_y]);
-	if(this_seq->id != NULL)
-		fprintf(file,"sequence-ID %s\n",this_seq->id);
-	fprintf(file,"Column: %d\nPos:%d\n",NAdd->cursor_x,NAdd->position);
-	switch(this_seq->elementtype)
-	{
-	case DNA:
-	case RNA:
-		fprintf(file,"#%s\n",
-		    this_seq->short_name);
-		break;
-	case PROTEIN:
-		fprintf(file,"%%%s\n",
-		    this_seq->short_name);
-		break;
-	case MASK:
-		fprintf(file,"@%s\n",
-		    this_seq->short_name);
-		break;
-	case TEXT:
-		fprintf(file,"%c%s\n",'"',
-		    this_seq->short_name);
-		break;
-	default:
-		break;
+	if (this_seq->id != NULL)
+		fprintf(file, "sequence-ID %s\n", this_seq->id);
+	fprintf(file, "Column: %d\nPos:%d\n", NAdd->cursor_x, NAdd->position);
+	switch (this_seq->elementtype) {
+		case DNA:
+		case RNA:
+			fprintf(file, "#%s\n", this_seq->short_name);
+			break;
+		case PROTEIN:
+			fprintf(file, "%%%s\n", this_seq->short_name);
+			break;
+		case MASK:
+			fprintf(file, "@%s\n", this_seq->short_name);
+			break;
+		case TEXT:
+			fprintf(file, "%c%s\n", '"', this_seq->short_name);
+			break;
+		default:
+			break;
 	}
-	if(this_seq->tmatrix)
-		for(j=0;j<this_seq->seqlen;j++)
-			putc(this_seq->tmatrix[getelem(this_seq,j)],file);
+	if (this_seq->tmatrix)
+		for (j = 0; j < this_seq->seqlen; j++)
+			putc(this_seq->tmatrix[getelem(this_seq, j)], file);
 	else
-		for(j=0;j<this_seq->seqlen;j++)
-			putc(getelem(this_seq,j),file);
+		for (j = 0; j < this_seq->seqlen; j++)
+			putc(getelem(this_seq, j), file);
 
 	fclose(file);
 	return;
 }
 
-ReadStatus(filename)
-char *filename;
+ReadStatus(filename) char *filename;
 {
 	/*
 	int i,j;
@@ -923,128 +886,129 @@ char *filename;
 			}
 		}
 	}
-	
+
 */
 }
 
-
-NormalizeOffset(aln)
-NA_Alignment *aln;
+NormalizeOffset(aln) NA_Alignment *aln;
 {
-	int i,j,offset = 99999999;
+	int i, j, offset = 99999999;
 
-	for(j=0;j<aln->numelements;j++)
-		offset = MIN(offset,aln->element[j].offset);
+	for (j = 0; j < aln->numelements; j++)
+		offset = MIN(offset, aln->element[j].offset);
 
-	for(j=0;j<aln->numelements;j++)
-		aln->element[j].offset -= offset;
+	for (j = 0; j < aln->numelements; j++) aln->element[j].offset -= offset;
 
 	aln->maxlen = -999999999;
-	for(j=0;j<aln->numelements;j++)
-		aln->maxlen = MAX(aln->element[j].seqlen+aln->element[j].offset,
-		    aln->maxlen);
+	for (j = 0; j < aln->numelements; j++)
+		aln->maxlen =
+		    MAX(aln->element[j].seqlen + aln->element[j].offset,
+			aln->maxlen);
 
 	aln->rel_offset += offset;
 
-	if(aln->numelements == 0)
-		aln->rel_offset = 0;
+	if (aln->numelements == 0) aln->rel_offset = 0;
 
 	return;
 }
 
-WriteCMask(aln,filename,method,maskable)
-NA_Alignment *aln;
+WriteCMask(aln, filename, method, maskable) NA_Alignment *aln;
 char *filename;
-int method,maskable;
+int method, maskable;
 {
-	int j,kk,mask = -1,k,offset,min_offset= -999999;
+	int j, kk, mask = -1, k, offset, min_offset = -999999;
 	char offset_str[100];
 	int *buf;
 	NA_Sequence *seqs;
 	FILE *file;
-	if(aln == NULL)
-		return;
-	if(aln->numelements == (int) NULL)
-		return;
+	if (aln == NULL) return;
+	if (aln->numelements == (int)NULL) return;
 	seqs = aln->element;
 
-	file = fopen(filename,"w");
-	if(file == NULL)
-	{
+	file = fopen(filename, "w");
+	if (file == NULL) {
 		Warning("Cannot open file for output");
-		return(1);
+		return (1);
 	}
-	if(maskable && (method != SELECT_REGION))
-	{
-		for(j=0;j<aln->numelements;j++)
-			if(seqs[j].elementtype == MASK && 
-			    seqs[j].selected)
+	if (maskable && (method != SELECT_REGION)) {
+		for (j = 0; j < aln->numelements; j++)
+			if (seqs[j].elementtype == MASK && seqs[j].selected)
 				mask = j;
 	}
-	for(j=0;j<aln->numelements;j++)
-	{
+	for (j = 0; j < aln->numelements; j++) {
 		SeqNorm(&(seqs[j]));
 	}
 
-	for(j=0;j<aln->numelements;j++)
-	{
-		if(method != SELECT_REGION)
+	for (j = 0; j < aln->numelements; j++) {
+		if (method != SELECT_REGION)
 			offset = seqs[j].offset;
 		else
-			for(offset=seqs[j].offset;
-			aln->selection_mask[offset] == '0';
-			offset++);
+			for (offset = seqs[j].offset;
+			     aln->selection_mask[offset] == '0'; offset++)
+				;
 
-		if(offset+aln->rel_offset != 0)
-			sprintf(offset_str,"(%d)",offset+aln->rel_offset);
+		if (offset + aln->rel_offset != 0)
+			sprintf(offset_str, "(%d)", offset + aln->rel_offset);
 		else
 			offset_str[0] = '\0';
-		
-		if(((j!=mask) && (seqs[j].selected) && method != SELECT_REGION) 
-		|| (method == SELECT_REGION && seqs[j].subselected)
-		|| method == ALL)
-		{
-			fprintf(file,"%c%s%s\n",
-			    seqs[j].elementtype == DNA?'#':
-			    seqs[j].elementtype == RNA?'#':
-			    seqs[j].elementtype == PROTEIN?'%':
-			    seqs[j].elementtype == TEXT?'"':
-			    seqs[j].elementtype == MASK?'@':'"',
+
+		if (((j != mask) && (seqs[j].selected) &&
+		     method != SELECT_REGION) ||
+		    (method == SELECT_REGION && seqs[j].subselected) ||
+		    method == ALL) {
+			fprintf(
+			    file, "%c%s%s\n",
+			    seqs[j].elementtype == DNA	     ? '#'
+			    : seqs[j].elementtype == RNA     ? '#'
+			    : seqs[j].elementtype == PROTEIN ? '%'
+			    : seqs[j].elementtype == TEXT    ? '"'
+			    : seqs[j].elementtype == MASK    ? '@'
+							     : '"',
 			    seqs[j].short_name,
-			    (offset+aln->rel_offset  == 0)? "":offset_str);
+			    (offset + aln->rel_offset == 0) ? "" : offset_str);
 
-			if(seqs[j].cmask != NULL)
-			{
+			if (seqs[j].cmask != NULL) {
+				buf =
+				    (int *)Calloc(seqs[j].seqlen, sizeof(int));
 
-				buf =(int*) Calloc(seqs[j].seqlen,sizeof(int) );
-
-				if(mask == -1)
-				{
-					for(k=0,kk=0;kk<seqs[j].seqlen;kk++)
-					{
-						if(method == SELECT_REGION)
-						{
-							if(aln->selection_mask[kk+offset]=='1')
-								buf[k++] = (getcmask( &(seqs[j]),kk+offset));
+				if (mask == -1) {
+					for (k = 0, kk = 0; kk < seqs[j].seqlen;
+					     kk++) {
+						if (method == SELECT_REGION) {
+							if (aln->selection_mask
+								[kk + offset] ==
+							    '1')
+								buf[k++] = (getcmask(
+								    &(seqs[j]),
+								    kk +
+									offset));
 						}
 
 						else
-							buf[k++] =( getcmask( &(seqs[j]),kk+offset) );
+							buf[k++] = (getcmask(
+							    &(seqs[j]),
+							    kk + offset));
 					}
 				}
-				else
-				{
-					for(k=0,kk=0;kk<seqs[j].seqlen;kk++)
-						if(getelem(&(seqs[mask]),kk+offset) == '1')
-							buf[k++] =(getcmask(&(seqs[j]), kk+offset));
-/*
-*			Looks like k might be one behind?
-*/
+				else {
+					for (k = 0, kk = 0; kk < seqs[j].seqlen;
+					     kk++)
+						if (getelem(&(seqs[mask]),
+							    kk + offset) == '1')
+							buf[k++] = (getcmask(
+							    &(seqs[j]),
+							    kk + offset));
+					/*
+					 *			Looks like k
+					 *might be one behind?
+					 */
 				}
-				fprintf(file,"name:%s\noffset:%d\nlength:%d\nstart:\n",
-						seqs[j].short_name,seqs[j].offset,k);
+				fprintf(
+				    file,
+				    "name:%s\noffset:%d\nlength:%d\nstart:\n",
+				    seqs[j].short_name, seqs[j].offset, k);
 
-				for(kk = 0; kk < k; kk++)
+				for (kk = 0; kk < k; kk++)
 					fprintf(file, "%d\n", buf[kk]);
 
 				Cfree(buf);
@@ -1052,5 +1016,5 @@ int method,maskable;
 		}
 	}
 	fclose(file);
-	return(0);
+	return (0);
 }
diff --git a/CORE/Makefile b/CORE/Makefile
index 8559d3b..0c81112 100755
--- a/CORE/Makefile
+++ b/CORE/Makefile
@@ -5,8 +5,8 @@ SRCS= ParseMenu.c main.c BasicDisplay.c EventHandler.c FileIO.c \
 DrawNA.c Free.c BuiltIn.c Edit.c Genbank.c Scroll.c ChooseFile.c \
 CutCopyPaste.c HGLfile.c
 
-LIBS= -lm -lxview -lolgx -lX11
-CFLAGS= -g -m32 -L/usr/lib32 -I/usr/include/xview
+LIBS= -lm -lxview -lolgx -lX11 -ltirpc
+CFLAGS= -g -m32 -L/usr/lib32 -I/usr/include
 CC = cc
 #	Possible defines, SUN4 SGI DEC HGL
 DEFINES =  -DLINUX
diff --git a/HGL_SRC/Makefile b/HGL_SRC/Makefile
index 9632d10..58c44c8 100755
--- a/HGL_SRC/Makefile
+++ b/HGL_SRC/Makefile
@@ -3,9 +3,9 @@ CC = cc
 FLAGS = -m32
 OPENWINHOME = ../usr
 MFILE = 
-INCDIR = -I/usr/include/xview
+INCDIR = -I/usr/include
 LIBDIR = -L/usr/lib32
-LIBS = -lxview -lolgx -lX11 
+LIBS = -lxview -lolgx -lX11 -ltirpc 
 
 libs.o = Alloc.o HGLfuncs.o