README.md

@@ -1,71 +0,0 @@
-# STADEN-LG
-
-STADEN Last Generation
-
-## Introduction
-
-<div  align="center"> 
-<img src="./desktop/staden-lg.png" width = "300" alt="logo" align=center />
-</div>
-
-This pkg is a fork of STADEN 1993 v12.1. Currently, I fixed the bug for compiling, but not completely.
-
-## Build
-
-You should clone this repo and cd to the repo get the `$pkgname` via `pwd` 
-
-```
-# build easy
-for pkgalone in ted newted abi alf Misc cop convert expGetSeq frog getMCH indexseqlibs bap/osp-bits
-do
-cd $pkgname/src/$pkgalone
-make
-done
-
-# compile x related
-cd $pkgname/src/staden
-bash gen_a.sh
-make mep dap sap splitp1 splitp2 splitp3 gip sethelp convert_project sapf nipf xmep xdap xsap
-cd $pkgname/src/bap
-make bap xbap
-for pkgalone in vepe update_subclones scf
-do
-cd $pkgname/src/$pkgalone
-make
-done
-```
-
-Or you can get this pkg from BioArchLinux repo.
-
-## Todo
-
-Following pkgs need your hands.
-
-- [ ] nip
-
-- [ ] sip
-
-- [ ] rep
-
-- [ ] lip
-
-- [ ] vep
-
-- [ ] nipl
-
-- [ ] pipl
-
-- [ ] sipl
-
-- [ ] xnip
-
-- [ ] xpip
-
-- [ ] xsip
-
-
-## License
-
-- Copyright (c) 1993 MEDICAL RESEARCH COUNCIL (MRC), UK. BSD License.
-
-- Copyright (c) 2023~ Everyone. GPL License.

Staden_install-alpha

@@ -0,0 +1,453 @@
+#! /bin/csh -f
+#
+# staden_install - version 2.4
+#
+#	This is a prototype installation program.
+#
+# 9 March 1992
+#	Modified for installation on Sun, Alliant, etc
+#	No longer install 2rs
+#
+# 20 November 1992
+#	Now includes convert, cop, frog, getMCH and scf
+#
+# 25 November 1992
+#	SGI supported
+# 
+# 19 May 1993
+#	DEC Alpha, Solaris supported
+# 
+# Written by sd@uk.ac.cam.mrc-lmb
+#
+
+# prelim
+set prog = $0 ; set prog = $prog:t
+
+# Machines supported: al sun dec sgi alpha solaris
+#set MACHINE = `echo $prog | sed 's/.*-//'`
+set MACHINE = alpha
+
+# For local (MRC-LMB) setup only
+#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
+set LOCAL = NO
+
+
+echo ""
+echo -n "Staden Package installation procedure - "
+switch (${MACHINE})
+	case "al":
+		echo "Alliant FX/2800 Concentrix version"
+		set MAKE = "make -sk"
+		breaksw
+	case "sun":
+		echo "SunOS version"
+		set MAKE = "make -sk"
+		breaksw
+	case "dec":
+		echo "DEC Ultrix (mips) version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "sgi":
+		echo "Silicon Graphics Iris version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "alpha":
+		echo "DEC Alpha OSF/1 version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "solaris":
+		echo "Solaris version"
+		set MAKE = "make -sk"
+		breaksw
+	default:
+		echo "Panic. Unknown version"
+		exit 1
+endsw
+echo ""
+echo "* starting initialization...please wait."
+echo ""
+
+# Binary fork of source directory
+if ($LOCAL == "YES") then
+    set DIR_BINARIES = ${MACHINE}-binaries
+    set DIR_PROGS = ${MACHINE}-bin
+else
+    set DIR_BINARIES = .
+    set DIR_PROGS = bin
+    set MAKE = "$MAKE -f makefile-${MACHINE}"
+endif
+
+init:
+# Set useful shell variables
+set YES="YES";
+set NO="NO"
+
+# set/unset some .cshrc envs.
+unset noclobber
+set noglob
+
+# set interrupt trap
+onintr end_failure
+
+# Make dir command
+set MKDIR = "mkdir"
+
+# Copy command
+set CP = "cp -p"
+
+# Install command
+#set INSTALL = "install"
+#set INSTALL = "mv"
+set INSTALL = "cp"
+
+# Set up default responses
+set DEF_STADEN_ROOT = `pwd`
+
+set DEF_REQ_NONX = "$YES"
+set DEF_REQ_X = "$YES"
+set DEF_REQ_TED = "$YES"
+set DEF_REQ_MISC = "$YES"
+
+# directories
+set DIR_SRC = $DEF_STADEN_ROOT/src
+set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
+set DIR_MISC = $DIR_SRC/Misc
+set DIR_STADEN = $DIR_SRC/staden
+set DIR_TED = $DIR_SRC/ted
+set DIR_ABI = $DIR_SRC/abi
+set DIR_ALF = $DIR_SRC/alf
+set DIR_BAP = $DIR_SRC/bap
+set DIR_OSP = $DIR_SRC/bap/osp-bits
+set DIR_CONVERT = $DIR_SRC/convert
+set DIR_COP = $DIR_SRC/cop
+set DIR_FROG = $DIR_SRC/frog
+set DIR_GETMCH = $DIR_SRC/getMCH
+set DIR_SCF = $DIR_SRC/scf
+
+
+main:
+
+	
+preamble:
+	echo ""
+	echo ""
+	echo "* Please answer the following questions."
+	echo "  Default answers to questions are given in square brackets."
+	echo "  If you require help at any stage respond with a ? to the question."
+	echo ""
+
+ask_staden_root:
+	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
+
+ask_require_nonx_progs: 
+	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
+	set ANS_REQ_NONX = $<
+	if ("$ANS_REQ_NONX" == "?") then
+		echo "* If you do not have X windows on your system you will require"
+		echo "  these.  However, you will require Tektronics terminal emulation."
+		echo "  If you do not require all of the non-X programs, you should abort"
+		echo "  and manually make the ones you require."
+		echo ""
+		goto ask_require_nonx_progs
+	else if ("$ANS_REQ_NONX" != "") then
+		if ("$ANS_REQ_NONX" =~ [yY]*) then
+			set ANS_REQ_NONX=$YES
+		else if ("$ANS_REQ_NONX" =~ [nN]*) then
+			set ANS_REQ_NONX=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_NONX=$DEF_REQ_NONX
+	endif
+
+ask_require_x_progs:
+	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
+	set ANS_REQ_X = $<
+	if ("$ANS_REQ_X" == "?") then
+		echo "* These are the programs that require X windows."
+		echo "  If you do not require all of the X programs, you should abort"
+		echo "  and manually make the ones you require."
+
+		echo ""
+		goto ask_require_x_progs
+	else if ("$ANS_REQ_X" != "") then
+		if ("$ANS_REQ_X" =~ [yY]*) then
+			set ANS_REQ_X=$YES
+		else if ("$ANS_REQ_X" =~ [nN]*) then
+			set ANS_REQ_X=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_X=$DEF_REQ_X
+	endif
+
+
+ask_require_ted:
+	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
+	set ANS_REQ_TED = $<
+	if ("$ANS_REQ_TED" == "?") then
+		echo "* This is the trace editor program.  It allows you to look at"
+		echo "  traces obtained from automated fluorescent sequencing machines."
+		echo ""
+		goto ask_require_ted
+	else if ("$ANS_REQ_TED" != "") then
+		if ("$ANS_REQ_TED" =~ [yY]*) then
+			set ANS_REQ_TED=$YES
+		else if ("$ANS_REQ_TED" =~ [nN]*) then
+			set ANS_REQ_TED=$NO
+		else
+			goto ask_require_ted
+		endif
+	else
+		set ANS_REQ_TED=$DEF_REQ_TED
+	endif
+
+
+
+ask_require_misc:
+	echo -n "Compile other programs [$DEF_REQ_MISC]? "
+	set ANS_REQ_MISC = $<
+	if ("$ANS_REQ_MISC" == "?") then
+		echo "* Other programs include:"
+		echo "    alfsplit"
+		echo "    getABISampleName"
+		echo ""
+		goto ask_require_misc
+	else if ("$ANS_REQ_MISC" != "") then
+		if ("$ANS_REQ_MISC" =~ [yY]*) then
+			set ANS_REQ_MISC=$YES
+		else if ("$ANS_REQ_MISC" =~ [nN]*) then
+			set ANS_REQ_MISC=$NO
+		else
+			goto ask_require_misc
+		endif
+	else
+		set ANS_REQ_MISC=$DEF_REQ_MISC
+	endif
+
+
+
+time_taken_warning:
+	echo ""
+	echo "The installation procedure is now ready to start."
+	echo ""
+	echo "**** Warning:"
+	echo "    The installation will take considerable time to complete.  If you"
+	echo "    are installing the whole Staden Package from scratch it could"
+	echo "    take as long as an hour for all exectuables to be compiled and"
+	echo "    installed."
+	echo ""
+
+ask_goahead:
+	echo -n "Proceed with the installation [YES]? " 
+	set ANSWER=$<
+	if ("$ANSWER" == "?") then
+		echo "* Final confirmation to proceed with the installation.  Answer"
+		echo "  YES to proceed; otherwise, answer NO to abort the installation."
+		echo ""
+		goto ask_goahead
+	else if ("$ANSWER" != "") then
+		if ("$ANSWER" =~ [nN]*) then
+			goto chickens_exit
+		else if ("$ANSWER" !~ [yY]*) then
+			goto ask_goahead
+		endif
+	endif
+
+installation_proper:
+
+# make binaries directory if it doesn't exist
+
+	if (! -d $DIR_BIN) then
+		$MKDIR $DIR_BIN
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
+		echo ""
+		echo "+ Compiling miscellaneous library"
+
+		pushd $DIR_MISC > /dev/null
+
+		cd $DIR_BINARIES
+	        $MAKE all
+
+		popd > /dev/null
+
+	endif
+
+        if ("$ANS_REQ_NONX" == "$YES") then
+		echo ""
+		echo "+ Installing non X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE nprogs lprogs
+                $INSTALL mep $DIR_BIN
+		$INSTALL nip $DIR_BIN
+		$INSTALL pip $DIR_BIN
+		$INSTALL sap $DIR_BIN
+		$INSTALL sapf $DIR_BIN
+		$INSTALL sip $DIR_BIN
+		$INSTALL splitp1 $DIR_BIN
+		$INSTALL splitp2 $DIR_BIN
+		$INSTALL splitp3 $DIR_BIN
+		$INSTALL sethelp $DIR_BIN
+		$INSTALL gip $DIR_BIN
+		$INSTALL nipl $DIR_BIN
+		$INSTALL pipl $DIR_BIN
+		$INSTALL sipl $DIR_BIN
+		$INSTALL dap $DIR_BIN
+		$INSTALL nipf $DIR_BIN
+		$INSTALL vep $DIR_BIN
+		$INSTALL rep $DIR_BIN
+		$INSTALL lip $DIR_BIN
+		#$INSTALL convert_project $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE bap
+                $INSTALL bap $DIR_BIN
+		popd > /dev/null
+
+	endif
+
+	if ("$ANS_REQ_TED" == "$YES") then
+		echo ""
+		echo "+ Installing Trace editor"
+
+		pushd $DIR_TED > /dev/null
+		cd $DIR_BINARIES
+                $MAKE ted
+		$INSTALL ted $DIR_BIN
+		popd > /dev/null
+	endif
+
+	if ("$ANS_REQ_X" == "$YES") then
+		echo ""
+		echo "+ Installing X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+                $MAKE xprogs
+		$INSTALL xmep $DIR_BIN
+		$INSTALL xnip $DIR_BIN
+		$INSTALL xpip $DIR_BIN
+		$INSTALL xsap $DIR_BIN
+		$INSTALL xsip $DIR_BIN
+		$INSTALL xdap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE xbap
+                $INSTALL xbap $DIR_BIN
+		popd > /dev/null
+
+
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES") then
+		echo ""
+		echo "+ Installing miscellaneous programs"
+
+		pushd $DIR_ABI > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL getABISampleName $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_ALF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE alfsplit
+		$INSTALL alfsplit $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_CONVERT > /dev/null
+		cd $DIR_BINARIES
+                $MAKE convert
+		$INSTALL convert $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_COP > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL cop $DIR_BIN
+		$INSTALL cop-bap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_FROG > /dev/null
+		cd $DIR_BINARIES
+                $MAKE frog
+		$INSTALL frog $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_GETMCH > /dev/null
+		cd $DIR_BINARIES
+                $MAKE trace2seq
+		$INSTALL trace2seq $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_SCF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE makeSCF
+		$INSTALL makeSCF $DIR_BIN
+		popd > /dev/null
+
+
+
+	endif
+
+
+installation_done:
+	echo ""
+	echo "+ Installation completed"
+	echo ""
+
+	echo "  Some further initialisation is required in order to use the"
+	echo "  package.  csh users should insert the following in their .login"
+	echo "  files:"
+	echo "  "
+	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
+	echo '  	source $STADENROOT/staden.login'
+	echo "  "
+	echo "  Users of the Bourne shell, sh, should insert the following in"
+	echo "  their .profile:"
+	echo "  "
+	echo "  	STADENROOT=$ANS_STADEN_ROOT"
+	echo "  	export STADENROOT"
+	echo '  	. $STADENROOT/staden.profile'
+	echo "  "
+	echo "  These initialisations will alter the shell's search path so that"
+	echo "  it can find the programs in the STADEN Package"
+	echo "  "
+
+normal_exit:
+	exit 0
+
+chickens_exit:
+	echo ""
+	echo "+ Installation cancelled"
+	echo ""
+
+	exit 0
+
+end_failure:
+	unset noglob
+	echo ""
+	echo "Aborted STADEN Package installation on `date`" 
+	echo ""
+	exit 1
+

Staden_install-dec

@@ -0,0 +1,453 @@
+#! /bin/csh -f
+#
+# staden_install - version 2.4
+#
+#	This is a prototype installation program.
+#
+# 9 March 1992
+#	Modified for installation on Sun, Alliant, etc
+#	No longer install 2rs
+#
+# 20 November 1992
+#	Now includes convert, cop, frog, getMCH and scf
+#
+# 25 November 1992
+#	SGI supported
+# 
+# 19 May 1993
+#	DEC Alpha, Solaris supported
+# 
+# Written by sd@uk.ac.cam.mrc-lmb
+#
+
+# prelim
+set prog = $0 ; set prog = $prog:t
+
+# Machines supported: al sun dec sgi alpha solaris
+#set MACHINE = `echo $prog | sed 's/.*-//'`
+set MACHINE = dec
+
+# For local (MRC-LMB) setup only
+#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
+set LOCAL = NO
+
+
+echo ""
+echo -n "Staden Package installation procedure - "
+switch (${MACHINE})
+	case "al":
+		echo "Alliant FX/2800 Concentrix version"
+		set MAKE = "make -sk"
+		breaksw
+	case "sun":
+		echo "SunOS version"
+		set MAKE = "make -sk"
+		breaksw
+	case "dec":
+		echo "DEC Ultrix (mips) version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "sgi":
+		echo "Silicon Graphics Iris version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "alpha":
+		echo "DEC Alpha OSF/1 version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "solaris":
+		echo "Solaris version"
+		set MAKE = "make -sk"
+		breaksw
+	default:
+		echo "Panic. Unknown version"
+		exit 1
+endsw
+echo ""
+echo "* starting initialization...please wait."
+echo ""
+
+# Binary fork of source directory
+if ($LOCAL == "YES") then
+    set DIR_BINARIES = ${MACHINE}-binaries
+    set DIR_PROGS = ${MACHINE}-bin
+else
+    set DIR_BINARIES = .
+    set DIR_PROGS = bin
+    set MAKE = "$MAKE -f makefile-${MACHINE}"
+endif
+
+init:
+# Set useful shell variables
+set YES="YES";
+set NO="NO"
+
+# set/unset some .cshrc envs.
+unset noclobber
+set noglob
+
+# set interrupt trap
+onintr end_failure
+
+# Make dir command
+set MKDIR = "mkdir"
+
+# Copy command
+set CP = "cp -p"
+
+# Install command
+#set INSTALL = "install"
+#set INSTALL = "mv"
+set INSTALL = "cp"
+
+# Set up default responses
+set DEF_STADEN_ROOT = `pwd`
+
+set DEF_REQ_NONX = "$YES"
+set DEF_REQ_X = "$YES"
+set DEF_REQ_TED = "$YES"
+set DEF_REQ_MISC = "$YES"
+
+# directories
+set DIR_SRC = $DEF_STADEN_ROOT/src
+set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
+set DIR_MISC = $DIR_SRC/Misc
+set DIR_STADEN = $DIR_SRC/staden
+set DIR_TED = $DIR_SRC/ted
+set DIR_ABI = $DIR_SRC/abi
+set DIR_ALF = $DIR_SRC/alf
+set DIR_BAP = $DIR_SRC/bap
+set DIR_OSP = $DIR_SRC/bap/osp-bits
+set DIR_CONVERT = $DIR_SRC/convert
+set DIR_COP = $DIR_SRC/cop
+set DIR_FROG = $DIR_SRC/frog
+set DIR_GETMCH = $DIR_SRC/getMCH
+set DIR_SCF = $DIR_SRC/scf
+
+
+main:
+
+	
+preamble:
+	echo ""
+	echo ""
+	echo "* Please answer the following questions."
+	echo "  Default answers to questions are given in square brackets."
+	echo "  If you require help at any stage respond with a ? to the question."
+	echo ""
+
+ask_staden_root:
+	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
+
+ask_require_nonx_progs: 
+	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
+	set ANS_REQ_NONX = $<
+	if ("$ANS_REQ_NONX" == "?") then
+		echo "* If you do not have X windows on your system you will require"
+		echo "  these.  However, you will require Tektronics terminal emulation."
+		echo "  If you do not require all of the non-X programs, you should abort"
+		echo "  and manually make the ones you require."
+		echo ""
+		goto ask_require_nonx_progs
+	else if ("$ANS_REQ_NONX" != "") then
+		if ("$ANS_REQ_NONX" =~ [yY]*) then
+			set ANS_REQ_NONX=$YES
+		else if ("$ANS_REQ_NONX" =~ [nN]*) then
+			set ANS_REQ_NONX=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_NONX=$DEF_REQ_NONX
+	endif
+
+ask_require_x_progs:
+	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
+	set ANS_REQ_X = $<
+	if ("$ANS_REQ_X" == "?") then
+		echo "* These are the programs that require X windows."
+		echo "  If you do not require all of the X programs, you should abort"
+		echo "  and manually make the ones you require."
+
+		echo ""
+		goto ask_require_x_progs
+	else if ("$ANS_REQ_X" != "") then
+		if ("$ANS_REQ_X" =~ [yY]*) then
+			set ANS_REQ_X=$YES
+		else if ("$ANS_REQ_X" =~ [nN]*) then
+			set ANS_REQ_X=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_X=$DEF_REQ_X
+	endif
+
+
+ask_require_ted:
+	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
+	set ANS_REQ_TED = $<
+	if ("$ANS_REQ_TED" == "?") then
+		echo "* This is the trace editor program.  It allows you to look at"
+		echo "  traces obtained from automated fluorescent sequencing machines."
+		echo ""
+		goto ask_require_ted
+	else if ("$ANS_REQ_TED" != "") then
+		if ("$ANS_REQ_TED" =~ [yY]*) then
+			set ANS_REQ_TED=$YES
+		else if ("$ANS_REQ_TED" =~ [nN]*) then
+			set ANS_REQ_TED=$NO
+		else
+			goto ask_require_ted
+		endif
+	else
+		set ANS_REQ_TED=$DEF_REQ_TED
+	endif
+
+
+
+ask_require_misc:
+	echo -n "Compile other programs [$DEF_REQ_MISC]? "
+	set ANS_REQ_MISC = $<
+	if ("$ANS_REQ_MISC" == "?") then
+		echo "* Other programs include:"
+		echo "    alfsplit"
+		echo "    getABISampleName"
+		echo ""
+		goto ask_require_misc
+	else if ("$ANS_REQ_MISC" != "") then
+		if ("$ANS_REQ_MISC" =~ [yY]*) then
+			set ANS_REQ_MISC=$YES
+		else if ("$ANS_REQ_MISC" =~ [nN]*) then
+			set ANS_REQ_MISC=$NO
+		else
+			goto ask_require_misc
+		endif
+	else
+		set ANS_REQ_MISC=$DEF_REQ_MISC
+	endif
+
+
+
+time_taken_warning:
+	echo ""
+	echo "The installation procedure is now ready to start."
+	echo ""
+	echo "**** Warning:"
+	echo "    The installation will take considerable time to complete.  If you"
+	echo "    are installing the whole Staden Package from scratch it could"
+	echo "    take as long as an hour for all exectuables to be compiled and"
+	echo "    installed."
+	echo ""
+
+ask_goahead:
+	echo -n "Proceed with the installation [YES]? " 
+	set ANSWER=$<
+	if ("$ANSWER" == "?") then
+		echo "* Final confirmation to proceed with the installation.  Answer"
+		echo "  YES to proceed; otherwise, answer NO to abort the installation."
+		echo ""
+		goto ask_goahead
+	else if ("$ANSWER" != "") then
+		if ("$ANSWER" =~ [nN]*) then
+			goto chickens_exit
+		else if ("$ANSWER" !~ [yY]*) then
+			goto ask_goahead
+		endif
+	endif
+
+installation_proper:
+
+# make binaries directory if it doesn't exist
+
+	if (! -d $DIR_BIN) then
+		$MKDIR $DIR_BIN
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
+		echo ""
+		echo "+ Compiling miscellaneous library"
+
+		pushd $DIR_MISC > /dev/null
+
+		cd $DIR_BINARIES
+	        $MAKE all
+
+		popd > /dev/null
+
+	endif
+
+        if ("$ANS_REQ_NONX" == "$YES") then
+		echo ""
+		echo "+ Installing non X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE nprogs lprogs
+                $INSTALL mep $DIR_BIN
+		$INSTALL nip $DIR_BIN
+		$INSTALL pip $DIR_BIN
+		$INSTALL sap $DIR_BIN
+		$INSTALL sapf $DIR_BIN
+		$INSTALL sip $DIR_BIN
+		$INSTALL splitp1 $DIR_BIN
+		$INSTALL splitp2 $DIR_BIN
+		$INSTALL splitp3 $DIR_BIN
+		$INSTALL sethelp $DIR_BIN
+		$INSTALL gip $DIR_BIN
+		$INSTALL nipl $DIR_BIN
+		$INSTALL pipl $DIR_BIN
+		$INSTALL sipl $DIR_BIN
+		$INSTALL dap $DIR_BIN
+		$INSTALL nipf $DIR_BIN
+		$INSTALL vep $DIR_BIN
+		$INSTALL rep $DIR_BIN
+		$INSTALL lip $DIR_BIN
+		#$INSTALL convert_project $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE bap
+                $INSTALL bap $DIR_BIN
+		popd > /dev/null
+
+	endif
+
+	if ("$ANS_REQ_TED" == "$YES") then
+		echo ""
+		echo "+ Installing Trace editor"
+
+		pushd $DIR_TED > /dev/null
+		cd $DIR_BINARIES
+                $MAKE ted
+		$INSTALL ted $DIR_BIN
+		popd > /dev/null
+	endif
+
+	if ("$ANS_REQ_X" == "$YES") then
+		echo ""
+		echo "+ Installing X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+                $MAKE xprogs
+		$INSTALL xmep $DIR_BIN
+		$INSTALL xnip $DIR_BIN
+		$INSTALL xpip $DIR_BIN
+		$INSTALL xsap $DIR_BIN
+		$INSTALL xsip $DIR_BIN
+		$INSTALL xdap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE xbap
+                $INSTALL xbap $DIR_BIN
+		popd > /dev/null
+
+
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES") then
+		echo ""
+		echo "+ Installing miscellaneous programs"
+
+		pushd $DIR_ABI > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL getABISampleName $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_ALF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE alfsplit
+		$INSTALL alfsplit $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_CONVERT > /dev/null
+		cd $DIR_BINARIES
+                $MAKE convert
+		$INSTALL convert $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_COP > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL cop $DIR_BIN
+		$INSTALL cop-bap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_FROG > /dev/null
+		cd $DIR_BINARIES
+                $MAKE frog
+		$INSTALL frog $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_GETMCH > /dev/null
+		cd $DIR_BINARIES
+                $MAKE trace2seq
+		$INSTALL trace2seq $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_SCF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE makeSCF
+		$INSTALL makeSCF $DIR_BIN
+		popd > /dev/null
+
+
+
+	endif
+
+
+installation_done:
+	echo ""
+	echo "+ Installation completed"
+	echo ""
+
+	echo "  Some further initialisation is required in order to use the"
+	echo "  package.  csh users should insert the following in their .login"
+	echo "  files:"
+	echo "  "
+	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
+	echo '  	source $STADENROOT/staden.login'
+	echo "  "
+	echo "  Users of the Bourne shell, sh, should insert the following in"
+	echo "  their .profile:"
+	echo "  "
+	echo "  	STADENROOT=$ANS_STADEN_ROOT"
+	echo "  	export STADENROOT"
+	echo '  	. $STADENROOT/staden.profile'
+	echo "  "
+	echo "  These initialisations will alter the shell's search path so that"
+	echo "  it can find the programs in the STADEN Package"
+	echo "  "
+
+normal_exit:
+	exit 0
+
+chickens_exit:
+	echo ""
+	echo "+ Installation cancelled"
+	echo ""
+
+	exit 0
+
+end_failure:
+	unset noglob
+	echo ""
+	echo "Aborted STADEN Package installation on `date`" 
+	echo ""
+	exit 1
+

Staden_install-sgi

@@ -0,0 +1,453 @@
+#! /bin/csh -f
+#
+# staden_install - version 2.4
+#
+#	This is a prototype installation program.
+#
+# 9 March 1992
+#	Modified for installation on Sun, Alliant, etc
+#	No longer install 2rs
+#
+# 20 November 1992
+#	Now includes convert, cop, frog, getMCH and scf
+#
+# 25 November 1992
+#	SGI supported
+# 
+# 19 May 1993
+#	DEC Alpha, Solaris supported
+# 
+# Written by sd@uk.ac.cam.mrc-lmb
+#
+
+# prelim
+set prog = $0 ; set prog = $prog:t
+
+# Machines supported: al sun dec sgi alpha solaris
+#set MACHINE = `echo $prog | sed 's/.*-//'`
+set MACHINE = sgi
+
+# For local (MRC-LMB) setup only
+#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
+set LOCAL = NO
+
+
+echo ""
+echo -n "Staden Package installation procedure - "
+switch (${MACHINE})
+	case "al":
+		echo "Alliant FX/2800 Concentrix version"
+		set MAKE = "make -sk"
+		breaksw
+	case "sun":
+		echo "SunOS version"
+		set MAKE = "make -sk"
+		breaksw
+	case "dec":
+		echo "DEC Ultrix (mips) version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "sgi":
+		echo "Silicon Graphics Iris version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "alpha":
+		echo "DEC Alpha OSF/1 version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "solaris":
+		echo "Solaris version"
+		set MAKE = "make -sk"
+		breaksw
+	default:
+		echo "Panic. Unknown version"
+		exit 1
+endsw
+echo ""
+echo "* starting initialization...please wait."
+echo ""
+
+# Binary fork of source directory
+if ($LOCAL == "YES") then
+    set DIR_BINARIES = ${MACHINE}-binaries
+    set DIR_PROGS = ${MACHINE}-bin
+else
+    set DIR_BINARIES = .
+    set DIR_PROGS = bin
+    set MAKE = "$MAKE -f makefile-${MACHINE}"
+endif
+
+init:
+# Set useful shell variables
+set YES="YES";
+set NO="NO"
+
+# set/unset some .cshrc envs.
+unset noclobber
+set noglob
+
+# set interrupt trap
+onintr end_failure
+
+# Make dir command
+set MKDIR = "mkdir"
+
+# Copy command
+set CP = "cp -p"
+
+# Install command
+#set INSTALL = "install"
+#set INSTALL = "mv"
+set INSTALL = "cp"
+
+# Set up default responses
+set DEF_STADEN_ROOT = `pwd`
+
+set DEF_REQ_NONX = "$YES"
+set DEF_REQ_X = "$YES"
+set DEF_REQ_TED = "$YES"
+set DEF_REQ_MISC = "$YES"
+
+# directories
+set DIR_SRC = $DEF_STADEN_ROOT/src
+set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
+set DIR_MISC = $DIR_SRC/Misc
+set DIR_STADEN = $DIR_SRC/staden
+set DIR_TED = $DIR_SRC/ted
+set DIR_ABI = $DIR_SRC/abi
+set DIR_ALF = $DIR_SRC/alf
+set DIR_BAP = $DIR_SRC/bap
+set DIR_OSP = $DIR_SRC/bap/osp-bits
+set DIR_CONVERT = $DIR_SRC/convert
+set DIR_COP = $DIR_SRC/cop
+set DIR_FROG = $DIR_SRC/frog
+set DIR_GETMCH = $DIR_SRC/getMCH
+set DIR_SCF = $DIR_SRC/scf
+
+
+main:
+
+	
+preamble:
+	echo ""
+	echo ""
+	echo "* Please answer the following questions."
+	echo "  Default answers to questions are given in square brackets."
+	echo "  If you require help at any stage respond with a ? to the question."
+	echo ""
+
+ask_staden_root:
+	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
+
+ask_require_nonx_progs: 
+	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
+	set ANS_REQ_NONX = $<
+	if ("$ANS_REQ_NONX" == "?") then
+		echo "* If you do not have X windows on your system you will require"
+		echo "  these.  However, you will require Tektronics terminal emulation."
+		echo "  If you do not require all of the non-X programs, you should abort"
+		echo "  and manually make the ones you require."
+		echo ""
+		goto ask_require_nonx_progs
+	else if ("$ANS_REQ_NONX" != "") then
+		if ("$ANS_REQ_NONX" =~ [yY]*) then
+			set ANS_REQ_NONX=$YES
+		else if ("$ANS_REQ_NONX" =~ [nN]*) then
+			set ANS_REQ_NONX=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_NONX=$DEF_REQ_NONX
+	endif
+
+ask_require_x_progs:
+	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
+	set ANS_REQ_X = $<
+	if ("$ANS_REQ_X" == "?") then
+		echo "* These are the programs that require X windows."
+		echo "  If you do not require all of the X programs, you should abort"
+		echo "  and manually make the ones you require."
+
+		echo ""
+		goto ask_require_x_progs
+	else if ("$ANS_REQ_X" != "") then
+		if ("$ANS_REQ_X" =~ [yY]*) then
+			set ANS_REQ_X=$YES
+		else if ("$ANS_REQ_X" =~ [nN]*) then
+			set ANS_REQ_X=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_X=$DEF_REQ_X
+	endif
+
+
+ask_require_ted:
+	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
+	set ANS_REQ_TED = $<
+	if ("$ANS_REQ_TED" == "?") then
+		echo "* This is the trace editor program.  It allows you to look at"
+		echo "  traces obtained from automated fluorescent sequencing machines."
+		echo ""
+		goto ask_require_ted
+	else if ("$ANS_REQ_TED" != "") then
+		if ("$ANS_REQ_TED" =~ [yY]*) then
+			set ANS_REQ_TED=$YES
+		else if ("$ANS_REQ_TED" =~ [nN]*) then
+			set ANS_REQ_TED=$NO
+		else
+			goto ask_require_ted
+		endif
+	else
+		set ANS_REQ_TED=$DEF_REQ_TED
+	endif
+
+
+
+ask_require_misc:
+	echo -n "Compile other programs [$DEF_REQ_MISC]? "
+	set ANS_REQ_MISC = $<
+	if ("$ANS_REQ_MISC" == "?") then
+		echo "* Other programs include:"
+		echo "    alfsplit"
+		echo "    getABISampleName"
+		echo ""
+		goto ask_require_misc
+	else if ("$ANS_REQ_MISC" != "") then
+		if ("$ANS_REQ_MISC" =~ [yY]*) then
+			set ANS_REQ_MISC=$YES
+		else if ("$ANS_REQ_MISC" =~ [nN]*) then
+			set ANS_REQ_MISC=$NO
+		else
+			goto ask_require_misc
+		endif
+	else
+		set ANS_REQ_MISC=$DEF_REQ_MISC
+	endif
+
+
+
+time_taken_warning:
+	echo ""
+	echo "The installation procedure is now ready to start."
+	echo ""
+	echo "**** Warning:"
+	echo "    The installation will take considerable time to complete.  If you"
+	echo "    are installing the whole Staden Package from scratch it could"
+	echo "    take as long as an hour for all exectuables to be compiled and"
+	echo "    installed."
+	echo ""
+
+ask_goahead:
+	echo -n "Proceed with the installation [YES]? " 
+	set ANSWER=$<
+	if ("$ANSWER" == "?") then
+		echo "* Final confirmation to proceed with the installation.  Answer"
+		echo "  YES to proceed; otherwise, answer NO to abort the installation."
+		echo ""
+		goto ask_goahead
+	else if ("$ANSWER" != "") then
+		if ("$ANSWER" =~ [nN]*) then
+			goto chickens_exit
+		else if ("$ANSWER" !~ [yY]*) then
+			goto ask_goahead
+		endif
+	endif
+
+installation_proper:
+
+# make binaries directory if it doesn't exist
+
+	if (! -d $DIR_BIN) then
+		$MKDIR $DIR_BIN
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
+		echo ""
+		echo "+ Compiling miscellaneous library"
+
+		pushd $DIR_MISC > /dev/null
+
+		cd $DIR_BINARIES
+	        $MAKE all
+
+		popd > /dev/null
+
+	endif
+
+        if ("$ANS_REQ_NONX" == "$YES") then
+		echo ""
+		echo "+ Installing non X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE nprogs lprogs
+                $INSTALL mep $DIR_BIN
+		$INSTALL nip $DIR_BIN
+		$INSTALL pip $DIR_BIN
+		$INSTALL sap $DIR_BIN
+		$INSTALL sapf $DIR_BIN
+		$INSTALL sip $DIR_BIN
+		$INSTALL splitp1 $DIR_BIN
+		$INSTALL splitp2 $DIR_BIN
+		$INSTALL splitp3 $DIR_BIN
+		$INSTALL sethelp $DIR_BIN
+		$INSTALL gip $DIR_BIN
+		$INSTALL nipl $DIR_BIN
+		$INSTALL pipl $DIR_BIN
+		$INSTALL sipl $DIR_BIN
+		$INSTALL dap $DIR_BIN
+		$INSTALL nipf $DIR_BIN
+		$INSTALL vep $DIR_BIN
+		$INSTALL rep $DIR_BIN
+		$INSTALL lip $DIR_BIN
+		#$INSTALL convert_project $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE bap
+                $INSTALL bap $DIR_BIN
+		popd > /dev/null
+
+	endif
+
+	if ("$ANS_REQ_TED" == "$YES") then
+		echo ""
+		echo "+ Installing Trace editor"
+
+		pushd $DIR_TED > /dev/null
+		cd $DIR_BINARIES
+                $MAKE ted
+		$INSTALL ted $DIR_BIN
+		popd > /dev/null
+	endif
+
+	if ("$ANS_REQ_X" == "$YES") then
+		echo ""
+		echo "+ Installing X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+                $MAKE xprogs
+		$INSTALL xmep $DIR_BIN
+		$INSTALL xnip $DIR_BIN
+		$INSTALL xpip $DIR_BIN
+		$INSTALL xsap $DIR_BIN
+		$INSTALL xsip $DIR_BIN
+		$INSTALL xdap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE xbap
+                $INSTALL xbap $DIR_BIN
+		popd > /dev/null
+
+
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES") then
+		echo ""
+		echo "+ Installing miscellaneous programs"
+
+		pushd $DIR_ABI > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL getABISampleName $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_ALF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE alfsplit
+		$INSTALL alfsplit $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_CONVERT > /dev/null
+		cd $DIR_BINARIES
+                $MAKE convert
+		$INSTALL convert $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_COP > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL cop $DIR_BIN
+		$INSTALL cop-bap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_FROG > /dev/null
+		cd $DIR_BINARIES
+                $MAKE frog
+		$INSTALL frog $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_GETMCH > /dev/null
+		cd $DIR_BINARIES
+                $MAKE trace2seq
+		$INSTALL trace2seq $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_SCF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE makeSCF
+		$INSTALL makeSCF $DIR_BIN
+		popd > /dev/null
+
+
+
+	endif
+
+
+installation_done:
+	echo ""
+	echo "+ Installation completed"
+	echo ""
+
+	echo "  Some further initialisation is required in order to use the"
+	echo "  package.  csh users should insert the following in their .login"
+	echo "  files:"
+	echo "  "
+	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
+	echo '  	source $STADENROOT/staden.login'
+	echo "  "
+	echo "  Users of the Bourne shell, sh, should insert the following in"
+	echo "  their .profile:"
+	echo "  "
+	echo "  	STADENROOT=$ANS_STADEN_ROOT"
+	echo "  	export STADENROOT"
+	echo '  	. $STADENROOT/staden.profile'
+	echo "  "
+	echo "  These initialisations will alter the shell's search path so that"
+	echo "  it can find the programs in the STADEN Package"
+	echo "  "
+
+normal_exit:
+	exit 0
+
+chickens_exit:
+	echo ""
+	echo "+ Installation cancelled"
+	echo ""
+
+	exit 0
+
+end_failure:
+	unset noglob
+	echo ""
+	echo "Aborted STADEN Package installation on `date`" 
+	echo ""
+	exit 1
+

Staden_install-solaris

@@ -0,0 +1,453 @@
+#! /bin/csh -f
+#
+# staden_install - version 2.4
+#
+#	This is a prototype installation program.
+#
+# 9 March 1992
+#	Modified for installation on Sun, Alliant, etc
+#	No longer install 2rs
+#
+# 20 November 1992
+#	Now includes convert, cop, frog, getMCH and scf
+#
+# 25 November 1992
+#	SGI supported
+# 
+# 19 May 1993
+#	DEC Alpha, Solaris supported
+# 
+# Written by sd@uk.ac.cam.mrc-lmb
+#
+
+# prelim
+set prog = $0 ; set prog = $prog:t
+
+# Machines supported: al sun dec sgi alpha solaris
+#set MACHINE = `echo $prog | sed 's/.*-//'`
+set MACHINE = solaris
+
+# For local (MRC-LMB) setup only
+#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
+set LOCAL = NO
+
+
+echo ""
+echo -n "Staden Package installation procedure - "
+switch (${MACHINE})
+	case "al":
+		echo "Alliant FX/2800 Concentrix version"
+		set MAKE = "make -sk"
+		breaksw
+	case "sun":
+		echo "SunOS version"
+		set MAKE = "make -sk"
+		breaksw
+	case "dec":
+		echo "DEC Ultrix (mips) version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "sgi":
+		echo "Silicon Graphics Iris version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "alpha":
+		echo "DEC Alpha OSF/1 version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "solaris":
+		echo "Solaris version"
+		set MAKE = "make -sk"
+		breaksw
+	default:
+		echo "Panic. Unknown version"
+		exit 1
+endsw
+echo ""
+echo "* starting initialization...please wait."
+echo ""
+
+# Binary fork of source directory
+if ($LOCAL == "YES") then
+    set DIR_BINARIES = ${MACHINE}-binaries
+    set DIR_PROGS = ${MACHINE}-bin
+else
+    set DIR_BINARIES = .
+    set DIR_PROGS = bin
+    set MAKE = "$MAKE -f makefile-${MACHINE}"
+endif
+
+init:
+# Set useful shell variables
+set YES="YES";
+set NO="NO"
+
+# set/unset some .cshrc envs.
+unset noclobber
+set noglob
+
+# set interrupt trap
+onintr end_failure
+
+# Make dir command
+set MKDIR = "mkdir"
+
+# Copy command
+set CP = "cp -p"
+
+# Install command
+#set INSTALL = "install"
+#set INSTALL = "mv"
+set INSTALL = "cp"
+
+# Set up default responses
+set DEF_STADEN_ROOT = `pwd`
+
+set DEF_REQ_NONX = "$YES"
+set DEF_REQ_X = "$YES"
+set DEF_REQ_TED = "$YES"
+set DEF_REQ_MISC = "$YES"
+
+# directories
+set DIR_SRC = $DEF_STADEN_ROOT/src
+set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
+set DIR_MISC = $DIR_SRC/Misc
+set DIR_STADEN = $DIR_SRC/staden
+set DIR_TED = $DIR_SRC/ted
+set DIR_ABI = $DIR_SRC/abi
+set DIR_ALF = $DIR_SRC/alf
+set DIR_BAP = $DIR_SRC/bap
+set DIR_OSP = $DIR_SRC/bap/osp-bits
+set DIR_CONVERT = $DIR_SRC/convert
+set DIR_COP = $DIR_SRC/cop
+set DIR_FROG = $DIR_SRC/frog
+set DIR_GETMCH = $DIR_SRC/getMCH
+set DIR_SCF = $DIR_SRC/scf
+
+
+main:
+
+	
+preamble:
+	echo ""
+	echo ""
+	echo "* Please answer the following questions."
+	echo "  Default answers to questions are given in square brackets."
+	echo "  If you require help at any stage respond with a ? to the question."
+	echo ""
+
+ask_staden_root:
+	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
+
+ask_require_nonx_progs: 
+	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
+	set ANS_REQ_NONX = $<
+	if ("$ANS_REQ_NONX" == "?") then
+		echo "* If you do not have X windows on your system you will require"
+		echo "  these.  However, you will require Tektronics terminal emulation."
+		echo "  If you do not require all of the non-X programs, you should abort"
+		echo "  and manually make the ones you require."
+		echo ""
+		goto ask_require_nonx_progs
+	else if ("$ANS_REQ_NONX" != "") then
+		if ("$ANS_REQ_NONX" =~ [yY]*) then
+			set ANS_REQ_NONX=$YES
+		else if ("$ANS_REQ_NONX" =~ [nN]*) then
+			set ANS_REQ_NONX=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_NONX=$DEF_REQ_NONX
+	endif
+
+ask_require_x_progs:
+	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
+	set ANS_REQ_X = $<
+	if ("$ANS_REQ_X" == "?") then
+		echo "* These are the programs that require X windows."
+		echo "  If you do not require all of the X programs, you should abort"
+		echo "  and manually make the ones you require."
+
+		echo ""
+		goto ask_require_x_progs
+	else if ("$ANS_REQ_X" != "") then
+		if ("$ANS_REQ_X" =~ [yY]*) then
+			set ANS_REQ_X=$YES
+		else if ("$ANS_REQ_X" =~ [nN]*) then
+			set ANS_REQ_X=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_X=$DEF_REQ_X
+	endif
+
+
+ask_require_ted:
+	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
+	set ANS_REQ_TED = $<
+	if ("$ANS_REQ_TED" == "?") then
+		echo "* This is the trace editor program.  It allows you to look at"
+		echo "  traces obtained from automated fluorescent sequencing machines."
+		echo ""
+		goto ask_require_ted
+	else if ("$ANS_REQ_TED" != "") then
+		if ("$ANS_REQ_TED" =~ [yY]*) then
+			set ANS_REQ_TED=$YES
+		else if ("$ANS_REQ_TED" =~ [nN]*) then
+			set ANS_REQ_TED=$NO
+		else
+			goto ask_require_ted
+		endif
+	else
+		set ANS_REQ_TED=$DEF_REQ_TED
+	endif
+
+
+
+ask_require_misc:
+	echo -n "Compile other programs [$DEF_REQ_MISC]? "
+	set ANS_REQ_MISC = $<
+	if ("$ANS_REQ_MISC" == "?") then
+		echo "* Other programs include:"
+		echo "    alfsplit"
+		echo "    getABISampleName"
+		echo ""
+		goto ask_require_misc
+	else if ("$ANS_REQ_MISC" != "") then
+		if ("$ANS_REQ_MISC" =~ [yY]*) then
+			set ANS_REQ_MISC=$YES
+		else if ("$ANS_REQ_MISC" =~ [nN]*) then
+			set ANS_REQ_MISC=$NO
+		else
+			goto ask_require_misc
+		endif
+	else
+		set ANS_REQ_MISC=$DEF_REQ_MISC
+	endif
+
+
+
+time_taken_warning:
+	echo ""
+	echo "The installation procedure is now ready to start."
+	echo ""
+	echo "**** Warning:"
+	echo "    The installation will take considerable time to complete.  If you"
+	echo "    are installing the whole Staden Package from scratch it could"
+	echo "    take as long as an hour for all exectuables to be compiled and"
+	echo "    installed."
+	echo ""
+
+ask_goahead:
+	echo -n "Proceed with the installation [YES]? " 
+	set ANSWER=$<
+	if ("$ANSWER" == "?") then
+		echo "* Final confirmation to proceed with the installation.  Answer"
+		echo "  YES to proceed; otherwise, answer NO to abort the installation."
+		echo ""
+		goto ask_goahead
+	else if ("$ANSWER" != "") then
+		if ("$ANSWER" =~ [nN]*) then
+			goto chickens_exit
+		else if ("$ANSWER" !~ [yY]*) then
+			goto ask_goahead
+		endif
+	endif
+
+installation_proper:
+
+# make binaries directory if it doesn't exist
+
+	if (! -d $DIR_BIN) then
+		$MKDIR $DIR_BIN
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
+		echo ""
+		echo "+ Compiling miscellaneous library"
+
+		pushd $DIR_MISC > /dev/null
+
+		cd $DIR_BINARIES
+	        $MAKE all
+
+		popd > /dev/null
+
+	endif
+
+        if ("$ANS_REQ_NONX" == "$YES") then
+		echo ""
+		echo "+ Installing non X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE nprogs lprogs
+                $INSTALL mep $DIR_BIN
+		$INSTALL nip $DIR_BIN
+		$INSTALL pip $DIR_BIN
+		$INSTALL sap $DIR_BIN
+		$INSTALL sapf $DIR_BIN
+		$INSTALL sip $DIR_BIN
+		$INSTALL splitp1 $DIR_BIN
+		$INSTALL splitp2 $DIR_BIN
+		$INSTALL splitp3 $DIR_BIN
+		$INSTALL sethelp $DIR_BIN
+		$INSTALL gip $DIR_BIN
+		$INSTALL nipl $DIR_BIN
+		$INSTALL pipl $DIR_BIN
+		$INSTALL sipl $DIR_BIN
+		$INSTALL dap $DIR_BIN
+		$INSTALL nipf $DIR_BIN
+		$INSTALL vep $DIR_BIN
+		$INSTALL rep $DIR_BIN
+		$INSTALL lip $DIR_BIN
+		#$INSTALL convert_project $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE bap
+                $INSTALL bap $DIR_BIN
+		popd > /dev/null
+
+	endif
+
+	if ("$ANS_REQ_TED" == "$YES") then
+		echo ""
+		echo "+ Installing Trace editor"
+
+		pushd $DIR_TED > /dev/null
+		cd $DIR_BINARIES
+                $MAKE ted
+		$INSTALL ted $DIR_BIN
+		popd > /dev/null
+	endif
+
+	if ("$ANS_REQ_X" == "$YES") then
+		echo ""
+		echo "+ Installing X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+                $MAKE xprogs
+		$INSTALL xmep $DIR_BIN
+		$INSTALL xnip $DIR_BIN
+		$INSTALL xpip $DIR_BIN
+		$INSTALL xsap $DIR_BIN
+		$INSTALL xsip $DIR_BIN
+		$INSTALL xdap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE xbap
+                $INSTALL xbap $DIR_BIN
+		popd > /dev/null
+
+
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES") then
+		echo ""
+		echo "+ Installing miscellaneous programs"
+
+		pushd $DIR_ABI > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL getABISampleName $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_ALF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE alfsplit
+		$INSTALL alfsplit $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_CONVERT > /dev/null
+		cd $DIR_BINARIES
+                $MAKE convert
+		$INSTALL convert $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_COP > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL cop $DIR_BIN
+		$INSTALL cop-bap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_FROG > /dev/null
+		cd $DIR_BINARIES
+                $MAKE frog
+		$INSTALL frog $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_GETMCH > /dev/null
+		cd $DIR_BINARIES
+                $MAKE trace2seq
+		$INSTALL trace2seq $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_SCF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE makeSCF
+		$INSTALL makeSCF $DIR_BIN
+		popd > /dev/null
+
+
+
+	endif
+
+
+installation_done:
+	echo ""
+	echo "+ Installation completed"
+	echo ""
+
+	echo "  Some further initialisation is required in order to use the"
+	echo "  package.  csh users should insert the following in their .login"
+	echo "  files:"
+	echo "  "
+	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
+	echo '  	source $STADENROOT/staden.login'
+	echo "  "
+	echo "  Users of the Bourne shell, sh, should insert the following in"
+	echo "  their .profile:"
+	echo "  "
+	echo "  	STADENROOT=$ANS_STADEN_ROOT"
+	echo "  	export STADENROOT"
+	echo '  	. $STADENROOT/staden.profile'
+	echo "  "
+	echo "  These initialisations will alter the shell's search path so that"
+	echo "  it can find the programs in the STADEN Package"
+	echo "  "
+
+normal_exit:
+	exit 0
+
+chickens_exit:
+	echo ""
+	echo "+ Installation cancelled"
+	echo ""
+
+	exit 0
+
+end_failure:
+	unset noglob
+	echo ""
+	echo "Aborted STADEN Package installation on `date`" 
+	echo ""
+	exit 1
+

Staden_install-sun

@@ -0,0 +1,453 @@
+#! /bin/csh -f
+#
+# staden_install - version 2.4
+#
+#	This is a prototype installation program.
+#
+# 9 March 1992
+#	Modified for installation on Sun, Alliant, etc
+#	No longer install 2rs
+#
+# 20 November 1992
+#	Now includes convert, cop, frog, getMCH and scf
+#
+# 25 November 1992
+#	SGI supported
+# 
+# 19 May 1993
+#	DEC Alpha, Solaris supported
+# 
+# Written by sd@uk.ac.cam.mrc-lmb
+#
+
+# prelim
+set prog = $0 ; set prog = $prog:t
+
+# Machines supported: al sun dec sgi alpha solaris
+#set MACHINE = `echo $prog | sed 's/.*-//'`
+set MACHINE = sun
+
+# For local (MRC-LMB) setup only
+#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
+set LOCAL = NO
+
+
+echo ""
+echo -n "Staden Package installation procedure - "
+switch (${MACHINE})
+	case "al":
+		echo "Alliant FX/2800 Concentrix version"
+		set MAKE = "make -sk"
+		breaksw
+	case "sun":
+		echo "SunOS version"
+		set MAKE = "make -sk"
+		breaksw
+	case "dec":
+		echo "DEC Ultrix (mips) version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "sgi":
+		echo "Silicon Graphics Iris version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "alpha":
+		echo "DEC Alpha OSF/1 version"
+		set MAKE = "gmake -sk"
+		breaksw
+	case "solaris":
+		echo "Solaris version"
+		set MAKE = "make -sk"
+		breaksw
+	default:
+		echo "Panic. Unknown version"
+		exit 1
+endsw
+echo ""
+echo "* starting initialization...please wait."
+echo ""
+
+# Binary fork of source directory
+if ($LOCAL == "YES") then
+    set DIR_BINARIES = ${MACHINE}-binaries
+    set DIR_PROGS = ${MACHINE}-bin
+else
+    set DIR_BINARIES = .
+    set DIR_PROGS = bin
+    set MAKE = "$MAKE -f makefile-${MACHINE}"
+endif
+
+init:
+# Set useful shell variables
+set YES="YES";
+set NO="NO"
+
+# set/unset some .cshrc envs.
+unset noclobber
+set noglob
+
+# set interrupt trap
+onintr end_failure
+
+# Make dir command
+set MKDIR = "mkdir"
+
+# Copy command
+set CP = "cp -p"
+
+# Install command
+#set INSTALL = "install"
+#set INSTALL = "mv"
+set INSTALL = "cp"
+
+# Set up default responses
+set DEF_STADEN_ROOT = `pwd`
+
+set DEF_REQ_NONX = "$YES"
+set DEF_REQ_X = "$YES"
+set DEF_REQ_TED = "$YES"
+set DEF_REQ_MISC = "$YES"
+
+# directories
+set DIR_SRC = $DEF_STADEN_ROOT/src
+set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
+set DIR_MISC = $DIR_SRC/Misc
+set DIR_STADEN = $DIR_SRC/staden
+set DIR_TED = $DIR_SRC/ted
+set DIR_ABI = $DIR_SRC/abi
+set DIR_ALF = $DIR_SRC/alf
+set DIR_BAP = $DIR_SRC/bap
+set DIR_OSP = $DIR_SRC/bap/osp-bits
+set DIR_CONVERT = $DIR_SRC/convert
+set DIR_COP = $DIR_SRC/cop
+set DIR_FROG = $DIR_SRC/frog
+set DIR_GETMCH = $DIR_SRC/getMCH
+set DIR_SCF = $DIR_SRC/scf
+
+
+main:
+
+	
+preamble:
+	echo ""
+	echo ""
+	echo "* Please answer the following questions."
+	echo "  Default answers to questions are given in square brackets."
+	echo "  If you require help at any stage respond with a ? to the question."
+	echo ""
+
+ask_staden_root:
+	set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
+
+ask_require_nonx_progs: 
+	echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
+	set ANS_REQ_NONX = $<
+	if ("$ANS_REQ_NONX" == "?") then
+		echo "* If you do not have X windows on your system you will require"
+		echo "  these.  However, you will require Tektronics terminal emulation."
+		echo "  If you do not require all of the non-X programs, you should abort"
+		echo "  and manually make the ones you require."
+		echo ""
+		goto ask_require_nonx_progs
+	else if ("$ANS_REQ_NONX" != "") then
+		if ("$ANS_REQ_NONX" =~ [yY]*) then
+			set ANS_REQ_NONX=$YES
+		else if ("$ANS_REQ_NONX" =~ [nN]*) then
+			set ANS_REQ_NONX=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_NONX=$DEF_REQ_NONX
+	endif
+
+ask_require_x_progs:
+	echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
+	set ANS_REQ_X = $<
+	if ("$ANS_REQ_X" == "?") then
+		echo "* These are the programs that require X windows."
+		echo "  If you do not require all of the X programs, you should abort"
+		echo "  and manually make the ones you require."
+
+		echo ""
+		goto ask_require_x_progs
+	else if ("$ANS_REQ_X" != "") then
+		if ("$ANS_REQ_X" =~ [yY]*) then
+			set ANS_REQ_X=$YES
+		else if ("$ANS_REQ_X" =~ [nN]*) then
+			set ANS_REQ_X=$NO
+		else
+			goto ask_require_nonx_progs
+		endif
+	else
+		set ANS_REQ_X=$DEF_REQ_X
+	endif
+
+
+ask_require_ted:
+	echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
+	set ANS_REQ_TED = $<
+	if ("$ANS_REQ_TED" == "?") then
+		echo "* This is the trace editor program.  It allows you to look at"
+		echo "  traces obtained from automated fluorescent sequencing machines."
+		echo ""
+		goto ask_require_ted
+	else if ("$ANS_REQ_TED" != "") then
+		if ("$ANS_REQ_TED" =~ [yY]*) then
+			set ANS_REQ_TED=$YES
+		else if ("$ANS_REQ_TED" =~ [nN]*) then
+			set ANS_REQ_TED=$NO
+		else
+			goto ask_require_ted
+		endif
+	else
+		set ANS_REQ_TED=$DEF_REQ_TED
+	endif
+
+
+
+ask_require_misc:
+	echo -n "Compile other programs [$DEF_REQ_MISC]? "
+	set ANS_REQ_MISC = $<
+	if ("$ANS_REQ_MISC" == "?") then
+		echo "* Other programs include:"
+		echo "    alfsplit"
+		echo "    getABISampleName"
+		echo ""
+		goto ask_require_misc
+	else if ("$ANS_REQ_MISC" != "") then
+		if ("$ANS_REQ_MISC" =~ [yY]*) then
+			set ANS_REQ_MISC=$YES
+		else if ("$ANS_REQ_MISC" =~ [nN]*) then
+			set ANS_REQ_MISC=$NO
+		else
+			goto ask_require_misc
+		endif
+	else
+		set ANS_REQ_MISC=$DEF_REQ_MISC
+	endif
+
+
+
+time_taken_warning:
+	echo ""
+	echo "The installation procedure is now ready to start."
+	echo ""
+	echo "**** Warning:"
+	echo "    The installation will take considerable time to complete.  If you"
+	echo "    are installing the whole Staden Package from scratch it could"
+	echo "    take as long as an hour for all exectuables to be compiled and"
+	echo "    installed."
+	echo ""
+
+ask_goahead:
+	echo -n "Proceed with the installation [YES]? " 
+	set ANSWER=$<
+	if ("$ANSWER" == "?") then
+		echo "* Final confirmation to proceed with the installation.  Answer"
+		echo "  YES to proceed; otherwise, answer NO to abort the installation."
+		echo ""
+		goto ask_goahead
+	else if ("$ANSWER" != "") then
+		if ("$ANSWER" =~ [nN]*) then
+			goto chickens_exit
+		else if ("$ANSWER" !~ [yY]*) then
+			goto ask_goahead
+		endif
+	endif
+
+installation_proper:
+
+# make binaries directory if it doesn't exist
+
+	if (! -d $DIR_BIN) then
+		$MKDIR $DIR_BIN
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
+		echo ""
+		echo "+ Compiling miscellaneous library"
+
+		pushd $DIR_MISC > /dev/null
+
+		cd $DIR_BINARIES
+	        $MAKE all
+
+		popd > /dev/null
+
+	endif
+
+        if ("$ANS_REQ_NONX" == "$YES") then
+		echo ""
+		echo "+ Installing non X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE nprogs lprogs
+                $INSTALL mep $DIR_BIN
+		$INSTALL nip $DIR_BIN
+		$INSTALL pip $DIR_BIN
+		$INSTALL sap $DIR_BIN
+		$INSTALL sapf $DIR_BIN
+		$INSTALL sip $DIR_BIN
+		$INSTALL splitp1 $DIR_BIN
+		$INSTALL splitp2 $DIR_BIN
+		$INSTALL splitp3 $DIR_BIN
+		$INSTALL sethelp $DIR_BIN
+		$INSTALL gip $DIR_BIN
+		$INSTALL nipl $DIR_BIN
+		$INSTALL pipl $DIR_BIN
+		$INSTALL sipl $DIR_BIN
+		$INSTALL dap $DIR_BIN
+		$INSTALL nipf $DIR_BIN
+		$INSTALL vep $DIR_BIN
+		$INSTALL rep $DIR_BIN
+		$INSTALL lip $DIR_BIN
+		#$INSTALL convert_project $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE bap
+                $INSTALL bap $DIR_BIN
+		popd > /dev/null
+
+	endif
+
+	if ("$ANS_REQ_TED" == "$YES") then
+		echo ""
+		echo "+ Installing Trace editor"
+
+		pushd $DIR_TED > /dev/null
+		cd $DIR_BINARIES
+                $MAKE ted
+		$INSTALL ted $DIR_BIN
+		popd > /dev/null
+	endif
+
+	if ("$ANS_REQ_X" == "$YES") then
+		echo ""
+		echo "+ Installing X programs"
+
+		pushd $DIR_STADEN > /dev/null
+		cd $DIR_BINARIES
+                $MAKE xprogs
+		$INSTALL xmep $DIR_BIN
+		$INSTALL xnip $DIR_BIN
+		$INSTALL xpip $DIR_BIN
+		$INSTALL xsap $DIR_BIN
+		$INSTALL xsip $DIR_BIN
+		$INSTALL xdap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_OSP > /dev/null
+		cd $DIR_BINARIES
+		$MAKE
+		popd > /dev/null		
+
+		pushd $DIR_BAP > /dev/null
+		cd $DIR_BINARIES
+	        $MAKE xbap
+                $INSTALL xbap $DIR_BIN
+		popd > /dev/null
+
+
+	endif
+
+	if ("$ANS_REQ_MISC" == "$YES") then
+		echo ""
+		echo "+ Installing miscellaneous programs"
+
+		pushd $DIR_ABI > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL getABISampleName $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_ALF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE alfsplit
+		$INSTALL alfsplit $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_CONVERT > /dev/null
+		cd $DIR_BINARIES
+                $MAKE convert
+		$INSTALL convert $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_COP > /dev/null
+		cd $DIR_BINARIES
+                $MAKE all
+		$INSTALL cop $DIR_BIN
+		$INSTALL cop-bap $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_FROG > /dev/null
+		cd $DIR_BINARIES
+                $MAKE frog
+		$INSTALL frog $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_GETMCH > /dev/null
+		cd $DIR_BINARIES
+                $MAKE trace2seq
+		$INSTALL trace2seq $DIR_BIN
+		popd > /dev/null
+
+		pushd $DIR_SCF > /dev/null
+		cd $DIR_BINARIES
+                $MAKE makeSCF
+		$INSTALL makeSCF $DIR_BIN
+		popd > /dev/null
+
+
+
+	endif
+
+
+installation_done:
+	echo ""
+	echo "+ Installation completed"
+	echo ""
+
+	echo "  Some further initialisation is required in order to use the"
+	echo "  package.  csh users should insert the following in their .login"
+	echo "  files:"
+	echo "  "
+	echo "  	setenv STADENROOT $ANS_STADEN_ROOT"
+	echo '  	source $STADENROOT/staden.login'
+	echo "  "
+	echo "  Users of the Bourne shell, sh, should insert the following in"
+	echo "  their .profile:"
+	echo "  "
+	echo "  	STADENROOT=$ANS_STADEN_ROOT"
+	echo "  	export STADENROOT"
+	echo '  	. $STADENROOT/staden.profile'
+	echo "  "
+	echo "  These initialisations will alter the shell's search path so that"
+	echo "  it can find the programs in the STADEN Package"
+	echo "  "
+
+normal_exit:
+	exit 0
+
+chickens_exit:
+	echo ""
+	echo "+ Installation cancelled"
+	echo ""
+
+	exit 0
+
+end_failure:
+	unset noglob
+	echo ""
+	echo "Aborted STADEN Package installation on `date`" 
+	echo ""
+	exit 1
+

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desktop/ted.desktop

@@ -1,8 +0,0 @@
-[Desktop Entry]
-X-Desktop-File-Install-Version=0.26
-Name=ted
-Comment=Xorg BAP
-Icon=/usr/share/icons/Xted.png
-Categories=Science
-Exec=ted
-Type=Application

desktop/xbap.desktop

@@ -1,8 +0,0 @@
-[Desktop Entry]
-X-Desktop-File-Install-Version=0.26
-Name=xbap
-Comment=Xorg BAP
-Icon=/usr/share/icons/Xbap.png
-Categories=Science
-Exec=xbap
-Type=Application

desktop/xdap.desktop

@@ -1,8 +0,0 @@
-[Desktop Entry]
-X-Desktop-File-Install-Version=0.26
-Name=xdap
-Comment=Xorg DAP
-Icon=/usr/share/icons/dap.png
-Categories=Science
-Exec=dbap
-Type=Application

desktop/xmep.desktop

@@ -1,8 +0,0 @@
-[Desktop Entry]
-X-Desktop-File-Install-Version=0.26
-Name=xmep
-Comment=Xorg MEP
-Icon=/usr/share/icons/xmep.png
-Categories=Science
-Exec=xmep
-Type=Application

desktop/xsap.desktop

@@ -1,8 +0,0 @@
-[Desktop Entry]
-X-Desktop-File-Install-Version=0.26
-Name=xsap
-Comment=Xorg SAP
-Icon=/usr/share/icons/xsap.png
-Categories=Science
-Exec=xsap
-Type=Application

shell/bap

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/bap

shell/dap

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/dap

shell/mep

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/mep

shell/nipf

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPNIP=/usr/share/staden-lg/help/dap_help NIPHELP=/usr/share/staden-lg/help/NIP.HLP NIPHPNT=/usr/share/staden-lg/help/NIP.PNT NIPMARG=/usr/share/staden-lg/help/NIP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/nipf

shell/sap

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/sap

shell/xbap

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPBAP=/usr/share/staden-lg/help/dap_help BAPHELP=/usr/share/staden-lg/help/BAP.HLP BAPHPNT=/usr/share/staden-lg/help/BAP.PNT BAPMARG=/usr/share/staden-lg/help/BAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xbap

shell/xdap

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPDAP=/usr/share/staden-lg/help/dap_help DAPHELP=/usr/share/staden-lg/help/DAP.HLP DAPHPNT=/usr/share/staden-lg/help/DAP.PNT DAPMARG=/usr/share/staden-lg/help/DAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xdap

shell/xmep

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPMEP=/usr/share/staden-lg/help/dap_help MEPHELP=/usr/share/staden-lg/help/MEP.HLP MEPHPNT=/usr/share/staden-lg/help/MEP.PNT MEPMARG=/usr/share/staden-lg/help/MEP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xmep

shell/xsap

@@ -1,2 +0,0 @@
-#!/bin/bash
-env STADTABL=/usr/share/staden-lg/tables STADUSER=/usr/share/staden-lg/userdata STADHELP=/usr/share/staden-lg/help HELPSAP=/usr/share/staden-lg/help/dap_help SAPHELP=/usr/share/staden-lg/help/SAP.HLP SAPHPNT=/usr/share/staden-lg/help/SAP.PNT SAPMARG=/usr/share/staden-lg/help/SAP.MRG TAGDB=/usr/share/staden-lg/tables/TAGDB /usr/share/staden-lg/bin/xsap

src/Misc/makefile

@@ -1,52 +0,0 @@
-#
-# Makefile for Miscellaneous routines - Alpha version 
-
-#
-# Objects made by this makefile
-#
-LIBS = misc.a
-
-#
-# Where the wild things are
-#
-SRC = .
-INCLUDES = -I$(SRC)
-
-#
-# Alpha Version
-#
-CC = cc
-CFLAGS = -g  $(INCLUDES)
-ARFLAGS = rv
-
-#
-# Objects
-#
-OBJS = \
-	crash.o \
-	date.o \
-	filenames.o \
-	files.o \
-	find.o \
-	shell.o \
-	strings.o
-
-#
-# Main dependency
-#
-$(LIBS) : $(OBJS)
-	/bin/rm -f $(LIBS) ;\
-	$(AR) $(ARFLAGS) $(LIBS) $(OBJS) ;\
-	ranlib $(LIBS)
-
-
-#
-# Special dependencies
-#
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-all : $(LIBS)
-
-clean :
-	/bin/rm -f $(OBJS) $(LIBS)

src/abi/makefile

@@ -1,43 +0,0 @@
-#
-# Makefile for abi - Alpha version
-#
-
-#
-# Programs made by this makefile
-#
-PROGS = getABISampleName 2rs
-all: $(PROGS)
-
-#
-# Where the wild things are
-#
-SRC = .
-
-#
-# Alpha
-#
-CC = cc
-CFLAGS = -g -I$(SRC)/../ted
-LD = cc
-LDFLAGS = -g
-
-#
-# Make the programs
-#
-getABISampleName: getABISampleName.o
-	$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
-
-2rs: 2rs.o
-	$(LD) $(LDFLAGS) -o 2rs 2rs.o
-
-#
-# Special dependencies
-#
-
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-all: $(PROGS)
-
-clean:
-	/bin/rm -f $(PROGS) *.o *~

src/alf/makefile

@@ -1,43 +0,0 @@
-#
-# Makefile for alf - Alpha version
-#
-
-#
-# Programs made by this makefile
-#
-PROGS = alfsplit
-
-#
-# Where the wild things are
-#
-SRC = .
-
-#
-# Alpha
-#
-CC = cc
-CFLAGS = -g  -I$(SRC)/../ted
-LD = cc
-LDFLAGS = -g 
-
-
-#
-# Make the programs
-#
-alfsplit: alfsplit.o
-	$(LD) $(LDFLAGS) -o alfsplit alfsplit.o $(LIBS)
-
-2rs: 2rs.o
-	$(LD) $(LDFLAGS) -o 2rs 2rs.o $(LIBS)
-
-
-#
-# Special dependencies
-#
-all: $(PROGS)
-
-clean:
-	/bin/rm -f $(PROGS) *.o *~
-
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<

src/bap/bap.f

@@ -93,9 +93,8 @@ C     DBAUTO
       CALL OPENGR(DEVNOS(10))
       WRITE(KBOUT,1000)
 1000  FORMAT(
-     +' BAP (Development assembly program) V12.1.1 2023',/,
-     +' Copyright: 1993 MRC Laboratory of Molecular Biology',/,
-     +' Copyleft: 2023 GPL')
+     +' BAP (Development assembly program) V12.1 May 1993',/,
+     +' Copyright: MRC Laboratory of Molecular Biology')
       IGORT = 0
       IDEV = KBOUT
 C   GET SCREEN AND MARGIN SIZES

src/bap/makefile

@@ -1,580 +0,0 @@
-# Makefile for staden X programs (Alpha version)
-# ---------------------------------------------------------
-
-# This makefile generates the following staden programs which
-# run under xterm (normal, `N') and those which run directly under X.
-NPROGS=      mep  nip   bap  sap  sip   splitp1 splitp2 splitp3 sethelp
-LPROGS=           nipl     
-XPROGS=     xmep xnip  xbap xsap xsip
-PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
-
-
-
-
-
-
-
-
-#
-# ``Interesting'' suffices that make needs to know about
-#
-.SUFFIXES: .a $(SUFFIXES)
-
-
-#
-# Directories
-#
-SRC = .
-STADENSRC=$(SRC)/../staden
-STADENBIN=$(STADENSRC)
-TEDSRC=$(SRC)/../ted
-TEDBIN=$(TEDSRC)
-OSPSRC=$(SRC)/osp-bits
-OSPBIN=$(OSPSRC)
-MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)
-# Use the ted sources compiled for staden executables
-INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC)
-
-
-#
-# Compilers and flags
-#
-CC= cc
-CFLAGS= -g $(INCLUDES)
-F77= gfortran
-FFLAGS= -g -fdec -std=legacy -C
-
-#FLIBS= -lfor -lUfor  -lots -lFutil
-FLIBS = -lm -lutil  
-XLIBS= -lXaw -lXt -lXmu -lXext -lX11
-LFLAGS= $(FLIBS)
-XLFLAGS= $(XLIBS) $(FLIBS)
-
-LD = gfortran
-XLD = cc
-LDFLAGS = -g -fdec -std=legacy -L/usr/lib -lgfortran
-
-#
-# Avoid compilation of objects in remote directories
-#
-$(STADENBIN)/%.o : $(STADENSRC)/%.f
-$(STADENBIN)/%.o : $(STADENSRC)/%.c
-$(TEDBIN)/%.o : $(TEDSRC)/%.f
-$(TEDBIN)/%.o : $(TEDSRC)/%.c
-
-#
-# Sequence library handling routines
-#
-SEQLIB=\
-	$(STADENBIN)/seqlibsubs.o
-
-
-
-#
-# The C objects, needed by every X program
-#
-CCORE=\
-	$(STADENBIN)/postscript.o\
-	$(TEDBIN)/Graph.o\
-	$(STADENBIN)/plotLog.o\
-	$(STADENBIN)/help.o\
-	$(STADENBIN)/dialogues.o\
-	$(STADENBIN)/userfacecom.o\
-	$(STADENBIN)/xmenu.o\
-	$(STADENBIN)/locks.o\
-	$(STADENBIN)/mcspec.o\
-	$(STADENBIN)/helpnmenu.o\
-	$(STADENBIN)/FtoC.o
-
-COBJS=\
-	$(STADENBIN)/main.o\
-	$(CCORE)
-
-COBJS2=\
-	xbapmain.o\
-	$(CCORE)
-
-
-#
-# Common objects, needed by every program
-#
-COMMONOBJSB=\
-	$(STADENBIN)/fmain.o\
-	$(STADENBIN)/seeme-aix.o\
-	$(STADENBIN)/nxspec.o\
-	$(STADENBIN)/userface.o\
-	$(STADENBIN)/userfacecom.o\
-	$(STADENBIN)/nxhelpmenu.o\
-	$(STADENBIN)/helpnmenu.o\
-	$(STADENBIN)/FtoC.o\
-	$(STADENBIN)/subs89.a
-
-COMMONOBJS=\
-	$(COMMONOBJSB)\
-	$(STADENBIN)/postscript.o
-
-SCOMMONOBJS=\
-	$(COMMONOBJSB)
-
-XCOMMONOBJS=\
-	$(STADENBIN)/seeme-aix.o\
-	$(STADENBIN)/xspec.o\
-	$(STADENBIN)/subs89.a\
-	$(COBJS)
-
-XCOMMONOBJS2=\
-	$(STADENBIN)/seeme-aix.o\
-	$(STADENBIN)/xspec.o\
-	$(STADENBIN)/subs89.a\
-	$(COBJS2)
-
-
-#
-# Building the programs
-# This should be just a linking phase because all of the object
-# files and library files are generated using implicit rules.
-# We use the fortran compiler to do linking.
-#
-GIP=\
-	$(STADENBIN)/gip.o
-
-GIPOBJS=\
-	$(GIP)\
-	$(SCOMMONOBJS)
-
-gip: $(GIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
-
-
-
-
-MEP=\
-	$(STADENBIN)/mep.o\
-	$(STADENBIN)/mepsub.o\
-	$(STADENBIN)/asubs89.a\
-	$(STADENBIN)/plot92.a
-
-MEPOBJS=\
-	$(MEP)\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o
-
-XMEPOBJS=\
-	$(MEP)\
-	$(STADENBIN)/xmepSpec.o\
-	$(XCOMMONOBJS)\
-	$(STADENBIN)/plX.o\
-	$(STADENBIN)/textOutput.o 
-
-mep: $(MEPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(MEPOBJS)  $(LFLAGS)
-
-xmep: $(XMEPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
-
-
-
-
-NIP=\
-	$(STADENBIN)/nip.o\
-	$(STADENBIN)/patternn.a\
-	$(STADENBIN)/patternnc.a\
-	$(STADENBIN)/anals89.a\
-	$(STADENBIN)/asubs89.a\
-	$(STADENBIN)/plot92.a $(SEQLIB)
-
-NIPOBJS=\
-	$(NIP)\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o
-
-XNIPOBJS=\
-	$(NIP)\
-	$(STADENBIN)/xnipSpec.o\
-	$(XCOMMONOBJS)\
-	$(STADENBIN)/plX.o\
-	$(STADENBIN)/textOutput.o 
-
-nip: $(NIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
-
-xnip: $(XNIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
-
-
-
-
-NIPL=\
-	$(STADENBIN)/nipl.o\
-	$(STADENBIN)/patternnc.a\
-	$(STADENBIN)/anals89.a\
-	$(STADENBIN)/asubs89.a\
-	$(SEQLIB)
-
-NIPLOBJS=\
-	$(NIPL)\
-	$(SCOMMONOBJS)
-
-nipl: $(NIPLOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
-
-
-
-
-PIP=\
-	$(STADENBIN)/pip.o\
-	$(STADENBIN)/analps89.a\
-	$(STADENBIN)/patternp.a\
-	$(STADENBIN)/patternpc.a\
-	$(STADENBIN)/asubs89.a\
-	$(STADENBIN)/plot92.a\
-	$(SEQLIB)
-
-PIPOBJS=\
-	$(PIP)\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o
-
-XPIPOBJS=\
-	$(PIP)\
-	$(STADENBIN)/xpipSpec.o\
-	$(XCOMMONOBJS)\
-	$(STADENBIN)/plX.o\
-	$(STADENBIN)/textOutput.o 
-
-pip: $(PIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(PIPOBJS)  $(LFLAGS)
-
-xpip:$(XPIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
-
-
-
-
-PIPL=\
-	$(STADENBIN)/pipl.o\
-	$(STADENBIN)/patternpc.a\
-	$(STADENBIN)/analps89.a\
-	$(STADENBIN)/asubs89.a\
-	$(SEQLIB)
-
-PIPLOBJS=\
-	$(PIPL)\
-	$(SCOMMONOBJS)
-
-pipl: $(PIPLOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS)  $(LFLAGS)
-
-
-
-#
-# Trace manager objects
-#
-STDTEDFILES=\
-	$(TEDBIN)/seq.o\
-	$(TEDBIN)/seqIOABI.o\
-	$(TEDBIN)/seqIOALF.o\
-	$(TEDBIN)/seqIOSCF.o\
-	$(TEDBIN)/seqIOPlain.o\
-	$(TEDBIN)/opp.o\
-	$(TEDBIN)/fpoint.o\
-	$(TEDBIN)/mach-io.o
-
-TMANOBJS=\
-	$(STADENBIN)/tman_main.o\
-	$(STADENBIN)/tman_display.o\
-	$(STADENBIN)/tman_traceDisplay.o\
-	$(STADENBIN)/tman_basesDisplay.o\
-	$(STADENBIN)/tman_context.o\
-	$(STADENBIN)/tman_gadgets.o\
-	$(STDTEDFILES)
-
-OSPOBJS=\
-	$(OSPBIN)/analysis.o\
-	$(OSPBIN)/our_allo.o\
-	$(OSPBIN)/paramIOX.o\
-	$(OSPBIN)/paramIO.o\
-	$(OSPBIN)/get_scores.o\
-	$(OSPBIN)/utils.o\
-	mess.o\
-	$(GNULIB)
-
-XHACK=\
-	$(STADENBIN)/SmeLine.o
-
-EDITOR=\
-	$(XHACK)\
-	$(STADENBIN)/xsapConEdit.o\
-	contigEditor.o\
-	edUtils.o\
-	$(STADENBIN)/undo.o\
-	$(STADENBIN)/Sheet.o\
-	$(STADENBIN)/select.o\
-	$(STADENBIN)/extend.o\
-	$(STADENBIN)/searchUtils.o\
-	edMenu.o\
-	oligo.o\
-	oligocom.o\
-	subclone.o\
-	myparams.o\
-	$(STADENBIN)/trans.o\
-	$(MISCBIN)/misc.a
-
-TAGEDITOR=\
-	$(STADENBIN)/tagEditor.o\
-	$(STADENBIN)/tagdbparse.o\
-	tagU2.o\
-	$(STADENBIN)/tagU1.o
-
-BAP=\
-	bap.o\
-	dbsysnew.o\
-	dbsyscommon.o\
-	actf.o\
-	dstrand.o\
-	oligo_sel.o\
-	llin.o\
-	guk.o\
-	$(STADENBIN)/asubs89.a\
-	$(STADENBIN)/plot92.a
-
-BAPOBJS=\
-	$(BAP)\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o\
-	$(STADENBIN)/conEdit.o\
-	tagU2.o\
-	$(OSPBIN)/analysis.o\
-	$(OSPBIN)/our_allo.o\
-	$(OSPBIN)/get_scores.o\
-	$(OSPBIN)/utils.o\
-	mess.o\
-	baponly.o\
-	oligocom.o
-
-XBAPOBJS=\
-	$(BAP)\
-	$(XCOMMONOBJS2)\
-	$(STADENBIN)/plX.o\
-	$(STADENBIN)/textOutput.o\
-	$(EDITOR)\
-	$(TMANOBJS)\
-	$(TAGEDITOR)\
-	$(OSPOBJS)
-
-bap:	$(BAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(BAPOBJS) $(LFLAGS)
-
-xbap:	$(XBAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XBAPOBJS) $(XLFLAGS)
-
-SAP=\
-	sap.o\
-	dbsyscommon.o\
-	dbsysold.o\
-	$(STADENBIN)/asubs89.a\
-	$(STADENBIN)/plot92.a
-
-SAPOBJS=\
-	$(SAP)\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o
-
-XSAPOBJS=\
-	$(SAP)\
-	$(STADENBIN)/xsapSpec.o\
-	$(XCOMMONOBJS)\
-	$(STADENBIN)/plX.o\
-	$(STADENBIN)/textOutput.o 
-
-sap: $(SAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
-
-xsap: $(XSAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
-
-
-
-
-SAPF=\
-	$(STADENBIN)/sapf.o\
-	$(STADENBIN)/dbsyscommon.o\
-	$(STADENBIN)/dbsysold.o\
-	$(STADENBIN)/asubs89.a\
-	$(STADENBIN)/plot92.a
-
-SAPFOBJS=\
-	$(SAPF)\
-	$(STADENBIN)/sapmen.o\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o
-
-sapf: $(SAPFOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
-
-
-
-
-
-
-SIP=\
-	$(STADENBIN)/sip.o\
-	$(STADENBIN)/dias89.a\
-	$(STADENBIN)/plot92.a\
-	$(SEQLIB)
-
-SIPOBJS=\
-	$(SIP)\
-	$(COMMONOBJS)\
-	$(STADENBIN)/pl4010.o
-
-XSIPOBJS=\
-	$(SIP)\
-	$(STADENBIN)/xsipSpec.o\
-	$(XCOMMONOBJS)\
-	$(STADENBIN)/plX.o\
-	$(STADENBIN)/textOutput.o 
-
-sip: $(SIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
-
-xsip: $(XSIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
-
-
-
-
-SIPL=\
-	$(STADENBIN)/sipl.o\
-	$(STADENBIN)/dias89.a\
-	$(SEQLIB)
-
-SIPLOBJS=\
-	$(SIPL)\
-	$(SCOMMONOBJS)
-
-sipl: $(SIPLOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
-
-
-
-
-SETHELP=\
-	$(STADENBIN)/sethelp.o
-
-SETHELPOBJS=\
-	$(SETHELP)\
-	$(SCOMMONOBJS)
-
-sethelp: $(SETHELPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
-
-
-
-
-SPLITP1=\
-	$(STADENBIN)/splitp1.o
-SPLITP1OBJS=\
-	$(SPLITP1)\
-	$(SCOMMONOBJS)
-
-splitp1: $(SPLITP1OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
-
-
-
-
-SPLITP2=\
-	$(STADENBIN)/splitp2.o
-SPLITP2OBJS=\
-	$(SPLITP2)\
-	$(SCOMMONOBJS)
-
-splitp2: $(SPLITP2OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
-
-
-
-
-
-SPLITP3=\
-	$(STADENBIN)/splitp3.o
-SPLITP3OBJS=\
-	$(SPLITP3)\
-	$(SCOMMONOBJS)
-
-splitp3: $(SPLITP3OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
-
-
-
-
-
-#
-# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
-# 
-%.o: $(SRC)/%.f
-	$(F77) $(FFLAGS) -c $<
-
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o: %.c
-	$(CC) $(CFLAGS) -c $<
-%.o: $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-
-
-
-#
-# The UNIX library (archive) mechanism is fairly weak so the following
-# procedure is used to generate libraries.
-#   * split the source file up into files which each contain
-#     a single function or subroutine
-#   * compile each of those files
-#   * insert the object files individually into the library
-# Each library is built by using a temporary directory.
-# The fortran compilations must be done sequentially in order to
-# avoid filling up the (small on this machine) /tmp directory
-# with compiler debugging information.
-#
-#%.a: $(SRC)/%.f
-#	BINDIR=`pwd`; \
-#	cd $(SRC); \
-#	SRCDIR=`pwd`; \
-#	TMPDIR=/tmp/staden$$$$; \
-#	if test ! -d $$TMPDIR; \
-#	then mkdir $$TMPDIR; \
-#	fi; \
-#	cd $$TMPDIR; \
-#	rm -f *.f *.o; \
-#	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
-#	$(F77) $(FFLAGS) -c *.f; \
-#	rm *.f; \
-#	rm -f $$BINDIR/$@; \
-#	ar rcv $$BINDIR/$@ *.o; \
-#	ranlib $$BINDIR/$@; \
-#	rm *.o; \
-#	cd $$BINDIR; \
-#	rm -r $$TMPDIR
-
-
-#%.a: $(SRC)/%.f
-#	$(F77) $(FFLAGS) -c *.f; 
-#	ar rcv $$BINDIR/$@ *.o; 
-
-
-
-all: $(NPROGS) $(XPROGS) $(LPROGS)
-
-nprogs: $(NPROGS)
-
-xprogs: $(XPROGS)
-
-lprogs: $(LPROGS)
-
-clean:
-	rm -f $(PROGS) *.o *.a *~

src/bap/mess.c

@@ -1,8 +1,8 @@
-/*
+/* 
   Program Name: mess
   File name: mess.c
   Purpose: put user information to the screen for the text version
-	 of osp--maybe error messages or any kind of user information
+         of osp--maybe error messages or any kind of user information
 	 or question.
 
   Last Update: Tuesday 13 August 1991
@@ -15,50 +15,47 @@
 */
 
 /* --- includes --- */
-#include <stdarg.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "defn.h"	/* IMPORT: stdio.h */
+#include "defn.h" /* IMPORT: stdio.h */
 #include "textOutput.h" /* IMPORT: UpdateTextOutput */
-/* int       vfprintf (FILE *stream, const char *format, va_list arglist);
- */
+#include <stdio.h>
+#include <stdarg.h>
+/* int       vfprintf (FILE *stream, const char *format, va_list arglist); */
 
 /* ---- Exports ---- */
 void messagef(char *format, ...)
 {
-	va_list args;
-	va_start(args, format);
-	vfprintf(stdout, format, args);
-	va_end(args);
-	UpdateTextOutput();
+    va_list args;
+    va_start (args,format);
+    vfprintf (stdout, format, args);
+    va_end(args);
+    UpdateTextOutput();
 }
 
 void message(char *message)
 {
-	/* prints the message to the screen*/
-	fprintf(stdout, "%s", message);
-	UpdateTextOutput();
-	return;
+  /* prints the message to the screen*/
+  fprintf(stdout,"%s",message);
+  UpdateTextOutput();
+  return;
 }
 
 void popupMessage(char *message)
 {
-	fprintf(stdout, "%s", message);
-	UpdateTextOutput();
-	return;
+  fprintf(stdout,"%s",message);
+  UpdateTextOutput();
+  return;
 }
 
+
 void popUpErrorMessage()
 {
-	fprintf(stdout,
-		"ERROR: Memory allocation problem.\nPlease exit and restart "
-		"this program\n");
-	/* since this is the text version I want the program to exit if this
-	   memory allocation error occurs*/
-	UpdateTextOutput();
-	sleep(10);
+  fprintf(stdout,"ERROR: Memory allocation problem.\nPlease exit and restart this program\n");
+/* since this is the text version I want the program to exit if this
+   memory allocation error occurs*/
+  UpdateTextOutput();
+  sleep(10);
+
+  exit();
 
-	exit(0);
 }
 

src/bap/osp-bits/makefile

@@ -1,50 +0,0 @@
-#
-# Makefile for osp (oligo selection program) - Alpha version
-#
-
-#
-# Programs made by this makefile
-#
-PROGS = subosp
-
-#
-# Where the wild things are
-#
-SRC = .
-
-#
-# X VERSION compilation flag
-#
-VERSION = SUBVERSION
-
-
-
-#
-# Compiler - debug on
-#
-CC= cc
-CFLAGS= -g -D$(VERSION)
-
-
-#
-# Object files
-#
-XOSPOBJS= our_allo.o analysis.o get_scores.o paramIO.o paramIOX.o utils.o
-
-#
-# Linking
-#
-subosp: $(XOSPOBJS)
-
-
-#
-# Miscellaneous
-#
-all: $(PROGS)
-
-clean:
-	rm -f $(PROGS) $(OSPOBJS) *~ 
- 
-%.o:	$(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-

src/convert/makefile

@@ -1,45 +0,0 @@
-#
-# Makefile for convert (Alpha version)
-#
-
-SRC = .
-MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)
-
-CC = cc
-CFLAGS = -g -I$(MISCSRC)
-LD = cc
-LDFLAGS = -g
-LIBS = $(MISCBIN)/misc.a
-
-#
-# Programs made by this makefile
-#
-PROGS = convert
-
-all : $(PROGS)
-
-#
-# Where the wild things are
-#
-
-OBJS = \
-	list.o \
-	main.o \
-	dapIO.o \
-	dapDB.o \
-	bapIO.o \
-	bapDB.o \
-	process.o \
-	flat_sd.o
-
-convert: $(OBJS)
-	$(LD) $(LDFLAGS) -o convert $(OBJS) $(LIBS) $(LDFLAGS)
-#
-# Special dependencies
-#
-%.o:$(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-clean :
-	/bin/rm -f $(PROGS) $(OBJS) *~

src/cop/makefile

@@ -1,114 +0,0 @@
-#
-# Makefile for COP (Check Out Project) - Alpha version
-#
-
-#
-# Programs made by this makefile
-#
-PROGS = cop cop-bap
-all: $(PROGS)
-#
-# Where the wild things are
-#
-SRC = .
-TEDSRC = $(SRC)/../ted
-MISCSRC = $(SRC)/../Misc
-MISCBIN = $(MISCSRC)
-CONVERTSRC = $(SRC)/../convert
-INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC)
-
-#
-# Alpha
-#
-CC = cc
-CFLAGS = -g $(INCLUDES)
-LD = cc
-LDFLAGS = -g 
-LIBFLAGS = 
-
-#
-# Main and miscellaneous routines
-#
-COPOBJ = \
-	cop.o
-
-COPBAPOBJ = \
-	cop-bap.o
-
-LIBS = \
-	$(MISCBIN)/misc.a
-
-#
-# For reading in xdap database
-#
-XDAPIO = \
-	dapIO.o
-
-XBAPIO = \
-	bapIO.o
-
-#
-# For reading in trace files
-#
-TRACES = \
-	getSeq.o \
-	seqIOABI.o \
-	seqIOALF.o \
-	seqIOSCF.o \
-	seqIOPlain.o \
-	opp.o \
-	seq.o \
-	fpoint.o\
-	mach-io.o
-
-#
-# For aligning sequences
-#
-ALIGN = \
-	llin.o
-
-#
-# The whole lot
-#
-OBJ = \
-	$(COPOBJ) \
-	$(XDAPIO) \
-	$(TRACES) \
-	$(ALIGN)
-
-OBJBAP = \
-	$(COPBAPOBJ) \
-	$(XBAPIO) \
-	$(TRACES) \
-	$(ALIGN)
-
-
-#
-# Cop
-#
-cop : $(OBJ)
-	$(LD) $(LDFLAGS) -o cop $(OBJ) $(LIBS) $(LIBFLAGS)
-
-cop-bap : $(OBJBAP)
-	$(LD) $(LDFLAGS) -o cop-bap $(OBJBAP) $(LIBS) $(LIBFLAGS)
-
-
-
-#
-# Special dependencies
-#
-
-all: $(PROGS)
-
-clean:
-	/bin/rm -f $(OBJ) $(PROGS) *~
-
-cop-bap.o: $(SRC)/cop.c
-	$(CC) -DBAP_VERSION $(CFLAGS) -o cop-bap.o -c $(SRC)/cop.c
-
-%.o: $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-%.o: $(TEDSRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-

src/expGetSeq/makefile

@@ -1,93 +0,0 @@
-#
-# Makefile for expGetSeq - Alpha version
-#
-
-#
-# Turning on the AUTO_CLIP switch allows ted to automatically
-# select a left (using the -enzyme option or the .enzyme in the
-# Xted file) and right cutoff on your sequence (using 2 out of
-# 5 N's)
-#
-# Turning on the SAVE_EDITS switch allows the user to maintain
-# copies of their edits, i.e. when you open up ted on a file
-# that you have already edited, the old edits show up in the
-# ted edit window.  The user may also call up any of their
-# past editing sessions.  
-#
-# Turning on the DEF_OUT  switch makes
-# trace_name.seq the default output file name
-#
-# Turning on the QUAL_CODE switch enables LaDeana's trace quality
-# clipping code.
-#
-# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
-# enables the overall trace quality check.
-#
-#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS  -DQUAL_CODE -DQUAL_CHECK
-SWITCHES = -DAUTO_CLIP -DQUAL_CODE
-
-#
-# Programs made by this makefile
-#
-PROGS = expGetSeq
-
-#
-# Where the wild things are
-#
-SRC = .
-TEDSRC = $(SRC)/../newted
-INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC)
-
-#
-# Compiler - debug on
-#
-CC= cc
-CFLAGS= -g  $(SWITCHES) $(INCLUDES)
-LD= cc
-LDFLAGS= -g
-
-
-#
-# Object files
-#
-OBJS=\
-	getMCH.o\
-	seq.o\
-	seqIOPlain.o\
-	seqIOABI.o\
-	seqIOEdit.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	opp.o\
-	fpoint.o\
-	match.o\
-	mach-io.o\
-	seqRead.o\
-	traceType.o
-
-
-#
-# Linking
-#
-expGetSeq: $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS)
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o : %.c
-	$(CC) $(CFLAGS) -c $<
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-%.o : $(TEDSRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-
-#
-# Special dependencies
-#
-clean:
-	rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
-
-all: $(PROGS)
-

src/frog/makefile

@@ -1,35 +0,0 @@
-CC = cc
-CFLAGS = -g 
-LD = cc
-LDFLAGS = -g
-LIBFLAGS =
-
-SRC = .
-PROGS = frog toad
-all: $(PROGS)
-
-FROGOBJ =\
-	frog.o\
-	mach-io.o
-
-frog : $(FROGOBJ)
-	$(LD) $(LDFLAGS) -o frog $(FROGOBJ) $(LIBFLAGS)
-
-
-TOADOBJ =\
-	toad.o\
-	scfIO.o\
-	mach-io.o
-
-toad : $(TOADOBJ)
-	$(LD) $(LDFLAGS) -o toad $(TOADOBJ) $(LIBFLAGS)
-
-
-#
-# Specials
-#
-%.o:$(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-clean:
-	/bin/rm -f $(PROGS) $(FROGOBJ)

src/getMCH/makefile

@@ -1,86 +0,0 @@
-#
-# Makefile for getMCH - Alpha version
-#
-
-#
-#Turning on the AUTO_CLIP switch allows ted to automatically
-#select a left (using the -enzyme option or the .enzyme in the
-#Xted file) and right cutoff on your sequence (using 2 out of
-#5 N's)
-#
-# Turning on the SAVE_EDITS switch allows the user to maintain
-# copies of their edits, i.e. when you open up ted on a file
-# that you have already edited, the old edits show up in the
-# ted edit window.  The user may also call up any of their
-# past editing sessions.  
-#
-#Turning on the DEF_OUT  switch makes
-# trace_name.seq the default output file name
-#
-#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS
-
-#
-# Programs made by this makefile
-#
-PROGS = getMCH trace2seq
-all: $(PROGS)
-#
-# Where the wild things are
-#
-SRC = .
-TEDSRC = $(SRC)/../ted
-INCLUDES = -I$(SRC) -I$(TEDSRC)
-
-#
-# Compiler - debug on
-#
-CC= cc
-CFLAGS= -g $(SWITCHES) $(INCLUDES)
-LD= cc
-LDFLAGS= -g
-LIBFLAGS =
-
-
-#
-# Object files
-#
-OBJS=\
-	getMCH.o\
-	seq.o\
-	seqIOPlain.o\
-	seqIOABI.o\
-	seqIOEdit.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	seqOutput.o\
-	opp.o\
-	fpoint.o\
-	match.o\
-	mach-io.o
-
-
-#
-# Linking
-#
-trace2seq getMCH: $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o : %.c
-	$(CC) $(CFLAGS) -c $<
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-%.o : $(TEDSRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-
-#
-# Special dependencies
-#
-clean:
-	rm -f $(PROGS) $(OBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
-
-all: $(PROGS)
-

src/indexseqlibs/excludewords.c

@@ -13,7 +13,7 @@ static FILE *out;
 
 static int line_comp(char *ex, char *in, int l)
 /*
-** Compare exclude line with cinline
+** Compare exclude line with inline
 */
 {
     return strncmp(ex,in+11,l);
@@ -28,13 +28,13 @@ static void process()
 */
 {
     char exline[MAXLINE];
-    char cinline[MAXLINE];
+    char inline[MAXLINE];
     char *exok, *inok;
     int compare;
 
 
     exok = fgets(exline,MAXLINE,ex);
-    inok = fgets(cinline,MAXLINE,in);
+    inok = fgets(inline,MAXLINE,in);
 
     while (exok && inok) {
 
@@ -43,15 +43,15 @@ static void process()
 	if (compare < 0)
 	    exok = fgets(exline,MAXLINE,ex);
 	else if (compare > 0) {
-	    fprintf(out,"%s",cinline);
-	    inok = fgets(cinline,MAXLINE,in);
+	    fprintf(out,"%s",inline);
+	    inok = fgets(inline,MAXLINE,in);
 	} else
-	    inok = fgets(cinline,MAXLINE,in);
+	    inok = fgets(inline,MAXLINE,in);
 
     }
 
-    while (inok = fgets(cinline,MAXLINE,in))
-	fprintf(out,"%s",cinline);
+    while (inok = fgets(inline,MAXLINE,in))
+	fprintf(out,"%s",inline);
 
 }
 

src/indexseqlibs/makefile

@@ -1,172 +0,0 @@
-#
-# indexseqlibs - Alpha version
-#
-
-all: $(PROGS)
-
-#
-# Programs need making
-#
-PROGS = \
-	addnl \
-	genbentryname1 \
-	entryname2 \
-	access4 \
-	access2 \
-	genbaccess1 \
-	title2 \
-	genbtitle1 \
-	emblentryname1 \
-	emblaccess1 \
-	embltitle1 \
-	pirentryname1 \
-	piraccess1 \
-	piraccess2 \
-	pirtitle1 \
-	pirtitle2 \
-	excludewords \
-	emblfreetext \
-	genbfreetext \
-	pirfreetext \
-	freetext2 \
-	freetext4 \
-	emblauthor \
-	genbauthor \
-	pirauthor \
-	hitNtrg \
-	division
-
-#
-# Where the wild things are
-#
-SRC = .
-
-#
-# Alpha
-#
-CC = cc
-CFLAGS = -g
-LD = cc
-LDFLAGS = -g
-
-#
-# Shared objects
-#
-OBJS = \
-	cdromheader.o \
-	mach-io.o
-
-#
-# Dependencies for programs
-#
-addnl : addnl.o
-	$(LD) $(LDFLAGS) -o $@ addnl.o
-
-genbentryname1 : genbentryname1.o
-	$(LD) $(LDFLAGS) -o $@ genbentryname1.o
-
-entryname2 : entryname2.o $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ entryname2.o $(OBJS)
-
-access4 : access4.o $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ access4.o $(OBJS)
-
-access2 : access2.o
-	$(LD) $(LDFLAGS) -o $@ access2.o
-
-genbaccess1 : genbaccess1.o
-	$(LD) $(LDFLAGS) -o $@ genbaccess1.o
-
-title2 : title2.o $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ title2.o $(OBJS)
-
-genbtitle1 : genbtitle1.o
-	$(LD) $(LDFLAGS) -o $@ genbtitle1.o
-
-emblentryname1 : emblentryname1.o
-	$(LD) $(LDFLAGS) -o $@ emblentryname1.o
-
-emblaccess1 : emblaccess1.o
-	$(LD) $(LDFLAGS) -o $@ emblaccess1.o
-
-embltitle1 : embltitle1.o
-	$(LD) $(LDFLAGS) -o $@ embltitle1.o
-
-pirentryname1 : pirentryname1.o
-	$(LD) $(LDFLAGS) -o $@ pirentryname1.o
-
-piraccess1 : piraccess1.o
-	$(LD) $(LDFLAGS) -o $@ piraccess1.o
-
-piraccess2 : piraccess2.o
-	$(LD) $(LDFLAGS) -o $@ piraccess2.o
-
-pirtitle1 : pirtitle1.o
-	$(LD) $(LDFLAGS) -o $@ pirtitle1.o
-
-pirtitle2 : pirtitle2.o
-	$(LD) $(LDFLAGS) -o $@ pirtitle2.o
-
-excludewords : excludewords.o
-	$(LD) $(LDFLAGS) -o $@ excludewords.o
-
-emblfreetext.o: $(SRC)/freetext.c
-	$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
-emblfreetext : emblfreetext.o
-	$(LD) $(LDFLAGS) -o $@ emblfreetext.o
-
-genbfreetext.o: $(SRC)/freetext.c
-	$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
-genbfreetext : genbfreetext.o
-	$(LD) $(LDFLAGS) -o $@ genbfreetext.o
-
-pirfreetext.o: $(SRC)/freetext.c
-	$(CC) $(CFLAGS) -DPIR -c -o $@ $<
-pirfreetext : pirfreetext.o
-	$(LD) $(LDFLAGS) -o $@ pirfreetext.o
-
-freetext2 : freetext2.o
-	$(LD) $(LDFLAGS) -o $@ freetext2.o
-
-freetext4 : freetext4.o $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ freetext4.o $(OBJS)
-
-emblauthor.o : $(SRC)/author.c
-	$(CC) $(CFLAGS) -DEMBL -c -o $@ $<
-emblauthor : emblauthor.o
-	$(LD) $(LDFLAGS) -o $@ emblauthor.o
-
-genbauthor.o : $(SRC)/author.c
-	$(CC) $(CFLAGS) -DGENBANK -c -o $@ $<
-genbauthor : genbauthor.o
-	$(LD) $(LDFLAGS) -o $@ genbauthor.o
-
-pirauthor.o : $(SRC)/author.c
-	$(CC) $(CFLAGS) -DPIR -c -o $@ $<
-pirauthor : pirauthor.o
-	$(LD) $(LDFLAGS) -o $@ pirauthor.o
-
-hitNtrg : hitNtrg.o $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ hitNtrg.o $(OBJS)
-
-division : division.o $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ division.o $(OBJS)
-
-
-
-
-#
-# Special dependencies
-#
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-
-
-
-all : $(PROGS)
-
-clean :
-	/bin/rm -f $(PROGS) *.o *~
-
-

src/newted/Graph.c

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/newted/Graph.h

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/newted/GraphP.h

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/newted/makefile

@@ -1,117 +0,0 @@
-#
-# Makefile for ted (trace editor) - Alpha fork
-#
-
-#
-# Turning on the AUTO_CLIP switch allows ted to automatically
-# select a left (using the -enzyme option or the .enzyme in the
-# Xted file) and right cutoff on your sequence (using 2 out of
-# 5 N's)
-#
-# Turning on the SAVE_EDITS switch allows the user to maintain
-# copies of their edits, i.e. when you open up ted on a file
-# that you have already edited, the old edits show up in the
-# ted edit window.  The user may also call up any of their
-# past editing sessions.  
-#
-# Turning on the DEF_OUT  switch makes
-# trace_name.seq the default output file name
-#
-# Turning on the QUAL_CODE switch enables LaDeana's trace quality
-# clipping code.
-#
-# Turning on the QUAL_CHECK switch (at the same time as QUAL_CODE)
-# enables the overall trace quality check.
-#
-#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS  -DQUAL_CODE -DQUAL_CHECK
-SWITCHES = -DAUTO_CLIP -DQUAL_CODE -DQUAL_CHECK
-
-
-#
-# Programs made by this makefile
-#
-PROGS = ted autoted
-
-#
-# Where the wild things are
-#
-SRC = .
-
-#
-# Compiler - debug on
-#
-CC= cc
-INCLUDES = -I$(SRC)
-CFLAGS= -g  $(SWITCHES) $(INCLUDES)
-LIBS= -lXaw -lXt -lXmu -lXext -lX11 
-#
-LD= cc
-LDFLAGS= -g 
-
-#
-# Object files
-#
-TEDOBJS=\
-	ted.o\
-	dialogues.o\
-	seq.o\
-	seqIOPlain.o\
-	seqIOABI.o\
-	help.o\
-	display.o\
-	traceDisplay.o\
-	basesDisplay.o\
-	Graph.o\
-	seqIOEdit.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	seqOutput.o\
-	opp.o\
-	info.o\
-	fpoint.o\
-	mach-io.o\
-	seqRead.o\
-	traceType.o\
-	match.o
-
-AUTOTEDOBJS=\
-	autoted.o\
-	seq.o\
-	seqIOPlain.o\
-	seqIOABI.o\
-	seqIOEdit.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	seqOutput.o\
-	opp.o\
-	traceType.o\
-	fpoint.o\
-	mach-io.o\
-	match.o\
-	seqRead.o
-
-
-
-#
-# Linking
-#
-ted: $(TEDOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
-autoted: $(AUTOTEDOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(AUTOTEDOBJS) $(LIBS)
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-
-#
-# Special dependencies
-#
-clean:
-	rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
-
-all: $(PROGS)
-

src/scf/makefile

@@ -1,67 +0,0 @@
-#
-# getMCH - Alpha version
-#
-
-#
-# Programs made by this makefile
-#
-PROGS = makeSCF
-
-#
-# SWITCHES - see ted makefile
-#
-#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS
-
-#
-# Where the wild things are
-#
-SRC = .
-TEDSRC = $(SRC)/../ted
-
-#
-# alpha
-#
-CC= cc
-CFLAGS= -g  $(SWITCHES) -I$(TEDSRC)
-LD= cc
-LDFLAGS= -g
-LIBFLAGS =
-
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-%.o : $(TEDSRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-#
-# Object files
-#
-OBJS=\
-	makeSCF.o\
-	writeSCF.o\
-	seq.o\
-	seqIOPlain.o\
-	seqIOABI.o\
-	seqIOEdit.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	seqOutput.o\
-	opp.o\
-	fpoint.o\
-	match.o\
-	mach-io.o
-
-
-#
-# Linking
-#
-makeSCF: $(OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(OBJS) $(LIBS) $(LIBFLAGS)
-
-#
-# Special dependencies
-#
-all: $(PROGS) 
-
-clean:
-	/bin/rm -f $(OBJS) $(PROGS) *~

src/staden/Sheet.c

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: Sheet.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/staden/Sheet.h

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: Sheet.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/staden/SheetP.h

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: SheetP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/staden/gen_a.sh

@@ -1,19 +0,0 @@
-#!/bin/bash
-#
-for fortran in $(ls *.f)
-do 
-  mkdir -p ${fortran%??}
-  cp $fortran ${fortran%??}
-
-  cd ${fortran%??}
-  fsplit ${fortran}
-  rm ${fortran}
-
-  gfortran  -g -fdec -std=legacy -C -c *.f
-  ar rcv ${fortran%??}.a *.o
-  ranlib ${fortran%??}.a
-
-  cd ..
-  cp ${fortran%??}/*.a .
-  rm -rf ${fortran%??}
-done

src/staden/makefile

@@ -1,603 +0,0 @@
-# Makefile for staden X programs (Alpha OSF/1.2 version)
-# ------------------------------------------------------
-
-# This makefile generates the following staden programs which
-# run under xterm (normal, `N') and those which run directly under X.
-NPROGS=      mep  nip   pip   dap  sap  sip   splitp1 splitp2 splitp3 gip sethelp convert_project rep lip sapf nipf vep
-LPROGS=           nipl  pipl            sipl
-XPROGS=     xmep xnip  xpip  xdap xsap xsip
-PROGS= $(NPROGS) $(LPROGS) $(XPROGS)
-
-#
-# ``Interesting'' suffices that make needs to know about
-#
-.SUFFIXES: .a $(SUFFIXES)
-
-#
-# Where the wild things are
-#
-SRC=.
-TEDSRC=$(SRC)/../ted
-MISCSRC=$(SRC)/../Misc
-MISCBIN=$(MISCSRC)
-INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC)
-
-#
-# Compilers and flags
-#
-CC= cc
-CFLAGS= -g $(INCLUDES)
-F77= gfortran
-FFLAGS= -g -fdec -std=legacy -L/usr/lib -lgfortran -C
-
-FLIBS = -lutil -lm
-#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm
-XLIBS= -lXaw -lXt -lXmu -lXext -lX11  
-LFLAGS= $(FLIBS)
-XLFLAGS= $(FLIBS) $(XLIBS) 
-
-LD = gfortran
-CLD = gfortran
-#CLD = cc
-LDFLAGS = -g # Comment out for faster linking when debugging
-
-
-
-#
-# Sequence library handling routines
-#
-SEQLIB=\
-	seqlibsubs.o
-
-
-#
-# The C objects, needed by every X program
-#
-CCORE=\
-	postscript.o\
-	Graph.o\
-	plotLog.o\
-	help.o\
-	dialogues.o\
-	userfacecom.o\
-	helpnmenu.o\
-	xmenu.o\
-	FtoC.o\
-	mcspec.o\
-	locks.o
-
-COBJS=\
-	main.o\
-	$(CCORE)
-
-XDAPCOBJS=\
-	xdapmain.o\
-	$(CCORE)
-
-
-#
-# Common objects, needed by every program
-#
-COMMONOBJSB=\
-	fmain.o\
-	seeme-aix.o\
-	nxspec.o\
-	userface.o\
-	userfacecom.o\
-	nxhelpmenu.o\
-	helpnmenu.o\
-	FtoC.o\
-	subs89.a
-
-COMMONOBJS=\
-	$(COMMONOBJSB)\
-	postscript.o
-
-SCOMMONOBJS=\
-	$(COMMONOBJSB)
-
-XCOMMONOBJS=\
-	seeme-aix.o\
-	xspec.o\
-	subs89.a\
-	$(COBJS)
-
-XDAPCOMMONOBJS=\
-	seeme-aix.o\
-	xspec.o\
-	subs89.a\
-	$(XDAPCOBJS)
-
-
-#
-# Building the programs
-# This should be just a linking phase because all of the object
-# files and library files are generated using implicit rules.
-# We use the fortran compiler to do linking.
-#
-GIP=\
-	gip.o
-
-GIPOBJS=\
-	$(GIP)\
-	$(SCOMMONOBJS)
-
-gip: $(GIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(GIPOBJS) $(LFLAGS)
-
-
-LIP=\
-	lip.o
- 
-LIPOBJS=\
-	$(LIP)\
-	$(SEQLIB)\
-	$(COMMONOBJS)
- 
-lip: $(LIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(LIPOBJS) $(LFLAGS)
-
-
-MEP=\
-	mep.o\
-	mepsub.o\
-	asubs89.a\
-	plot92.a
-
-MEPOBJS=\
-	$(MEP)\
-	$(COMMONOBJS)\
-	pl4010.o
-
-XMEPOBJS=\
-	$(MEP)\
-	$(XCOMMONOBJS)\
-	plX.o\
-	textOutput.o 
-
-mep: $(MEPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(MEPOBJS)  $(LFLAGS)
-
-xmep: $(XMEPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(XMEPOBJS) $(XLFLAGS)
-
-
-
-
-NIP=\
-	nip.o\
-	patternn.a\
-	patternnc.a\
-	anals89.a\
-	asubs89.a\
-	plot92.a \
-	$(SEQLIB)
-
-NIPOBJS=\
-	$(NIP)\
-	$(COMMONOBJS)\
-	pl4010.o
-
-XNIPOBJS=\
-	$(NIP)\
-	$(XCOMMONOBJS)\
-	plX.o\
-	textOutput.o 
-
-nip: $(NIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(NIPOBJS) $(LFLAGS)
-
-xnip: $(XNIPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(XNIPOBJS) $(XLFLAGS)
-
-
-
-
-NIPL=\
-	nipl.o\
-	patternnc.a\
-	anals89.a\
-	asubs89.a\
-	$(SEQLIB)
-
-NIPLOBJS=\
-	$(NIPL)\
-	$(SCOMMONOBJS)
-
-nipl: $(NIPLOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(NIPLOBJS) $(LFLAGS)
-
-
-
-NIPF=\
-	nipf.o\
-	asubs89.a\
-	plot92.a
-
-NIPFOBJS=\
-	$(NIPF)\
-	$(COMMONOBJS)\
-	pl4010.o
-
-
-nipf: $(NIPFOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(NIPFOBJS) $(LFLAGS)
-
-
-
-
-
-PIP=\
-	pip.o\
-	analps89.a\
-	patternp.a\
-	patternpc.a\
-	asubs89.a\
-	plot92.a\
-	$(SEQLIB)
-
-PIPOBJS=\
-	$(PIP)\
-	$(COMMONOBJS)\
-	pl4010.o
-
-XPIPOBJS=\
-	$(PIP)\
-	$(XCOMMONOBJS)\
-	plX.o\
-	textOutput.o 
-
-pip: $(PIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(PIPOBJS)  $(LFLAGS)
-
-xpip:$(XPIPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(XPIPOBJS) $(XLFLAGS)
-
-
-
-
-PIPL=\
-	pipl.o\
-	patternpc.a\
-	analps89.a\
-	asubs89.a\
-	$(SEQLIB)
-
-PIPLOBJS=\
-	$(PIPL)\
-	$(SCOMMONOBJS)
-
-pipl: $(PIPLOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(PIPLOBJS)  $(LFLAGS)
-
-
-
-#
-# Trace manager objects
-#
-STDTEDFILES=\
-	seq.o\
-	seqIOABI.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	seqIOPlain.o\
-	opp.o\
-	fpoint.o\
-	mach-io.o
-
-TMANOBJS=\
-	tman_main.o\
-	tman_display.o\
-	tman_traceDisplay.o\
-	tman_basesDisplay.o\
-	tman_context.o\
-	tman_gadgets.o\
-	$(STDTEDFILES)
-
-# Some versions of X11R4 may have a bug in SmeLine.c
-XHACK=\
-	SmeLine.o
-
-EDITOR=\
-	$(XHACK)\
-	xsapConEdit.o\
-	contigEditor.o\
-	edUtils.o\
-	undo.o\
-	Sheet.o\
-	select.o\
-	extend.o\
-	searchUtils.o\
-	edMenu.o\
-	trans.o\
-	$(MISCBIN)/misc.a
-
-TAGEDITOR=\
-	tagEditor.o\
-	tagdbparse.o\
-	tagU2.o\
-	tagU1.o
-
-DAP=\
-	dap.o\
-	dbsysnew.o\
-	dbsyscommon.o\
-	asubs89.a\
-	plot92.a
-
-DAPOBJS=\
-	$(DAP)\
-	$(COMMONOBJS)\
-	pl4010.o\
-	conEdit.o\
-	tagU2.o
-
-XDAPOBJS=\
-	$(DAP)\
-	$(XDAPCOMMONOBJS)\
-	plX.o\
-	textOutput.o\
-	$(EDITOR)\
-	$(TMANOBJS)\
-	$(TAGEDITOR)
-
-dap: $(DAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(DAPOBJS) $(LFLAGS)
-
-xdap: $(XDAPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(XDAPOBJS) $(XLFLAGS)
-
-convert_project: cvt.o
-	$(CC) $(CFLAGS) -o $@ cvt.o
-
-SAP=\
-	sap.o\
-	dbsyscommon.o\
-	dbsysold.o\
-	asubs89.a\
-	plot92.a
-
-SAPOBJS=\
-	$(SAP)\
-	$(COMMONOBJS)\
-	pl4010.o
-
-XSAPOBJS=\
-	$(SAP)\
-	$(XCOMMONOBJS)\
-	plX.o\
-	textOutput.o 
-
-sap: $(SAPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SAPOBJS) $(LFLAGS)
-
-xsap: $(XSAPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(XSAPOBJS) $(XLFLAGS)
-
-
-
-
-SAPF=\
-	sapf.o\
-	dbsyscommon.o\
-	dbsysold.o\
-	asubs89.a\
-	plot92.a
-
-SAPFOBJS=\
-	$(SAPF)\
-	sapmen.o\
-	$(COMMONOBJS)\
-	pl4010.o
-
-sapf: $(SAPFOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SAPFOBJS) $(LFLAGS)
-
-
-
-
-
-
-SIP=\
-	sip.o\
-	dias89.a\
-	plot92.a\
-	$(SEQLIB)
-
-SIPOBJS=\
-	$(SIP)\
-	$(COMMONOBJS)\
-	pl4010.o
-
-XSIPOBJS=\
-	$(SIP)\
-	$(XCOMMONOBJS)\
-	plX.o\
-	textOutput.o 
-
-sip: $(SIPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SIPOBJS) $(LFLAGS)
-
-xsip: $(XSIPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(XSIPOBJS) $(XLFLAGS)
-
-
-
-
-SIPL=\
-	sipl.o\
-	dias89.a\
-	$(SEQLIB)
-
-SIPLOBJS=\
-	$(SIPL)\
-	$(SCOMMONOBJS)
-
-sipl: $(SIPLOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SIPLOBJS) $(LFLAGS)
-
-
-
-
-SETHELP=\
-	sethelp.o
-
-SETHELPOBJS=\
-	$(SETHELP)
-
-sethelp: $(SETHELPOBJS)
-	$(CLD) $(LDFLAGS) -o $@ $(SETHELPOBJS) $(LFLAGS)
-
-
-
-
-SPLITP1=\
-	splitp1.o
-SPLITP1OBJS=\
-	$(SPLITP1)\
-	$(SCOMMONOBJS)
-
-splitp1: $(SPLITP1OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SPLITP1OBJS) $(LFLAGS)
-
-
-
-
-SPLITP2=\
-	splitp2.o
-SPLITP2OBJS=\
-	$(SPLITP2)\
-	$(SCOMMONOBJS)
-
-splitp2: $(SPLITP2OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SPLITP2OBJS) $(LFLAGS)
-
-
-
-
-
-SPLITP3=\
-	splitp3.o
-SPLITP3OBJS=\
-	$(SPLITP3)\
-	$(SCOMMONOBJS)
-
-splitp3: $(SPLITP3OBJS)
-	$(LD) $(LDFLAGS) -o $@ $(SPLITP3OBJS) $(LFLAGS)
-
-
-
-REP=\
-	rep.o\
-	dias89.a\
-	subs89.a
-
-REPOBJS=\
-	$(REP)\
-	$(COMMONOBJS)
- 
-rep:	$(REPOBJS)
-	$(F77) $(LDFLAGS) -o $@ $(REPOBJS) $(LFLAGS)
-
-
-
-
-
-VEP=\
-	vep.o\
-	dias89.a\
-	subs89.a
-
-
-VEPOBJS=\
-	$(VEP)\
-	$(SCOMMONOBJS)
-
-
-vep: $(VEPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(VEPOBJS)  $(LFLAGS)
-
-
-
-
-#
-# Special dependencies
-#
-#
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o: $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-%.o: $(TEDSRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
-# 
-%.o: $(SRC)/%.f
-	$(F77) $(FFLAGS) -c $<
-
-
-#
-# The UNIX library (archive) mechanism is fairly weak so the following
-# procedure is used to generate libraries.
-#   * split the source file up into files which each contain
-#     a single function or subroutine
-#   * compile each of those files
-#   * insert the object files individually into the library
-# Each library is built by using a temporary directory.
-# The fortran compilations must be done sequentially in order to
-# avoid filling up the (small on this machine) /tmp directory
-# with compiler debugging information.
-#
-%.a: $(SRC)/%.f
-	sh gen_a.sh
-
-#	BINDIR=`pwd`; \
-#	cd $(SRC); \
-#	SRCDIR=`pwd`; \
-#
-#	TMPDIR=/tmp/staden$$$$; \
-#	if test ! -d $$TMPDIR; \
-#	then mkdir $$TMPDIR; \
-#	fi; \
-#	cd $$TMPDIR; \
-#	rm -f *.f *.o; \
-#
-#	fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \
-#	$(F77) $(FFLAGS) -c *.f; \
-#
-##	rm *.f; \
-#
-#	rm -f $@; \
-#	ar rcv $@ *.o; \
-#	ranlib $@; \
-##rm *.o; \
-#
-#	cd $$BINDIR; \
-#	rm -r $$TMPDIR
-
-
-
-#.f.a:
-#	$(F77) $(FFLAGS) -c $<
-#	ar rcv $@ $*.o
-#	ranlib $@
-#	rm $*.o
-
-all: $(PROGS)
-
-nprogs: $(NPROGS)
-
-xprogs: $(XPROGS)
-
-lprogs: $(LPROGS)
-
-clean:
-	rm -f $(PROGS) *.a *.o *~
-
-lint:
-	lint -Q -Nn5000 -DNOSTRDUP $(INCLUDES) *.c
-
-

src/staden/seeme-dec.f

@@ -162,8 +162,7 @@ C  so tell the user
                 JRECL=1
                 OPEN(UNIT=IDEV,FILE=FILNAM,STATUS='OLD',
      +               READONLY,
-C     +               RECORDTYPE='STREAM',
-     +               ERR=100)
+     +               RECORDTYPE='STREAM',ERR=100)
       END IF
       IOK=0
       RETURN
@@ -670,7 +669,6 @@ C
       WRITE(*,*)'END IN GETRSL'
       END
       INTEGER FUNCTION SEEKRS(IDEV,IREC)
-      EXTERNAL FSEEK
-C      INTEGER FSEEK
+      INTEGER FSEEK
       SEEKRS = FSEEK(IDEV,IREC,0)
       END

src/staden/userfacecom.c

@@ -2,10 +2,9 @@
 #include <stdlib.h>
 #include <string.h>
 #include <sys/types.h>
-
-#include "FtoC.h" /* IMPORT: Fstr2Cstr and Cstr2Fstr */
-#include "helpnmenu.h"
 #include "userface.h"
+#include "helpnmenu.h"
+#include "FtoC.h" /* IMPORT: Fstr2Cstr and Cstr2Fstr */
 
 /*
  * Prompts the user with either one yes/no question or another.
@@ -17,21 +16,21 @@
  *    1 = no
  *   -1 = cancel
  */
-int yesono(int choice, char *prompt1, char *prompt2)
-{
-	int a;
+int yesono(int choice, char *prompt1, char *prompt2) {
+    int a;
 
-	switch (choice) {
-		case 0:
-			return yesno(prompt1);
-		case 1:
-			a = yesno(prompt2);
-			if (a >= 0) a ^= 1;
-			return a;
-		default:
-			fputs("yesno() called with bad 'choice'\n", stderr);
-			return -1;
-	}
+    switch(choice) {
+    case 0:
+	return yesno(prompt1);
+    case 1:
+	a = yesno(prompt2);
+	if (a>=0)
+	    a ^= 1;
+	return a;
+    default:
+	fputs("yesno() called with bad 'choice'\n", stderr);
+	return -1;
+    }
 }
 
 /*--------------------------------------------------------------------------*\
@@ -42,33 +41,51 @@ int yesono(int choice, char *prompt1, char *prompt2)
 |*									    *|
 \*--------------------------------------------------------------------------*/
 
-void getint_x(int_f *MININ_p, int_f *MAXIN_p, int_f *DEF_p, char *PROMPT_p,
-	      int_f *VALUE_p, /* out: result */
-	      int_f *KBIN_p, int_f *KBOUT_p, int_f *IHELPS_p, int_f *IHELPE_p,
-	      char *HELPF_p, int_f *IDEVH_p, int_f *IOK_p, /* out: status */
-	      int_fl PROMPT_l, int_fl HELPF_l)
+void getint_x(int_f *MININ_p,
+	      int_f *MAXIN_p,
+	      int_f *DEF_p,
+	      char  *PROMPT_p,
+	      int_f *VALUE_p,  /* out: result */
+	      int_f *KBIN_p,
+	      int_f *KBOUT_p,
+	      int_f *IHELPS_p,
+	      int_f *IHELPE_p,
+	      char  *HELPF_p,
+	      int_f *IDEVH_p,
+	      int_f *IOK_p,    /* out: status */
+	      int_fl PROMPT_l,
+	      int_fl HELPF_l)
 /*
  * Prompt for an integer in the range *MININ_p <= i <= *MAXIN_p
  * IOK=0 => OK
  * IOK=1 => Cancel
  */
 {
-	char prompt[256];
-	int status;
+    char prompt[256];
+    int status;
 
-	Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
+    Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
 
-	*VALUE_p =
-	    getint((int)*MININ_p, (int)*MAXIN_p, (int)*DEF_p, prompt, &status);
-	*IOK_p = (int_f)((status < 0) ? 1 : 0);
+    *VALUE_p = getint((int)*MININ_p, (int)*MAXIN_p, (int)*DEF_p,
+		      prompt, &status);
+    *IOK_p = (int_f)((status < 0)? 1:0);
 
-	return;
+    return;
 }
 
-void getrl_x(float *MININ_p, float *MAXIN_p, float *DEF_p, char *PROMPT_p,
-	     float *VALUE_p, /* out: result */
-	     int_f *KBIN_p, int_f *KBOUT_p, int_f *IHELPS_p, int_f *IHELPE_p,
-	     char *HELPF_p, int_f *IDEVH_p, int_f *IOK_p, int_fl PROMPT_l,
+void getrl_x(float *MININ_p,
+	     float *MAXIN_p,
+	     float *DEF_p,
+	     char  *PROMPT_p,
+	     float *VALUE_p,  /* out: result */
+	     int_f *KBIN_p,
+	     int_f *KBOUT_p,
+	     int_f *IHELPS_p,
+	     int_f *IHELPE_p,
+	     char  *HELPF_p,
+	     int_f *IDEVH_p,
+	     int_f *IOK_p,
+	     int_fl PROMPT_l,
 	     int_fl HELPF_l)
 /*
  * Prompt for a real in the range *MININ_p <= i <= *MAXIN_p
@@ -77,21 +94,30 @@ void getrl_x(float *MININ_p, float *MAXIN_p, float *DEF_p, char *PROMPT_p,
  * IOK=1 => Cancel
  */
 {
-	char prompt[256];
-	int status;
+    char prompt[256];
+    int status;
 
-	Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
+    Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
 
-	*VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 2);
-	*IOK_p = (int_f)((status < 0) ? 1 : 0);
+    *VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 2);
+    *IOK_p = (int_f)((status < 0)? 1:0);
 
-	return;
+    return;
 }
 
-void getrls_x(float *MININ_p, float *MAXIN_p, float *DEF_p, char *PROMPT_p,
-	      float *VALUE_p, /* out: result */
-	      int_f *KBIN_p, int_f *KBOUT_p, int_f *IHELPS_p, int_f *IHELPE_p,
-	      char *HELPF_p, int_f *IDEVH_p, int_f *IOK_p, int_fl PROMPT_l,
+void getrls_x(float *MININ_p,
+	      float *MAXIN_p,
+	      float *DEF_p,
+	      char  *PROMPT_p,
+	      float *VALUE_p,  /* out: result */
+	      int_f *KBIN_p,
+	      int_f *KBOUT_p,
+	      int_f *IHELPS_p,
+	      int_f *IHELPE_p,
+	      char  *HELPF_p,
+	      int_f *IDEVH_p,
+	      int_f *IOK_p,
+	      int_fl PROMPT_l,
 	      int_fl HELPF_l)
 /*
  * Prompt for a real in the range *MININ_p <= i <= *MAXIN_p
@@ -100,20 +126,27 @@ void getrls_x(float *MININ_p, float *MAXIN_p, float *DEF_p, char *PROMPT_p,
  * IOK=1 => Cancel
  */
 {
-	char prompt[256];
-	int status;
+    char prompt[256];
+    int status;
 
-	Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
+    Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
 
-	*VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 10);
-	*IOK_p = (int_f)((status < 0) ? 1 : 0);
+    *VALUE_p = getfloat(*MININ_p, *MAXIN_p, *DEF_p, prompt, &status, 10);
+    *IOK_p = (int_f)((status < 0)? 1:0);
 
-	return;
+    return;
 }
 
-void yesno_x(int_f *ANSWER_p, char *PROMPT_p, int_f *IHELPS_p, int_f *IHELPE_p,
-	     char *HELPF_p, int_f *IDEVH_p, int_f *KBIN_p, int_f *KBOUT_p,
-	     int_fl PROMPT_l, int_fl HELPF_l)
+void yesno_x(int_f *ANSWER_p,
+	     char  *PROMPT_p,
+	     int_f *IHELPS_p,
+	     int_f *IHELPE_p,
+	     char  *HELPF_p,
+	     int_f *IDEVH_p,
+	     int_f *KBIN_p,
+	     int_f *KBOUT_p,
+	     int_fl PROMPT_l,
+	     int_fl HELPF_l)
 /*
  * Prompt the user with *PROMPT_l and get a YES or NO response.
  * ANSWER=-1 => Cancel
@@ -121,35 +154,48 @@ void yesno_x(int_f *ANSWER_p, char *PROMPT_p, int_f *IHELPS_p, int_f *IHELPE_p,
  * ANSWER=1  => NO
  */
 {
-	char prompt[256];
+    char prompt[256];
 
-	Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
-	*ANSWER_p = (int_f)yesno(prompt);
+    Fstr2Cstr(PROMPT_p, PROMPT_l, prompt, (int_fl)sizeof(prompt));
+    *ANSWER_p = (int_f)yesno(prompt);
 }
 
-void yesono_x(int_f *CHOICE_p, char *P1_p, char *P2_p, int_f *IHELPS_p,
-	      int_f *IHELPE_p, char *HELPF_p, int_f *IDEVH_p, int_f *KBIN_p,
-	      int_f *KBOUT_p, int_fl P1_l, int_fl P2_l, int_fl HELPF_l)
+void yesono_x(int_f *CHOICE_p,
+	      char  *P1_p,
+	      char  *P2_p,
+	      int_f *IHELPS_p,
+	      int_f *IHELPE_p,
+	      char  *HELPF_p,
+	      int_f *IDEVH_p,
+	      int_f *KBIN_p,
+	      int_f *KBOUT_p,
+	      int_fl P1_l,
+	      int_fl P2_l,
+	      int_fl HELPF_l)
 /*
  * If CHOICE is 0, present a YESNO dialogue with prompt P1.
  * If CHOICE is 1, present a YESNO dialogue with prompt P2.
  */
 {
-	char prompt1[256], prompt2[256];
+    char prompt1[256], prompt2[256];
 
-	Fstr2Cstr(P1_p, P1_l, prompt1, (int_fl)sizeof(prompt1));
-	Fstr2Cstr(P2_p, P2_l, prompt2, (int_fl)sizeof(prompt2));
+    Fstr2Cstr(P1_p, P1_l, prompt1, (int_fl)sizeof(prompt1));
+    Fstr2Cstr(P2_p, P2_l, prompt2, (int_fl)sizeof(prompt2));
 
-	*CHOICE_p = (int_f)yesono(*CHOICE_p, prompt1, prompt2);
+    *CHOICE_p = (int_f)yesono(*CHOICE_p, prompt1, prompt2);
 }
 
-void gtstr_x(char *P_p,	      /* prompt */
-	     char *STRING_p,  /* default value (if *LENGTH_p > 0) */
-	     char *NEW_p,     /* out: dialogue result */
+void gtstr_x(char  *P_p,      /* prompt */
+	     char  *STRING_p, /* default value (if *LENGTH_p > 0) */
+	     char  *NEW_p,    /* out: dialogue result */
 	     int_f *LENGTH_p, /* in:  significant length of *STRING_p
-				out: significant length of *NEW_p */
-	     int_f *KBOUT_p, int_f *KBIN_p, int_f *INFLAG_p, /* out: status */
-	     int_fl P_l, int_fl STRING_l, int_fl NEW_l)
+			 	out: significant length of *NEW_p */
+	     int_f *KBOUT_p,
+	     int_f *KBIN_p,
+	     int_f *INFLAG_p, /* out: status */
+	     int_fl P_l,
+	     int_fl STRING_l,
+	     int_fl NEW_l)
 /*
  * Prompt with P for a string, default value STRING.
  * Return new string in NEW.
@@ -159,43 +205,43 @@ void gtstr_x(char *P_p,	      /* prompt */
  * INFLAG=3 => LENGTH=0 and NEW full of blanks (ie default)
  */
 {
-	char question[256], def[256];
-	char *defptr;
-	int ret;
+    char question[256], def[256];
+    char *defptr;
+    int ret;
 
-	Fstr2Cstr(P_p, P_l, question, (int_fl)sizeof(question));
-	if (*LENGTH_p > 0) {
-		Fstr2Cstr(STRING_p, STRING_l, def, (int_fl)sizeof(def));
-		defptr = def;
-	}
-	else
-		defptr = 0;
+    Fstr2Cstr(P_p, P_l, question, (int_fl)sizeof(question));
+    if (*LENGTH_p > 0) {
+	Fstr2Cstr(STRING_p, STRING_l, def, (int_fl)sizeof(def));
+	defptr = def;
+    } else
+	defptr = 0;
 
-	ret =
-	    gtstr(question, defptr, NEW_p, (size_t)((NEW_l == 1) ? 40 : NEW_l));
-	switch (ret) {
-		case -1:
-			*INFLAG_p = 2;
-			*LENGTH_p = 1;
-			return;
-		case 0:
-			*INFLAG_p = 0;
-			*LENGTH_p = (int_f)strlen(NEW_p);
-			Cstr2Fstr(NEW_p, NEW_p, NEW_l);
-			return;
-		case 1:
-			*INFLAG_p = 3;
-			*LENGTH_p = 0;
-	}
+    ret = gtstr(question, defptr, NEW_p, (size_t)((NEW_l==1)?40:NEW_l));
+    switch(ret) {
+    case -1:
+	*INFLAG_p = 2;
+	*LENGTH_p = 1;
+	return;
+    case 0:
+	*INFLAG_p = 0;
+	*LENGTH_p = (int_f)strlen(NEW_p);
+	Cstr2Fstr(NEW_p, NEW_p, NEW_l);
+	return;
+    case 1:
+	*INFLAG_p = 3;
+	*LENGTH_p = 0;
+    }
 }
 
-void getstr_x(char *P_p,       /* prompt */
-	      char *STRING_p,  /* default value (if *LENGTH_p > 0) */
-	      char *NEW_p,     /* out: dialogue result */
+void getstr_x(char  *P_p,      /* prompt */
+	      char  *STRING_p, /* default value (if *LENGTH_p > 0) */
+	      char  *NEW_p,    /* out: dialogue result */
 	      int_f *MAXSTR_p, /* array length of *STRING_p and *NEW_p */
 	      int_f *LENGTH_p, /* in:  significant length of *STRING_p
 				 out: significant length of *NEW_p */
-	      int_f *KBOUT_p, int_f *KBIN_p, int_f *INFLAG_p, /* out: status */
+	      int_f *KBOUT_p,
+	      int_f *KBIN_p,
+	      int_f *INFLAG_p, /* out: status */
 	      int_fl P_l)
 /*
  * Present a dialogue requesting a string result with the given prompt
@@ -206,16 +252,31 @@ void getstr_x(char *P_p,       /* prompt */
  * given *STRING_p and *NEW_p.
  */
 {
-	gtstr_x(P_p, STRING_p, NEW_p, LENGTH_p, KBOUT_p, KBIN_p, INFLAG_p, P_l,
-		*MAXSTR_p, *MAXSTR_p);
+    gtstr_x(P_p,
+	    STRING_p,
+	    NEW_p,   
+	    LENGTH_p,
+	    KBOUT_p,
+	    KBIN_p,
+	    INFLAG_p,
+	    P_l,
+	    *MAXSTR_p,
+	    *MAXSTR_p);
 }
 
-void radion_x(char *TITLE_p, char *PROMPT_p, /* Actually: *PROMPT_p[*NB_p] */
-	      int_f *NB_p,		     /* Number of buttons (1..NB) */
-	      int_f *CHOICE_p,		     /* in:  default button
-					       out: selected button */
-	      int_f *IHELPS_p, int_f *IHELPE_p, char *HELPF_p, int_f *IDEVH_p,
-	      int_f *KBIN_p, int_f *KBOUT_p, int_fl TITLE_l, int_fl PROMPT_l,
+void radion_x(char  *TITLE_p,
+	      char  *PROMPT_p, /* Actually: *PROMPT_p[*NB_p] */
+	      int_f *NB_p,     /* Number of buttons (1..NB) */
+	      int_f *CHOICE_p, /* in:  default button
+			         out: selected button */
+	      int_f *IHELPS_p,
+	      int_f *IHELPE_p,
+	      char  *HELPF_p,
+	      int_f *IDEVH_p,
+	      int_f *KBIN_p,
+	      int_f *KBOUT_p,
+	      int_fl TITLE_l,
+	      int_fl PROMPT_l,
 	      int_fl HELPF_l)
 /*
  * Present a ``radio button'' dialogue allowing the user to select
@@ -225,32 +286,37 @@ void radion_x(char *TITLE_p, char *PROMPT_p, /* Actually: *PROMPT_p[*NB_p] */
  * CHOICE=-1      => Cancel
  */
 {
-	char **opt, title[256];
-	int i, numopts = (int)*NB_p;
+    char **opt, title[256];
+    int i, numopts = (int)*NB_p;
 
-	/* initialise options array */
-	opt = (char **)malloc(numopts * sizeof(char *));
-	opt[0] = (char *)malloc((unsigned int)((PROMPT_l + 1) * numopts));
-	for (i = 0; i < numopts; i++) {
-		opt[i] = opt[0] + (PROMPT_l + 1) * i;
-		Fstr2Cstr(PROMPT_p + (i * PROMPT_l), PROMPT_l, opt[i],
-			  PROMPT_l + 1);
-	}
+    /* initialise options array */
+    opt = (char **)malloc(numopts * sizeof(char *));
+    opt[0] = (char *)malloc((unsigned int)((PROMPT_l+1) * numopts));
+    for (i=0; i<numopts; i++) {
+	opt[i] = opt[0] + (PROMPT_l+1)*i;
+	Fstr2Cstr(PROMPT_p+(i*PROMPT_l), PROMPT_l, opt[i], PROMPT_l+1);
+    }
 
-	Fstr2Cstr(TITLE_p, TITLE_l, title, (int_fl)sizeof(title));
+    Fstr2Cstr(TITLE_p, TITLE_l, title, (int_fl)sizeof(title));
 
-	*CHOICE_p = (int_f)radion(title, opt, *NB_p, *CHOICE_p);
-
-	free((void *)opt[0]);
-	free((void *)opt);
-	return;
+    *CHOICE_p = (int_f)radion(title, opt, *NB_p, *CHOICE_p);
+    
+    free((void *)opt[0]);
+    free((void *)opt);
+    return;
 }
 
-void check4_x(char *P1_p, char *P2_p, char *P3_p, char *P4_p, int_f *C1_p,
-	      int_f *C2_p, int_f *C3_p, int_f *C4_p, int_f *IHELPS_p,
-	      int_f *IHELPE_p, char *HELPF_p, int_f *IDEVH_p, int_f *KBIN_p,
-	      int_f *KBOUT_p, int_f *IOK_p, int_fl P1_l, int_fl P2_l,
-	      int_fl P3_l, int_fl P4_l, int_fl HELPF_l)
+void check4_x(char  *P1_p, char  *P2_p, char  *P3_p, char  *P4_p,
+	      int_f *C1_p, int_f *C2_p, int_f *C3_p, int_f *C4_p,
+	      int_f *IHELPS_p,
+	      int_f *IHELPE_p,
+	      char  *HELPF_p,
+	      int_f *IDEVH_p,
+	      int_f *KBIN_p,
+	      int_f *KBOUT_p,
+	      int_f *IOK_p,
+	      int_fl P1_l, int_fl P2_l, int_fl P3_l, int_fl P4_l,
+	      int_fl HELPF_l)
 /*
  * Present a ``checkbox'' dialogue allowing the user to alter the
  * Boolean state of four items.
@@ -260,28 +326,25 @@ void check4_x(char *P1_p, char *P2_p, char *P3_p, char *P4_p, int_f *C1_p,
  * IOK=1 => Cancel
  */
 {
-	int ret;
-	char *prompts[4];
-	int *bools[4];
+    int ret;
+    char *prompts[4];
+    int *bools[4];
 
-	prompts[0] = P1_p;
-	bools[0] = (int *)C1_p;
-	prompts[1] = P2_p;
-	bools[1] = (int *)C2_p;
-	prompts[2] = P3_p;
-	bools[2] = (int *)C3_p;
-	prompts[3] = P4_p;
-	bools[3] = (int *)C4_p;
+    prompts[0] = P1_p; bools[0] = (int *)C1_p;
+    prompts[1] = P2_p; bools[1] = (int *)C2_p;
+    prompts[2] = P3_p; bools[2] = (int *)C3_p;
+    prompts[3] = P4_p; bools[3] = (int *)C4_p;
 
-	ret = checkn(4, prompts, bools);
+    ret = checkn(4, prompts, bools);
 
-	if (ret == 0)
-		*IOK_p = 0;
-	else
-		*IOK_p = 1;
+    if (ret == 0)
+	*IOK_p = 0;
+    else
+	*IOK_p = 1;
 }
 
-void getopt_x(int_f *KBIN_p, int_f *KOPT_p,
+void getopt_x(int_f *KBIN_p,
+	      int_f *KOPT_p,
 	      int_f *IOPT_p) /* out: option number selected */
 /*
  * Select a function to execute
@@ -290,51 +353,58 @@ void getopt_x(int_f *KBIN_p, int_f *KOPT_p,
  * KOPT=3 => menu option requested
  */
 {
-	*IOPT_p = (int_f)getcopt((int *)KOPT_p);
-	switch (*KOPT_p) {
-		case -3:
-		case -2:
-			*KOPT_p = 0;
-			*IOPT_p = 2;
-			break;
-		case -1:
-			*KOPT_p = 0;
-			*IOPT_p = 1;
-			break;
-	}
+    *IOPT_p = (int_f)getcopt((int *)KOPT_p);
+    switch(*KOPT_p) {
+    case -3:
+    case -2:
+	*KOPT_p = 0;
+	*IOPT_p = 2;
+	break;
+    case -1:
+	*KOPT_p = 0;
+	*IOPT_p = 1;
+	break;
+    }
 }
 
-void showfi_x(int_f *KBOUT_p, char *STRING_p, int_fl STRING_l)
+void showfi_x(int_f *KBOUT_p,
+	      char  *STRING_p,
+	      int_fl STRING_l)
 /*
  * Display `STRING', the name of the current file(s).
  */
 {
-	char func[256];
+    char func[256];
 
-	Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
-	showfi(func);
+    Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
+    showfi(func);
 }
 
-void showfu_x(int_f *KBOUT_p, char *STRING_p, int_fl STRING_l)
+
+void showfu_x(int_f *KBOUT_p,
+	      char  *STRING_p,
+	      int_fl  STRING_l)
 /*
  * Display `STRING', the name of the current function.
  */
 {
-	char func[256];
+    char func[256];
 
-	Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
-	showfu(func);
+    Fstr2Cstr(STRING_p, STRING_l, func, (int_fl)sizeof(func));
+    showfu(func);
 }
 
-void errom_x(int_f *KBOUT_p, char *STRING_p, int_fl STRING_l)
+void errom_x(int_f *KBOUT_p,
+	     char  *STRING_p,
+	     int_fl  STRING_l)
 /*
  * Display the error message `STRING'.
  */
 {
-	char err[256];
+    char err[256];
 
-	Fstr2Cstr(STRING_p, STRING_l, err, (int_fl)sizeof(err));
-	errom(err);
+    Fstr2Cstr(STRING_p, STRING_l, err, (int_fl)sizeof(err));
+    errom(err);
 }
 
 void busy_x(int_f *KBOUT_p)
@@ -343,7 +413,7 @@ void busy_x(int_f *KBOUT_p)
  * next dialogue function is called.
  */
 {
-	busy();
+    busy();
 }
 
 /*
@@ -351,8 +421,10 @@ void busy_x(int_f *KBOUT_p)
  *    0 for ok
  *   -1 for cancel
  */
-void bpause_x(int_f *KBIN_p, int_f *KBOUT_p, int_f *IOK_p)
-{
-	*IOK_p = (int_f)bpause();
+void bpause_x(int_f *KBIN_p,
+	      int_f *KBOUT_p,
+	      int_f *IOK_p) {
+
+    *IOK_p = (int_f)bpause();
 }
 

src/ted/Graph.c

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/ted/Graph.h

@@ -1,3 +1,5 @@
+#include <X11/copyright.h>
+
 /* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */
 
@@ -42,35 +44,38 @@
 
 /* define any special resource names here that are not in <X11/StringDefs.h> */
 
-#define XtNgraphResource "graphResource"
-#define XtCGraphResource "GraphResource"
+#define XtNgraphResource		"graphResource"
+#define XtCGraphResource		"GraphResource"
+
+#define XtNdimBackground                "dimBackground"
+#define XtNexposeCallback               "exposeCallback"
+#define XtNgraphColour1                 "graphColour1"
+#define XtNgraphColour2                 "graphColour2"
+#define XtNgraphColour3                 "graphColour3"
+#define XtNgraphColour4                 "graphColour4"
+#define XtNresizeCallback               "resizeCallback"
 
-#define XtNdimBackground "dimBackground"
-#define XtNexposeCallback "exposeCallback"
-#define XtNgraphColour1 "graphColour1"
-#define XtNgraphColour2 "graphColour2"
-#define XtNgraphColour3 "graphColour3"
-#define XtNgraphColour4 "graphColour4"
-#define XtNresizeCallback "resizeCallback"
 
 /* declare specific GraphWidget class and instance datatypes */
 
-typedef struct _GraphClassRec *GraphWidgetClass;
-typedef struct _GraphRec *GraphWidget;
+typedef struct _GraphClassRec  *GraphWidgetClass;
+typedef struct _GraphRec       *GraphWidget;
+
 
 /* declare the class constant */
 
 extern WidgetClass graphWidgetClass;
 
+
 /* ---- Exported procedures ---- */
 
 extern Pixel GraphColour1(Widget w);
 extern Pixel GraphColour2(Widget w);
 extern Pixel GraphColour3(Widget w);
 extern Pixel GraphColour4(Widget w);
-extern GC GraphGC1(Widget w);
-extern GC GraphGC2(Widget w);
-extern GC GraphGC3(Widget w);
-extern GC GraphGC4(Widget w);
+extern GC    GraphGC1(Widget w);
+extern GC    GraphGC2(Widget w);
+extern GC    GraphGC3(Widget w);
+extern GC    GraphGC4(Widget w);
 
 #endif /* _Graph_h */

src/ted/GraphP.h

@@ -1,3 +1,4 @@
+#include <X11/copyright.h>
 
 /* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */
 /* Copyright	Massachusetts Institute of Technology	1987, 1988 */

src/ted/makefile

@@ -1,90 +0,0 @@
-#
-# Makefile for ted (trace editor) - Alpha fork
-#
-
-#
-#Turning on the AUTO_CLIP switch allows ted to automatically
-#select a left (using the -enzyme option or the .enzyme in the
-#Xted file) and right cutoff on your sequence (using 2 out of
-#5 N's)
-#
-# Turning on the SAVE_EDITS switch allows the user to maintain
-# copies of their edits, i.e. when you open up ted on a file
-# that you have already edited, the old edits show up in the
-# ted edit window.  The user may also call up any of their
-# past editing sessions.  
-#
-#Turning on the DEF_OUT  switch makes
-# trace_name.seq the default output file name
-#
-#SWITCHES = -DAUTO_CLIP  -DDEF_OUT  -DSAVE_EDITS
-SWITCHES = -DAUTO_CLIP
-
-#
-# Programs made by this makefile
-#
-PROGS = ted
-
-#
-# Where the wild things are
-#
-SRC = .
-
-#
-# Compiler - debug on
-#
-CC= gfortran
-INCLUDES = -I$(SRC)
-CFLAGS= -g $(SWITCHES) $(INCLUDES)
-LIBS= -lXaw -lXt -lXmu -lXext -lX11 
-#-ldnet_stub
-#
-LD= gfortran
-LDFLAGS= -g 
-
-#
-# Object files
-#
-TEDOBJS=\
-	ted.o\
-	dialogues.o\
-	seq.o\
-	seqIOPlain.o\
-	seqIOABI.o\
-	help.o\
-	display.o\
-	traceDisplay.o\
-	basesDisplay.o\
-	Graph.o\
-	seqIOEdit.o\
-	seqIOALF.o\
-	seqIOSCF.o\
-	seqOutput.o\
-	opp.o\
-	info.o\
-	fpoint.o\
-	mach-io.o\
-	seqRead.o
-
-
-#
-# Linking
-#
-ted: $(TEDOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(TEDOBJS) $(LIBS)
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o : $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-
-#
-# Special dependencies
-#
-clean:
-	rm -f ted $(TEDOBJS) *~ *.aux *.log *.bbl *.blg *.dvi *.ps
-
-all: $(PROGS)
-

src/update_subclones/makefile

@@ -1,42 +0,0 @@
-#
-# Makefile for subclonedb
-#
-
-#
-# Programs made by this makefile
-#
-PROGS = update_subclones
-
-#
-# Where the wild things are
-#
-SRC = .
-MISCSRC = $(SRC)/../Misc
-MISCBIN = $(MISCSRC)
-INCLUDES = -I$(SRC) -I$(MISCSRC)
-
-#
-# Alpha
-#
-CC = cc
-CFLAGS = -g $(INCLUDES)
-LD = cc
-LDFLAGS = -g 
-
-#
-# Here they are
-#
-
-update_subclones : update_subclones.o $(MISCBIN)/misc.a
-	$(LD) $(LDFLAGS) -o update_subclones update_subclones.o $(MISCBIN)/misc.a
-
-#
-# Special dependencies
-#
-all: $(PROGS)
-
-clean:
-	/bin/rm -f $(PROGS)
-
-%.o: $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<

src/vepe/makefile

@@ -1,137 +0,0 @@
-# Makefile for vepe - Alpha version
-# -------------------------------
-
-PROGS= vepe
-
-all: $(PROGS)
-
-
-
-
-
-#
-# ``Interesting'' suffices that make needs to know about
-#
-.SUFFIXES: .a $(SUFFIXES)
-
-
-#
-# Directories
-#
-SRC = .
-#STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden
-STADENSRC=$(SRC)/../staden
-STADENBIN=$(STADENSRC)
-# Use the ted sources compiled for staden executables
-INCLUDES= -I$(STADENSRC)
-
-
-#
-# Compilers and flags
-#
-# debug on
-CC= cc
-CFLAGS= -g $(INCLUDES)
-F77= gfortran
-FFLAGS= -g
-LD= gfortran
-LDFLAGS= -g 
-
-FLAGS = -lutil -lm
-#FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil
-XLIBS= -lXaw -lXt -lXmu -lXext -lX11
-#LFLAGS= $(FLIBS)
-XLFLAGS= $(FLIBS) $(XLIBS)
-
-#
-# Avoid compilation of objects in remote directories
-#
-$(STADENBIN)/%.o : $(STADENSRC)/%.f
-$(STADENBIN)/%.o : $(STADENSRC)/%.c
-
-#
-# Common objects, needed by every program
-#
-COMMONOBJS=\
-	$(STADENBIN)/seeme-aix.o\
-	$(STADENBIN)/nxspec.o\
-	$(STADENBIN)/userface.o\
-	$(STADENBIN)/userfacecom.o\
-	$(STADENBIN)/helpnmenu.o\
-	$(STADENBIN)/nxhelpmenu.o\
-	$(STADENBIN)/FtoC.o\
-	$(STADENBIN)/subs89.a\
-
-
-#
-# Building the programs
-# This should be just a linking phase because all of the object
-# files and library files are generated using implicit rules.
-# We use the fortran compiler to do linking.
-#
-
-#
-# Vector excision program
-#
-
-VEP=\
-	vep.o\
-	$(STADENBIN)/dias89.a\
-	$(STADENBIN)/subs89.a
-
-
-VEPOBJS=\
-	$(VEP)\
-	$(COMMONOBJS)
-
-
-vep: $(VEPOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(VEPOBJS)  $(LFLAGS)
-
-
-
-VEPE=\
-	vepe.o\
-	$(STADENBIN)/dias89.a\
-	expio.o\
-	expFileIO.o
-
-
-VEPEOBJS=\
-	$(VEPE)\
-	$(COMMONOBJS)
-
-
-vepe: $(VEPEOBJS)
-	$(LD) $(LDFLAGS) -o $@ $(VEPEOBJS)  $(LFLAGS)
-
-COBJS =  expFileIO.o testc.o
-FOBJS =  expFileIO.o testf.o
-
-
-testc: $(COBJS)
-	$(CC) $(CFLAGS) -o $@ $(COBJS)
-
-testf:  $(FOBJS)
-	$(F77) $(FFLAGS) -o $@ $(FOBJS)
-
-
-#
-# Files requiring simple C compilation (thing.c -> thing.o)
-# 
-%.o: %.c
-	$(CC) $(CFLAGS) -c $<
-%.o: $(SRC)/%.c
-	$(CC) $(CFLAGS) -c $<
-
-#
-# Files requiring simple FORTRAN compilation (thing.f -> thing.o)
-# 
-%.o: $(SRC)/%.f
-	$(F77) $(FFLAGS) -c $<
-
-clean:
-	rm -f $(PROGS) *.o *.a *~
-
-
-install: clean all