diff -up EMBOSS-6.4.0/emboss/acd/epscan.acd.fixconflict EMBOSS-6.4.0/emboss/acd/epscan.acd

--- EMBOSS-6.4.0/emboss/acd/epscan.acd.fixconflict	2012-02-27 09:53:58.673872826 -0500

+++ EMBOSS-6.4.0/emboss/acd/epscan.acd	2012-02-27 09:54:48.345441143 -0500

@@ -0,0 +1,63 @@

+application: epscan [

+  documentation: "Scans protein sequence(s) with fingerprints from

+                  the PRINTS database"

+  groups: "Protein:Motifs"

+    relations: "EDAM:0000158 topic Sequence motifs"

+    relations: "EDAM:0000382 operation Sequence motif recognition (protein)"

+    relations: "EDAM:0000347 operation Sequence database search

+                (by motif or pattern)"

+    relations: "EDAM:0000340 operation Protein secondary database search"

+]

+

+section: input [

+  information: "Input section"

+  type: "page"

+]

+

+  seqall: sequence [

+    parameter: "Y"

+    type: "Protein"

+    relations: "EDAM:0002886 data Sequence record (protein)"

+  ]

+

+endsection: input

+

+section: required [

+  information: "Required section"

+  type: "page"

+]

+

+  integer: emin [

+    standard: "Y"

+    minimum: "1"

+    maximum: "20"

+    default: "2"

+    information: "Minimum number of elements per fingerprint"

+    relations: "EDAM:0002527 data Parameter or primitive"

+  ]

+

+  integer: emax [

+    standard: "Y"

+    minimum: "$(emin)"

+    maximum: "20"

+    failrange: "N"

+    trueminimum: "N"

+    default: "20"

+    information: "Maximum number of elements per fingerprint"

+    relations: "EDAM:0002527 data Parameter or primitive"

+  ]

+

+endsection: required

+

+section: output [

+  information: "Output section"

+  type: "page"

+]

+

+  outfile: outfile [

+    parameter: "Y"

+    knowntype: "pscan output"

+    relations: "EDAM:0001420 data Sequence-profile alignment (fingerprint)"

+  ]

+

+endsection: output

diff -up EMBOSS-6.4.0/emboss/acd/Makefile.am.fixconflict EMBOSS-6.4.0/emboss/acd/Makefile.am

--- EMBOSS-6.4.0/emboss/acd/Makefile.am.fixconflict	2012-02-27 09:46:48.379612489 -0500

+++ EMBOSS-6.4.0/emboss/acd/Makefile.am	2012-02-27 09:46:59.796513263 -0500

@@ -54,7 +54,7 @@ pkgdata2_DATA = needle.acd needleall.acd

 	pepwheel.acd pepwindow.acd pepwindowall.acd plotcon.acd plotorf.acd \

 	polydot.acd preg.acd prettyplot.acd prettyseq.acd \

 	primersearch.acd printsextract.acd profit.acd \

-	prophecy.acd prophet.acd prosextract.acd pscan.acd psiphi.acd \

+	prophecy.acd prophet.acd prosextract.acd epscan.acd psiphi.acd \

 	rebaseextract.acd recoder.acd redata.acd remap.acd restover.acd \

 	restrict.acd revseq.acd seealso.acd \

 	seqcount.acd seqmatchall.acd \

diff -up EMBOSS-6.4.0/emboss/acd/Makefile.fixconflict EMBOSS-6.4.0/emboss/acd/Makefile

--- EMBOSS-6.4.0/emboss/acd/Makefile.fixconflict	2012-02-27 09:47:30.481246583 -0500

+++ EMBOSS-6.4.0/emboss/acd/Makefile	2012-02-27 09:47:33.853217278 -0500

@@ -299,7 +299,7 @@ pkgdata2_DATA = needle.acd needleall.acd

 	pepwheel.acd pepwindow.acd pepwindowall.acd plotcon.acd plotorf.acd \

 	polydot.acd preg.acd prettyplot.acd prettyseq.acd \

 	primersearch.acd printsextract.acd profit.acd \

-	prophecy.acd prophet.acd prosextract.acd pscan.acd psiphi.acd \

+	prophecy.acd prophet.acd prosextract.acd epscan.acd psiphi.acd \

 	rebaseextract.acd recoder.acd redata.acd remap.acd restover.acd \

 	restrict.acd revseq.acd seealso.acd \

 	seqcount.acd seqmatchall.acd \

diff -up EMBOSS-6.4.0/emboss/acd/Makefile.in.fixconflict EMBOSS-6.4.0/emboss/acd/Makefile.in

--- EMBOSS-6.4.0/emboss/acd/Makefile.in.fixconflict	2012-02-27 09:47:10.357421484 -0500

+++ EMBOSS-6.4.0/emboss/acd/Makefile.in	2012-02-27 09:47:16.506368036 -0500

@@ -299,7 +299,7 @@ pkgdata2_DATA = needle.acd needleall.acd

 	pepwheel.acd pepwindow.acd pepwindowall.acd plotcon.acd plotorf.acd \

 	polydot.acd preg.acd prettyplot.acd prettyseq.acd \

 	primersearch.acd printsextract.acd profit.acd \

-	prophecy.acd prophet.acd prosextract.acd pscan.acd psiphi.acd \

+	prophecy.acd prophet.acd prosextract.acd epscan.acd psiphi.acd \

 	rebaseextract.acd recoder.acd redata.acd remap.acd restover.acd \

 	restrict.acd revseq.acd seealso.acd \

 	seqcount.acd seqmatchall.acd \

diff -up EMBOSS-6.4.0/emboss/acd/printsextract.acd.fixconflict EMBOSS-6.4.0/emboss/acd/printsextract.acd

--- EMBOSS-6.4.0/emboss/acd/printsextract.acd.fixconflict	2012-02-27 09:48:16.922842970 -0500

+++ EMBOSS-6.4.0/emboss/acd/printsextract.acd	2012-02-27 09:48:27.680749468 -0500

@@ -1,5 +1,5 @@

 application: printsextract [

-  documentation: "Extract data from PRINTS database for use by pscan"

+  documentation: "Extract data from PRINTS database for use by epscan"

   groups: "Utils:Database creation"

   gui: "no"

   batch: "no"

diff -up EMBOSS-6.4.0/emboss/data/edamtoacd.dat.fixconflict EMBOSS-6.4.0/emboss/data/edamtoacd.dat

--- EMBOSS-6.4.0/emboss/data/edamtoacd.dat.fixconflict	2012-02-27 09:47:52.084058836 -0500

+++ EMBOSS-6.4.0/emboss/data/edamtoacd.dat	2012-02-27 09:47:57.107015183 -0500

@@ -159,7 +159,7 @@ outfile        |  "EDAM:Primer report"

 outfile        |  "EDAM:Primer report"                                       | knowntype:"primersearch output"                 

 outfile        |  "EDAM:Sequence-profile alignment report"                   | knowntype:"profit output"                       

 outfile        |  "EDAM:Sequence profile record"                             | knowntype:"prophecy output"                     

-outfile        |  "EDAM:Fingerprint alignment report"                        | knowntype:"pscan output"                        

+outfile        |  "EDAM:Fingerprint alignment report"                        | knowntype:"epscan output"                        

 outfile        |  "EDAM:Restriction enzyme report"                           | knowntype:"redata output"                       

 outfile        |  "EDAM:Restriction map report"                              | knowntype:"remap output"                        

 outfile        |  "EDAM:EMBOSS restover recognition site report"             | knowntype:"restover output"                        

diff -up EMBOSS-6.4.0/emboss/epscan.c.fixconflict EMBOSS-6.4.0/emboss/epscan.c

--- EMBOSS-6.4.0/emboss/epscan.c.fixconflict	2012-02-27 09:48:44.891599888 -0500

+++ EMBOSS-6.4.0/emboss/epscan.c	2012-02-27 09:48:40.234640361 -0500

@@ -0,0 +1,481 @@

+/* @source pscan application

+**

+** Reports fingerprints in a protein sequence

+** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

+** @@

+**

+** This program is free software; you can redistribute it and/or

+** modify it under the terms of the GNU General Public License

+** as published by the Free Software Foundation; either version 2

+** of the License, or (at your option) any later version.

+**

+** This program is distributed in the hope that it will be useful,

+** but WITHOUT ANY WARRANTY; without even the implied warranty of

+** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

+** GNU General Public License for more details.

+**

+** You should have received a copy of the GNU General Public License

+** along with this program; if not, write to the Free Software

+** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.

+******************************************************************************/

+

+#include "emboss.h"

+

+

+

+

+static void pscan_print_hits(AjPFile outf, AjPList l, ajuint nmotifs,

+			     ajuint begin);

+

+

+

+

+/* @prog pscan ****************************************************************

+**

+** Scans proteins using PRINTS

+**

+******************************************************************************/

+

+int main(int argc, char **argv)

+{

+    AjPSeqall seqall;

+    AjPSeq seq   = NULL;

+    AjPFile outf = NULL;

+    ajint begin;

+    ajint end;

+    ajuint emin;

+    ajuint emax;

+

+    AjPFile mfile = NULL;

+    EmbPMatPrints s = NULL;

+    AjPList l = NULL;

+    AjPStr strand = NULL;

+    AjPStr substr = NULL;

+    AjPStr name = NULL;

+

+    AjBool all;

+    AjBool ordered;

+

+    ajint hits;

+    ajint nmotifs;

+

+    embInit("pscan", argc, argv);

+

+    seqall = ajAcdGetSeqall("sequence");

+    outf   = ajAcdGetOutfile("outfile");

+    emin   = ajAcdGetInt("emin");

+    emax   = ajAcdGetInt("emax");

+

+    substr = ajStrNew();

+    name   = ajStrNew();

+

+    all = ordered = ajTrue;

+

+

+

+    while(ajSeqallNext(seqall, &seq))

+    {

+	begin = ajSeqallGetseqBegin(seqall);

+	end   = ajSeqallGetseqEnd(seqall);

+

+	ajStrAssignC(&name,ajSeqGetNameC(seq));

+	strand = ajSeqGetSeqCopyS(seq);

+

+	ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1);

+

+	nmotifs = 0;

+	ajDebug("pscan sequence '%S'\n", ajSeqGetNameS(seq));

+	embMatPrintsInit(&mfile);

+	ajDebug("pscan prints file '%F'\n", mfile);

+	l = ajListNew();

+	while((s = embMatProtReadInt(mfile)))

+	{

+	    ajDebug("pscan file '%F' read\n", mfile);

+	    if(s->n >= emin && s->n <= emax)

+	    {

+		hits=embMatProtScanInt(substr,name,s,&l,&all,&ordered,

+					    1);

+		if(hits)

+		    ++nmotifs;

+	    }

+	    embMatProtDelInt(&s);

+	}

+

+	pscan_print_hits(outf, l, nmotifs, begin);

+	ajListFree(&l);

+

+

+	ajStrDel(&strand);

+	ajFileClose(&mfile);

+    }

+

+    ajStrDel(&substr);

+    ajStrDel(&name);

+

+    ajSeqallDel(&seqall);

+    ajSeqDel(&seq;;

+    ajFileClose(&outf);

+

+    embExit();

+

+    return 0;

+}

+

+

+

+

+/* @funcstatic pscan_print_hits ***********************************************

+**

+** Undocumented.

+**

+** @param [u] outf [AjPFile] outfile

+** @param [u] l [AjPList] hits

+** @param [r] nmotifs [ajuint] number of hits

+** @param [r] begin [ajuint] start position

+** @@

+******************************************************************************/

+

+static void pscan_print_hits(AjPFile outf, AjPList l, ajuint nmotifs,

+			     ajuint begin)

+{

+    EmbPMatMatch mm;

+    ajuint i;

+    ajuint j;

+    AjBool found;

+    ajuint nleft;

+    ajuint maxelem = 0;

+    ajuint maxhpm;

+    ajuint hpm = 0;

+

+    nleft = nmotifs;

+

+

+    ajFmtPrintF(outf,"\n\nCLASS 1\n");

+    ajFmtPrintF(outf,"Fingerprints with all elements in order\n\n");

+

+

+    found = ajTrue;

+

+    while(found && nleft)

+    {

+	found = ajFalse;

+	maxelem = 0;

+	for(i=0;i

+	{

+	    ajListPop(l,(void **)&mm;;

+	    if(mm->all && mm->ordered)

+	    {

+		maxelem = AJMAX(maxelem,mm->n);

+		found = ajTrue;

+	    }

+	    hpm = mm->hpm;

+

+	    ajListPushAppend(l,(void *)mm);

+	    for(j=1;j

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajListPushAppend(l,(void *)mm);

+	    }

+	}

+

+

+	if(found)

+	{

+	    found = ajFalse;

+	    for(i=0;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		hpm = mm->hpm;

+

+		if(mm->all && mm->ordered && maxelem==mm->n)

+		    break;

+		ajListPushAppend(l,(void *)mm);

+

+		for(j=1;j

+		{

+		    ajListPop(l,(void **)&mm;;

+		    ajListPushAppend(l,(void *)mm);

+		}

+	    }

+

+	    if(mm->all && mm->ordered && maxelem==mm->n)

+	    {

+		ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",

+			    ajStrGetPtr(mm->cod),mm->n);

+		ajFmtPrintF(outf,"    Accession number %s\n",

+			    ajStrGetPtr(mm->acc));

+		ajFmtPrintF(outf,"    %s\n",ajStrGetPtr(mm->tit));

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    for(i=1;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    --nleft;

+	}

+

+    }

+

+    ajFmtPrintF(outf,"\n\nCLASS 2\n");

+    ajFmtPrintF(outf,"All elements match but not all in the "

+		"correct order\n\n");

+

+    found = ajTrue;

+

+    while(found && nleft)

+    {

+	found = ajFalse;

+	maxelem = 0;

+

+	for(i=0;i

+	{

+	    ajListPop(l,(void **)&mm;;

+	    if(mm->all)

+	    {

+		maxelem = AJMAX(maxelem,mm->n);

+		found = ajTrue;

+	    }

+	    hpm = mm->hpm;

+	    ajListPushAppend(l,(void *)mm);

+

+	    for(j=1;j

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajListPushAppend(l,(void *)mm);

+	    }

+	}

+

+	if(found)

+	{

+

+	    found=ajFalse;

+	    for(i=0;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		hpm = mm->hpm;

+		if(mm->all && maxelem==mm->n)

+		    break;

+		ajListPushAppend(l,(void *)mm);

+

+		for(j=1;j

+		{

+		    ajListPop(l,(void **)&mm;;

+		    ajListPushAppend(l,(void *)mm);

+		}

+	    }

+

+	    if(mm->all && maxelem==mm->n)

+	    {

+		ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",

+			    ajStrGetPtr(mm->cod),mm->n);

+		ajFmtPrintF(outf,"    Accession number %s\n",

+			    ajStrGetPtr(mm->acc));

+		ajFmtPrintF(outf,"    %s\n",ajStrGetPtr(mm->tit));

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    for(i=1;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    --nleft;

+	}

+

+    }

+

+

+

+

+    ajFmtPrintF(outf,"\n\nCLASS 3\n");

+    ajFmtPrintF(outf,

+		"Not all elements match but those that do are in order\n\n");

+

+    found = ajTrue;

+

+    while(found && nleft)

+    {

+	found  = ajFalse;

+	maxhpm = 0;

+	for(i=0;i

+	{

+	    ajListPop(l,(void **)&mm;;

+	    if(mm->ordered)

+	    {

+		maxhpm = AJMAX(maxelem,mm->hpm);

+		found  = ajTrue;

+	    }

+	    hpm = mm->hpm;

+	    ajListPushAppend(l,(void *)mm);

+

+	    for(j=1;j

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajListPushAppend(l,(void *)mm);

+	    }

+	}

+

+

+	if(found)

+	{

+	    found = ajFalse;

+	    for(i=0;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		hpm = mm->hpm;

+

+		if(mm->ordered && maxhpm==mm->hpm)

+		    break;

+		ajListPushAppend(l,(void *)mm);

+

+		for(j=1;j

+		{

+		    ajListPop(l,(void **)&mm;;

+		    ajListPushAppend(l,(void *)mm);

+		}

+	    }

+

+	    if(mm->ordered && maxhpm==mm->hpm)

+	    {

+		ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",

+			    ajStrGetPtr(mm->cod),mm->n);

+		ajFmtPrintF(outf,"    Accession number %s\n",

+			    ajStrGetPtr(mm->acc));

+		ajFmtPrintF(outf,"    %s\n",ajStrGetPtr(mm->tit));

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    for(i=1;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    --nleft;

+	}

+

+    }

+

+

+

+

+    ajFmtPrintF(outf,"\n\nCLASS 4\n");

+    ajFmtPrintF(outf,

+		"Remaining partial matches\n\n");

+

+    found = ajTrue;

+

+    while(found && nleft)

+    {

+	found = ajFalse;

+	maxhpm = 0;

+

+	for(i=0;i

+	{

+	    ajListPop(l,(void **)&mm;;

+	    maxhpm = AJMAX(maxelem,mm->hpm);

+	    found = ajTrue;

+

+	    hpm = mm->hpm;

+	    ajListPushAppend(l,(void *)mm);

+	    for(j=1;j

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajListPushAppend(l,(void *)mm);

+	    }

+	}

+

+

+	if(found)

+	{

+	    found = ajFalse;

+	    for(i=0;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		hpm = mm->hpm;

+

+		if(maxhpm==mm->hpm)

+		    break;

+		ajListPushAppend(l,(void *)mm);

+

+		for(j=1;j

+		{

+		    ajListPop(l,(void **)&mm;;

+		    ajListPushAppend(l,(void *)mm);

+		}

+	    }

+

+	    if(maxhpm==mm->hpm)

+	    {

+		ajFmtPrintF(outf,"Fingerprint %s Elements %d\n",

+			    ajStrGetPtr(mm->cod),mm->n);

+		ajFmtPrintF(outf,"    Accession number %s\n",

+			    ajStrGetPtr(mm->acc));

+		ajFmtPrintF(outf,"    %s\n",ajStrGetPtr(mm->tit));

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    for(i=1;i

+	    {

+		ajListPop(l,(void **)&mm;;

+		ajFmtPrintF(outf,"  Element %d Threshold %d%% Score %d%%\n",

+			    mm->element+1, mm->thresh, mm->score);

+		ajFmtPrintF(outf,"             Start position %d Length %d\n",

+			    mm->start+begin,mm->len);

+

+		embMatMatchDel(&mm;;

+	    }

+

+	    --nleft;

+	}

+

+    }

+

+

+    while(ajListPop(l,(void **)&mm))

+	if(mm)

+	    embMatMatchDel(&mm;;

+

+    return;

+}

diff -up EMBOSS-6.4.0/emboss/Makefile.am.fixconflict EMBOSS-6.4.0/emboss/Makefile.am

--- EMBOSS-6.4.0/emboss/Makefile.am.fixconflict	2012-02-27 09:48:55.526507467 -0500

+++ EMBOSS-6.4.0/emboss/Makefile.am	2012-02-27 09:52:54.611429591 -0500

@@ -80,7 +80,7 @@ pepwheel pepwindow pepwindowall \

 plotcon plotorf polydot preg \

 prettyplot prettyseq primersearch printsextract \

 profit prophecy prophet \

-prosextract pscan psiphi \

+prosextract epscan psiphi \

 rebaseextract recoder redata remap  \

 restover restrict revseq \

 seealso seqcount seqmatchall seqret seqretsetall seqretsplit \

@@ -301,7 +301,7 @@ profit_SOURCES = profit.c

 prophecy_SOURCES = prophecy.c

 prophet_SOURCES = prophet.c

 prosextract_SOURCES = prosextract.c

-pscan_SOURCES = pscan.c

+epscan_SOURCES = pscan.c

 psiphi_SOURCES = psiphi.c

 rebaseextract_SOURCES = rebaseextract.c

 recoder_SOURCES = recoder.c

diff -up EMBOSS-6.4.0/emboss/Makefile.in.fixconflict EMBOSS-6.4.0/emboss/Makefile.in

--- EMBOSS-6.4.0/emboss/Makefile.in.fixconflict	2012-02-27 09:49:12.123363211 -0500

+++ EMBOSS-6.4.0/emboss/Makefile.in	2012-02-27 09:52:34.681602796 -0500

@@ -109,7 +109,7 @@ bin_PROGRAMS = aaindexextract$(EXEEXT) a

 	plotorf$(EXEEXT) polydot$(EXEEXT) preg$(EXEEXT) \

 	prettyplot$(EXEEXT) prettyseq$(EXEEXT) primersearch$(EXEEXT) \

 	printsextract$(EXEEXT) profit$(EXEEXT) prophecy$(EXEEXT) \

-	prophet$(EXEEXT) prosextract$(EXEEXT) pscan$(EXEEXT) \

+	prophet$(EXEEXT) prosextract$(EXEEXT) epscan$(EXEEXT) \

 	psiphi$(EXEEXT) rebaseextract$(EXEEXT) recoder$(EXEEXT) \

 	redata$(EXEEXT) remap$(EXEEXT) restover$(EXEEXT) \

 	restrict$(EXEEXT) revseq$(EXEEXT) seealso$(EXEEXT) \

@@ -1837,10 +1837,10 @@ prosextract_DEPENDENCIES = ../nucleus/li

 	../ajax/ensembl/libensembl.la ../ajax/graphics/libajaxg.la \

 	../ajax/core/libajax.la $(EXTRA_LDS) ../ajax/pcre/libepcre.la \

 	../plplot/libeplplot.la $(am__DEPENDENCIES_1)

-am_pscan_OBJECTS = pscan.$(OBJEXT)

-pscan_OBJECTS = $(am_pscan_OBJECTS)

-pscan_LDADD = $(LDADD)

-pscan_DEPENDENCIES = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \

+am_epscan_OBJECTS = pscan.$(OBJEXT)

+epscan_OBJECTS = $(am_epscan_OBJECTS)

+epscan_LDADD = $(LDADD)

+epscan_DEPENDENCIES = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \

 	../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \

 	../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \

 	$(EXTRA_LDS) ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \

@@ -2592,7 +2592,7 @@ SOURCES = $(aaindexextract_SOURCES) $(ab

 	$(preg_SOURCES) $(prettyplot_SOURCES) $(prettyseq_SOURCES) \

 	$(prima_SOURCES) $(primers_SOURCES) $(primersearch_SOURCES) \

 	$(printsextract_SOURCES) $(profit_SOURCES) $(prophecy_SOURCES) \

-	$(prophet_SOURCES) $(prosextract_SOURCES) $(pscan_SOURCES) \

+	$(prophet_SOURCES) $(prosextract_SOURCES) $(epscan_SOURCES) \

 	$(psiphi_SOURCES) $(rebaseextract_SOURCES) $(recoder_SOURCES) \

 	$(redata_SOURCES) $(remap_SOURCES) $(restover_SOURCES) \

 	$(restrict_SOURCES) $(revseq_SOURCES) $(seealso_SOURCES) \

@@ -2701,7 +2701,7 @@ DIST_SOURCES = $(aaindexextract_SOURCES)

 	$(preg_SOURCES) $(prettyplot_SOURCES) $(prettyseq_SOURCES) \

 	$(prima_SOURCES) $(primers_SOURCES) $(primersearch_SOURCES) \

 	$(printsextract_SOURCES) $(profit_SOURCES) $(prophecy_SOURCES) \

-	$(prophet_SOURCES) $(prosextract_SOURCES) $(pscan_SOURCES) \

+	$(prophet_SOURCES) $(prosextract_SOURCES) $(epscan_SOURCES) \

 	$(psiphi_SOURCES) $(rebaseextract_SOURCES) $(recoder_SOURCES) \

 	$(redata_SOURCES) $(remap_SOURCES) $(restover_SOURCES) \

 	$(restrict_SOURCES) $(revseq_SOURCES) $(seealso_SOURCES) \

@@ -3172,7 +3172,7 @@ profit_SOURCES = profit.c

 prophecy_SOURCES = prophecy.c

 prophet_SOURCES = prophet.c

 prosextract_SOURCES = prosextract.c

-pscan_SOURCES = pscan.c

+epscan_SOURCES = pscan.c

 psiphi_SOURCES = psiphi.c

 rebaseextract_SOURCES = rebaseextract.c

 recoder_SOURCES = recoder.c

@@ -3990,9 +3990,9 @@ prophet$(EXEEXT): $(prophet_OBJECTS) $(p

 prosextract$(EXEEXT): $(prosextract_OBJECTS) $(prosextract_DEPENDENCIES) 

 	@rm -f prosextract$(EXEEXT)

 	$(LINK) $(prosextract_OBJECTS) $(prosextract_LDADD) $(LIBS)

-pscan$(EXEEXT): $(pscan_OBJECTS) $(pscan_DEPENDENCIES) 

-	@rm -f pscan$(EXEEXT)

-	$(LINK) $(pscan_OBJECTS) $(pscan_LDADD) $(LIBS)

+epscan$(EXEEXT): $(epscan_OBJECTS) $(epscan_DEPENDENCIES) 

+	@rm -f epscan$(EXEEXT)

+	$(LINK) $(epscan_OBJECTS) $(epscan_LDADD) $(LIBS)

 psiphi$(EXEEXT): $(psiphi_OBJECTS) $(psiphi_DEPENDENCIES) 

 	@rm -f psiphi$(EXEEXT)

 	$(LINK) $(psiphi_OBJECTS) $(psiphi_LDADD) $(LIBS)

@@ -4456,7 +4456,7 @@ distclean-compile:

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/prophecy.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/prophet.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/prosextract.Po@am__quote@

-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pscan.Po@am__quote@

+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/epscan.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/psiphi.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/rebaseextract.Po@am__quote@

 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/recoder.Po@am__quote@