diff -up EMBOSS-6.6.0/emboss/acd/epscan.acd.fixconflict EMBOSS-6.6.0/emboss/acd/epscan.acd
--- EMBOSS-6.6.0/emboss/acd/epscan.acd.fixconflict 2015-10-30 09:50:32.562390934 -0400
+++ EMBOSS-6.6.0/emboss/acd/epscan.acd 2015-10-30 09:50:32.562390934 -0400
@@ -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-6.6.0/emboss/acd/Makefile.am.fixconflict EMBOSS-6.6.0/emboss/acd/Makefile.am
--- EMBOSS-6.6.0/emboss/acd/Makefile.am.fixconflict 2013-07-15 17:25:46.000000000 -0400
+++ EMBOSS-6.6.0/emboss/acd/Makefile.am 2015-10-30 09:50:32.562390934 -0400
@@ -264,7 +264,7 @@ profit.acd \
prophecy.acd \
prophet.acd \
prosextract.acd \
-pscan.acd \
+epscan.acd \
psiphi.acd \
rebaseextract.acd \
recoder.acd \
diff -up EMBOSS-6.6.0/emboss/acd/Makefile.in.fixconflict EMBOSS-6.6.0/emboss/acd/Makefile.in
--- EMBOSS-6.6.0/emboss/acd/Makefile.in.fixconflict 2013-07-15 17:27:30.000000000 -0400
+++ EMBOSS-6.6.0/emboss/acd/Makefile.in 2015-10-30 09:50:32.562390934 -0400
@@ -532,7 +532,7 @@ profit.acd \
prophecy.acd \
prophet.acd \
prosextract.acd \
-pscan.acd \
+epscan.acd \
psiphi.acd \
rebaseextract.acd \
recoder.acd \
diff -up EMBOSS-6.6.0/emboss/acd/printsextract.acd.fixconflict EMBOSS-6.6.0/emboss/acd/printsextract.acd
--- EMBOSS-6.6.0/emboss/acd/printsextract.acd.fixconflict 2012-03-12 13:46:17.000000000 -0400
+++ EMBOSS-6.6.0/emboss/acd/printsextract.acd 2015-10-30 09:50:32.562390934 -0400
@@ -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-6.6.0/emboss/data/edamtoacd.dat.fixconflict EMBOSS-6.6.0/emboss/data/edamtoacd.dat
--- EMBOSS-6.6.0/emboss/data/edamtoacd.dat.fixconflict 2009-09-30 12:53:21.000000000 -0400
+++ EMBOSS-6.6.0/emboss/data/edamtoacd.dat 2015-10-30 09:50:32.563390927 -0400
@@ -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-6.6.0/emboss/epscan.c.fixconflict EMBOSS-6.6.0/emboss/epscan.c
--- EMBOSS-6.6.0/emboss/epscan.c.fixconflict 2015-10-30 09:50:32.563390927 -0400
+++ EMBOSS-6.6.0/emboss/epscan.c 2015-10-30 09:50:32.563390927 -0400
@@ -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<nleft;++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<hpm;++j)
+ {
+ ajListPop(l,(void **)&mm);
+ ajListPushAppend(l,(void *)mm);
+ }
+ }
+
+
+ if(found)
+ {
+ found = ajFalse;
+ for(i=0;i<nleft;++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<hpm;++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<hpm;++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<nleft;++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<hpm;++j)
+ {
+ ajListPop(l,(void **)&mm);
+ ajListPushAppend(l,(void *)mm);
+ }
+ }
+
+ if(found)
+ {
+
+ found=ajFalse;
+ for(i=0;i<nleft;++i)
+ {
+ ajListPop(l,(void **)&mm);
+ hpm = mm->hpm;
+ if(mm->all && maxelem==mm->n)
+ break;
+ ajListPushAppend(l,(void *)mm);
+
+ for(j=1;j<hpm;++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<hpm;++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<nleft;++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<hpm;++j)
+ {
+ ajListPop(l,(void **)&mm);
+ ajListPushAppend(l,(void *)mm);
+ }
+ }
+
+
+ if(found)
+ {
+ found = ajFalse;
+ for(i=0;i<nleft;++i)
+ {
+ ajListPop(l,(void **)&mm);
+ hpm = mm->hpm;
+
+ if(mm->ordered && maxhpm==mm->hpm)
+ break;
+ ajListPushAppend(l,(void *)mm);
+
+ for(j=1;j<hpm;++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<hpm;++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<nleft;++i)
+ {
+ ajListPop(l,(void **)&mm);
+ maxhpm = AJMAX(maxelem,mm->hpm);
+ found = ajTrue;
+
+ hpm = mm->hpm;
+ ajListPushAppend(l,(void *)mm);
+ for(j=1;j<hpm;++j)
+ {
+ ajListPop(l,(void **)&mm);
+ ajListPushAppend(l,(void *)mm);
+ }
+ }
+
+
+ if(found)
+ {
+ found = ajFalse;
+ for(i=0;i<nleft;++i)
+ {
+ ajListPop(l,(void **)&mm);
+ hpm = mm->hpm;
+
+ if(maxhpm==mm->hpm)
+ break;
+ ajListPushAppend(l,(void *)mm);
+
+ for(j=1;j<hpm;++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<hpm;++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-6.6.0/emboss/Makefile.am.fixconflict EMBOSS-6.6.0/emboss/Makefile.am
--- EMBOSS-6.6.0/emboss/Makefile.am.fixconflict 2015-10-30 09:50:32.554390990 -0400
+++ EMBOSS-6.6.0/emboss/Makefile.am 2015-10-30 09:51:26.065016794 -0400
@@ -309,7 +309,7 @@ profit \
prophecy \
prophet \
prosextract \
-pscan \
+epscan \
psiphi \
rebaseextract \
recoder \
@@ -587,7 +587,7 @@ profit_SOURCES = profit.c
prophecy_SOURCES = prophecy.c
prophet_SOURCES = prophet.c
prosextract_SOURCES = prosextract.c
-pscan_SOURCES = pscan.c
+epscan_SOURCES = epscan.c
psiphi_SOURCES = psiphi.c
rebaseextract_SOURCES = rebaseextract.c
recoder_SOURCES = recoder.c
diff -up EMBOSS-6.6.0/emboss/Makefile.in.fixconflict EMBOSS-6.6.0/emboss/Makefile.in
--- EMBOSS-6.6.0/emboss/Makefile.in.fixconflict 2013-07-15 17:27:30.000000000 -0400
+++ EMBOSS-6.6.0/emboss/Makefile.in 2015-10-30 09:50:32.565390913 -0400
@@ -142,7 +142,7 @@ 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$(EXEEXT) refseqget$(EXEEXT) remap$(EXEEXT) \
restover$(EXEEXT) restrict$(EXEEXT) revseq$(EXEEXT) \
@@ -1993,10 +1993,10 @@ prosextract_DEPENDENCIES = ../nucleus/li
../ajax/core/libajax.la $(am__append_3) \
../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
$(am__DEPENDENCIES_1)
-am_pscan_OBJECTS = pscan.$(OBJEXT)
-pscan_OBJECTS = $(am_pscan_OBJECTS)
-pscan_LDADD = $(LDADD)
-pscan_DEPENDENCIES = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \
+am_epscan_OBJECTS = epscan.$(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 \
$(am__append_3) ../ajax/pcre/libepcre.la \
@@ -2821,7 +2821,7 @@ 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) $(refseqget_SOURCES) $(remap_SOURCES) \
$(restover_SOURCES) $(restrict_SOURCES) $(revseq_SOURCES) \
@@ -2934,7 +2934,7 @@ 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) $(refseqget_SOURCES) $(remap_SOURCES) \
$(restover_SOURCES) $(restrict_SOURCES) $(revseq_SOURCES) \
@@ -3414,7 +3414,7 @@ profit_SOURCES = profit.c
prophecy_SOURCES = prophecy.c
prophet_SOURCES = prophet.c
prosextract_SOURCES = prosextract.c
-pscan_SOURCES = pscan.c
+epscan_SOURCES = epscan.c
psiphi_SOURCES = psiphi.c
rebaseextract_SOURCES = rebaseextract.c
recoder_SOURCES = recoder.c
@@ -4266,9 +4266,9 @@ prophet$(EXEEXT): $(prophet_OBJECTS) $(p
prosextract$(EXEEXT): $(prosextract_OBJECTS) $(prosextract_DEPENDENCIES) $(EXTRA_prosextract_DEPENDENCIES)
@rm -f prosextract$(EXEEXT)
$(LINK) $(prosextract_OBJECTS) $(prosextract_LDADD) $(LIBS)
-pscan$(EXEEXT): $(pscan_OBJECTS) $(pscan_DEPENDENCIES) $(EXTRA_pscan_DEPENDENCIES)
- @rm -f pscan$(EXEEXT)
- $(LINK) $(pscan_OBJECTS) $(pscan_LDADD) $(LIBS)
+epscan$(EXEEXT): $(epscan_OBJECTS) $(epscan_DEPENDENCIES) $(EXTRA_epscan_DEPENDENCIES)
+ @rm -f epscan$(EXEEXT)
+ $(LINK) $(epscan_OBJECTS) $(epscan_LDADD) $(LIBS)
psiphi$(EXEEXT): $(psiphi_OBJECTS) $(psiphi_DEPENDENCIES) $(EXTRA_psiphi_DEPENDENCIES)
@rm -f psiphi$(EXEEXT)
$(LINK) $(psiphi_OBJECTS) $(psiphi_LDADD) $(LIBS)
@@ -4748,7 +4748,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(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@