Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian....@packages.debian.org Usertags: pu
X-CC: debian-med-packag...@lists.alioth.debian.org
Hi,
it appears that profphd in stretch is unusable because it requires an older
perl version (and reject stretch perl version). As such, package should be
removed *or* attached patch could be applied to make it work with current
perl version.
It applies to strech with no additional feature or stuff, those patches
only fix issue of perl version to allow software to run.
Thanks for your advice and patch consideration.
Olivier (on behalf of debian-med team)
Author: Tatiana Malygina <merlett...@gmail.com>
Description: fix error "Negative repeat count does nothing at" for various
lines (including possible places where this error might appear -
by semi-autoreplacement)
Last-Update: 2016-08-24
--- a/src/prof/scr/lib/lib-prof.pl
+++ b/src/prof/scr/lib/lib-prof.pl
@@ -1,5 +1,6 @@
#use Data::Dumper;
use Carp qw| cluck :DEFAULT |;
+use List::Util qw[max];
no warnings 'deprecated';
#------------------------------------------------------------------------------#
# Copyright Sep, 1998 #
@@ -4401,7 +4402,7 @@
# loop over all alis
foreach $itAli (@wantNum){
$hssp{"fin",$itAli}.=$hssp{"ali",$itAli,$itRes};
- $hssp{"fin",$itAli}.="." x (1 + $insMax - length($hssp{"ali",$itAli,$itRes}));
+ $hssp{"fin",$itAli}.="." x max(1 + $insMax - length($hssp{"ali",$itAli,$itRes}), 0);
}
}
# ------------------------------
@@ -11580,7 +11581,7 @@
next if ($rdb{$kwd}=~/^\s*$/);
$tmp{$kwd}=1;
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$rdb{$kwd});
+ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$rdb{$kwd});
# other info
if ($kwd =~ /prot_nfar/ && $#otherDistance){
@@ -11595,7 +11596,7 @@
$val= $rdb{$kwd,$other};
$kwd2=$kwd.$other;}
$tmp=$kwd2; $tmp=~tr/[a-z]/[A-Z]/;
- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$val);
+ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$val);
}}
}
@@ -11618,7 +11619,7 @@
next if ($rdb{$kwd}=~/^\s*$/);
$tmp{$kwd}=1;
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$rdb{$kwd});}
+ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$rdb{$kwd});}
push(@tmpwrt,@tmp2,"# ") if ($#tmp2 > 3);
# ------------------------------
@@ -11634,7 +11635,7 @@
@tmpval=split(/\t/,$rdb{$kwd});
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
foreach $tmpval (@tmpval){
- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhiteHtm-length($tmp)) .": ".$tmpval);
+ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhiteHtm-length($tmp), 0) .": ".$tmpval);
}
}
push(@tmpwrt,@tmp2,"# ") if ($#tmp2>3);
@@ -11649,7 +11650,7 @@
next if ($rdb{$kwd}=~/^\s*$/);
$tmp{$kwd}=1;
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
- push(@tmp2,"# VALUE ".$tmp. " " x ($numwhite-length($tmp)) .": ".$rdb{$kwd});}
+ push(@tmp2,"# VALUE ".$tmp. " " x max($numwhite-length($tmp), 0) .": ".$rdb{$kwd});}
if ($#tmp2>3) { push(@tmpwrt,@tmp2,"# ");
$Lnet=1;} else {$Lnet=0;}
@@ -11830,12 +11831,12 @@
# ------------------------------
# notation: header: protein
- $tmp="HEADER". " " x ($numwhite-6) . ": PROTEIN";
+ $tmp="HEADER". " " x max($numwhite-6, 0) . ": PROTEIN";
push(@tmp2,
"# ",
# "# NOTATION "."-" x length($tmp),
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp))
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0)
);
foreach $kwd ("prot_id","prot_name","prot_nres","prot_nchn","prot_kchn",
"prot_nali","prot_nfar"){
@@ -11843,60 +11844,60 @@
next if (! defined $tmp{$kwd});
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
$tmpcontd=$kwd." contd";
- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": ";
- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": ";
+ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": ";
+ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": ";
$notation=$par{"notation",$kwd};
$notation=~s/\n/\n$tmpdescontd/g;
push(@tmp2,$tmpdes.$notation);}
# ------------------------------
# notation: header: alignment
- $tmp="HEADER". " " x ($numwhite-6) . ": ALIGNMENT";
+ $tmp="HEADER". " " x max($numwhite-6, 0) . ": ALIGNMENT";
push(@tmp2,
"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));
foreach $kwd ("ali_orig","ali_used","ali_para"
){
next if (! defined $par{"notation",$kwd});
next if (! defined $tmp{$kwd});
$tmpcontd=$kwd." contd";
- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": ";
- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": ";
+ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": ";
+ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": ";
$notation=$par{"notation",$kwd};
$notation=~s/\n/\n$tmpdescontd/g;
push(@tmp2,$tmpdes.$notation);}
# ------------------------------
# notation: header: network
- $tmp="HEADER". " " x ($numwhite-6) . ": INTERNAL";
+ $tmp="HEADER". " " x max($numwhite-6, 0) . ": INTERNAL";
push(@tmp2,
"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));
foreach $kwd ("prof_fpar","prof_nnet","prof_fnet","prof_mode"){
next if (! defined $par{"notation",$kwd});
next if (! defined $tmp{$kwd});
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
$tmpcontd=$kwd." contd";
- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": ";
- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": ";
+ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": ";
+ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": ";
$notation=$par{"notation",$kwd};
push(@tmp2,$tmpdes.$notation);}
# ------------------------------
# notation: body: protein
push(@tmp2,"# ");
- $tmp="BODY ". " " x ($numwhite-5) . ": PROTEIN";
+ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROTEIN";
push(@tmp2,
"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));
foreach $kwd ("No","AA","CHN"){
next if (! defined $par{"notation",$kwd});
$tmp=$kwd; $tmp=~tr/[a-z]/[A-Z]/;
- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": ";
- $tmpdescontd="# NOTATION ".$tmpcontd. " " x ($numwhite-length($tmpcontd)) .": ";
+ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": ";
+ $tmpdescontd="# NOTATION ".$tmpcontd. " " x max($numwhite-length($tmpcontd), 0) .": ";
$notation=$par{"notation",$kwd};
$notation=~s/\n/\n$tmpdescontd/g;
push(@tmp2,$tmpdes.$notation);}
@@ -11906,11 +11907,11 @@
$#tmp=0;
if ($whichPROFloc =~ /^(3|both)$/){
- $tmp="BODY ". " " x ($numwhite-5) . ": PROF";
+ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROF";
push(@tmp,
"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));}
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));}
else {
push(@tmp,
"# ");}
@@ -11950,7 +11951,7 @@
$tmp=$kwd;
# $tmp=~tr/[a-z]/[A-Z]/;
# split annotations too long
- $tmpdes= "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)) .": ";
+ $tmpdes= "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0) .": ";
$notation=$par{"notation",$kwd};
# no new line in RDB
$notation=~s/\n/ /g;
@@ -11958,22 +11959,22 @@
# insert header
if ($kwd =~ /ACC/ && ! defined $tmp{"acc"}){
$tmp{"acc"}=1;
- $tmp="BODY ". " " x ($numwhite-5) . ": PROFacc";
+ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROFacc";
push(@tmp,"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));}
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));}
elsif ($kwd =~ /HEL/ && ! defined $tmp{"sec"}){
$tmp{"sec"}=1;
- $tmp="BODY ". " " x ($numwhite-5) . ": PROFsec";
+ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROFsec";
push(@tmp,"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));}
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));}
elsif ($kwd =~ /MN/ && ! defined $tmp{"htm"}){
$tmp{"htm"}=1;
- $tmp="BODY ". " " x ($numwhite-5) . ": PROFhtm";
+ $tmp="BODY ". " " x max($numwhite-5, 0) . ": PROFhtm";
push(@tmp,"# ",
"# "."-" x 72,
- "# NOTATION ".$tmp. " " x ($numwhite-length($tmp)));}
+ "# NOTATION ".$tmp. " " x max($numwhite-length($tmp), 0));}
# ------------------------------
# add to final
@@ -11984,7 +11985,7 @@
if (defined $PROF_SKIP){
$tmp="NOTE";
push(@tmp,
- "# NOTATION ".$tmp." " x ($numwhite-length($tmp)) .": ".$par{"notation","prof_skip"});}
+ "# NOTATION ".$tmp." " x max($numwhite-length($tmp), 0) .": ".$par{"notation","prof_skip"});}
push(@tmp2,
@tmp,
"# " ,
@@ -12048,10 +12049,10 @@
$white="10";
print
# "--- ------------------------------------------------------------------\n",
- "--- PROF: ",$dateLoc, " " x ($white-length($dateLoc)),
+ "--- PROF: ",$dateLoc, " " x max($white-length($dateLoc), 0),
" run time=",&fctRunTime($timeBegLoc),"\n";
print
- "--- N proteins: ",$nfileInLoc," " x ($white-length($nfileInLoc)),
+ "--- N proteins: ",$nfileInLoc," " x max($white-length($nfileInLoc), 0),
" time per protein=",&fctSeconds2time((time-$timeBegLoc)/$nfileInLoc),"\n"
if ($nfileInLoc > 2);
Author: Tatiana Malygina <merlett...@gmail.com>
Last-Update: 2016-09-11
Description: fixes warning message
"""
Useless use of greediness modifier '?' in regex; marked by <-- HERE in
m/^(.{59}? <-- HERE \S*[\., \-\;\:])/ at
/usr/share/profphd/prof/scr/lib/lib-profwrt.pl line 2303.
"""
which appears when 'prof' is run with 'ascii' parameter, i.e.
prof /usr/share/profphd/prof/exa/1ppt.hssp fileRdb=1ppt.rdbProfSec sec ascii
--- profphd-1.0.42.orig/src/prof/scr/lib/lib-profwrt.pl
+++ profphd-1.0.42/src/prof/scr/lib/lib-profwrt.pl
@@ -2300,7 +2300,7 @@
# long lines: to split
$lentmp=$len-12;
while (length($tmp)>=$len){
- $tmp=~s/^(.{$lentmp}?\S*[\., \-\;\:])//;
+ $tmp=~s/^(.{$lentmp}\S*[\., \-\;\:])//;
last if (! defined $1);
print $fhoutLoc
$1. " " x ($len-length($1)) ."#\n";
Author: Tatiana Malygina <merlett...@gmail.com>
Description: remove perlbrew to use latest perl 5.22
Last-Update: 2016-08-23
--- a/src/prof/prof
+++ b/src/prof/prof
@@ -35,7 +35,7 @@
echoerr ""
}
-if [ ${PERL_VER} -ge ${PERL_BAD} ]
+if [ ${PERL_VER} -le ${PERL_BAD} ]
then
## Do stuff with perl 5.10.1 if perlbrew installed
if [ -x ${PERLBREW_PATH} ]
Author: Tatiana Malygina <merlett...@gmail.com>
Description: fix error "Modification of non-creatable array value attempted,
subscript -1 at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 7739"
Last-Update: 2016-09-11
--- profphd-1.0.42.orig/src/prof/scr/lib/lib-prof.pl
+++ profphd-1.0.42/src/prof/scr/lib/lib-prof.pl
@@ -7720,7 +7720,7 @@
# --------------------------------------------------
# get helix lengths
- $#tmpbeg=$#tmpbeg=$#tmpend=$prev=$cth=0;
+ $#tmpbeg=$prev=$cth=0; $#tmpend=$#tmplen=1;
foreach $itres (1..$rdb{"NROWS"}){
next if ($prof_skip{$itres} || ! defined $rdb{$itres,"PHEL"});
if ($rdb{$itres,"PHEL"} ne "H") {
@@ -7832,7 +7832,7 @@
# --------------------------------------------------
# get helix lengths
- $#tmpbeg=$#tmpbeg=$#tmpend=$prev=$cte=0;
+ $#tmpbeg=$prev=$cte=0; $#tmpend=$#tmplen=1;
foreach $itres (1..$rdb{"NROWS"}){
next if ($prof_skip{$itres} || ! defined $rdb{$itres,"PHEL"});
if ($rdb{$itres,"PHEL"} ne "E") {
Author: Tatiana Malygina <merlett...@gmail.com>
Description: change defined(@array) to @array to use with perl 5.22
Last-Update: 2016-08-22
--- a/src/prof/embl/scr/lib-col.pl
+++ b/src/prof/embl/scr/lib-col.pl
@@ -338,7 +338,7 @@
$#dir2=$Lok=0;
return(0,"no input file") if (! defined $fileInLoc);
$chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
- $#dir=0 if (! defined @dir);
+ $#dir=0 if (! @dir);
$Lscreen=0 if (! defined $Lscreen);
if (-d $Lscreen) {
@dir=($Lscreen,@dir);
@@ -1070,7 +1070,7 @@
$#dir2=$Lok=0;
return(0,"no input file") if (! defined $fileInLoc);
$chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
- $#dir=0 if (! defined @dir);
+ $#dir=0 if (! @dir);
$Lscreen=0 if (! defined $Lscreen);
if (-d $Lscreen) {
@dir=($Lscreen,@dir);
@@ -1208,7 +1208,7 @@
# of all numbers wanted (i.e. = $want[M])
undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around!
- $#want=0 if (! defined @want);
+ $#want=0 if (! @want);
$LreadAll=0;
# ------------------------------
# digest input
@@ -1261,7 +1261,7 @@
# sort the array
@wantNum= sort bynumber (@wantNum);
# too many wanted
- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
+ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
$#tmp=0;
foreach $want (@wantNum){
if ($want <= $locNum[$#locNum]){
@@ -1695,7 +1695,7 @@
$ifirLoc=0 if (! defined $ifirLoc || ($ifirLoc eq "*") );
$ilasLoc=0 if (! defined $ilasLoc || ($ilasLoc eq "*") );
$chainLoc=0 if (! defined $chainLoc || ($chainLoc eq "*") );
- $#kwdRd=0 if (! defined @kwdRd);
+ $#kwdRd=0 if (! @kwdRd);
undef %tmp;
if ($#kwdRd>0){
foreach $tmp(@kwdRd){
@@ -3518,7 +3518,7 @@
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."phdHtmGetBest";$fhinLoc="FHIN_"."phdHtmGetBest";
# check arguments
- return(&errSbr("no input!")) if (! defined @tmp || $#tmp==0);
+ return(&errSbr("no input!")) if (! @tmp || $#tmp==0);
$minLenLoc=18 if ($minLenLoc == 0);
$max=0;
@@ -5569,7 +5569,7 @@
# out: $file (id or 0 for error)
#--------------------------------------------------------------------------------
return($idLoc) if (-e $idLoc); # already existing directory
- $#dirLoc=0 if (! defined @dirLoc);
+ $#dirLoc=0 if (! @dirLoc);
if (! defined $Lscreen){$Lscreen=0;}
elsif (-d $Lscreen) {@dirLoc=($Lscreen,@dirLoc);$Lscreen=0;}
@dirSwissLoc=("/data/swissprot/current/"); # swiss dir's
--- a/src/prof/embl/scr/conv_phd2hssp.pl
+++ b/src/prof/embl/scr/conv_phd2hssp.pl
@@ -310,7 +310,7 @@
$par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"};}}}}
# ------------------------------
# push array of output files
- if (! defined @fileOut){$#fileOut=0;}
+ if (! @fileOut){$#fileOut=0;}
foreach $kwd (@kwdDef){
if ($kwd=~/^fileOut/){
push(@fileOut,$par{"$kwd"});}}
@@ -327,7 +327,7 @@
$par{"$kwd"}=$par{"dirWork"}.$par{"$kwd"};}}}}
# ------------------------------
# array of Work files
- if (! defined @fileWork){$#fileWork=0;}
+ if (! @fileWork){$#fileWork=0;}
foreach $kwd (@kwdDef){
if (($kwd=~/^file/)&&($kwd!~/^fileIn/)&&($kwd!~/^fileOut/)){
push(@fileWork,$par{"$kwd"});}}
@@ -511,4 +511,3 @@
}
close($fhoutLoc);
}
-
--- a/src/prof/embl/scr/lib/all5.pl
+++ b/src/prof/embl/scr/lib/all5.pl
@@ -377,7 +377,7 @@
@tmp=split(/[\s\t]+/,$_); foreach $tmp (@tmp){$tmp=~s/\s//g;}
if ($itrow==1){ # only first time: check numbers passed
- @colNumLoc=(1..$#tmp) if (! defined @colNumLoc || ! @colNumLoc); }
+ @colNumLoc=(1..$#tmp) if (! @colNumLoc || ! @colNumLoc); }
# read columns
foreach $itcol (@colNumLoc) {
--- a/src/prof/embl/scr/lib/br.pl
+++ b/src/prof/embl/scr/lib/br.pl
@@ -1770,7 +1770,7 @@
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."phdHtmGetBest";$fhinLoc="FHIN_"."phdHtmGetBest";
# check arguments
- return(&errSbr("no input!")) if (! defined @tmp || $#tmp==0);
+ return(&errSbr("no input!")) if (! @tmp || $#tmp==0);
$minLenLoc=18 if ($minLenLoc == 0);
$max=0;
@@ -4438,17 +4438,17 @@
# in GLOBAL: @NUM, @SEQ, @SEC(HE ), @ACC, @RISEC, @RIACC
# out: 1 if ok
#----------------------------------------------------------------------
- if (! defined @NUM || $#NUM == 0 || ! defined @SEQ || $#SEQ == 0 ||
- ! defined @SEC || $#SEC == 0 || ! defined @ACC || $#ACC == 0 ||
- ! defined @RISEC || $#RISEC == 0 ||
- ! defined @RIACC || $#RIACC == 0 ) {
+ if (! @NUM || $#NUM == 0 || ! @SEQ || $#SEQ == 0 ||
+ ! @SEC || $#SEC == 0 || ! @ACC || $#ACC == 0 ||
+ ! @RISEC || $#RISEC == 0 ||
+ ! @RIACC || $#RIACC == 0 ) {
print "*** ERROR in wrt_dssp_phd: not all arguments defined!!\n";
- print "*** missing NUM\n" if (! defined @NUM || $#NUM == 0);
- print "*** missing SEQ\n" if (! defined @SEQ || $#SEQ == 0 );
- print "*** missing SEC\n" if (! defined @SEC || $#SEC == 0);
- print "*** missing ACC\n" if (! defined @ACC || $#ACC == 0);
- print "*** missing RISEC\n" if (! defined @RISEC || $#RISEC == 0);
- print "*** missing RIACC\n" if (! defined @RIACC || $#RIACC == 0);
+ print "*** missing NUM\n" if (! @NUM || $#NUM == 0);
+ print "*** missing SEQ\n" if (! @SEQ || $#SEQ == 0 );
+ print "*** missing SEC\n" if (! @SEC || $#SEC == 0);
+ print "*** missing ACC\n" if (! @ACC || $#ACC == 0);
+ print "*** missing RISEC\n" if (! @RISEC || $#RISEC == 0);
+ print "*** missing RIACC\n" if (! @RIACC || $#RIACC == 0);
return(0);}
print $fhoutLoc
--- a/src/prof/embl/scr/lib/file.pl
+++ b/src/prof/embl/scr/lib/file.pl
@@ -244,7 +244,7 @@
$sbrName="lib-br:"."fileListWrt";$fhoutLoc="FHOUT_"."fileListWrt";
# check arguments
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
- return(0,"*** $sbrName: not def \@list!") if (! defined @listLoc || ! @listLoc);
+ return(0,"*** $sbrName: not def \@list!") if (! @listLoc || ! @listLoc);
$#tmp=0; # ------------------------------
foreach $file (@listLoc){ # check existence
if (-e $file) {
@@ -254,7 +254,7 @@
else { print $fhErrSbr "-*- WARN $sbrName missing file=$file,\n";}}
@listLoc=@tmp;
- return(0,"*** $sbrName: after check none in\@list!") if (! defined @listLoc || ! @listLoc);
+ return(0,"*** $sbrName: after check none in\@list!") if (! @listLoc || ! @listLoc);
# open file
&open_file("$fhoutLoc",">$fileOutLoc") ||
return(0,"*** ERROR $sbrName: fileNew=$fileOutLoc, not created\n",0);
@@ -1019,7 +1019,7 @@
# EXA: 1 MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
# EXA: 51 QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
#--------------------------------------------------------------------------------
- return(0) if (! defined @tmp || ! $#tmp);
+ return(0) if (! @tmp || ! $#tmp);
$ctLocFlag=$already_sequence=0;
foreach $tmp (@tmp){
last if ($tmp=~/^\#/); # avoid being too friendly to GCG!
--- a/src/prof/embl/scr/lib/formats.pl
+++ b/src/prof/embl/scr/lib/formats.pl
@@ -2472,7 +2472,7 @@
$#dir2=$Lok=0;
return(0,"no input file") if (! defined $fileInLoc);
$chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
- $#dir=0 if (! defined @dir);
+ $#dir=0 if (! @dir);
$Lscreen=0 if (! defined $Lscreen);
if (-d $Lscreen) {
@dir=($Lscreen,@dir);
@@ -3808,7 +3808,7 @@
open("$fhout",">$fileOutLoc") ||
return(0,"*** $sbrName cannot open fileOutLoc=$fileOutLoc\n");
# avoid warning
- $#NUM=0 if (! defined @NUM);
+ $#NUM=0 if (! @NUM);
# ------------------------------
if ($Levalsec){ # write PP2dotpred format
@@ -6056,7 +6056,7 @@
# out: $file (id or 0 for error)
#--------------------------------------------------------------------------------
return($idLoc) if (-e $idLoc); # already existing directory
- $#dirLoc=0 if (! defined @dirLoc);
+ $#dirLoc=0 if (! @dirLoc);
if (! defined $LscreenLoc){
$LscreenLoc=0;}
elsif (-d $Lscreen) {
--- a/src/prof/embl/scr/lib/hssp.pl
+++ b/src/prof/embl/scr/lib/hssp.pl
@@ -718,7 +718,7 @@
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
- return(0,"*** $sbrName: not def \@takeLoc!") if (! defined @takeLoc || $#takeLoc<1);
+ return(0,"*** $sbrName: not def \@takeLoc!") if (! @takeLoc || $#takeLoc<1);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# open files
&open_file("$fhinLoc","$fileInLoc") ||
@@ -1062,7 +1062,7 @@
$#dir2=$Lok=0;
return(0,"no input file") if (! defined $fileInLoc);
$chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
- $#dir=0 if (! defined @dir);
+ $#dir=0 if (! @dir);
$Lscreen=0 if (! defined $Lscreen);
if (-d $Lscreen) {
@dir=($Lscreen,@dir);
@@ -1205,7 +1205,7 @@
# of all numbers wanted (i.e. = $want[M])
undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around!
- $#want=0 if (! defined @want);
+ $#want=0 if (! @want);
$LreadAll=0;
# ------------------------------
# digest input
@@ -1260,7 +1260,7 @@
# sort the array
@wantNum= sort bynumber (@wantNum);
# too many wanted
- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
+ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
$#tmp=0;
foreach $want (@wantNum){
if ($want <= $locNum[$#locNum]){
@@ -1817,7 +1817,7 @@
$ifirLoc=0 if (! defined $ifirLoc || ($ifirLoc eq "*") );
$ilasLoc=0 if (! defined $ilasLoc || ($ilasLoc eq "*") );
$chainLoc=0 if (! defined $chainLoc || ($chainLoc eq "*") );
- $#kwdRd=0 if (! defined @kwdRd);
+ $#kwdRd=0 if (! @kwdRd);
undef %tmp;
if ($#kwdRd>0){
foreach $tmp(@kwdRd){
--- a/src/prof/embl/scr/lib/scr.pl
+++ b/src/prof/embl/scr/lib/scr.pl
@@ -884,7 +884,7 @@
$par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}}
# ------------------------------
# push array of output files
- $#fileOut=0 if (! defined @fileOut);
+ $#fileOut=0 if (! @fileOut);
foreach $kwd (@kwdFileOut){
push(@fileOut,$par{$kwd});}
# ------------------------------
@@ -1013,7 +1013,7 @@
printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}}
# ------------------------------
# input files
- if (defined @fileIn && $#fileIn>1){
+ if (@fileIn && $#fileIn>1){
# get dirs
$#tmpdir=0;
undef %tmpdir;
@@ -1036,10 +1036,10 @@
$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
print $fhTraceLocSbr "\n";}}
- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
+ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
$tmp=0;
$tmp=$fileIn if (defined $fileIn && $fileIn);
- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
+ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1);
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
print $fhTraceLocSbr "--- \n";
@@ -1463,7 +1463,7 @@
# ------------------------------
# (1) find in arguments passed
# ------------------------------
- if (defined @argLoc && $#argLoc > 0) {
+ if (@argLoc && $#argLoc > 0) {
foreach $arg (@argLoc) {
if ($arg=~/^ARCH=(\S+)/i) {
$archFound=$1;
@@ -1708,7 +1708,7 @@
# check arguments
return(&errSbr("not def nperlineLoc!")) if (! defined $nperlineLoc);
return(&errSbr("not def LnumLoc!")) if (! defined $LnumLoc);
- return(&errSbr("not def ARRAYtmpLoc!")) if (! defined @tmpLoc);
+ return(&errSbr("not def ARRAYtmpLoc!")) if (! @tmpLoc);
return(&errSbr("empty ARRAYtmpLoc!")) if (! $#tmpLoc);
# return(&errSbr("not def !")) if (! defined $);
--- a/src/prof/embl/scr/pack/copf.pm
+++ b/src/prof/embl/scr/pack/copf.pm
@@ -1847,7 +1847,7 @@
$par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}}
# ------------------------------
# push array of output files
- $#fileOut=0 if (! defined @fileOut);
+ $#fileOut=0 if (! @fileOut);
foreach $kwd (@kwdFileOut){
push(@fileOut,$par{$kwd});}
# ------------------------------
@@ -1973,7 +1973,7 @@
printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}}
# ------------------------------
# input files
- if (defined @fileIn && $#fileIn>1){
+ if (@fileIn && $#fileIn>1){
# get dirs
$#tmpdir=0; undef %tmpdir;
foreach $file (@fileIn){
@@ -1995,10 +1995,10 @@
$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
print $fhTraceLocSbr "\n";}}
- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
+ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
$tmp=0;
$tmp=$fileIn if (defined $fileIn && $fileIn);
- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
+ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1);
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
print $fhTraceLocSbr "--- \n";
@@ -4441,7 +4441,7 @@
# ------------------------------
# (1) find in arguments passed
# ------------------------------
- if (defined @argLoc && $#argLoc > 0) {
+ if (@argLoc && $#argLoc > 0) {
foreach $arg (@argLoc) {
if ($arg=~/^ARCH=(\S+)/i) {
$archFound=$1;
@@ -4726,7 +4726,7 @@
# of all numbers wanted (i.e. = $want[M])
undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around!
- $#want=0 if (! defined @want);
+ $#want=0 if (! @want);
$LreadAll=0;
# ------------------------------
# digest input
@@ -4779,7 +4779,7 @@
# sort the array
@wantNum= sort bynumber (@wantNum);
# too many wanted
- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
+ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
$#tmp=0;
foreach $want (@wantNum){
if ($want <= $locNum[$#locNum]){
--- a/src/prof/embl/scr/pack/hssp_filter.pm
+++ b/src/prof/embl/scr/pack/hssp_filter.pm
@@ -1324,7 +1324,7 @@
$par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"} if (-d $par{"dirOut"});}}
# ------------------------------
# push array of output files
- $#fileOut=0 if (! defined @fileOut);
+ $#fileOut=0 if (! @fileOut);
foreach $kwd (@kwdFileOut){
push(@fileOut,$par{"$kwd"});}
# ------------------------------
@@ -1450,7 +1450,7 @@
printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{"$kwd"};}}
# ------------------------------
# input files
- if (defined @fileIn && $#fileIn>1){
+ if (@fileIn && $#fileIn>1){
# get dirs
$#tmpdir=0; undef %tmpdir;
foreach $file (@fileIn){
@@ -1472,10 +1472,10 @@
$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
print $fhTraceLocSbr "\n";}}
- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
+ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
$tmp=0;
$tmp=$fileIn if (defined $fileIn && $fileIn);
- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
+ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1);
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
print $fhTraceLocSbr "--- \n";
@@ -1700,7 +1700,7 @@
# ------------------------------
# (1) find in arguments passed
# ------------------------------
- if (defined @argLoc && $#argLoc > 0) {
+ if (@argLoc && $#argLoc > 0) {
foreach $arg (@argLoc) {
if ($arg=~/^ARCH=(\S+)/i) {
$archFound=$1;
@@ -2193,7 +2193,7 @@
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
- return(0,"*** $sbrName: not def \@takeLoc!") if (! defined @takeLoc || $#takeLoc<1);
+ return(0,"*** $sbrName: not def \@takeLoc!") if (! @takeLoc || $#takeLoc<1);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# open files
&open_file("$fhinLoc","$fileInLoc") ||
@@ -2246,7 +2246,7 @@
$#dir2=$Lok=0;
return(0,"no input file") if (! defined $fileInLoc);
$chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
- $#dir=0 if (! defined @dir);
+ $#dir=0 if (! @dir);
$Lscreen=0 if (! defined $Lscreen);
# passed dir instead of Lscreen
if (-d $Lscreen) { @dir=($Lscreen,@dir);
--- a/src/prof/scr/conv_prof2hssp.pl
+++ b/src/prof/scr/conv_prof2hssp.pl
@@ -310,7 +310,7 @@
$par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"};}}}}
# ------------------------------
# push array of output files
- if (! defined @fileOut){$#fileOut=0;}
+ if (! @fileOut){$#fileOut=0;}
foreach $kwd (@kwdDef){
if ($kwd=~/^fileOut/){
push(@fileOut,$par{"$kwd"});}}
@@ -327,7 +327,7 @@
$par{"$kwd"}=$par{"dirWork"}.$par{"$kwd"};}}}}
# ------------------------------
# array of Work files
- if (! defined @fileWork){$#fileWork=0;}
+ if (! @fileWork){$#fileWork=0;}
foreach $kwd (@kwdDef){
if (($kwd=~/^file/)&&($kwd!~/^fileIn/)&&($kwd!~/^fileOut/)){
push(@fileWork,$par{"$kwd"});}}
@@ -511,4 +511,3 @@
}
close($fhoutLoc);
}
-
--- a/src/prof/scr/lib/dead_code.pl
+++ b/src/prof/scr/lib/dead_code.pl
@@ -15,7 +15,7 @@
#-------------------------------------------------------------------------------
$SBR4=""."nnJury"; $fhinLoc="FHIN_"."nnJury";$fhoutLoc="FHOUT_"."nnJury";
# check arguments
- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc ||
+ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc ||
! @fileOutNetLoc);
# --------------------------------------------------
# loop over all output files
@@ -1338,4 +1338,3 @@
print $FHTRACE $tmpWrt; }
return($itVec);
} # end of assVec_strLocRel
-
--- a/src/prof/scr/lib/lib-col.pl
+++ b/src/prof/scr/lib/lib-col.pl
@@ -652,7 +652,7 @@
}
# ------------------------------
# push array of output files
- $#fileOut=0 if (! defined @fileOut);
+ $#fileOut=0 if (! @fileOut);
foreach $kwd (@kwdFileOut){
push(@fileOut,$par{$kwd});}
# ------------------------------
@@ -773,7 +773,7 @@
printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}}
# ------------------------------
# input files
- if (defined @fileIn && $#fileIn>1){
+ if (@fileIn && $#fileIn>1){
# get dirs
$#tmpdir=0;
undef %tmpdir;
@@ -796,10 +796,10 @@
$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
print $fhTraceLocSbr "\n";}}
- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
+ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
$tmp=0;
$tmp=$fileIn if (defined $fileIn && $fileIn);
- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
+ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1);
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
print $fhTraceLocSbr "--- \n";
@@ -2320,7 +2320,7 @@
# EXA: 1 MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
# EXA: 51 QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
#--------------------------------------------------------------------------------
- return(0) if (! defined @tmp || ! $#tmp);
+ return(0) if (! @tmp || ! $#tmp);
$ctLocFlag=$already_sequence=0;
foreach $tmp (@tmp){
last if ($tmp=~/^\#/); # avoid being too friendly to GCG!
@@ -2752,7 +2752,7 @@
# in: @tmp:
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
- return(0) if (! defined @tmp || ! $#tmp);
+ return(0) if (! @tmp || ! $#tmp);
foreach $tmp (@tmp){
return(0) if ($tmp=~/[^A-Z.~_![:space:]]/i);
}
--- a/src/prof/scr/lib/lib-prof.pl
+++ b/src/prof/scr/lib/lib-prof.pl
@@ -426,7 +426,7 @@
return(&errSbr("missing par{extBlastMat}!", $SBR6)) if (! defined $par{"extBlastMat"} ||
length($par{"extBlastMat"}) < 3);
return(&errSbr("missing Hash_ARRAYhssp!", $SBR6)) if (! %hssp);
- return(&errSbr("missing Norm_ARRAYaa!", $SBR6)) if (! defined @aa || ! @aa);
+ return(&errSbr("missing Norm_ARRAYaa!", $SBR6)) if (! @aa || ! @aa);
@@ -2820,7 +2820,7 @@
return(&errSbr("not def acc3Thresh1!",$SBR6),0) if (! defined $acc3Thresh1);
return(&errSbr("not def acc3Thresh2!",$SBR6),0) if (! defined $acc3Thresh2);
return(&errSbr("bitaccLoc < 1!",$SBR6),0) if ($bitaccLoc<1);
- return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! defined @vecLoc || $#vecLoc<1);
+ return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! @vecLoc || $#vecLoc<1);
$undecidedLoc=$bitaccLoc*0.5 if (! defined $undecidedLoc);
@@ -2884,7 +2884,7 @@
# check arguments
return(&errSbr("not def accRelLoc!", $SBR6),0) if (! defined $accRelLoc);
return(&errSbr("not def acc2Thresh!", $SBR6),0) if (! defined $acc2Thresh);
- return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! defined @prdLoc || $#prdLoc<1);
+ return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! @prdLoc || $#prdLoc<1);
# ------------------------------
# fast end for others
@@ -2944,7 +2944,7 @@
return(&errSbr("not def accRelLoc!", $SBR6),0) if (! defined $accRelLoc);
return(&errSbr("not def acc3Thresh1!",$SBR6),0) if (! defined $acc3Thresh1);
return(&errSbr("not def acc3Thresh2!",$SBR6),0) if (! defined $acc3Thresh2);
- return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! defined @prdLoc || $#prdLoc<1);
+ return(&errSbr("no vector (prdLoc)!", $SBR6),0) if (! @prdLoc || $#prdLoc<1);
# ------------------------------
# compile averages over each state
@@ -3002,7 +3002,7 @@
# check arguments
return(&errSbr("not def modepredLoc!",$SBR6),0) if (! defined $modepredLoc);
return(&errSbr("not def posWinLoc!",$SBR6),0) if (! defined $posWinLoc);
- return(&errSbr("not def outnum2symLoc!",$SBR6),0) if (! defined @outnum2symLoc ||
+ return(&errSbr("not def outnum2symLoc!",$SBR6),0) if (! @outnum2symLoc ||
$#outnum2symLoc<1);
return(&errSbr("numout must be > 1, here",$SBR6),0) if ($#outnum2symLoc<2);
return(&errSbr("undefined symbol for posWinLoc=$posWinLoc, outnum2symLoc=".
@@ -3055,7 +3055,7 @@
return(&errSbr("not def modepredLoc!",$SBR6),0) if (! defined $modepredLoc);
return(&errSbr("not def bitaccLoc!",$SBR6),0) if (! defined $bitaccLoc);
return(&errSbr("bitaccLoc < 1!",$SBR6),0) if ($bitaccLoc<1);
- return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! defined @vecLoc || $#vecLoc<1);
+ return(&errSbr("no vector (vecLoc,$SBR6)!"),0) if (! @vecLoc || $#vecLoc<1);
# --------------------------------------------------
# distinguish prediction modes
# --------------------------------------------------
@@ -5309,7 +5309,7 @@
# ------------------------------
# symbols for output units
- if (! defined @outnum2sym || ! $#outnum2sym){
+ if (! @outnum2sym || ! $#outnum2sym){
foreach $itout (1..$numoutLoc){
push(@outnum2sym,$ptrGlob{"outnum2sym",$itout});
}}
@@ -6073,7 +6073,7 @@
$SBR4=""."nn3rdProcessOnesam";
# check arguments
return(&errSbr("not def modepredLoc!",$SBR4)) if (! defined $modepredLoc);
- return(&errSbr("not def outputs!",$SBR4)) if (! defined @tmp);
+ return(&errSbr("not def outputs!",$SBR4)) if (! @tmp);
$#out=$sum=0;
foreach $itout (1..$#tmp){
@@ -6734,7 +6734,7 @@
$LverbLoc=0; # temporary writes
# $LverbLoc=1;
# check arguments
- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc ||
+ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc ||
! @fileOutNetLoc);
@winoutJoinLoc=split(/,/,$winoutJoinLoc);
@@ -6991,7 +6991,7 @@
#-------------------------------------------------------------------------------
$SBR4=""."nnJurySpecial"; $fhinLoc="FHIN_"."nnJurySpecial";$fhoutLoc="FHOUT_"."nnJurySpecial";
# check arguments
- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc ||
+ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc ||
! @fileOutNetLoc);
# --------------------------------------------------
# loop over all output files
@@ -7118,7 +7118,7 @@
#-------------------------------------------------------------------------------
$SBR4=""."nnJuryWeight"; $fhinLoc="FHIN_"."nnJuryWeight";$fhoutLoc="FHOUT_"."nnJuryWeight";
# check arguments
- return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! defined @fileOutNetLoc ||
+ return(&errSbr("not def fileOutNetLoc!",$SBR4)) if (! @fileOutNetLoc ||
! @fileOutNetLoc);
@winoutJoinLoc=split(/,/,$winoutJoinLoc);
@@ -8099,7 +8099,7 @@
# out GLOBAL: @codeUnitIn1st
# out GLOBAL: @num_codeUnitIn (if $Ldobuild2nd)
# --------------------------------------------------
- if (! defined @codeUnitIn1st) {
+ if (! @codeUnitIn1st) {
($Lok,$msg)=
&decode_inputUnits1st($winHalf,$modeinLoc,$numaaLoc
); return(&errSbrMsg("spoiled decode_inputUnits1st(1)",
@@ -8631,7 +8631,7 @@
# ------------------------------
# add additional local information: go through window
- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
+ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){
foreach $scale (@hydrophobicityScalesWanted) {
push(@vecIn,$prot{$itwin,$scale});
@@ -8641,7 +8641,7 @@
# local info: once per window
# sum over hydrophobicity (i+2,+3,+4)
- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
+ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
foreach $scale (@hydrophobicityScalesWantedSum) {
push(@vecIn,split(/,/,$prot{$itres,$scale."sum",($winHalf*2+1)}));
}}
@@ -8730,7 +8730,7 @@
# ------------------------------
# add additional local information: go through window
- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
+ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){
foreach $scale (@hydrophobicityScalesWanted) {
push(@vecIn,$prot{$itwin,$scale});
@@ -8740,7 +8740,7 @@
# local info: once per window
# sum over hydrophobicity (i+2,+3,+4)
- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
+ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
foreach $scale (@hydrophobicityScalesWantedSum) {
push(@vecIn,split(/,/,$prot{$itres,$scale."sum",($winHalf*2+1)}));
}}
@@ -8858,7 +8858,7 @@
# ------------------------------
# add additional local information: go through window
- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
+ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){
foreach $scale (@hydrophobicityScalesWanted) {
if (defined $prot_hydro{$itwin,$scale}){
@@ -8871,7 +8871,7 @@
# local info: once per window
# sum over hydrophobicity (i+2,+3,+4)
- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
+ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
foreach $scale (@hydrophobicityScalesWantedSum) {
if (defined $prot_hydro{$itres,$scale."sum",($winHalf*2+1)}){
push(@vecIn,split(/,/,$prot_hydro{$itres,$scale."sum",($winHalf*2+1)}));}
@@ -8943,7 +8943,7 @@
# ------------------------------
# add additional local information: go through window
- if (defined @hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
+ if (@hydrophobicityScalesWanted && $#hydrophobicityScalesWanted){
$#tmp=0;
foreach $itwin (($itres-$winHalf) .. ($itres+$winHalf)){
foreach $scale (@hydrophobicityScalesWanted) {
@@ -8957,7 +8957,7 @@
# ------------------------------
# local info: once per window
# sum over hydrophobicity (i+2,+3,+4)
- if (defined @hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
+ if (@hydrophobicityScalesWantedSum && $#hydrophobicityScalesWantedSum){
$#tmp=0;
foreach $scale (@hydrophobicityScalesWantedSum) {
if (defined $prot_hydro{$itres,$scale."sum",($winHalf*2+1)}){
@@ -9572,7 +9572,7 @@
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."phdHtmGetBest";$fhinLoc="FHIN_"."phdHtmGetBest";
# check arguments
- return(&errSbr("no input!")) if (! defined @tmp || $#tmp==0);
+ return(&errSbr("no input!")) if (! @tmp || $#tmp==0);
$minLenLoc=18 if ($minLenLoc == 0);
$max=0;
