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Author: Tatiana Malygina <merlettaia@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;
|