|  line  | 
 true  | 
 false  | 
 branch  | 
 
| 
47
 | 
 0  | 
 2  | 
 if (not defined $format) { }  | 
 
| 
49
 | 
 1  | 
 1  | 
 unless (defined $range)  | 
 
| 
50
 | 
 1  | 
 1  | 
 if ($format eq 'BLINKER')  | 
 
| 
61
 | 
 0  | 
 2  | 
 if ($format eq 'GIZA') { }  | 
 
| 
 | 
 1  | 
 1  | 
 elsif ($format eq 'BLINKER') { }  | 
 
| 
 | 
 1  | 
 0  | 
 elsif ($format eq 'NAACL') { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($format eq 'TALP') { }  | 
 
| 
119
 | 
 0  | 
 0  | 
 unless (defined $outputFH)  | 
 
| 
120
 | 
 0  | 
 0  | 
 if ($representation eq 'matrix')  | 
 
| 
121
 | 
 0  | 
 0  | 
 unless (defined $mark)  | 
 
| 
122
 | 
 0  | 
 0  | 
 unless (defined $maxRows)  | 
 
| 
123
 | 
 0  | 
 0  | 
 unless (defined $maxCols)  | 
 
| 
127
 | 
 0  | 
 0  | 
 if ($format eq 'latex')  | 
 
| 
136
 | 
 0  | 
 0  | 
 if ($$alSet{'format'} ne 'GIZA' and not $$FH{'source'} && $$FH{'target'})  | 
 
| 
144
 | 
 0  | 
 0  | 
 if ($representation eq 'matrix') { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($representation eq 'enumlinks') { }  | 
 
| 
153
 | 
 0  | 
 0  | 
 if ($format eq 'latex')  | 
 
| 
162
 | 
 0  | 
 0  | 
 if ($$alSet{'format'} eq 'GIZA') { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($$alSet{'format'} eq 'NAACL' or $$alSet{'format'} eq 'BLINKER' or $$alSet{'format'} eq 'TALP') { }  | 
 
| 
166
 | 
 0  | 
 0  | 
 unless ($$alSet{'location'}{'source'})  | 
 
| 
216
 | 
 1  | 
 0  | 
 unless (defined $weighted)  | 
 
| 
230
 | 
 0  | 
 1  | 
 if ($$answerAlSet{'format'} eq 'NAACL' and $alignMode eq 'as-is' and $$answerAlSet{'firstSentPair'} == 1) { }  | 
 
| 
231
 | 
 0  | 
 0  | 
 unless my $answerFH = 'IO::File'->new('<' . $$answerAlSet{'location'}{'sourceToTarget'})  | 
 
| 
237
 | 
 0  | 
 0  | 
 if ($answerFH->eof)  | 
 
| 
243
 | 
 0  | 
 0  | 
 if ($$answerAlSet{'lastSentPair'} eq 'eof') { }  | 
 
| 
278
 | 
 0  | 
 1  | 
 if ($$submissionAlSet{'format'} eq 'NAACL' and $alignMode eq 'as-is' and $$submissionAlSet{'firstSentPair'} == 1) { }  | 
 
| 
279
 | 
 0  | 
 0  | 
 unless my $submissionFH = 'IO::File'->new('<' . $$submissionAlSet{'location'}{'sourceToTarget'})  | 
 
| 
286
 | 
 0  | 
 0  | 
 if ($submissionFH->eof)  | 
 
| 
292
 | 
 0  | 
 0  | 
 if ($$submissionAlSet{'lastSentPair'} eq 'eof') { }  | 
 
| 
337
 | 
 0  | 
 1  | 
 if ($weighted)  | 
 
| 
379
 | 
 0  | 
 1  | 
 if ($weighted) { }  | 
 
| 
413
 | 
 54  | 
 5  | 
 if (defined $sureAnswer{$alignment})  | 
 
| 
414
 | 
 54  | 
 0  | 
 if (not $weighted) { }  | 
 
| 
422
 | 
 54  | 
 5  | 
 if (defined $sureAnswer{$alignment} or defined $possibleAnswer{$alignment})  | 
 
| 
423
 | 
 54  | 
 0  | 
 if (not $weighted) { }  | 
 
| 
431
 | 
 54  | 
 5  | 
 if (defined $sureAnswer{$alignment})  | 
 
| 
432
 | 
 54  | 
 0  | 
 if (not $weighted) { }  | 
 
| 
440
 | 
 1  | 
 0  | 
 if (scalar keys %sureSubmission != 0) { }  | 
 
| 
445
 | 
 1  | 
 0  | 
 if (scalar keys %sureAnswer != 0) { }  | 
 
| 
450
 | 
 1  | 
 0  | 
 if ($sureRecall != 0 and $surePrecision != 0) { }  | 
 
| 
458
 | 
 1  | 
 0  | 
 if (scalar(keys %sureSubmission) + scalar(keys %possibleSubmission) != 0) { }  | 
 
| 
463
 | 
 1  | 
 0  | 
 if (scalar(keys %sureAnswer) + scalar(keys %possibleAnswer) != 0) { }  | 
 
| 
468
 | 
 1  | 
 0  | 
 if ($possibleRecall != 0 and $possiblePrecision != 0) { }  | 
 
| 
475
 | 
 1  | 
 0  | 
 if (scalar(keys %sureSubmission) + scalar(keys %possibleSubmission) != 0) { }  | 
 
| 
489
 | 
 0  | 
 0  | 
 if (ref $AlignmentSub eq 'ARRAY')  | 
 
| 
490
 | 
 0  | 
 0  | 
 if ($$AlignmentSub[0] eq 'Lingua::Alignment::eliminateWord')  | 
 
| 
491
 | 
 0  | 
 0  | 
 if (@$AlignmentSub < 3) { }  | 
 
| 
494
 | 
 0  | 
 0  | 
 unless ($$alSet{'location'}{$side} and $$newLocation{$side})  | 
 
| 
505
 | 
 0  | 
 0  | 
 unless (defined $selectSubgroups)  | 
 
| 
506
 | 
 0  | 
 0  | 
 unless (defined $alignMode)  | 
 
| 
507
 | 
 0  | 
 0  | 
 unless (defined $$globals{'minPhraseFrequency'})  | 
 
| 
508
 | 
 0  | 
 0  | 
 unless (defined $$globals{'extendGroups'})  | 
 
| 
509
 | 
 0  | 
 0  | 
 unless (defined $$globals{'onlyGroups'})  | 
 
| 
510
 | 
 0  | 
 0  | 
 unless (defined $$globals{'defaultActionGrouping'})  | 
 
| 
511
 | 
 0  | 
 0  | 
 unless (defined $$globals{'defaultActionGeneral'})  | 
 
| 
512
 | 
 0  | 
 0  | 
 unless (defined $$globals{'verbose'})  | 
 
| 
521
 | 
 0  | 
 0  | 
 if ($selectSubgroups == 0)  | 
 
| 
539
 | 
 0  | 
 0  | 
 unless ($selectSubgroups)  | 
 
| 
546
 | 
 0  | 
 0  | 
 if ($$globals{'onlyGroups'} == 0)  | 
 
| 
568
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
583
 | 
 0  | 
 0  | 
 if ($j <= @{$$al{'sourceAl'};})  | 
 
| 
584
 | 
 0  | 
 0  | 
 if ($j == @{$$al{'sourceAl'};}) { }  | 
 
| 
590
 | 
 0  | 
 0  | 
 if ($newAnchorSource - $lastAnchorSource != 1 and not $sourcePerturbed{$lastAnchorSource + 1}) { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($newAnchorTarget - $lastAnchorTarget != 1 and not $targetPerturbed{$lastAnchorTarget + 1}) { }  | 
 
| 
595
 | 
 0  | 
 0  | 
 unless ($al->isAnchor($i, 'target'))  | 
 
| 
597
 | 
 0  | 
 0  | 
 unless ($anchorsInTarget)  | 
 
| 
599
 | 
 0  | 
 0  | 
 if ($newPerturbationDetected)  | 
 
| 
621
 | 
 0  | 
 0  | 
 if ($selectSubgroups) { }  | 
 
| 
624
 | 
 0  | 
 0  | 
 if (do {
	($ruleApplied = $perturbation->applyGrouping($groupKeys, $subGroupKeys, $globals)) > 0
}) { }  | 
 
| 
632
 | 
 0  | 
 0  | 
 if ($ruleApplied == -1) { }  | 
 
| 
644
 | 
 0  | 
 0  | 
 if ($ind > 0)  | 
 
| 
649
 | 
 0  | 
 0  | 
 if ($ind > 0)  | 
 
| 
662
 | 
 0  | 
 0  | 
 if ($newFormat eq 'NAACL' and not $selectSubgroups)  | 
 
| 
663
 | 
 0  | 
 0  | 
 if (exists $$newFH{'source'})  | 
 
| 
666
 | 
 0  | 
 0  | 
 if (exists $$newFH{'target'})  | 
 
| 
675
 | 
 0  | 
 0  | 
 if ($internalSentPairNum % 1000 == 0) { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($internalSentPairNum % 100 == 0) { }  | 
 
| 
679
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
680
 | 
 0  | 
 0  | 
 if ($selectSubgroups)  | 
 
| 
682
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
686
 | 
 0  | 
 0  | 
 if ($$globals{'onlyGroups'} == 0)  | 
 
| 
696
 | 
 0  | 
 0  | 
 if ($selectSubgroups == 0)  | 
 
| 
700
 | 
 0  | 
 0  | 
 if ($selectSubgroups) { }  | 
 
| 
701
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
702
 | 
 0  | 
 0  | 
 unless open GROUPS, ">$ENV/groups"  | 
 
| 
705
 | 
 0  | 
 0  | 
 if ($count >= $$globals{'minPhraseFrequency'})  | 
 
| 
709
 | 
 0  | 
 0  | 
 if ($$globals{'onlyGroups'} == 0)  | 
 
| 
710
 | 
 0  | 
 0  | 
 unless open SUBGROUPS, ">$ENV/subGroups"  | 
 
| 
713
 | 
 0  | 
 0  | 
 if ($count >= $$globals{'minPhraseFrequency'})  | 
 
| 
729
 | 
 0  | 
 0  | 
 if (not defined $newFormat) { }  | 
 
| 
736
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
739
 | 
 0  | 
 0  | 
 unless open CS, "<$corpSrc"  | 
 
| 
740
 | 
 0  | 
 0  | 
 unless open CT, "<$corpTrg"  | 
 
| 
752
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
763
 | 
 0  | 
 0  | 
 if ($newcorp{$pair})  | 
 
| 
768
 | 
 0  | 
 0  | 
 if ($cntToFind == 0)  | 
 
| 
769
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
773
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
774
 | 
 0  | 
 0  | 
 if ($inputSentPairNum % 100000 == 0)  | 
 
| 
775
 | 
 0  | 
 0  | 
 if ($inputSentPairNum % 10000 == 0)  | 
 
| 
778
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
787
 | 
 0  | 
 0  | 
 if (exists $found{"$s ||| $t"}) { }  | 
 
| 
808
 | 
 0  | 
 0  | 
 if (not defined $newFormat) { }  | 
 
| 
816
 | 
 0  | 
 0  | 
 unless open CS, "<$corpSrc"  | 
 
| 
817
 | 
 0  | 
 0  | 
 unless open CT, "<$corpTrg"  | 
 
| 
827
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
840
 | 
 0  | 
 0  | 
 if (not $newcorp{"$s ||| $t"}) { }  | 
 
| 
849
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
865
 | 
 0  | 
 0  | 
 if ($verbose > 2)  | 
 
| 
866
 | 
 0  | 
 0  | 
 if ($verbose > 2)  | 
 
| 
868
 | 
 0  | 
 0  | 
 if ($numcs < $sMin or $numcs > $sMax or $numct < $tMin or $numct > $tMax) { }  | 
 
| 
886
 | 
 0  | 
 0  | 
 if ($sLcs == 0 or $tLcs == 0) { }  | 
 
| 
892
 | 
 0  | 
 0  | 
 if ($verbose > 1)  | 
 
| 
898
 | 
 0  | 
 0  | 
 if ($lcs > $bestLcs) { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($lcs == $bestLcs) { }  | 
 
| 
908
 | 
 0  | 
 0  | 
 if ($verbose > 1)  | 
 
| 
909
 | 
 0  | 
 0  | 
 if ($cnt2 > 0 and $cnt2 % 100000 == 0) { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($cnt2 > 0 and $cnt2 % 1000 == 0) { }  | 
 
| 
917
 | 
 0  | 
 0  | 
 if ($cntCharLevel > 1) { }  | 
 
| 
931
 | 
 0  | 
 0  | 
 if ($lcs > $bestLcs)  | 
 
| 
941
 | 
 0  | 
 0  | 
 if ($cntGoodLength == 0) { }  | 
 
| 
944
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
948
 | 
 0  | 
 0  | 
 if ($cntCharLevel == 1) { }  | 
 
| 
954
 | 
 0  | 
 0  | 
 if ($verbose > 2)  | 
 
| 
970
 | 
 0  | 
 0  | 
 if ($$change[0] eq '-') { }  | 
 
| 
982
 | 
 0  | 
 0  | 
 if ($numDel == 0) { }  | 
 
| 
1003
 | 
 0  | 
 0  | 
 if ($verbose > 2)  | 
 
| 
1017
 | 
 0  | 
 0  | 
 if ($$change[0] eq '-') { }  | 
 
| 
1028
 | 
 0  | 
 0  | 
 if ($numDel == 0) { }  | 
 
| 
1046
 | 
 0  | 
 0  | 
 if ($verbose > 0)  | 
 
| 
1070
 | 
 1  | 
 1  | 
 unless (ref $location)  | 
 
| 
1081
 | 
 0  | 
 2  | 
 if ($numLimits == 0 or $numLimits > 2) { }  | 
 
| 
 | 
 1  | 
 1  | 
 elsif ($numLimits == 1) { }  | 
 
| 
1088
 | 
 0  | 
 2  | 
 if (not $limits[0] =~ /\d+/ or $limits[0] == 0) { }  | 
 
| 
1093
 | 
 1  | 
 1  | 
 if (not $limits[1] =~ /\d+/ or $limits[1] == 0) { }  | 
 
| 
1107
 | 
 0  | 
 1  | 
 if ($$refToLocation{'source'})  | 
 
| 
1109
 | 
 0  | 
 0  | 
 if ($sourceFileName =~ /^(EN|FR)\.sample.\d+$/)  | 
 
| 
1115
 | 
 1  | 
 0  | 
 if (not $$refToLocation{'sampleNum'})  | 
 
| 
1127
 | 
 0  | 
 2  | 
 if ($openMode eq '>')  | 
 
| 
1128
 | 
 0  | 
 0  | 
 if ($format eq 'BLINKER')  | 
 
| 
1135
 | 
 0  | 
 0  | 
 if ($oldFiles{$newFile} and $key ne 'sampleNum')  | 
 
| 
1143
 | 
 0  | 
 0  | 
 if ($format eq 'BLINKER') { }  | 
 
| 
1146
 | 
 0  | 
 0  | 
 if ($$location{'targetToSource'})  | 
 
| 
1149
 | 
 0  | 
 0  | 
 if ($$location{'source'})  | 
 
| 
1152
 | 
 0  | 
 0  | 
 if ($$location{'target'})  | 
 
| 
1158
 | 
 0  | 
 2  | 
 if ($format eq 'GIZA') { }  | 
 
| 
 | 
 1  | 
 1  | 
 elsif ($format eq 'NAACL' or $format eq 'TALP') { }  | 
 
| 
 | 
 1  | 
 0  | 
 elsif ($format eq 'BLINKER') { }  | 
 
| 
1159
 | 
 0  | 
 0  | 
 unless $FH{'sourceToTarget'} = 'IO::File'->new($openMode . $$location{'sourceToTarget'})  | 
 
| 
1160
 | 
 0  | 
 0  | 
 if ($$location{'targetToSource'})  | 
 
| 
1161
 | 
 0  | 
 0  | 
 unless $FH{'targetToSource'} = 'IO::File'->new($openMode . $$location{'targetToSource'})  | 
 
| 
1164
 | 
 1  | 
 0  | 
 if ($$location{'source'})  | 
 
| 
1165
 | 
 0  | 
 1  | 
 unless $FH{'source'} = 'IO::File'->new($openMode . $$location{'source'})  | 
 
| 
1167
 | 
 1  | 
 0  | 
 if ($$location{'target'})  | 
 
| 
1168
 | 
 0  | 
 1  | 
 unless $FH{'target'} = 'IO::File'->new($openMode . $$location{'target'})  | 
 
| 
1170
 | 
 0  | 
 1  | 
 unless $FH{'sourceToTarget'} = 'IO::File'->new($openMode . $$location{'sourceToTarget'})  | 
 
| 
1171
 | 
 0  | 
 1  | 
 if ($$location{'targetToSource'})  | 
 
| 
1172
 | 
 0  | 
 0  | 
 unless $FH{'targetToSource'} = 'IO::File'->new($openMode . $$location{'targetToSource'})  | 
 
| 
1175
 | 
 0  | 
 1  | 
 if ($$location{'source'})  | 
 
| 
1176
 | 
 0  | 
 0  | 
 unless $FH{'source'} = 'IO::File'->new($openMode . $$location{'source'})  | 
 
| 
1178
 | 
 0  | 
 1  | 
 if ($$location{'target'})  | 
 
| 
1179
 | 
 0  | 
 0  | 
 unless $FH{'target'} = 'IO::File'->new($openMode . $$location{'target'})  | 
 
| 
1192
 | 
 0  | 
 0  | 
 if ($type eq 'dir') { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif ($type eq 'file') { }  | 
 
| 
1193
 | 
 0  | 
 0  | 
 unless (-e $path and -d _)  | 
 
| 
1198
 | 
 0  | 
 0  | 
 if ($path =~ m[/])  | 
 
| 
1200
 | 
 0  | 
 0  | 
 unless (-e $dir)  | 
 
| 
1215
 | 
 0  | 
 2  | 
 if ($$alSet{'format'} eq 'TALP') { }  | 
 
| 
 | 
 0  | 
 2  | 
 elsif ($$alSet{'format'} eq 'GIZA') { }  | 
 
| 
 | 
 1  | 
 1  | 
 elsif ($$alSet{'format'} eq 'NAACL') { }  | 
 
| 
 | 
 1  | 
 0  | 
 elsif ($$alSet{'format'} eq 'BLINKER') { }  | 
 
| 
1217
 | 
 0  | 
 0  | 
 if ($FH{'source'})  | 
 
| 
1220
 | 
 0  | 
 0  | 
 if ($FH{'target'})  | 
 
| 
1223
 | 
 0  | 
 0  | 
 if ($FH{'sourceToTarget'})  | 
 
| 
1226
 | 
 0  | 
 0  | 
 if ($FH{'targetToSource'})  | 
 
| 
1235
 | 
 0  | 
 0  | 
 if ($FH{'targetToSource'})  | 
 
| 
1243
 | 
 0  | 
 0  | 
 if ($FH{'source'})  | 
 
| 
1246
 | 
 0  | 
 0  | 
 if ($FH{'target'})  | 
 
| 
1253
 | 
 0  | 
 0  | 
 if ($FH{'sourceToTarget'}->eof)  | 
 
| 
1257
 | 
 0  | 
 0  | 
 if ($FH{'targetToSource'})  | 
 
| 
1262
 | 
 0  | 
 0  | 
 if ($FH{'targetToSource'}->eof)  | 
 
| 
1269
 | 
 0  | 
 1  | 
 if ($FH{'source'})  | 
 
| 
1274
 | 
 0  | 
 1  | 
 if ($FH{'target'})  | 
 
| 
1287
 | 
 0  | 
 2  | 
 if ($format eq 'GIZA') { }  | 
 
| 
 | 
 1  | 
 1  | 
 elsif ($format eq 'NAACL' or $format eq 'TALP') { }  | 
 
| 
 | 
 1  | 
 0  | 
 elsif ($format eq 'BLINKER') { }  | 
 
| 
1289
 | 
 0  | 
 0  | 
 if ($$FH{'targetToSource'})  | 
 
| 
1293
 | 
 1  | 
 0  | 
 if ($$FH{'source'})  | 
 
| 
1296
 | 
 1  | 
 0  | 
 if ($$FH{'target'})  | 
 
| 
1299
 | 
 1  | 
 0  | 
 if ($$FH{'sourceToTarget'})  | 
 
| 
1302
 | 
 0  | 
 1  | 
 if ($$FH{'targetToSource'})  | 
 
| 
1306
 | 
 0  | 
 1  | 
 if ($$FH{'source'})  | 
 
| 
1309
 | 
 0  | 
 1  | 
 if ($$FH{'target'})  | 
 
| 
1325
 | 
 0  | 
 22  | 
 if (not defined $alignMode or $alignMode =~ /^as.?is$/i) { }  | 
 
| 
 | 
 0  | 
 22  | 
 elsif ($alignMode =~ /^null.?align$/i) { }  | 
 
| 
 | 
 22  | 
 0  | 
 elsif ($alignMode =~ /^no.?null.?align$/i) { }  | 
 
| 
1334
 | 
 0  | 
 22  | 
 if ($$alSet{'format'} eq 'TALP') { }  | 
 
| 
 | 
 0  | 
 22  | 
 elsif ($$alSet{'format'} eq 'GIZA') { }  | 
 
| 
 | 
 11  | 
 11  | 
 elsif ($$alSet{'format'} eq 'NAACL') { }  | 
 
| 
 | 
 11  | 
 0  | 
 elsif ($$alSet{'format'} eq 'BLINKER') { }  | 
 
| 
1335
 | 
 0  | 
 0  | 
 if ($$alSet{'lastSentPair'} eq 'eof') { }  | 
 
| 
1340
 | 
 0  | 
 0  | 
 if ($theEnd) { }  | 
 
| 
1343
 | 
 0  | 
 0  | 
 if ($$alFH{'source'})  | 
 
| 
1346
 | 
 0  | 
 0  | 
 if ($$alFH{'target'})  | 
 
| 
1349
 | 
 0  | 
 0  | 
 if ($$alFH{'sourceToTarget'})  | 
 
| 
1352
 | 
 0  | 
 0  | 
 if ($$alFH{'targetToSource'})  | 
 
| 
1359
 | 
 0  | 
 0  | 
 if ($$alSet{'lastSentPair'} eq 'eof') { }  | 
 
| 
1364
 | 
 0  | 
 0  | 
 if ($theEnd) { }  | 
 
| 
1370
 | 
 0  | 
 0  | 
 if ($$alFH{'targetToSource'})  | 
 
| 
1380
 | 
 0  | 
 11  | 
 if ($$alSet{'lastSentPair'} eq 'eof') { }  | 
 
| 
1385
 | 
 1  | 
 10  | 
 if ($theEnd) { }  | 
 
| 
1388
 | 
 10  | 
 0  | 
 if ($$alFH{'source'})  | 
 
| 
1393
 | 
 10  | 
 0  | 
 if ($$alFH{'target'})  | 
 
| 
1401
 | 
 10  | 
 0  | 
 if ($num == $sentPairNum)  | 
 
| 
1410
 | 
 0  | 
 10  | 
 if ($$alFH{'targetToSource'})  | 
 
| 
1414
 | 
 0  | 
 0  | 
 if ($num == $sentPairNum)  | 
 
| 
1428
 | 
 11  | 
 0  | 
 if ($$alSet{'lastSentPair'} eq 'eof') { }  | 
 
| 
1433
 | 
 1  | 
 10  | 
 if ($theEnd) { }  | 
 
| 
1436
 | 
 0  | 
 10  | 
 if ($$alFH{'source'})  | 
 
| 
1439
 | 
 0  | 
 10  | 
 if ($$alFH{'target'})  | 
 
| 
1445
 | 
 0  | 
 10  | 
 if ($$alSet{'location'}{'targetToSource'})  | 
 
| 
1454
 | 
 0  | 
 20  | 
 if ($alignMode eq 'null-align') { }  | 
 
| 
 | 
 20  | 
 0  | 
 elsif ($alignMode eq 'no-null-align') { }  | 
 
| 
1467
 | 
 0  | 
 0  | 
 if ($$newLocation{'source'}) { }  | 
 
| 
1470
 | 
 0  | 
 0  | 
 if ($$alSet{'firstSentPair'} != 1 or $$alSet{'format'} ne $newFormat)  | 
 
| 
1477
 | 
 0  | 
 0  | 
 if ($$newLocation{'target'}) { }  | 
 
| 
1480
 | 
 0  | 
 0  | 
 if ($$alSet{'firstSentPair'} != 1 or $$alSet{'format'} ne $newFormat)  | 
 
| 
1488
 | 
 0  | 
 0  | 
 if ($newFormat eq 'BLINKER') { }  | 
 
| 
 | 
 0  | 
 0  | 
 elsif (exists $$alSet{'location'}{'sampleNum'}) { }  | 
 
| 
1501
 | 
 0  | 
 0  | 
 if (not defined $newFormat) { }  | 
 
| 
1513
 | 
 0  | 
 0  | 
 if (defined $AlignmentSub)  | 
 
| 
1515
 | 
 0  | 
 0  | 
 if (ref $AlignmentSub eq 'ARRAY') { }  | 
 
| 
1537
 | 
 0  | 
 0  | 
 if (not defined $newFormat) { }  | 
 
| 
1556
 | 
 0  | 
 0  | 
 if (@{$$clusters[$c]{'source'};} > 1 or @{$$clusters[$c]{'target'};} > 1)  | 
 
| 
1560
 | 
 0  | 
 0  | 
 if ($clone->isIn('sourceAl', $j, $k))  | 
 
| 
1593
 | 
 0  | 
 149  | 
 if (scalar @components < 3)  | 
 
| 
1601
 | 
 0  | 
 0  | 
 if (scalar @components == 3 or scalar @components == 4 and $components[3] =~ /^[\d\.]+$/ || $components[3] eq 'S' or scalar @components == 5 and $components[3] eq 'S' || $components[4] eq 'S')  | 
 
| 
1607
 | 
 0  | 
 0  | 
 if (scalar @components == 4 and $components[3] eq 'P' or scalar @components == 5 and $components[3] eq 'P' || $components[4] eq 'P')  |