/dports/benchmarks/inferno/inferno-0.10.9/tests/ |
H A D | diff-folded.rs | 14 infile1: &str, in test_diff_folded() 35 differential::from_files(options, infile1, infile2, &mut result)?; in test_diff_folded() 84 fn test_diff_folded_logs<F>(infile1: &str, infile2: &str, asserter: F) in test_diff_folded_logs() 92 infile1: &str, in test_diff_folded_logs_with_options() 100 let r1 = BufReader::new(File::open(infile1).unwrap()); in test_diff_folded_logs_with_options() 109 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_default() localVariable 118 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_normalize() localVariable 131 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_strip_hex() localVariable 144 let infile1 = "./tests/data/diff-folded/before_fractionals.txt"; in diff_folded_fractional_samples() localVariable 195 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_cli() localVariable [all …]
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/src/unit_test/ |
H A D | stat_utils.cpp | 48 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local 69 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local 74 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST() 90 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local 95 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST() 111 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local 115 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST() 133 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local 137 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST() 155 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local [all …]
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Alignment/ |
H A D | Exonerate.pm | 226 my ($self,$infile1) = @_; 227 $self->{'input'} = $infile1 if(defined $infile1); 273 my ($fh,$infile1); 276 ($fh, $infile1) = $self->io->tempfile(); 277 my $temp = Bio::SeqIO->new( -file => ">$infile1", 284 push @infilearr, $infile1; 288 ($fh, $infile1) = $self->io->tempfile(); 289 my $temp = Bio::SeqIO->new( -file => ">$infile1", 294 $infile1 = $query; 296 return $infile1;
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H A D | Sim4.pm | 249 my ($temp,$infile1, $infile2, $est_first,$seq); 253 ($est_first,$infile1,$infile2)= $self->_setinput($self->cdna_seq,$self->genomic_seq); 254 …if (!($infile1 && $infile2)) {$self->throw("Bad input data (sequences need an id ) or less than 2 … 260 my @exon_sets = $self->_run($est_first,$infile1,$infile2,$param_string); 280 my ($self,$estfirst,$infile1,$infile2,$param_string) = @_; 290 my $commandstring = $self->executable." $infile1 $infile2 $param_string > $outfile";
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H A D | Lagan.pm | 197 my ($infile1, $infile2) = $self->_setinput($executable, $input1, $input2); 200 $infile1, 322 my ($fh, $infile1, $infile2, $temp1, $temp2, $seq1, $seq2); 333 ($fh, $infile1) = $self->io->tempfile(); 342 push @infilearr, $infile1; 344 $infile1 = \@infilearr; 349 ($fh, $infile1) = $self->io->tempfile(); 390 return ($infile1, $infile2);
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H A D | Blat.pm | 527 my ($self,$infile1) = @_; 528 if (defined $infile1) { 529 $self->{'input'} = $infile1; 546 my ($self,$infile1) = @_; 547 $self->{'db'} = $infile1 if(defined $infile1);
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/dports/math/plplot-ada/plplot-5.15.0/scripts/ |
H A D | compare.c | 53 FILE *infile1, *infile2; in main() local 65 infile1 = fopen( argv[1], "r" ); in main() 66 if ( infile1 == NULL ) { in main() 80 fseek( infile1, 0L, SEEK_END ); in main() 82 size1 = ftell( infile1 ); in main() 92 fseek( infile1, SKIPHEADER, SEEK_END ); in main() 98 fread( contents1, sizeof(char), (size_t)(size1-SKIPHEADER), infile1 ); in main()
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/dports/math/plplot/plplot-5.15.0/scripts/ |
H A D | compare.c | 53 FILE *infile1, *infile2; in main() local 65 infile1 = fopen( argv[1], "r" ); in main() 66 if ( infile1 == NULL ) { in main() 80 fseek( infile1, 0L, SEEK_END ); in main() 82 size1 = ftell( infile1 ); in main() 92 fseek( infile1, SKIPHEADER, SEEK_END ); in main() 98 fread( contents1, sizeof(char), (size_t)(size1-SKIPHEADER), infile1 ); in main()
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/dports/math/gap/gap-4.11.0/pkg/digraphs-1.1.1/extern/edge-addition-planarity-suite-Version_3.0.0.5/c/ |
H A D | planarityUtils.c | 132 FILE *infile1 = NULL, *infile2 = NULL; in TextFilesEqual() local 135 infile1 = fopen(file1Name, "r"); in TextFilesEqual() 138 if (infile1 == NULL || infile2 == NULL) in TextFilesEqual() 145 while ((c1 = fgetc(infile1)) != EOF) in TextFilesEqual() 184 if (infile1 != NULL) fclose(infile1); in TextFilesEqual() 194 FILE *infile1 = NULL, *infile2 = NULL; in BinaryFilesEqual() local 197 infile1 = fopen(file1Name, "r"); in BinaryFilesEqual() 200 if (infile1 == NULL || infile2 == NULL) in BinaryFilesEqual() 207 while ((c1 = fgetc(infile1)) != EOF) in BinaryFilesEqual() 235 if (infile1 != NULL) fclose(infile1); in BinaryFilesEqual()
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/dports/math/planarity/edge-addition-planarity-suite-Version_3.0.1.1/c/ |
H A D | planarityUtils.c | 143 FILE *infile1 = NULL, *infile2 = NULL; in TextFilesEqual() local 146 infile1 = fopen(file1Name, "r"); in TextFilesEqual() 149 if (infile1 == NULL || infile2 == NULL) in TextFilesEqual() 156 while ((c1 = fgetc(infile1)) != EOF) in TextFilesEqual() 195 if (infile1 != NULL) fclose(infile1); in TextFilesEqual() 205 FILE *infile1 = NULL, *infile2 = NULL; in BinaryFilesEqual() local 208 infile1 = fopen(file1Name, "r"); in BinaryFilesEqual() 211 if (infile1 == NULL || infile2 == NULL) in BinaryFilesEqual() 218 while ((c1 = fgetc(infile1)) != EOF) in BinaryFilesEqual() 246 if (infile1 != NULL) fclose(infile1); in BinaryFilesEqual()
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/dports/graphics/mapserver/mapserver-7.6.4/mapscript/perl/examples/ |
H A D | distanceToShape.pl | 18 my ($infile1, $infile1_shpid, $infile2, $infile2_shpid, $distance); 20 GetOptions("infile1=s", \$infile1, "infile1_shpid=s", \$infile1_shpid, "infile2=s", \$infile2, "inf… 22 if(!$infile1 or !$infile1_shpid or !$infile2 or !$infile2_shpid) { 28 my $inshpf1 = new mapscript::shapefileObj($infile1, -1) or die "Unable to open shapefile $infile1."; 39 print "Distance between shape $infile1/$infile1_shpid and shape $infile2/$infile2_shpid is $distanc…
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H A D | shp_in_shp.pl | 16 my ($infile1, $infile1_shpid, $infile2, $infile2_shpid, $within); 18 GetOptions("infile1=s", \$infile1, "infile1_shpid=s", \$infile1_shpid, "infile2=s", \$infile2, "inf… 21 if(!$infile1 or !defined($infile1_shpid) or !$infile2 or !defined($infile2_shpid)) { 27 my $inshpf1 = new mapscript::shapefileObj($infile1, -1) or die "Unable to open shapefile $infile1."; 45 print "Shape $infile1/$infile1_shpid is $within shape $infile2/$infile2_shpid\n";
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/ |
H A D | Signalp.pm | 196 my $infile1 = $self->_writeSeqFile($seq); 198 $self->_input($infile1); 201 unlink $infile1; 206 my $infile1; 209 $infile1 = $self->_writeSeqFile($tmpseq); 212 $self->_input($infile1); 231 my ($self,$infile1) = @_; 232 $self->{'input'} = $infile1 if(defined $infile1);
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H A D | Coil.pm | 211 my $infile1 = $self->_writeSeqFile($seq); 213 $self->_input($infile1); 216 unlink $infile1; 244 my ($self,$infile1) = @_; 245 if(defined $infile1){ 247 $self->{'input'}=$infile1;
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H A D | Seg.pm | 182 my $infile1 = $self->_writeSeqFile($seq); 184 $self->_input($infile1); 187 unlink $infile1; 214 my ($self,$infile1) = @_; 215 if(defined $infile1){ 217 $self->{'input'}=$infile1;
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H A D | Prints.pm | 190 my $infile1 = $self->_writeSeqFile($seq); 192 $self->_input($infile1); 195 unlink $infile1; 222 my ($self,$infile1) = @_; 224 if(defined $infile1){ 226 $self->{'input'}=$infile1;
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H A D | Profile.pm | 189 my $infile1 = $self->_writeSeqFile($seq); 191 $self->_input($infile1); 194 unlink $infile1; 223 my ($self,$infile1) = @_; 224 if(defined $infile1){ 225 $self->{'input'}=$infile1;
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H A D | Tmhmm.pm | 233 my $infile1 = $self->_writeSeqFile($seq); 235 $self->_input($infile1); 238 unlink $infile1; 266 my ($self,$infile1) = @_; 267 if (defined $infile1){ 269 $self->{'input'}=$infile1;
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H A D | Infernal.pm | 514 my $infile1 = $self->_writeSeqFile(@seq); 515 return $self->_run($infile1); 517 my $infile1 = $self->_writeAlignFile(@seq); 518 return $self->_run($infile1); 540 my $infile1 = $self->_writeSeqFile(@seq); 541 return $self->_run(-seq_files => [$infile1]); 562 my $infile1 = $self->_writeSeqFile(@seq); 563 return $self->_run(-seq_files => [$infile1]); 568 my $infile1 = $self->_writeAlignFile($seq[0]); 612 my $infile1 = $self->_writeAlignFile(@seq); [all …]
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H A D | Genscan.pm | 175 my $infile1 = $self->_writeSeqFile($seq); 176 $self->_set_input($infile1); 230 my ($self,$infile1) = @_; 231 $self->{'input'}=$infile1;
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/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_TCoffee_tool.py | 35 self.infile1 = "Fasta/fa01" 58 cmdline = TCoffeeCommandline(t_coffee_exe, infile=self.infile1) 63 records = list(SeqIO.parse(self.infile1, "fasta")) 74 cmdline.infile = self.infile1 86 records = list(SeqIO.parse(self.infile1, "fasta")) 97 cmdline.infile = self.infile1 112 records = list(SeqIO.parse(self.infile1, "fasta")) 124 infile=self.infile1, 138 records = list(SeqIO.parse(self.infile1, "fasta")) 151 infile=self.infile1, [all …]
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H A D | test_Mafft_tool.py | 76 self.infile1 = "Fasta/f002" 85 cmdline = MafftCommandline(mafft_exe, input=self.infile1) 101 cmdline.set_parameter("input", self.infile1) 113 cmdline.input = self.infile1 126 cmdline = MafftCommandline(mafft_exe, input=self.infile1, phylipout=True) 143 mafft_exe, input=self.infile1, phylipout=True, namelength=50 160 cmdline.set_parameter("input", self.infile1)
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H A D | test_Dialign_tool.py | 49 self.infile1 = "Fasta/f002" 64 cmdline = DialignCommandline(dialign_exe, input=self.infile1) 74 cmdline.set_parameter("input", self.infile1) 87 cmdline.input = self.infile1 99 cmdline.set_parameter("input", self.infile1)
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H A D | test_BWA_tool.py | 77 self.infile1 = "BWA/HNSCC1_1_truncated.fastq" 150 self.do_aln(self.infile1, self.saifile1) 153 cmdline.set_parameter("read_file", self.infile1) 170 self.do_aln(self.infile1, self.saifile1) 177 cmdline.set_parameter("read_file1", self.infile1) 195 cmdline.set_parameter("read_file1", self.infile1)
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/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/SuperReadsR/src/ |
H A D | rename_filter_fastq.cc | 67 std::ifstream infile1(path1); in main() local 68 if(!infile1.good()) in main() 87 while(infile1.good()) { in main() 88 const char* res = parse_write(infile1, out, read_number++); in main() 91 …valid fastq format (" << res << ") in file '" << path1 << "' around position " << infile1.tellg()); in main()
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