1
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5
6 package uk.ac.ebi.intenz.tools.sib.translator;
7
8 import uk.ac.ebi.xchars.domain.EncodingType;
9 import org.apache.log4j.Logger;
10 import java.util.Iterator;
11
12 import uk.ac.ebi.intenz.tools.sib.translator.helper.DataHolder;
13
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15
16
17
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20
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23
24
25 public class CALineTest extends BaseLineTest {
26
27 Logger LOGGER = Logger.getLogger(CALineTest.class);
28
29
30 public void populateTests(){
31 dataHolders.add(new DataHolder("1.1.1.3", "<stereo>L</stereo>-homoserine + NAD(P)<smallsup>+</smallsup> = <stereo>L</stereo>-aspartate 4-semialdehyde + NAD(P)H + H<smallsup>+</smallsup>",
32 "L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H") );
33 dataHolders.add(new DataHolder("1.1.1.21",
34 "alditol + NAD(P)<smallsup>+</smallsup> = aldose + NAD(P)H + H<smallsup>+</smallsup>",
35 "Alditol + NAD(P)(+) = aldose + NAD(P)H"));
36 dataHolders.add(new DataHolder("1.1.1.22", "UDP-glucose + <b>2</b> NAD<smallsup>+</smallsup> + H<smallsub>2</smallsub>O = UDP-glucuronate + <b>2</b> NADH + <b>2</b> H<smallsup>+</smallsup>",
37 "UDP-glucose + 2 NAD(+) + H(2)O = UDP-glucuronate + 2 NADH"));
38 dataHolders.add(new DataHolder("1.1.1.34", "(<stereo>R</stereo>)-mevalonate + CoA + <b>2</b> NADP<smallsup>+</smallsup> = (<stereo>S</stereo>)-3-hydroxy-3-methylglutaryl-CoA + <b>2</b> NADPH + <b>2</b> H<smallsup>+</smallsup>",
39 "(R)-mevalonate + CoA + 2 NADP(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH"));
40 dataHolders.add(new DataHolder("1.1.1.62", "estradiol-17<greek>beta</greek> + NAD(P)<smallsup>+</smallsup> = estrone + NAD(P)H + H<smallsup>+</smallsup>",
41 "Estradiol-17-beta + NAD(P)(+) = estrone + NAD(P)H"));
42 dataHolders.add(new DataHolder("1.1.1.62","estradiol-17<greek>beta</greek> + NAD(P)<smallsup>+</smallsup> = estrone + NAD(P)H + H<smallsup>+</smallsup>",
43 "Estradiol-17-beta + NAD(P)(+) = estrone + NAD(P)H"));
44 dataHolders.add(new DataHolder("1.1.1.92", "<stereo>D</stereo>-glycerate + NAD(P)<smallsup>+</smallsup> + CO<smallsub>2</smallsub> = 2-hydroxy-3-oxosuccinate + NAD(P)H + <b>2</b> H<smallsup>+</smallsup>",
45 "D-glycerate + NAD(P)(+) + CO(2) = 2-hydroxy-3-oxosuccinate + NAD(P)H"));
46 dataHolders.add(new DataHolder("1.1.1.100",
47 "(3<stereo>R</stereo>)-3-hydroxyacyl-<protein>acyl-carrier-protein</protein> + NADP<smallsup>+</smallsup> = 3-oxoacyl-<protein>acyl-carrier-protein</protein> + NADPH + H<smallsup>+</smallsup>",
48 "(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH"));
49 dataHolders.add(new DataHolder("1.1.1.145",
50 "a 3<greek>beta</greek>-hydroxy-<greek>Delta</greek><smallsup>5</smallsup>-steroid + NAD<smallsup>+</smallsup> = a 3-oxo-<greek>Delta</greek><smallsup>5</smallsup>-steroid + NADH + H<smallsup>+</smallsup>",
51 "A 3-beta-hydroxy-Delta(5)-steroid + NAD(+) = a 3-oxo-Delta(5)-steroid + NADH"));
52 dataHolders.add(new DataHolder("1.1.1.160","(<plusmn/>)-5-[(<ital>tert</ital>-butylamino)-2'-hydroxypropoxy]-1,2,3,4-tetrahydro-1-naphthol + NADP<smallsup>+</smallsup> = (<plusmn/>)-5-[(<ital>tert</ital>-butylamino)-2'-hydroxypropoxy]-3,4-dihydro-1(2<element>H</element>)-naphthalenone + NADPH + H<smallsup>+</smallsup>",
53 "(+-)-5-((tert-butylamino)-2'-hydroxypropoxy)-1,2,3,4-tetrahydro-1-naphthol + NADP(+) = (+-)-5-((tert-butylamino)-2'-hydroxypropoxy)-3,4-dihydro-1(2H)-naphthalenone + NADPH"));
54 dataHolders.add(new DataHolder("1.1.1.177",
55 "<ital>sn</ital>-glycerol 3-phosphate + NADP<smallsup>+</smallsup> = <stereo>D</stereo>-glyceraldehyde 3-phosphate + NADPH + H<smallsup>+</smallsup>",
56 "sn-glycerol 3-phosphate + NADP(+) = D-glyceraldehyde 3-phosphate + NADPH"));
57 dataHolders.add(new DataHolder("1.1.1.261",
58 "<ital>sn</ital>-glycerol-1-phosphate + NAD(P)<smallsup>+</smallsup> = glycerone phosphate + NAD(P)H + H<smallsup>+</smallsup>",
59 "sn-glycerol-1-phosphate + NAD(P)(+) = glycerone phosphate + NAD(P)H"));
60 dataHolders.add(new DataHolder("1.2.2.2", "pyruvate + ferricytochrome <ital>b</ital><smallsub>1</smallsub> + H<smallsub>2</smallsub>O = acetate + CO<smallsub>2</smallsub> + ferrocytochrome <ital>b</ital><smallsub>1</smallsub>",
61 "Pyruvate + ferricytochrome b1 + H(2)O = acetate + CO(2) + ferrocytochrome b1"));
62 dataHolders.add(new DataHolder("1.3.1.42", "8-[(1<stereo>R</stereo>,2<stereo>R</stereo>)-3-oxo-2-{(<stereo>Z</stereo>)-pent-2-enyl}cyclopentyl]octanoate + NADP<smallsup>+</smallsup> = (15<stereo>Z</stereo>)-12-oxophyto-10,15-dienoate + NADPH + H<smallsup>+</smallsup>",
63 "8-((1R,2R)-3-oxo-2-((Z)-pent-2-enyl)cyclopentyl)octanoate + NADP(+) = (15Z)-12-oxophyto-10,15-dienoate + NADPH"));
64 dataHolders.add(new DataHolder("1.6.2.5", "NADPH + H<smallsup>+</smallsup> + <b>2</b> ferricytochrome <ital>c</ital><smallsub>2</smallsub> = NADP<smallsup>+</smallsup> + <b>2</b> ferrocytochrome <ital>c</ital><smallsub>2</smallsub>",
65 "NADPH + 2 ferricytochrome c2 = NADP(+) + 2 ferrocytochrome c2"));
66 dataHolders.add(new DataHolder("1.7.1.4", "ammonium hydroxide + <b>3</b> NAD(P)<smallsup>+</smallsup> + H<smallsub>2</smallsub>O = nitrite + <b>3</b> NAD(P)H + <b>3</b> H<smallsup>+</smallsup>",
67 "Ammonium hydroxide + 3 NAD(P)(+) + H(2)O = nitrite + 3 NAD(P)H"));
68 dataHolders.add( new DataHolder("1.13.12.5","<ital>Renilla</ital> luciferin + O<smallsub>2</smallsub> = oxidized <ital>Renilla</ital> luciferin + CO<smallsub>2</smallsub> + h<greek>nu</greek>",
69 "Renilla luciferin + O(2) = oxidized Renilla luciferin + CO(2) + light"));
70 dataHolders.add(new DataHolder("1.14.13.39", "<stereo>L</stereo>-arginine + <b>n</b> NADPH + <b>n</b> H<smallsup>+</smallsup> + <b>m</b> O<smallsub>2</smallsub> = citrulline + nitric oxide + <b>n</b> NADP<smallsup>+</smallsup>",
71 "L-arginine + n NADPH + m O(2) = citrulline + nitric oxide + n NADP(+)"));
72 dataHolders.add(new DataHolder("1.14.13.70", "obtusifoliol + <b>3</b> O<smallsub>2</smallsub> + <b>3</b> NADPH + <b>3</b> H<smallsup>+</smallsup> = 4<greek>alpha</greek>-methyl-5<greek>alpha</greek>-ergosta-8,14,24(28)-trien-3<greek>beta</greek>-ol + formate + <b>3</b> NADP<smallsup>+</smallsup> + <b>3</b> H<smallsub>2</smallsub>O",
73 "Obtusifoliol + 3 O(2) + 3 NADPH = 4-alpha-methyl-5-alpha-ergosta-8,14,24(28)-trien-3-beta-ol + formate + 3 NADP(+) + 3 H(2)O"));
74 dataHolders.add(new DataHolder("1.14.13.78", "<ital>ent</ital>-kaur-16-en-19-al + NADPH + O<smallsub>2</smallsub> = <ital>ent</ital>-kaur-16-en-19-oate + NADP<smallsup>+</smallsup> + H<smallsub>2</smallsub>O",
75 "Ent-kaur-16-en-19-al + NADPH + O(2) = ent-kaur-16-en-19-oate + NADP(+) + H(2)O"));
76 dataHolders.add(new DataHolder("1.17.4.3", "(<stereo>E</stereo>)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H<smallsub>2</smallsub>O + protein-disulfide = 2-<element>C</element>-methyl-<stereo>D</stereo>-erythritol 2,4-cyclodiphosphate + protein-dithiol",
77 "(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H(2)O + protein-disulfide = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-dithiol"));
78 dataHolders.add(new DataHolder("2.1.1.44", "<element>S</element>-adenosyl-<stereo>L</stereo>-methionine + <element>N</element><smallsup><greek>alpha</greek></smallsup>,<element>N</element><smallsup><greek>alpha</greek></smallsup>-dimethyl-<stereo>L</stereo>-histidine = <element>S</element>-adenosyl-<stereo>L</stereo>-homocysteine + <element>N</element><smallsup><greek>alpha</greek></smallsup>,<element>N</element><smallsup><greek>alpha</greek></smallsup>,<element>N</element><smallsup><greek>alpha</greek></smallsup>-trimethyl-<stereo>L</stereo>-histidine",
79 "S-adenosyl-L-methionine + N(alpha),N(alpha)-dimethyl-L-histidine = S-adenosyl-L-homocysteine + N(alpha),N(alpha),N(alpha)-trimethyl-L-histidine"));
80 dataHolders.add(new DataHolder("2.1.1.56","<element>S</element>-adenosyl-<stereo>L</stereo>-methionine + G(5')pppR-RNA = <element>S</element>-adenosyl-<stereo>L</stereo>-homocysteine + m<smallsup>7</smallsup>G(5')pppR-RNA",
81 "S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(7)G(5')pppR-RNA"));
82 dataHolders.add(new DataHolder("2.1.1.57", "<element>S</element>-adenosyl-<stereo>L</stereo>-methionine + m<smallsup>7</smallsup>G(5')pppR-RNA = <element>S</element>-adenosyl-<stereo>L</stereo>-homocysteine + m<smallsup>7</smallsup>G(5')pppRm-RNA",
83 "S-adenosyl-L-methionine + m(7)G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(7)G(5')pppRm-RNA"));
84 dataHolders.add(new DataHolder("2.1.1.62","<element>S</element>-adenosyl-<stereo>L</stereo>-methionine + m<smallsup>7</smallsup>G(5')pppAm = <element>S</element>-adenosyl-<stereo>L</stereo>-homocysteine + m<smallsup>7</smallsup>G(5')pppm<smallsup>6</smallsup>Am",
85 "S-adenosyl-L-methionine + m(7)G(5')pppAm = S-adenosyl-L-homocysteine + m(7)G(5')pppm(6)Am"));
86
87
88 dataHolders.add(new DataHolder("2.3.1.85",
89 "acetyl-CoA + <b><ital>n</ital></b> malonyl-CoA + <b>2<ital>n</ital></b> NADPH + <b>2<ital>n</ital></b> H<smallsup>+</smallsup> = a long-chain fatty acid + <b>(<ital>n</ital>+1)</b> CoA + <b><ital>n</ital></b> CO<smallsub>2</smallsub> + <b>2<ital>n</ital></b> NADP<smallsup>+</smallsup>",
90 "Acetyl-CoA + n malonyl-CoA + 2n NADPH = a long-chain fatty acid + (n+1) CoA + n CO(2) + 2n NADP(+)"));
91 dataHolders.add(new DataHolder("2.3.1.59", "acetyl-CoA + gentamicin C<smallsub>1a</smallsub> = CoA + <element>N</element><smallsup>2'</smallsup>-acetylgentamicin C<smallsub>1a</smallsub>",
92 "Acetyl-CoA + gentamicin C(1a) = CoA + N(2')-acetylgentamicin C(1a)"));
93 dataHolders.add( new DataHolder("2.3.2.12","peptidyl-tRNA<smallsub>1</smallsub> + aminoacyl-tRNA<smallsub>2</smallsub> = tRNA<smallsub>1</smallsub> + peptidyl(aminoacyl-tRNA<smallsub>2</smallsub>)",
94 "Peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidyl(aminoacyl-tRNA(2))"));
95 dataHolders.add(new DataHolder("2.4.1.92",
96 "1-<element>O</element>-[<element>O</element>-2-(acetylamino)-2-deoxy-<stereo>beta</stereo>-<stereo>D</stereo>-galactopyranosyl-(1<arrow>right</arrow>4)-<element>O</element>-[<element>N</element>-acetyl-<stereo>alpha</stereo>-neuraminosyl-(2<arrow>right</arrow>3)]-<element>O</element>-<stereo>beta</stereo>-<stereo>D</stereo>-galactopyranosyl-(1<arrow>right</arrow>4)-<stereo>beta</stereo>-<stereo>D</stereo>-glucopyranosyl]-ceramide",
97 "1-O-(O-2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl-(1->4)-O-(N-acetyl-alpha-neuraminosyl-(2->3))-O-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl)-ceramide"));
98
99
100
101
102 dataHolders.add( new DataHolder("2.4.1.155",
103 "UDP-<element>N</element>-acetyl-<stereo>D</stereo>-glucosamine + 6-(2-[<element>N</element>-acetyl-<greek>beta</greek>-<stereo>D</stereo>-glucosaminyl]-<greek>alpha</greek>-<stereo>D</stereo>-mannosyl)-<greek>beta</greek>-<stereo>D</stereo>-mannosyl-R = UDP + 6-(2,6-bis[<element>N</element>-acetyl-<greek>beta</greek>-<stereo>D</stereo>-glucosaminyl]-<greek>alpha</greek>-<stereo>D</stereo>-mannosyl)-<greek>beta</greek>-<stereo>D</stereo>-mannosyl-R",
104 "UDP-N-acetyl-D-glucosamine + 6-(2-(N-acetyl-beta-D-glucosaminyl)-alpha-D-mannosyl)-beta-D-mannosyl-R = UDP + 6-(2,6-bis(N-acetyl-beta-D-glucosaminyl)-alpha-D-mannosyl)-beta-D-mannosyl-R"));
105 dataHolders.add(new DataHolder("2.4.1.212","<b><ital>n</ital></b> UDP-<element>N</element>-acetyl-<stereo>D</stereo>-glucosamine + <b><ital>n</ital></b> UDP-<stereo>D</stereo>-glucuronate = [<greek>beta</greek>-<element>N</element>-acetyl-<stereo>D</stereo>-glucosaminyl(1<arrow>right</arrow>4)<greek>beta</greek>-<stereo>D</stereo>-glucuronosyl(1<arrow>right</arrow>3)]<smallsub><b><ital>n</ital></b></smallsub> + <b>2<ital>n</ital></b> UDP",
106 "n UDP-N-acetyl-D-glucosamine + n UDP-D-glucuronate = (beta-N-acetyl-D-glucosaminyl(1->4)-beta-D-glucuronosyl(1->3))(n) + 2n UDP"));
107 dataHolders.add(new DataHolder("2.4.2.30",
108 "NAD<smallsup>+</smallsup> + (ADP-<stereo>D</stereo>-ribosyl)<smallsub><ital>n</ital></smallsub>-acceptor = nicotinamide + (ADP-<stereo>D</stereo>-ribosyl)<smallsub><ital>n</ital>+1</smallsub>-acceptor + H<smallsup>+</smallsup>",
109 "NAD(+) + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor"));
110 dataHolders.add( new DataHolder("2.4.99.7",
111 "CMP-<element>N</element>-acetylneuraminate + <element>N</element>-acetyl-<greek>alpha</greek>-neuraminyl-(2<arrow>right</arrow>3)-<greek>beta</greek>-<stereo>D</stereo>-galactosyl-(1<arrow>right</arrow>3)-<element>N</element>-acetyl-<stereo>D</stereo>-galactosaminyl-R = CMP + <element>N</element>-acetyl-<greek>alpha</greek>-neuraminyl-(2<arrow>right</arrow>3)-<greek>beta</greek>-<stereo>D</stereo>-galactosyl-(1<arrow>right</arrow>3)-[<element>N</element>-acetyl-<greek>alpha</greek>-neuraminyl-(2<arrow>right</arrow>6)]-<element>N</element>-acetyl-<stereo>D</stereo>-galactosaminyl-R",
112 "CMP-N-acetylneuraminate + N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->3)-N-acetyl-D-galactosaminyl-R = CMP + N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->3)-(N-acetyl-alpha-neuraminyl-(2->6))-N-acetyl-D-galactosaminyl-R"));
113 dataHolders.add(new DataHolder("2.5.1.61", "<b>4</b> porphobilinogen + H<smallsub>2</smallsub>O = hydroxymethylbilane + <b>4</b> NH<smallsub>3</smallsub>",
114 "4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3)"));
115
116 dataHolders.add(new DataHolder("2.7.7.50",
117 "GTP + (5')ppPur-mRNA = diphosphate + G(5')pppPur-mRNA",
118 "GTP + (5')ppPur-mRNA = diphosphate + G(5')pppPur-mRNA"));
119
120 dataHolders.add(new DataHolder("2.7.8.7",
121 "CoA-[4'-phosphopantetheine] + apo-<protein>acyl-carrier-protein</protein> = adenosine 3',5'-bisphosphate + holo-<protein>acyl-carrier-protein</protein>",
122 "CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]"));
123
124
125 dataHolders.add(new DataHolder("3.1.3.56","<stereo>D</stereo>-<ital>myo</ital>-inositol 1,4,5-trisphosphate + H<smallsub>2</smallsub>O = <ital>myo</ital>-inositol 1,4-bisphosphate + phosphate",
126 "D-myo-inositol 1,4,5-trisphosphate + H(2)O = myo-inositol 1,4-bisphosphate + phosphate"));
127 dataHolders.add(new DataHolder("3.2.1.120",
128 "Hydrolysis of 1,4-<greek>beta</greek>-<stereo>D</stereo>-glucosidic links in oligoxyloglucans so as to remove successive isoprimeverose (i.e. <greek>alpha</greek>-xylo-1,6-<greek>beta</greek>-<stereo>D</stereo>-glucosyl-) residues from the non-reducing chain ends",
129 "Hydrolysis of 1,4-beta-D-glucosidic links in oligoxyloglucans so as to remove successive isoprimeverose (i.e. alpha-xylo-1,6-beta-D-glucosyl-) residues from the non-reducing chain ends"));
130 dataHolders.add( new DataHolder("3.4.21.42",
131 "Cleavage of Arg<scissile/>Ala bond in complement component C4 to form C4a and C4b, and Lys(or Arg)<scissile/>Lys bond in complement component C2 to form C2a and C2b: the <quotes/>classical<quotes/> pathway C3 convertase",
132 "Cleavage of Arg-|-Ala bond in complement component C4 to form C4a and C4b, and Lys(or Arg)-|-Lys bond in complement component C2 to form C2a and C2b: the 'classical' pathway C3 convertase"));
133 dataHolders.add( new DataHolder("3.4.23.18","Generally favours hydrophobic residues in P1 and P1', but also accepts Lys in P1, which leads to activation of trypsinogen",
134 "Generally favors hydrophobic residues in P1 and P1', but also accepts Lys in P1, which leads to activation of trypsinogen"));
135
136 dataHolders.add( new DataHolder("3.4.24.52",
137 "Cleavage of only two bonds: 10-His<scissile/>Leu-11 and 14-Ala<scissile/>Leu-15, in the insulin B chain.",
138 "Cleavage of only two bonds: 10-His-|-Leu-11 and 14-Ala-|-Leu-15, in the insulin B chain."));
139 dataHolders.add(new DataHolder("3.5.4.30", "dCTP + <b>2</b> H<smallsub>2</smallsub>O = dUMP + diphosphate + NH<smallsub>3</smallsub>",
140 "dCTP + 2 H(2)O = dUMP + diphosphate + NH(3)"));
141 dataHolders.add( new DataHolder("3.6.3.8",
142 "ATP + H<smallsub>2</smallsub>O + Ca<smallsup>2+</smallsup><smallsub><stereo>cis</stereo></smallsub> = ADP + phosphate + Ca<smallsup>2+</smallsup><smallsub><stereo>trans</stereo></smallsub>",
143 "ATP + H(2)O + Ca(2+)(Cis) = ADP + phosphate + Ca(2+)(Trans)"));
144 dataHolders.add(new DataHolder("4.1.1.2",
145 "oxalate + H<smallsup>+</smallsup> = formate + CO<smallsub>2</smallsub>",
146 "Oxalate = formate + CO(2)"));
147 dataHolders.add(new DataHolder("4.1.1.4",
148 "acetoacetate + H<smallsup>+</smallsup> = acetone + CO<smallsub>2</smallsub>",
149 "Acetoacetate = acetone + CO(2)"));
150
151
152
153
154
155 dataHolders.add(new DataHolder("4.1.1.83",
156 "(4-hydroxyphenyl)acetate + H<smallsup>+</smallsup> = 4-methylphenol + CO<smallsub>2</smallsub>",
157 "(4-hydroxyphenyl)acetate = 4-methylphenol + CO(2)"));
158 dataHolders.add(new DataHolder("4.1.1.85",
159 "3-dehydro-<stereo>L</stereo>-gulonate 6-phosphate + H<smallsup>+</smallsup> = <stereo>L</stereo>-xylulose 5-phosphate + CO<smallsub>2</smallsub>",
160 "3-dehydro-L-gulonate 6-phosphate = L-xylulose 5-phosphate + CO(2)"));
161 dataHolders.add(new DataHolder("4.2.1.106",
162 "7<stereo>alpha</stereo>,12<stereo>alpha</stereo>-dihydroxy-3-oxochol-4-enoate = 12<stereo>alpha</stereo>-hydroxy-3-oxochola-4,6-dienoate + H<smallsub>2</smallsub>O",
163 "7-alpha,12-alpha-dihydroxy-3-oxochol-4-enoate = 12-alpha-hydroxy-3-oxochola-4,6-dienoate + H(2)O"));
164 dataHolders.add(new DataHolder("6.2.1.23",
165 "ATP + an <greek>alpha</greek><greek>omega</greek>-dicarboxylic acid = AMP + diphosphate + an <locant>omega</locant>-carboxyacyl-CoA",
166 "ATP + an alpha-omega-dicarboxylic acid = AMP + diphosphate + an omega-carboxyacyl-CoA"));
167
168 dataHolders.add(new DataHolder("unknown",
169 "[tRNA]-guanine + queuine = [tRNA]-queuine + guanine",
170 "[tRNA]-guanine + queuine = [tRNA]-queuine + guanine"));
171 dataHolders.add(new DataHolder("3.6.1.66",
172 "dITP + H<smallsub>2</smallsub>O = dIMP + diphosphate",
173 "dITP + H(2)O = dIMP + diphosphate"));
174 }
175
176 public CALineTest(String name) {
177 super(name);
178 }
179
180 public void setUp() throws Exception {
181 super.setUp();
182 }
183
184 public void tearDown() throws Exception {
185 super.tearDown();
186 }
187
188
189
190
191 public void testData(){
192 Iterator iter = dataHolders.iterator();
193 while ( iter.hasNext() ) {
194 DataHolder reactionData = (DataHolder) iter.next();
195 String translated = translator.toASCII(reactionData.getIntenzData(), true, false);
196 String translatedString = sc.xml2Display( translated, EncodingType.SWISSPROT_CODE);
197 if( !translatedString.equals(reactionData.getEnzymeData()) ){
198 LOGGER.error("ASSERT FALSE - EC "+reactionData.getEC()+" ORIGINAL IntEnz XML \n"+reactionData.getIntenzData()+"\n"+translatedString+" SHOULD BE \n"+reactionData.getEnzymeData());
199 assertFalse(true);
200 }
201 }
202 }
203 }