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1 | 1 | package org.biojava.nbio.core.sequence.io.embl; |
2 | 2 |
|
3 | 3 | /** |
4 | | - * This class should parse the data of embl file identification |
| 4 | + * |
| 5 | + * This class contains the processed data of embl file |
| 6 | + * Primary accession number |
| 7 | + * Sequence version number |
| 8 | + * Topology: 'circular' or 'linear' |
| 9 | + * Molecule type |
| 10 | + * Data class |
| 11 | + * Taxonomic division |
| 12 | + * Sequence length |
| 13 | + * @since 5.0.0 |
5 | 14 | * @author Noor Aldeen Al Mbaidin |
6 | 15 | */ |
7 | 16 | public class EmblId { |
8 | 17 |
|
9 | 18 |
|
10 | | - private String PrimaryAccession; |
11 | | - private String SequenceVersion; |
12 | | - private String Topology; |
13 | | - private String MoleculeType; |
14 | | - private String DataClass; |
15 | | - private String TaxonomicDivision; |
16 | | - private String SequenceLength; |
| 19 | + private String primaryAccession; |
| 20 | + private String sequenceVersion; |
| 21 | + private String topology; |
| 22 | + private String moleculeType; |
| 23 | + private String dataClass; |
| 24 | + private String taxonomicDivision; |
| 25 | + private String sequenceLength; |
17 | 26 |
|
18 | 27 | public EmblId() { |
19 | 28 | } |
20 | 29 |
|
| 30 | + /** |
| 31 | + * |
| 32 | + * @return String |
| 33 | + */ |
21 | 34 | public String getPrimaryAccession() { |
22 | | - return PrimaryAccession; |
| 35 | + return primaryAccession; |
23 | 36 | } |
24 | 37 |
|
25 | 38 | public void setPrimaryAccession(String primaryAccession) { |
26 | | - PrimaryAccession = primaryAccession; |
| 39 | + this.primaryAccession = primaryAccession; |
27 | 40 | } |
28 | 41 |
|
| 42 | + /** |
| 43 | + * return the sequence version |
| 44 | + * @return String |
| 45 | + */ |
29 | 46 | public String getSequenceVersion() { |
30 | | - return SequenceVersion; |
| 47 | + return sequenceVersion; |
31 | 48 | } |
32 | 49 |
|
33 | 50 | public void setSequenceVersion(String sequenceVersion) { |
34 | | - SequenceVersion = sequenceVersion; |
| 51 | + this.sequenceVersion = sequenceVersion; |
35 | 52 | } |
36 | 53 |
|
37 | 54 | public String getTopology() { |
38 | | - return Topology; |
| 55 | + return topology; |
39 | 56 | } |
40 | 57 |
|
41 | 58 | public void setTopology(String topology) { |
42 | | - Topology = topology; |
| 59 | + this.topology = topology; |
43 | 60 | } |
44 | 61 |
|
| 62 | + /** |
| 63 | + * Molecule type this represents the type of molecule as stored |
| 64 | + * @return String |
| 65 | + */ |
45 | 66 | public String getMoleculeType() { |
46 | | - return MoleculeType; |
| 67 | + return moleculeType; |
47 | 68 | } |
48 | 69 |
|
49 | 70 | public void setMoleculeType(String moleculeType) { |
50 | | - MoleculeType = moleculeType; |
| 71 | + this.moleculeType = moleculeType; |
51 | 72 | } |
52 | 73 |
|
53 | 74 | public String getDataClass() { |
54 | | - return DataClass; |
| 75 | + return dataClass; |
55 | 76 | } |
56 | 77 |
|
57 | 78 | public void setDataClass(String dataClass) { |
58 | | - DataClass = dataClass; |
| 79 | + this.dataClass = dataClass; |
59 | 80 | } |
60 | 81 |
|
| 82 | + /** |
| 83 | + * |
| 84 | + * @return String |
| 85 | + */ |
61 | 86 | public String getTaxonomicDivision() { |
62 | | - return TaxonomicDivision; |
| 87 | + return taxonomicDivision; |
63 | 88 | } |
64 | 89 |
|
65 | 90 | public void setTaxonomicDivision(String taxonomicDivision) { |
66 | | - TaxonomicDivision = taxonomicDivision; |
| 91 | + this.taxonomicDivision = taxonomicDivision; |
67 | 92 | } |
68 | 93 |
|
| 94 | + /** |
| 95 | + * Sequence length The last item on the ID line is the length of the |
| 96 | + * sequence (the total number of bases in the sequence). This number includes |
| 97 | + * base positions reported as present but undetermined (coded as "N"). |
| 98 | + * @return String |
| 99 | + */ |
69 | 100 | public String getSequenceLength() { |
70 | | - return SequenceLength; |
| 101 | + return sequenceLength; |
71 | 102 | } |
72 | 103 |
|
73 | 104 | public void setSequenceLength(String sequenceLength) { |
74 | | - SequenceLength = sequenceLength; |
| 105 | + this.sequenceLength = sequenceLength; |
75 | 106 | } |
76 | 107 |
|
77 | 108 | } |
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