Last change
on this file was
5800,
checked in by westram, 16 years ago
|
- translate_gene_sequence() defaults to EMBL
1 (if no codon specified) and to codon_start 0
- added fixEmptyQualifiers():
- searches for empty data and replaces it by '<empty>' (currently only done for qualifier 'replace')
- called before writing features to
- silently skip empty lines before or after sections
|
File size:
1.5 KB
|
Line | |
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1 | // ================================================================ // |
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2 | // // |
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3 | // File : Feature.h // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in November 2006 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // ================================================================ // |
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11 | #ifndef FEATURE_H |
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12 | #define FEATURE_H |
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13 | |
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14 | #ifndef TYPES_H |
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15 | #include "types.h" |
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16 | #endif |
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17 | #ifndef LOCATION_H |
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18 | #include "Location.h" |
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19 | #endif |
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20 | |
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21 | class Feature { |
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22 | string type; |
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23 | LocationPtr location; |
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24 | stringMap qualifiers; // qualifiers with content (content of multiple identical qualifiers gets merged) |
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25 | |
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26 | public: |
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27 | Feature(const string& Type, const string& locationString); |
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28 | |
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29 | void addQualifiedEntry(const string& qualifier, const string& value); |
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30 | |
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31 | string createGeneName() const; // creates a (non-unique) default name for gene |
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32 | |
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33 | const string& getType() const { return type; } |
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34 | const Location& getLocation() const { return *location; } |
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35 | const stringMap& getQualifiers() const { return qualifiers; } |
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36 | |
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37 | void expectLocationInSequence(long seqLength) const; |
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38 | |
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39 | void fixEmptyQualifiers(); |
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40 | }; |
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41 | |
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42 | |
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43 | #else |
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44 | #error Feature.h included twice |
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45 | #endif // FEATURE_H |
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46 | |
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