← Back to branch summary

~ubuntu-branches/debian/jessie/ugene/jessie

« back to all changes in this revision

Viewing changes to src/plugins_3rdparty/uhmmer/src/u_search/HMMSearchTask.h

  • Committer: Package Import Robot
  • Author(s): Steffen Moeller
  • Date: 2011-11-02 13:29:07 UTC
  • mfrom: (1.2.1) (3.1.11 natty)
  • Revision ID: package-import@ubuntu.com-20111102132907-o34gwnt0uj5g6hen
Tags: 1.9.8+repack-1
* First release to Debian
  - added README.Debian
  - increased policy version to 3.9.2
  - added URLs for version control system
* Added debug package.

Show diffs side-by-side

added added

removed removed

Lines of Context:
src/plugins_3rdparty/uhmmer/src/u_search/HMMSearchTask.h
1
 
/*****************************************************************
2
 
* Unipro UGENE - Integrated Bioinformatics Suite
3
 
* Copyright (C) 2008 Unipro, Russia (http://ugene.unipro.ru)
4
 
* All Rights Reserved
5
 
* 
6
 
*     This source code is distributed under the terms of the
7
 
*     GNU General Public License. See the files COPYING and LICENSE
8
 
*     for details.
9
 
*****************************************************************/
10
 
 
11
 
#ifndef _GB2_HMMSEARCH_TASK_H_
12
 
#define _GB2_HMMSEARCH_TASK_H_
13
 
 
14
 
#include "uhmmsearch.h"
15
 
 
16
 
#include <core_api/LRegion.h>
17
 
#include <core_api/Task.h>
18
 
#include <datatype/DNASequence.h>
19
 
#include <datatype/AnnotationData.h>
20
 
#include <util_tasks/SequenceWalkerTask.h>
21
 
 
22
 
struct plan7_s;
23
 
 
24
 
namespace GB2 {
25
 
 
26
 
class DNATranslation;
27
 
 
28
 
class HMMSearchTaskResult {
29
 
public:
30
 
    HMMSearchTaskResult() : evalue(0), score(0), onCompl(false), onAmino(false){} 
31
 
    float   evalue;
32
 
    float   score;
33
 
    bool    onCompl;
34
 
    bool    onAmino;
35
 
    LRegion r;
36
 
 
37
 
};
38
 
 
39
 
class HMMSearchTaskCachedResult : public HMMSearchTaskResult {
40
 
public:
41
 
        HMMSearchTaskCachedResult() {}
42
 
    LRegion globalReg;
43
 
 
44
 
};
45
 
 
46
 
class HMMSearchTask: public Task, SequenceWalkerCallback {
47
 
    Q_OBJECT
48
 
public:
49
 
    HMMSearchTask(plan7_s* hmm, const DNASequence& seq, const UHMMSearchSettings& s);
50
 
 
51
 
    virtual void prepare();
52
 
    
53
 
    const QList<HMMSearchTaskResult>& getResults() const {return results;}
54
 
 
55
 
    virtual void onRegion(SequenceWalkerSubtask* t, TaskStateInfo& stateInfo);
56
 
 
57
 
        Task::ReportResult report();
58
 
 
59
 
    QList<SharedAnnotationData> getResultsAsAnnotations(const QString& name) const;
60
 
 
61
 
private:
62
 
    bool checkAlphabets(int hmmAl, DNAAlphabet* seqAl, DNATranslation*& complTrans, DNATranslation*& aminoTrans);
63
 
private:
64
 
    plan7_s*                    hmm;
65
 
    DNASequence                 seq;
66
 
    UHMMSearchSettings          settings;
67
 
    DNATranslation*             complTrans;
68
 
    DNATranslation*             aminoTrans;
69
 
    QList<HMMSearchTaskResult>  results;
70
 
        QList<HMMSearchTaskResult>  resultsCompl;
71
 
        QList<HMMSearchTaskCachedResult>  cacheDirect;
72
 
        QList<HMMSearchTaskCachedResult>  cacheCompl;
73
 
};
74
 
 
75
 
 
76
 
 
77
 
}//namespace
78
 
#endif