xtandemparamwidget.cpp 5.31 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148

/*******************************************************************************
 * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
 *
 * This file is part of XTPcpp.
 *
 *     XTPcpp is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     XTPcpp is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
 *implementation
 ******************************************************************************/

#include "xtandemparamwidget.h"

#include "../../project_view/projectwindow.h"
#include "ui_xtandem_view_widget.h"
#include <QDebug>
#include <files/tandemparametersfile.h>


XtandemParamWidget::XtandemParamWidget(QWidget *parent)
  : QWidget(parent), ui(new Ui::XtandemParamWidget)
{
  qDebug() << "begin";
  ui->setupUi(this);

  qDebug() << "end";
}

XtandemParamWidget::~XtandemParamWidget()
{
  qDebug() << "XtandemParamWidget::~XtandemParamWidget";
  delete ui;
  qDebug() << "end";
}

void
XtandemParamWidget::setAutomaticXTandemParameters(QString params_file)
{
  qDebug() << "begin ";
  // TandemParametersFile param_file(params_file);
  TandemParametersFile param_file("/home/trenne/test_tandem.xml");
  TandemParameters xtandem_parameters = param_file.getTandemParameters();

  setSpectrumParameters(xtandem_parameters);
  setProteinParameters(xtandem_parameters);
  setResidueParameters(xtandem_parameters);
  setScoringParameters(xtandem_parameters);
  setRefineParameters(xtandem_parameters);
  setOutputParameters(xtandem_parameters);

  qDebug() << "end ";
}

void
XtandemParamWidget::setSpectrumParameters(TandemParameters xtandem_parameters)
{
}

void
XtandemParamWidget::setProteinParameters(TandemParameters xtandem_parameters)
{
}

void
XtandemParamWidget::setResidueParameters(TandemParameters xtandem_parameters)
{
  ui->fixedModificationsLineEdit->setText(
    xtandem_parameters.getValue("residue, modification mass"));
  ui->fixedModifications1LineEdit->setText(
    xtandem_parameters.getValue("residue, modification mass 1"));
  ui->fixedModifications2LineEdit->setText(
    xtandem_parameters.getValue("residue, modification mass 2"));

  ui->potentialModificationsLineEdit->setText(
    xtandem_parameters.getValue("residue, potential modification mass"));
  ui->potentialModificationsMotifLineEdit->setText(
    xtandem_parameters.getValue("residue, potential modification motif"));
}

void
XtandemParamWidget::setScoringParameters(TandemParameters xtandem_parameters)
{
}

void
XtandemParamWidget::setRefineParameters(TandemParameters xtandem_parameters)
{
  ui->useOfTheRefinementModuleLineEdit->setText(
    xtandem_parameters.getValue("refine"));
  ui->maximumEValueToAcceptPeptideLineEdit->setText(
    xtandem_parameters.getValue("refine, maximum valid expectation value"));

  ui->peptideNTerPotentialModificationsLineEdit->setText(
    xtandem_parameters.getValue("refine, potential N-terminus modifications"));
  ui->peptideCTerPotentialModificationsLineEdit->setText(
    xtandem_parameters.getValue("refine, potential C-terminus modifications"));

  ui->alterFixedModificationsLineEdit->setText(
    xtandem_parameters.getValue("refine, modification mass"));
  ui->alterFixedModifications1LineEdit->setText(
    xtandem_parameters.getValue("refine, modification mass 1"));
  ui->alterFixedModifications2LineEdit->setText(
    xtandem_parameters.getValue("refine, modification mass 2"));

  ui->alterFixedModificationsLineEdit->setText(
    xtandem_parameters.getValue("refine, potential modification mass"));
  ui->alterFixedModifications1LineEdit->setText(
    xtandem_parameters.getValue("refine, potential modification mass 1"));
  ui->alterFixedModifications2LineEdit->setText(
    xtandem_parameters.getValue("refine, potential modification mass 2"));

  ui->potentialModificationsMotifLineEdit_2->setText(
    xtandem_parameters.getValue("refine, potential modification motif"));
  ui->potentialModificationsMotif1LineEdit->setText(
    xtandem_parameters.getValue("refine, potential modification motif 1"));
  ui->potentialModificationsMotif2LineEdit->setText(
    xtandem_parameters.getValue("refine, potential modification motif 2"));

  ui->usePotentialModificationsInRefinementModuleLineEdit->setText(
    xtandem_parameters.getValue(
      "refine, use potential modifications for full refinement"));
  ui->useSemiEnzymaticCleavageRulesLineEdit_2->setText(
    xtandem_parameters.getValue("refine, cleavage semi"));
  ui->cleavageAtEachResiduesLineEdit->setText(
    xtandem_parameters.getValue("refine, unanticipated cleavage"));
  ui->spectrumIntensityModelSynthesisLineEdit->setText(
    xtandem_parameters.getValue("refine, spectrum synthesis"));
  ui->pointMutationsLineEdit->setText(
    xtandem_parameters.getValue("refine, point mutations"));
}

void
XtandemParamWidget::setOutputParameters(TandemParameters xtandem_parameters)
{
}