From e786ed45c8664a8abd05e1aacd3e0cd5666e5544 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 14 Oct 2017 19:04:28 +0200
Subject: [PATCH] WIP: refinement module
---
src/core/tandem_run/tandemparameters.cpp | 6 +-
.../edit_tandem_preset_dialog.ui | 506 ++++++++++++++++--
.../edittandempresetdialog.cpp | 72 ++-
3 files changed, 521 insertions(+), 63 deletions(-)
diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index aa73215be..3a3cc9ebe 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -95,13 +95,13 @@ void TandemParameters::setParamLabelValue(const QString & label, const QString &
throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be Daltons or ppm (not %2)").arg(label).arg(value));
}
}
- if ((label == "spectrum, parent monoisotopic mass isotope error") || (label == "spectrum, use neutral loss window") || (label == "spectrum, use contrast angle") || (label == "protein, cleavage semi") || (label == "protein, quick acetyl") || (label == "protein, quick pyrolidone") || (label == "protein, stP bias") || (label == "scoring, cyclic permutation") || (label == "scoring, include reverse") || (label == "scoring, y ions") || (label == "scoring, b ions") || (label == "scoring, c ions") || (label == "scoring, z ions") || (label == "scoring, a ions") || (label == "scoring, x ions") || (label == "refine")) {
+ if ((label == "spectrum, parent monoisotopic mass isotope error") || (label == "spectrum, use neutral loss window") || (label == "spectrum, use contrast angle") || (label == "protein, cleavage semi") || (label == "protein, quick acetyl") || (label == "protein, quick pyrolidone") || (label == "protein, stP bias") || (label == "scoring, cyclic permutation") || (label == "scoring, include reverse") || (label == "scoring, y ions") || (label == "scoring, b ions") || (label == "scoring, c ions") || (label == "scoring, z ions") || (label == "scoring, a ions") || (label == "scoring, x ions") || (label == "refine") || (label == "refine, use potential modifications for full refinement") || (label == "refine, cleavage semi") ) {
if ((value != "yes") && (value != "no")) {
throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be yes or no (not %2)").arg(label).arg(value));
}
}
-
-
+
+
if ((label == "spectrum, parent monoisotopic mass error minus") || (label == "spectrum, parent monoisotopic mass error plus")|| (label == "spectrum, dynamic range") || (label == "spectrum, minimum parent m+h") || (label == "protein, cleavage C-terminal mass change")|| (label == "protein, cleavage N-terminal mass change") || (label == "protein, C-terminal residue modification mass") || (label == "protein, N-terminal residue modification mass") || (label == "refine, maximum valid expectation value")) {
bool ok;
value.toDouble(&ok);
diff --git a/src/gui/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui b/src/gui/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
index 35eb9eca7..546bd9a2f 100644
--- a/src/gui/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
+++ b/src/gui/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
@@ -1708,14 +1708,119 @@
<property name="geometry">
<rect>
<x>0</x>
- <y>0</y>
- <width>1012</width>
- <height>468</height>
+ <y>-96</y>
+ <width>998</width>
+ <height>564</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout_14">
<item>
<layout class="QGridLayout" name="gridLayout_5">
+ <item row="12" column="1">
+ <widget class="QLineEdit" name="refpmmotif2_edit"/>
+ </item>
+ <item row="8" column="2">
+ <widget class="QPushButton" name="refpmm1_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="1">
+ <widget class="QLineEdit" name="refpmmotif1_edit"/>
+ </item>
+ <item row="12" column="2">
+ <widget class="QPushButton" name="refpmmotif2_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="12" column="0">
+ <widget class="QLabel" name="label_59">
+ <property name="text">
+ <string>Potential modifications motif 2</string>
+ </property>
+ </widget>
+ </item>
+ <item row="13" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_22">
+ <item>
+ <widget class="QRadioButton" name="rupmffr_yes_radio_button">
+ <property name="text">
+ <string>yes</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">rupmffr_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="rupmffr_no_radio_button">
+ <property name="text">
+ <string>no</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">rupmffr_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_20">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item row="13" column="0">
+ <widget class="QLabel" name="label_60">
+ <property name="text">
+ <string>Use potential modifications in refinement module</string>
+ </property>
+ </widget>
+ </item>
+ <item row="8" column="0">
+ <widget class="QLabel" name="label_55">
+ <property name="text">
+ <string>Alter potential modifications 1</string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="0">
+ <widget class="QLabel" name="label_53">
+ <property name="text">
+ <string>Alter fixed modifications 2</string>
+ </property>
+ </widget>
+ </item>
+ <item row="7" column="0">
+ <widget class="QLabel" name="label_54">
+ <property name="text">
+ <string>Alter potential modifications</string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="2">
+ <widget class="QPushButton" name="refmm2_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="6" column="1">
+ <widget class="QLineEdit" name="refmm2_edit"/>
+ </item>
+ <item row="5" column="1">
+ <widget class="QLineEdit" name="refmm1_edit"/>
+ </item>
<item row="1" column="0">
<widget class="QLabel" name="label_48">
<property name="text">
@@ -1737,10 +1842,13 @@
</property>
</widget>
</item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="rmvev_edit"/>
+ </item>
<item row="0" column="0">
<widget class="QLabel" name="label_29">
<property name="text">
- <string>Control the use of the refinment module</string>
+ <string>Use of the refinement module</string>
</property>
</widget>
</item>
@@ -1788,8 +1896,8 @@
</item>
</layout>
</item>
- <item row="1" column="1">
- <widget class="QLineEdit" name="rmvev_edit"/>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="refpntm_edit"/>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_50">
@@ -1798,6 +1906,9 @@
</property>
</widget>
</item>
+ <item row="3" column="1">
+ <widget class="QLineEdit" name="refpctm_edit"/>
+ </item>
<item row="2" column="2">
<widget class="QPushButton" name="refpntm_push_button">
<property name="text">
@@ -1805,22 +1916,23 @@
</property>
</widget>
</item>
- <item row="3" column="2">
- <widget class="QPushButton" name="refpctm_push_button">
+ <item row="10" column="0">
+ <widget class="QLabel" name="label_57">
<property name="text">
- <string>?</string>
+ <string>Potential modifications motif</string>
</property>
</widget>
</item>
- <item row="2" column="1">
- <widget class="QLineEdit" name="refpntm_edit"/>
- </item>
- <item row="3" column="1">
- <widget class="QLineEdit" name="refpctm_edit"/>
- </item>
<item row="4" column="1">
<widget class="QLineEdit" name="refmm_edit"/>
</item>
+ <item row="3" column="2">
+ <widget class="QPushButton" name="refpctm_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
<item row="4" column="0">
<widget class="QLabel" name="label_51">
<property name="text">
@@ -1828,6 +1940,9 @@
</property>
</widget>
</item>
+ <item row="7" column="1">
+ <widget class="QLineEdit" name="refpmm_edit"/>
+ </item>
<item row="5" column="0">
<widget class="QLabel" name="label_52">
<property name="text">
@@ -1842,32 +1957,172 @@
</property>
</widget>
</item>
- <item row="6" column="0">
- <widget class="QLabel" name="label_53">
+ <item row="8" column="1">
+ <widget class="QLineEdit" name="refpmm1_edit"/>
+ </item>
+ <item row="5" column="2">
+ <widget class="QPushButton" name="refmm1_push_button">
<property name="text">
- <string>Alter fixed modifications 2</string>
+ <string>?</string>
</property>
</widget>
</item>
- <item row="5" column="2">
- <widget class="QPushButton" name="refmm1_push_button">
+ <item row="9" column="1">
+ <widget class="QLineEdit" name="refpmm2_edit"/>
+ </item>
+ <item row="9" column="0">
+ <widget class="QLabel" name="label_56">
+ <property name="text">
+ <string>Alter potential modifications 2</string>
+ </property>
+ </widget>
+ </item>
+ <item row="7" column="2">
+ <widget class="QPushButton" name="refpmm_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="6" column="2">
- <widget class="QPushButton" name="refmm2_push_button">
+ <item row="9" column="2">
+ <widget class="QPushButton" name="refpmm2_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="5" column="1">
- <widget class="QLineEdit" name="refmm1_edit"/>
+ <item row="10" column="1">
+ <widget class="QLineEdit" name="refpmmotif_edit"/>
</item>
- <item row="6" column="1">
- <widget class="QLineEdit" name="refmm2_edit"/>
+ <item row="11" column="0">
+ <widget class="QLabel" name="label_58">
+ <property name="text">
+ <string>Potential modifications motif 1</string>
+ </property>
+ </widget>
+ </item>
+ <item row="10" column="2">
+ <widget class="QPushButton" name="refpmmotif_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="2">
+ <widget class="QPushButton" name="refpmmotif1_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="13" column="2">
+ <widget class="QPushButton" name="rupmffr_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="14" column="0">
+ <widget class="QLabel" name="label_61">
+ <property name="text">
+ <string>Use semi-enzymatic cleavage rules</string>
+ </property>
+ </widget>
+ </item>
+ <item row="14" column="2">
+ <widget class="QPushButton" name="rcsemi_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="14" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_23">
+ <item>
+ <widget class="QRadioButton" name="rcsemi_yes_radio_button">
+ <property name="text">
+ <string>yes</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">rcsemi_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="rcsemi_no_radio_button">
+ <property name="text">
+ <string>no</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">rcsemi_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_21">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
+ </item>
+ <item row="15" column="0">
+ <widget class="QLabel" name="label_62">
+ <property name="text">
+ <string>Cleavage at each residues</string>
+ </property>
+ </widget>
+ </item>
+ <item row="15" column="2">
+ <widget class="QPushButton" name="ruc_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="15" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_24">
+ <item>
+ <widget class="QRadioButton" name="ruc_yes_radio_button">
+ <property name="text">
+ <string>yes</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">ruc_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="ruc_no_radio_button">
+ <property name="text">
+ <string>no</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">ruc_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_22">
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ <property name="sizeHint" stdset="0">
+ <size>
+ <width>40</width>
+ <height>20</height>
+ </size>
+ </property>
+ </spacer>
+ </item>
+ </layout>
</item>
</layout>
</item>
@@ -2870,8 +3125,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>999</x>
- <y>183</y>
+ <x>1017</x>
+ <y>104</y>
</hint>
<hint type="destinationlabel">
<x>1130</x>
@@ -2886,8 +3141,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>1021</x>
- <y>224</y>
+ <x>1017</x>
+ <y>138</y>
</hint>
<hint type="destinationlabel">
<x>1076</x>
@@ -2902,8 +3157,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>1000</x>
- <y>252</y>
+ <x>1017</x>
+ <y>172</y>
</hint>
<hint type="destinationlabel">
<x>1070</x>
@@ -2918,8 +3173,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>963</x>
- <y>286</y>
+ <x>1017</x>
+ <y>206</y>
</hint>
<hint type="destinationlabel">
<x>1064</x>
@@ -2934,8 +3189,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>1007</x>
- <y>320</y>
+ <x>1017</x>
+ <y>240</y>
</hint>
<hint type="destinationlabel">
<x>1523</x>
@@ -2950,8 +3205,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>993</x>
- <y>356</y>
+ <x>1017</x>
+ <y>274</y>
</hint>
<hint type="destinationlabel">
<x>1523</x>
@@ -2966,8 +3221,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>960</x>
- <y>396</y>
+ <x>1017</x>
+ <y>308</y>
</hint>
<hint type="destinationlabel">
<x>993</x>
@@ -2975,6 +3230,150 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>refpmm_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>342</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1132</x>
+ <y>813</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpmm1_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>376</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1090</x>
+ <y>791</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpmm2_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>410</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1076</x>
+ <y>798</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpmmotif_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>444</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1001</x>
+ <y>999</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpmmotif1_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>478</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>933</x>
+ <y>948</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpmmotif2_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>512</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>920</x>
+ <y>916</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>rupmffr_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>546</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>807</x>
+ <y>1069</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>rcsemi_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1017</x>
+ <y>580</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>789</x>
+ <y>874</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>ruc_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>965</x>
+ <y>597</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>865</x>
+ <y>1011</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>doCopy()</slot>
@@ -2987,23 +3386,26 @@
<slot>doSelectDir()</slot>
</slots>
<buttongroups>
+ <buttongroup name="sci_button_group"/>
+ <buttongroup name="sbi_button_group"/>
+ <buttongroup name="pqp_button_group"/>
<buttongroup name="syi_button_group"/>
- <buttongroup name="szi_button_group"/>
- <buttongroup name="refine_button_group"/>
- <buttongroup name="spmmeu_button_group"/>
+ <buttongroup name="spmmie_button_group"/>
+ <buttongroup name="sfmmeu_button_group"/>
<buttongroup name="pstpb_button_group"/>
+ <buttongroup name="pqa_button_group"/>
+ <buttongroup name="sxi_button_group"/>
+ <buttongroup name="sir_button_group"/>
+ <buttongroup name="sunlw_button_group"/>
+ <buttongroup name="spmmeu_button_group"/>
<buttongroup name="sai_button_group"/>
<buttongroup name="pcsemi_button_group"/>
- <buttongroup name="pqp_button_group"/>
- <buttongroup name="sbi_button_group"/>
<buttongroup name="suca_button_group"/>
- <buttongroup name="sir_button_group"/>
+ <buttongroup name="refine_button_group"/>
+ <buttongroup name="rupmffr_button_group"/>
<buttongroup name="scp_button_group"/>
- <buttongroup name="sci_button_group"/>
- <buttongroup name="spmmie_button_group"/>
- <buttongroup name="sxi_button_group"/>
- <buttongroup name="sfmmeu_button_group"/>
- <buttongroup name="sunlw_button_group"/>
- <buttongroup name="pqa_button_group"/>
+ <buttongroup name="szi_button_group"/>
+ <buttongroup name="ruc_button_group"/>
+ <buttongroup name="rcsemi_button_group"/>
</buttongroups>
</ui>
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index c1659f113..cd614096c 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -354,16 +354,31 @@ void EditTandemPresetDialog::doHelp() {
{
html_doc.setFileName(":/tandem/resources/html_doc/refpctm.html");
}
-if ((senderObjName == "refmm_push_button")|| (senderObjName == "refmm1_push_button")|| (senderObjName == "refmm2_push_button"))
+ if ((senderObjName == "refmm_push_button")|| (senderObjName == "refmm1_push_button")|| (senderObjName == "refmm2_push_button"))
{
html_doc.setFileName(":/tandem/resources/html_doc/refmm.html");
}
-
-
- _tandem_params.setParamLabelValue("residue, potential modification mass", ui->rpmm_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification mass 1", ui->rpmm1_edit->text());
- _tandem_params.setParamLabelValue("residue, potential modification mass 2", ui->rpmm2_edit->text());
-
+ if ((senderObjName == "refpmm_push_button")|| (senderObjName == "refpmm1_push_button")|| (senderObjName == "refpmm2_push_button"))
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/refpmm.html");
+ }
+ if ((senderObjName == "refpmmotif_push_button")|| (senderObjName == "refpmmotif1_push_button")|| (senderObjName == "refpmmotif2_push_button"))
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/refpmmotif.html");
+ }
+ if(senderObjName == "rupmffr_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/rupmffr.html");
+ }
+ if(senderObjName == "rcsemi_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/rcsemi.html");
+ }
+ if(senderObjName == "ruc_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/ruc.html");
+ }
+
if (html_doc.open(QFile::ReadOnly | QFile::Text)) {
QTextStream in(&html_doc);
ui->doc_plain_text_edit->setHtml(in.readAll());
@@ -498,7 +513,24 @@ void EditTandemPresetDialog::readUi() {
_tandem_params.setParamLabelValue("refine, modification mass", ui->refmm_edit->text());
_tandem_params.setParamLabelValue("refine, modification mass 1", ui->refmm1_edit->text());
_tandem_params.setParamLabelValue("refine, modification mass 2", ui->refmm2_edit->text());
-
+ _tandem_params.setParamLabelValue("refine, potential modification mass", ui->refpmm_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification mass 1", ui->refpmm1_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification mass 2", ui->refpmm2_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification motif", ui->refpmmotif_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification motif 1", ui->refpmmotif1_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential modification motif 2", ui->refpmmotif2_edit->text());
+ _tandem_params.setParamLabelValue("refine, use potential modifications for full refinement", "no");
+ if (ui->rupmffr_yes_radio_button->isChecked()) {
+ _tandem_params.setParamLabelValue("refine, use potential modifications for full refinement", "yes");
+ }
+ _tandem_params.setParamLabelValue("refine, cleavage semi", "no");
+ if (ui->rcsemi_yes_radio_button->isChecked()) {
+ _tandem_params.setParamLabelValue("refine, cleavage semi", "yes");
+ }
+ _tandem_params.setParamLabelValue("refine, unanticipated cleavage", "no");
+ if (ui->ruc_yes_radio_button->isChecked()) {
+ _tandem_params.setParamLabelValue("refine, unanticipated cleavage", "yes");
+ }
}
catch (pappso::PappsoException & error) {
@@ -740,14 +772,38 @@ void EditTandemPresetDialog::populate() {
//<note type="input" label="refine, modification mass 2"></note>
ui->refmm2_edit->setText(_tandem_params.getValue("refine, modification mass 2"));
//<note type="input" label="refine, potential modification mass">15.99491@M</note>
+ ui->refpmm_edit->setText(_tandem_params.getValue("refine, potential modification mass"));
//<note type="input" label="refine, potential modification mass 1"></note>
+ ui->refpmm1_edit->setText(_tandem_params.getValue("refine, potential modification mass 1"));
//<note type="input" label="refine, potential modification mass 2"></note>
+ ui->refpmm2_edit->setText(_tandem_params.getValue("refine, potential modification mass 2"));
//<note type="input" label="refine, potential modification motif"></note>
+ ui->refpmmotif_edit->setText(_tandem_params.getValue("refine, potential modification motif"));
//<note type="input" label="refine, potential modification motif 1"></note>
+ ui->refpmmotif1_edit->setText(_tandem_params.getValue("refine, potential modification motif 1"));
//<note type="input" label="refine, potential modification motif 2"></note>
+ ui->refpmmotif2_edit->setText(_tandem_params.getValue("refine, potential modification motif 2"));
//<note type="input" label="refine, use potential modifications for full refinement">yes</note>
+ ui->rupmffr_yes_radio_button->setChecked(true);
+ ui->rupmffr_no_radio_button->setChecked(false);
+ if ( _tandem_params.getValue("refine, use potential modifications for full refinement") == "no" ) { // -1 for not found
+ ui->rupmffr_yes_radio_button->setChecked(false);
+ ui->rupmffr_no_radio_button->setChecked(true);
+ }
//<note type="input" label="refine, cleavage semi">no</note>
+ ui->rcsemi_yes_radio_button->setChecked(true);
+ ui->rcsemi_no_radio_button->setChecked(false);
+ if ( _tandem_params.getValue("refine, cleavage semi") == "no" ) { // -1 for not found
+ ui->rcsemi_yes_radio_button->setChecked(false);
+ ui->rcsemi_no_radio_button->setChecked(true);
+ }
//<note type="input" label="refine, unanticipated cleavage">no</note>
+ ui->ruc_yes_radio_button->setChecked(true);
+ ui->ruc_no_radio_button->setChecked(false);
+ if ( _tandem_params.getValue("refine, unanticipated cleavage") == "no" ) { // -1 for not found
+ ui->ruc_yes_radio_button->setChecked(false);
+ ui->ruc_no_radio_button->setChecked(true);
+ }
//<note type="input" label="refine, spectrum synthesis">yes</note>
//<note type="input" label="refine, point mutations">no</note>
--
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