diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index 429b09e907ed27ad31f4f8608b74147723fc9d21..aa73215bee25e50cfa4ba55c143c208d01181e3c 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -95,14 +95,14 @@ 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")) {
+ 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 ((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")) {
+ 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);
if (!ok) {// not an integer
@@ -124,7 +124,7 @@ void TandemParameters::setParamLabelValue(const QString & label, const QString &
}
}
- //text "protein, cleavage site" "protein, modified residue mass file" "residue, modification mass"
+ //text "protein, cleavage site" "protein, modified residue mass file" "residue, modification mass" || (label == "refine, potential N-terminus modifications") || (label == "refine, potential C-terminus modifications")
_map_label_value.insert(label, value);
}
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 6b95bb51a39d413ff24436854dc51066edbb8164..0706ba23401f76265557a5a76f8d552badd02be0 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
@@ -100,7 +100,7 @@
<item>
<widget class="QTabWidget" name="tabWidget">
<property name="currentIndex">
- <number>3</number>
+ <number>4</number>
</property>
<widget class="QWidget" name="spectrum_tab">
<property name="sizePolicy">
@@ -1716,13 +1716,108 @@
<layout class="QVBoxLayout" name="verticalLayout_14">
<item>
<layout class="QGridLayout" name="gridLayout_5">
+ <item row="1" column="0">
+ <widget class="QLabel" name="label_48">
+ <property name="text">
+ <string>Maximum E-value to accept peptide </string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <widget class="QPushButton" name="rmvev_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QPushButton" name="refine_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
<item row="0" column="0">
<widget class="QLabel" name="label_29">
<property name="text">
- <string>TextLabel</string>
+ <string>Control the use of the refinment module</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_49">
+ <property name="text">
+ <string>Peptide N-ter potential modifications</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_21">
+ <item>
+ <widget class="QRadioButton" name="refine_yes_radio_button">
+ <property name="text">
+ <string>&yes</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">refine_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="refine_no_radio_button">
+ <property name="text">
+ <string>no</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">refine_button_group</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_19">
+ <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="1" column="1">
+ <widget class="QLineEdit" name="rmvev_edit"/>
+ </item>
+ <item row="3" column="0">
+ <widget class="QLabel" name="label_50">
+ <property name="text">
+ <string>Peptide C-ter potential modifications</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QPushButton" name="refpntm_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="2">
+ <widget class="QPushButton" name="refpctm_push_button">
+ <property name="text">
+ <string>?</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>
</layout>
</item>
<item>
@@ -2717,6 +2812,70 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>refine_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>999</x>
+ <y>183</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1130</x>
+ <y>-101</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>rmvev_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1021</x>
+ <y>224</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1076</x>
+ <y>-66</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpntm_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1000</x>
+ <y>252</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1070</x>
+ <y>-37</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>refpctm_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>963</x>
+ <y>286</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1064</x>
+ <y>-12</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>doCopy()</slot>
@@ -2729,22 +2888,23 @@
<slot>doSelectDir()</slot>
</slots>
<buttongroups>
- <buttongroup name="spmmie_button_group"/>
- <buttongroup name="scp_button_group"/>
- <buttongroup name="spmmeu_button_group"/>
- <buttongroup name="suca_button_group"/>
- <buttongroup name="sfmmeu_button_group"/>
- <buttongroup name="pcsemi_button_group"/>
- <buttongroup name="pqa_button_group"/>
<buttongroup name="pqp_button_group"/>
- <buttongroup name="pstpb_button_group"/>
- <buttongroup name="sunlw_button_group"/>
+ <buttongroup name="suca_button_group"/>
<buttongroup name="sir_button_group"/>
- <buttongroup name="syi_button_group"/>
+ <buttongroup name="sfmmeu_button_group"/>
<buttongroup name="sbi_button_group"/>
- <buttongroup name="sci_button_group"/>
<buttongroup name="szi_button_group"/>
+ <buttongroup name="spmmeu_button_group"/>
<buttongroup name="sai_button_group"/>
+ <buttongroup name="pcsemi_button_group"/>
+ <buttongroup name="spmmie_button_group"/>
+ <buttongroup name="sci_button_group"/>
+ <buttongroup name="scp_button_group"/>
+ <buttongroup name="pqa_button_group"/>
<buttongroup name="sxi_button_group"/>
+ <buttongroup name="sunlw_button_group"/>
+ <buttongroup name="pstpb_button_group"/>
+ <buttongroup name="syi_button_group"/>
+ <buttongroup name="refine_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 743f036302232c27ed5695451f0bb092cdc6db91..a25b8313a2b5d03c3fe6efa8c2759384aa5db099 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -338,6 +338,22 @@ void EditTandemPresetDialog::doHelp() {
{
html_doc.setFileName(":/tandem/resources/html_doc/sxi.html");
}
+ if(senderObjName == "refine_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/refine.html");
+ }
+ if(senderObjName == "rmvev_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/rmvev.html");
+ }
+ if(senderObjName == "refpntm_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/refpntm.html");
+ }
+ if(senderObjName == "refpctm_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/refpctm.html");
+ }
@@ -468,6 +484,15 @@ void EditTandemPresetDialog::readUi() {
if (ui->sxi_yes_radio_button->isChecked()) {
_tandem_params.setParamLabelValue("scoring, x ions", "yes");
}
+ _tandem_params.setParamLabelValue("refine", "no");
+ if (ui->refine_yes_radio_button->isChecked()) {
+ _tandem_params.setParamLabelValue("refine", "yes");
+ }
+ _tandem_params.setParamLabelValue("refine, maximum valid expectation value", ui->rmvev_edit->text());
+
+ _tandem_params.setParamLabelValue("refine, potential N-terminus modifications", ui->refpntm_edit->text());
+ _tandem_params.setParamLabelValue("refine, potential C-terminus modifications", ui->refpctm_edit->text());
+
}
catch (pappso::PappsoException & error) {
QMessageBox::warning(this,tr("Error in parameters :"), error.qwhat());
@@ -686,6 +711,36 @@ void EditTandemPresetDialog::populate() {
ui->sxi_no_radio_button->setChecked(true);
}
+
+ //<note type="input" label="refine">yes</note>
+ ui->refine_yes_radio_button->setChecked(true);
+ ui->refine_no_radio_button->setChecked(false);
+ if ( _tandem_params.getValue("refine") == "no" ) { // -1 for not found
+ ui->refine_yes_radio_button->setChecked(false);
+ ui->refine_no_radio_button->setChecked(true);
+ }
+ //<note type="input" label="refine, maximum valid expectation value">0.01</note>
+ ui->rmvev_edit->setText(_tandem_params.getValue("refine, maximum valid expectation value"));
+
+ //<note type="input" label="refine, potential N-terminus modifications">+42.01056@[</note>
+ ui->refpntm_edit->setText(_tandem_params.getValue("refine, potential N-terminus modifications"));
+ //<note type="input" label="refine, potential C-terminus modifications"></note>
+ ui->refpctm_edit->setText(_tandem_params.getValue("refine, potential C-terminus modifications"));
+ //<note type="input" label="refine, modification mass">57.02146@C</note>
+ //<note type="input" label="refine, modification mass 1"></note>
+ //<note type="input" label="refine, modification mass 2"></note>
+ //<note type="input" label="refine, potential modification mass">15.99491@M</note>
+ //<note type="input" label="refine, potential modification mass 1"></note>
+ //<note type="input" label="refine, potential modification mass 2"></note>
+ //<note type="input" label="refine, potential modification motif"></note>
+ //<note type="input" label="refine, potential modification motif 1"></note>
+ //<note type="input" label="refine, potential modification motif 2"></note>
+ //<note type="input" label="refine, use potential modifications for full refinement">yes</note>
+ //<note type="input" label="refine, cleavage semi">no</note>
+ //<note type="input" label="refine, unanticipated cleavage">no</note>
+ //<note type="input" label="refine, spectrum synthesis">yes</note>
+ //<note type="input" label="refine, point mutations">no</note>
+
qDebug() << "EditTandemPresetDialog::populate end";
}