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 bcc70d87bfc40a692feb7ad3ed777e0c1e64e892..18a225b3b0db961e6b3ca048e2de8ccd83229e8a 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
@@ -133,48 +133,55 @@
<x>0</x>
<y>0</y>
<width>998</width>
- <height>598</height>
+ <height>700</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout_3">
<item>
<layout class="QGridLayout" name="gridLayout_2">
- <item row="15" column="2">
+ <item row="9" column="0">
+ <widget class="QLabel" name="label_78">
+ <property name="text">
+ <string>Neutral loss mass</string>
+ </property>
+ </widget>
+ </item>
+ <item row="18" column="2">
<widget class="QPushButton" name="suca_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="13" column="0">
+ <item row="16" column="0">
<widget class="QLabel" name="label_15">
<property name="text">
<string>Minimum parent MH+ to be considered</string>
</property>
</widget>
</item>
- <item row="12" column="0">
+ <item row="15" column="0">
<widget class="QLabel" name="label_14">
<property name="text">
<string>Minimu m/z fragment to be considered</string>
</property>
</widget>
</item>
- <item row="11" column="0">
+ <item row="14" column="0">
<widget class="QLabel" name="label_13">
<property name="text">
<string>Minimum number of peaks for a spectrum to be considered</string>
</property>
</widget>
</item>
- <item row="12" column="2">
+ <item row="15" column="2">
<widget class="QPushButton" name="smfmz_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="11" column="2">
+ <item row="14" column="2">
<widget class="QPushButton" name="smp_push_button">
<property name="text">
<string>?</string>
@@ -261,6 +268,9 @@
</property>
</widget>
</item>
+ <item row="2" column="1">
+ <widget class="QLineEdit" name="parent_ion_upper_window_edit"/>
+ </item>
<item row="1" column="0">
<widget class="QLabel" name="label_2">
<property name="text">
@@ -268,6 +278,9 @@
</property>
</widget>
</item>
+ <item row="1" column="1">
+ <widget class="QLineEdit" name="parent_ion_lower_window_edit"/>
+ </item>
<item row="3" column="2">
<widget class="QPushButton" name="spmmie_push_button">
<property name="sizePolicy">
@@ -281,15 +294,12 @@
</property>
</widget>
</item>
- <item row="2" column="1">
- <widget class="QLineEdit" name="parent_ion_upper_window_edit"/>
- </item>
- <item row="1" column="1">
- <widget class="QLineEdit" name="parent_ion_lower_window_edit"/>
- </item>
<item row="4" column="1">
<widget class="QLineEdit" name="smpc_edit"/>
</item>
+ <item row="7" column="1">
+ <widget class="QLineEdit" name="sfmme_edit"/>
+ </item>
<item row="2" column="0">
<widget class="QLabel" name="label_3">
<property name="text">
@@ -297,9 +307,6 @@
</property>
</widget>
</item>
- <item row="7" column="1">
- <widget class="QLineEdit" name="sfmme_edit"/>
- </item>
<item row="3" column="0">
<widget class="QLabel" name="label_4">
<property name="text">
@@ -342,6 +349,9 @@
</property>
</widget>
</item>
+ <item row="12" column="1">
+ <widget class="QLineEdit" name="sdr_edit"/>
+ </item>
<item row="7" column="0">
<widget class="QLabel" name="label_7">
<property name="text">
@@ -356,8 +366,8 @@
</property>
</widget>
</item>
- <item row="9" column="1">
- <widget class="QLineEdit" name="sdr_edit"/>
+ <item row="13" column="1">
+ <widget class="QLineEdit" name="stp_edit"/>
</item>
<item row="8" column="0">
<widget class="QLabel" name="label_10">
@@ -366,92 +376,89 @@
</property>
</widget>
</item>
- <item row="9" column="2">
+ <item row="12" column="2">
<widget class="QPushButton" name="sdr_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="10" column="1">
- <widget class="QLineEdit" name="stp_edit"/>
- </item>
- <item row="9" column="0">
+ <item row="12" column="0">
<widget class="QLabel" name="label_11">
<property name="text">
<string>Set the dynamic range to score spectra</string>
</property>
</widget>
</item>
- <item row="10" column="0">
+ <item row="13" column="0">
<widget class="QLabel" name="label_12">
<property name="text">
<string>Maximum number of peaks to use in a spectrum</string>
</property>
</widget>
</item>
- <item row="10" column="2">
+ <item row="13" column="2">
<widget class="QPushButton" name="stp_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="14" column="2">
+ <item row="16" column="1">
+ <widget class="QLineEdit" name="smpmh_edit"/>
+ </item>
+ <item row="17" column="2">
<widget class="QPushButton" name="spsbs_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="13" column="2">
+ <item row="16" column="2">
<widget class="QPushButton" name="smpmh_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="13" column="1">
- <widget class="QLineEdit" name="smpmh_edit"/>
+ <item row="15" column="1">
+ <widget class="QLineEdit" name="smfmz_edit"/>
</item>
<item row="14" column="1">
+ <widget class="QLineEdit" name="smp_edit"/>
+ </item>
+ <item row="17" column="1">
<widget class="QLineEdit" name="spsbs_edit">
<property name="enabled">
<bool>false</bool>
</property>
</widget>
</item>
- <item row="12" column="1">
- <widget class="QLineEdit" name="smfmz_edit"/>
- </item>
- <item row="11" column="1">
- <widget class="QLineEdit" name="smp_edit"/>
+ <item row="19" column="1">
+ <widget class="QLineEdit" name="st_edit"/>
</item>
- <item row="14" column="0">
+ <item row="17" column="0">
<widget class="QLabel" name="label_16">
<property name="text">
<string>Alter how protein sequences are retrieved from FASTA files</string>
</property>
</widget>
</item>
- <item row="16" column="2">
+ <item row="19" column="2">
<widget class="QPushButton" name="st_push_button">
<property name="text">
<string>?</string>
</property>
</widget>
</item>
- <item row="16" column="1">
- <widget class="QLineEdit" name="st_edit"/>
- </item>
- <item row="16" column="0">
+ <item row="19" column="0">
<widget class="QLabel" name="label_17">
<property name="text">
<string>Set number of threads</string>
</property>
</widget>
</item>
- <item row="15" column="0">
+ <item row="18" column="0">
<widget class="QLabel" name="label_18">
<property name="text">
<string>Use contrast angle</string>
@@ -606,7 +613,7 @@
</item>
</layout>
</item>
- <item row="15" column="1">
+ <item row="18" column="1">
<layout class="QHBoxLayout" name="horizontalLayout_8">
<item>
<widget class="QRadioButton" name="suca_yes_radio_button">
@@ -643,6 +650,84 @@
</item>
</layout>
</item>
+ <item row="10" column="0">
+ <widget class="QLabel" name="label_79">
+ <property name="text">
+ <string>Neutral loss window (Daltons)</string>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="0">
+ <widget class="QLabel" name="label_80">
+ <property name="text">
+ <string>Noise suppression routine</string>
+ </property>
+ </widget>
+ </item>
+ <item row="9" column="1">
+ <widget class="QLineEdit" name="snlm_edit"/>
+ </item>
+ <item row="10" column="1">
+ <widget class="QLineEdit" name="snlw_edit"/>
+ </item>
+ <item row="9" column="2">
+ <widget class="QPushButton" name="snlm_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="10" column="2">
+ <widget class="QPushButton" name="snlw_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="2">
+ <widget class="QPushButton" name="suns_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="11" column="1">
+ <layout class="QHBoxLayout" name="horizontalLayout_37">
+ <item>
+ <widget class="QRadioButton" name="suns_yes_radio_button">
+ <property name="text">
+ <string>yes</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">buttonGroup_8</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="suns_no_radio_button">
+ <property name="text">
+ <string>no</string>
+ </property>
+ <attribute name="buttonGroup">
+ <string notr="true">buttonGroup_8</string>
+ </attribute>
+ </widget>
+ </item>
+ <item>
+ <spacer name="horizontalSpacer_35">
+ <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>
<item>
@@ -3287,7 +3372,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>506</y>
+ <y>608</y>
</hint>
<hint type="destinationlabel">
<x>1588</x>
@@ -3303,7 +3388,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>540</y>
+ <y>642</y>
</hint>
<hint type="destinationlabel">
<x>1674</x>
@@ -3319,7 +3404,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>574</y>
+ <y>676</y>
</hint>
<hint type="destinationlabel">
<x>1611</x>
@@ -3335,7 +3420,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>608</y>
+ <y>710</y>
</hint>
<hint type="destinationlabel">
<x>1711</x>
@@ -3351,7 +3436,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>642</y>
+ <y>744</y>
</hint>
<hint type="destinationlabel">
<x>1642</x>
@@ -3367,7 +3452,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>676</y>
+ <y>778</y>
</hint>
<hint type="destinationlabel">
<x>1579</x>
@@ -3383,7 +3468,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>710</y>
+ <y>812</y>
</hint>
<hint type="destinationlabel">
<x>1734</x>
@@ -3399,7 +3484,7 @@
<hints>
<hint type="sourcelabel">
<x>1017</x>
- <y>744</y>
+ <y>846</y>
</hint>
<hint type="destinationlabel">
<x>1734</x>
@@ -4166,8 +4251,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>990</x>
- <y>158</y>
+ <x>1017</x>
+ <y>200</y>
</hint>
<hint type="destinationlabel">
<x>1005</x>
@@ -4182,8 +4267,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>961</x>
- <y>195</y>
+ <x>1017</x>
+ <y>234</y>
</hint>
<hint type="destinationlabel">
<x>985</x>
@@ -4198,8 +4283,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>982</x>
- <y>223</y>
+ <x>1017</x>
+ <y>268</y>
</hint>
<hint type="destinationlabel">
<x>1061</x>
@@ -4214,8 +4299,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>999</x>
- <y>258</y>
+ <x>1017</x>
+ <y>302</y>
</hint>
<hint type="destinationlabel">
<x>1092</x>
@@ -4230,8 +4315,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>960</x>
- <y>294</y>
+ <x>1017</x>
+ <y>336</y>
</hint>
<hint type="destinationlabel">
<x>906</x>
@@ -4246,8 +4331,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>1009</x>
- <y>332</y>
+ <x>1017</x>
+ <y>370</y>
</hint>
<hint type="destinationlabel">
<x>1096</x>
@@ -4262,8 +4347,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>949</x>
- <y>361</y>
+ <x>1017</x>
+ <y>404</y>
</hint>
<hint type="destinationlabel">
<x>380</x>
@@ -4278,8 +4363,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>942</x>
- <y>397</y>
+ <x>1017</x>
+ <y>438</y>
</hint>
<hint type="destinationlabel">
<x>710</x>
@@ -4294,8 +4379,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>978</x>
- <y>429</y>
+ <x>1017</x>
+ <y>472</y>
</hint>
<hint type="destinationlabel">
<x>476</x>
@@ -4310,8 +4395,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>948</x>
- <y>463</y>
+ <x>1017</x>
+ <y>506</y>
</hint>
<hint type="destinationlabel">
<x>656</x>
@@ -4326,8 +4411,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>1011</x>
- <y>489</y>
+ <x>1017</x>
+ <y>540</y>
</hint>
<hint type="destinationlabel">
<x>680</x>
@@ -4342,8 +4427,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>965</x>
- <y>533</y>
+ <x>1017</x>
+ <y>574</y>
</hint>
<hint type="destinationlabel">
<x>1011</x>
@@ -4358,8 +4443,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>963</x>
- <y>562</y>
+ <x>1017</x>
+ <y>608</y>
</hint>
<hint type="destinationlabel">
<x>1385</x>
@@ -4374,8 +4459,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>974</x>
- <y>601</y>
+ <x>1017</x>
+ <y>642</y>
</hint>
<hint type="destinationlabel">
<x>1399</x>
@@ -4383,6 +4468,54 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>snlm_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>981</x>
+ <y>493</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1580</x>
+ <y>493</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>snlw_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>961</x>
+ <y>519</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1580</x>
+ <y>523</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>suns_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>993</x>
+ <y>554</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1580</x>
+ <y>560</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>doCopy()</slot>
@@ -4395,38 +4528,39 @@
<slot>doSelectDir()</slot>
</slots>
<buttongroups>
- <buttongroup name="sai_button_group"/>
- <buttongroup name="sir_button_group"/>
<buttongroup name="sbi_button_group"/>
- <buttongroup name="refine_button_group"/>
+ <buttongroup name="buttonGroup_5"/>
+ <buttongroup name="sunlw_button_group"/>
+ <buttongroup name="pqa_button_group"/>
+ <buttongroup name="suca_button_group"/>
+ <buttongroup name="scp_button_group"/>
+ <buttongroup name="buttonGroup"/>
<buttongroup name="sfmmeu_button_group"/>
<buttongroup name="pcsemi_button_group"/>
- <buttongroup name="buttonGroup"/>
- <buttongroup name="ruc_button_group"/>
- <buttongroup name="spmmeu_button_group"/>
- <buttongroup name="buttonGroup_7"/>
<buttongroup name="sxi_button_group"/>
- <buttongroup name="pqp_button_group"/>
- <buttongroup name="sunlw_button_group"/>
+ <buttongroup name="buttonGroup_2"/>
+ <buttongroup name="sai_button_group"/>
+ <buttongroup name="buttonGroup_7"/>
+ <buttongroup name="sir_button_group"/>
<buttongroup name="pstpb_button_group"/>
- <buttongroup name="buttonGroup_3"/>
- <buttongroup name="buttonGroup_5"/>
- <buttongroup name="sci_button_group"/>
- <buttongroup name="rpm_button_group"/>
+ <buttongroup name="spmmie_button_group"/>
+ <buttongroup name="rcsemi_button_group"/>
+ <buttongroup name="rss_button_group"/>
+ <buttongroup name="ruc_button_group"/>
+ <buttongroup name="buttonGroup_6"/>
<buttongroup name="ospec_button_group"/>
- <buttongroup name="suca_button_group"/>
- <buttongroup name="rupmffr_button_group"/>
<buttongroup name="szi_button_group"/>
- <buttongroup name="buttonGroup_4"/>
<buttongroup name="oresu_button_group"/>
- <buttongroup name="buttonGroup_2"/>
- <buttongroup name="pqa_button_group"/>
- <buttongroup name="spmmie_button_group"/>
- <buttongroup name="buttonGroup_6"/>
- <buttongroup name="rss_button_group"/>
<buttongroup name="mzid_button_group"/>
- <buttongroup name="scp_button_group"/>
+ <buttongroup name="spmmeu_button_group"/>
+ <buttongroup name="sci_button_group"/>
+ <buttongroup name="pqp_button_group"/>
<buttongroup name="syi_button_group"/>
- <buttongroup name="rcsemi_button_group"/>
+ <buttongroup name="rupmffr_button_group"/>
+ <buttongroup name="buttonGroup_4"/>
+ <buttongroup name="refine_button_group"/>
+ <buttongroup name="buttonGroup_3"/>
+ <buttongroup name="rpm_button_group"/>
+ <buttongroup name="buttonGroup_8"/>
</buttongroups>
</ui>
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index cc7b41badd0cd3c25e50defdcea226eed7b75cc3..59c8f8a6c4486eb3945ac9b34198ba104319cb3c 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -78,7 +78,7 @@ void EditTandemPresetDialog::setTandemParametersFile(const TandemParametersFile
_preset_directory = settings.value("path/tandemrun_preset_directory", "").toString();
_p_tandem_preset_file->setDirectory(QDir(_preset_directory));
}
-
+
fillPresetComboBox();
populate();
@@ -223,6 +223,18 @@ void EditTandemPresetDialog::doHelp() {
{
html_doc.setFileName(":/tandem/resources/html_doc/sunlw.html");
}
+ if(senderObjName == "snlm_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/snlm.html");
+ }
+ if(senderObjName == "snlw_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/snlw.html");
+ }
+ if(senderObjName == "suns_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/suns.html");
+ }
if(senderObjName == "sdr_push_button")
{
html_doc.setFileName(":/tandem/resources/html_doc/sdr.html");
@@ -492,6 +504,14 @@ void EditTandemPresetDialog::readUi() {
_tandem_params.setParamLabelValue("spectrum, use neutral loss window", "yes");
}
+ _tandem_params.setParamLabelValue("spectrum, neutral loss mass", ui->snlm_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, neutral loss window", ui->snlw_edit->text());
+ _tandem_params.setParamLabelValue("spectrum, use noise suppression", "no");
+ if (ui->suns_yes_radio_button->isChecked()) {
+ _tandem_params.setParamLabelValue("spectrum, use noise suppression", "yes");
+ }
+
+
_tandem_params.setParamLabelValue("spectrum, dynamic range", ui->sdr_edit->text());
_tandem_params.setParamLabelValue("spectrum, total peaks", ui->stp_edit->text());
_tandem_params.setParamLabelValue("spectrum, minimum peaks", ui->smp_edit->text());
@@ -692,6 +712,20 @@ void EditTandemPresetDialog::populate() {
ui->sunlw_no_radio_button->setChecked(true);
}
+
+
+ //<note type="input" label="spectrum, neutral loss mass">18.01057</note>
+ ui->snlm_edit->setText(_tandem_params.getValue("spectrum, neutral loss mass"));
+ //<note type="input" label="spectrum, neutral loss window">0.02</note>
+ ui->snlw_edit->setText(_tandem_params.getValue("spectrum, neutral loss window"));
+ //<note type="input" label="spectrum, use noise suppression">yes</note>
+ ui->suns_yes_radio_button->setChecked(true);
+ ui->suns_no_radio_button->setChecked(false);
+ if ( _tandem_params.getValue("spectrum, use noise suppression") == "no" ) { // -1 for not found
+ ui->suns_yes_radio_button->setChecked(false);
+ ui->suns_no_radio_button->setChecked(true);
+ }
+
//<note type="input" label="spectrum, dynamic range">100.0</note>
ui->sdr_edit->setText(_tandem_params.getValue("spectrum, dynamic range"));