diff --git a/src/core/tandem_run/tandemparameters.cpp b/src/core/tandem_run/tandemparameters.cpp
index 973aeabe072d6d6a39ee4aa513ff0561411f79f9..67140d5bb7658e39c7b77a0675a2148489b5627e 100644
--- a/src/core/tandem_run/tandemparameters.cpp
+++ b/src/core/tandem_run/tandemparameters.cpp
@@ -95,20 +95,21 @@ 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")) {
+ if ((label == "spectrum, parent monoisotopic mass isotope error") || (label == "spectrum, use neutral loss window") || (label == "spectrum, use contrast angle") || (label == "protein, 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") ) {
+
+ 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")) {
bool ok;
value.toDouble(&ok);
if (!ok) {// not an integer
throw pappso::ExceptionNotPossible(QObject::tr("%1 value must be a number (not %2)").arg(label).arg(value));
}
}
-
-
+
+
if ((label == "spectrum, maximum parent charge") || (label == "spectrum, total peaks") || (label == "spectrum, minimum peaks") || (label == "spectrum, sequence batch size") || (label == "spectrum, threads")) {
bool ok;
value.toInt(&ok);
@@ -122,6 +123,8 @@ void TandemParameters::setParamLabelValue(const QString & label, const QString &
}
}
+ //text "protein, cleavage site"
+
_map_label_value.insert(label, value);
}
void TandemParameters::setMethodName(const QString & method) {
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 e17633d2fa35cf16910b45b93aa2c93490e3577b..65e1fb4cac180463372aeb6b97480174cdeb6e08 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>0</number>
+ <number>1</number>
</property>
<widget class="QWidget" name="spectrum_tab">
<property name="sizePolicy">
@@ -131,7 +131,7 @@
<property name="geometry">
<rect>
<x>0</x>
- <y>-162</y>
+ <y>0</y>
<width>976</width>
<height>598</height>
</rect>
@@ -565,23 +565,128 @@
<x>0</x>
<y>0</y>
<width>990</width>
- <height>436</height>
+ <height>468</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout_6">
<item>
<layout class="QGridLayout" name="gridLayout_3">
+ <item row="3" column="2">
+ <widget class="QLineEdit" name="pcntmc_edit"/>
+ </item>
+ <item row="2" column="0">
+ <widget class="QLabel" name="label_19">
+ <property name="text">
+ <string>Moiety added to peptide C-terminus by cleavage</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="3">
+ <widget class="QPushButton" name="pcntmc_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
<item row="0" column="0">
<widget class="QLabel" name="label_5">
<property name="text">
- <string>TextLabel</string>
+ <string>Define protein cleavage site</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_6">
<property name="text">
- <string>TextLabel</string>
+ <string>Use semi enzymatic cleavage rules</string>
+ </property>
+ </widget>
+ </item>
+ <item row="3" column="0">
+ <widget class="QLabel" name="label_20">
+ <property name="text">
+ <string>Moiety added to peptide N-terminus by cleavage</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="3">
+ <widget class="QPushButton" name="pcctmc_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="3">
+ <widget class="QPushButton" name="pcs_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="0" column="2">
+ <widget class="QLineEdit" name="pcs_edit"/>
+ </item>
+ <item row="1" column="3">
+ <widget class="QPushButton" name="pcsemi_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="1" column="2">
+ <widget class="QComboBox" name="pcsemi_combo_box">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <item>
+ <property name="text">
+ <string>yes</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>no</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item row="4" column="0">
+ <widget class="QLabel" name="label_21">
+ <property name="text">
+ <string>Moiety added to protein C-terminus</string>
+ </property>
+ </widget>
+ </item>
+ <item row="2" column="2">
+ <widget class="QLineEdit" name="pcctmc_edit"/>
+ </item>
+ <item row="5" column="0">
+ <widget class="QLabel" name="label_22">
+ <property name="text">
+ <string>Moiety added to protein N-terminus</string>
+ </property>
+ </widget>
+ </item>
+ <item row="4" column="2">
+ <widget class="QLineEdit" name="pctrmm_edit"/>
+ </item>
+ <item row="5" column="2">
+ <widget class="QLineEdit" name="pntrmm_edit"/>
+ </item>
+ <item row="4" column="3">
+ <widget class="QPushButton" name="pctrmm_push_button">
+ <property name="text">
+ <string>?</string>
+ </property>
+ </widget>
+ </item>
+ <item row="5" column="3">
+ <widget class="QPushButton" name="pntrmm_push_button">
+ <property name="text">
+ <string>?</string>
</property>
</widget>
</item>
@@ -673,7 +778,7 @@
<hints>
<hint type="sourcelabel">
<x>1343</x>
- <y>654</y>
+ <y>687</y>
</hint>
<hint type="destinationlabel">
<x>881</x>
@@ -689,7 +794,7 @@
<hints>
<hint type="sourcelabel">
<x>1429</x>
- <y>654</y>
+ <y>687</y>
</hint>
<hint type="destinationlabel">
<x>879</x>
@@ -705,7 +810,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>55</y>
+ <y>200</y>
</hint>
<hint type="destinationlabel">
<x>1728</x>
@@ -721,7 +826,7 @@
<hints>
<hint type="sourcelabel">
<x>1030</x>
- <y>130</y>
+ <y>113</y>
</hint>
<hint type="destinationlabel">
<x>1542</x>
@@ -737,7 +842,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>89</y>
+ <y>234</y>
</hint>
<hint type="destinationlabel">
<x>720</x>
@@ -753,7 +858,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>123</y>
+ <y>268</y>
</hint>
<hint type="destinationlabel">
<x>1181</x>
@@ -769,7 +874,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>157</y>
+ <y>302</y>
</hint>
<hint type="destinationlabel">
<x>1037</x>
@@ -785,7 +890,7 @@
<hints>
<hint type="sourcelabel">
<x>944</x>
- <y>130</y>
+ <y>113</y>
</hint>
<hint type="destinationlabel">
<x>707</x>
@@ -801,7 +906,7 @@
<hints>
<hint type="sourcelabel">
<x>909</x>
- <y>55</y>
+ <y>200</y>
</hint>
<hint type="destinationlabel">
<x>400</x>
@@ -817,7 +922,7 @@
<hints>
<hint type="sourcelabel">
<x>909</x>
- <y>89</y>
+ <y>234</y>
</hint>
<hint type="destinationlabel">
<x>464</x>
@@ -833,7 +938,7 @@
<hints>
<hint type="sourcelabel">
<x>909</x>
- <y>123</y>
+ <y>268</y>
</hint>
<hint type="destinationlabel">
<x>798</x>
@@ -849,7 +954,7 @@
<hints>
<hint type="sourcelabel">
<x>909</x>
- <y>157</y>
+ <y>302</y>
</hint>
<hint type="destinationlabel">
<x>970</x>
@@ -865,7 +970,7 @@
<hints>
<hint type="sourcelabel">
<x>1313</x>
- <y>76</y>
+ <y>68</y>
</hint>
<hint type="destinationlabel">
<x>1737</x>
@@ -881,7 +986,7 @@
<hints>
<hint type="sourcelabel">
<x>1430</x>
- <y>76</y>
+ <y>68</y>
</hint>
<hint type="destinationlabel">
<x>1796</x>
@@ -897,7 +1002,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>191</y>
+ <y>336</y>
</hint>
<hint type="destinationlabel">
<x>1209</x>
@@ -913,7 +1018,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>225</y>
+ <y>370</y>
</hint>
<hint type="destinationlabel">
<x>1247</x>
@@ -929,7 +1034,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>259</y>
+ <y>404</y>
</hint>
<hint type="destinationlabel">
<x>1142</x>
@@ -945,7 +1050,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>293</y>
+ <y>438</y>
</hint>
<hint type="destinationlabel">
<x>1322</x>
@@ -961,7 +1066,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>327</y>
+ <y>472</y>
</hint>
<hint type="destinationlabel">
<x>1259</x>
@@ -977,7 +1082,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>361</y>
+ <y>506</y>
</hint>
<hint type="destinationlabel">
<x>1588</x>
@@ -993,7 +1098,7 @@
<hints>
<hint type="sourcelabel">
<x>995</x>
- <y>395</y>
+ <y>540</y>
</hint>
<hint type="destinationlabel">
<x>1674</x>
@@ -1008,8 +1113,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>977</x>
- <y>417</y>
+ <x>995</x>
+ <y>574</y>
</hint>
<hint type="destinationlabel">
<x>1611</x>
@@ -1024,8 +1129,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>933</x>
- <y>437</y>
+ <x>995</x>
+ <y>608</y>
</hint>
<hint type="destinationlabel">
<x>1711</x>
@@ -1040,8 +1145,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>968</x>
- <y>484</y>
+ <x>995</x>
+ <y>642</y>
</hint>
<hint type="destinationlabel">
<x>1642</x>
@@ -1056,8 +1161,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>945</x>
- <y>513</y>
+ <x>995</x>
+ <y>676</y>
</hint>
<hint type="destinationlabel">
<x>1579</x>
@@ -1072,8 +1177,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>966</x>
- <y>559</y>
+ <x>995</x>
+ <y>710</y>
</hint>
<hint type="destinationlabel">
<x>1734</x>
@@ -1088,8 +1193,8 @@
<slot>doHelp()</slot>
<hints>
<hint type="sourcelabel">
- <x>922</x>
- <y>586</y>
+ <x>995</x>
+ <y>744</y>
</hint>
<hint type="destinationlabel">
<x>1734</x>
@@ -1097,6 +1202,102 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>pcs_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>984</x>
+ <y>181</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1735</x>
+ <y>195</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>pcsemi_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>990</x>
+ <y>220</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1678</x>
+ <y>257</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>pcctmc_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>981</x>
+ <y>253</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1454</x>
+ <y>274</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>pcntmc_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>974</x>
+ <y>287</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1486</x>
+ <y>295</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>pctrmm_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>989</x>
+ <y>323</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1511</x>
+ <y>354</y>
+ </hint>
+ </hints>
+ </connection>
+ <connection>
+ <sender>pntrmm_push_button</sender>
+ <signal>clicked()</signal>
+ <receiver>EditTandemPresetView</receiver>
+ <slot>doHelp()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>968</x>
+ <y>358</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1577</x>
+ <y>370</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>doCopy()</slot>
diff --git a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
index a60263cca8e29f12e51d4049f4f74c1b98fd8ce5..b6669878099a08ce0ea10f725946b110f8a63c21 100644
--- a/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
+++ b/src/gui/edit_tandem_preset_dialog/edittandempresetdialog.cpp
@@ -245,6 +245,32 @@ void EditTandemPresetDialog::doHelp() {
{
html_doc.setFileName(":/tandem/resources/html_doc/st.html");
}
+ if(senderObjName == "pcs_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/pcs.html");
+ }
+ if(senderObjName == "pcsemi_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/pcsemi.html");
+ }
+
+ if(senderObjName == "pcctmc_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/pcctmc.html");
+ }
+ if(senderObjName == "pcntmc_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/pcntmc.html");
+ }
+ if(senderObjName == "pctrmm_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/pctrmm.html");
+ }
+ if(senderObjName == "pntrmm_push_button")
+ {
+ html_doc.setFileName(":/tandem/resources/html_doc/pntrmm.html");
+ }
+
if (html_doc.open(QFile::ReadOnly | QFile::Text)) {
QTextStream in(&html_doc);
@@ -285,6 +311,13 @@ void EditTandemPresetDialog::readUi() {
_tandem_params.setParamLabelValue("spectrum, use contrast angle", ui->suca_combo_box->currentText());
_tandem_params.setParamLabelValue("spectrum, threads", ui->st_edit->text());
+
+ _tandem_params.setParamLabelValue("protein, cleavage site", ui->pcs_edit->text());
+ _tandem_params.setParamLabelValue("protein, cleavage semi", ui->pcsemi_combo_box->currentText());
+ _tandem_params.setParamLabelValue("protein, cleavage C-terminal mass change", ui->pcctmc_edit->text());
+ _tandem_params.setParamLabelValue("protein, cleavage N-terminal mass change", ui->pcntmc_edit->text());
+
+
}
catch (pappso::PappsoException & error) {
QMessageBox::warning(this,tr("Error in parameters :"), error.qwhat());
@@ -348,7 +381,7 @@ void EditTandemPresetDialog::populate() {
ui->smfmz_edit->setText(_tandem_params.getValue("spectrum, minimum fragment mz"));
//<note type="input" label="spectrum, minimum parent m+h">500.0</note>
ui->smpmh_edit->setText(_tandem_params.getValue("spectrum, minimum parent m+h"));
-
+
//<note type="input" label="spectrum, sequence batch size">1000</note>
ui->spsbs_edit->setText(_tandem_params.getValue("spectrum, sequence batch size"));
//<note type="input" label="spectrum, use contrast angle">no</note>
@@ -358,6 +391,26 @@ void EditTandemPresetDialog::populate() {
}
//<note type="input" label="spectrum, threads">1</note>
ui->st_edit->setText(_tandem_params.getValue("spectrum, threads"));
+
+
+ //<note type="input" label="protein, cleavage site">[RK]|{P}</note>
+ ui->pcs_edit->setText(_tandem_params.getValue("protein, cleavage site"));
+ //<note type="input" label="protein, cleavage semi">no</note>
+ index = ui->pcsemi_combo_box->findText(_tandem_params.getValue("protein, cleavage semi"));
+ if ( index != -1 ) { // -1 for not found
+ ui->pcsemi_combo_box->setCurrentIndex(index);
+ }
+
+
+ //<note type="input" label="protein, cleavage C-terminal mass change">+17.00305</note>
+ ui->pcctmc_edit->setText(_tandem_params.getValue("protein, cleavage C-terminal mass change"));
+ //<note type="input" label="protein, cleavage N-terminal mass change">+1.00794</note>
+ ui->pcntmc_edit->setText(_tandem_params.getValue("protein, cleavage N-terminal mass change"));
+
+ //<note type="input" label="protein, C-terminal residue modification mass">0.0</note>
+ ui->pctrmm_edit->setText(_tandem_params.getValue("protein, C-terminal residue modification mass"));
+ //<note type="input" label="protein, N-terminal residue modification mass">0.0</note>
+ ui->pntrmm_edit->setText(_tandem_params.getValue("protein, N-terminal residue modification mass"));
qDebug() << "EditTandemPresetDialog::populate end";
}