Commit 5bc1c1e1 authored by Renne Thomas's avatar Renne Thomas
Browse files

Remove noise suppression

parent 60bbae60
......@@ -185,7 +185,6 @@ TandemParameters::setParamLabelValue(const QString &label, const QString &value)
(label == "output, parameters") || (label == "output, performance") ||
(label == "output, histograms") ||
(label == "output, path hashing") ||
(label == "spectrum, use noise suppression") ||
(label == "spectrum, use conditioning") ||
(label == "protein, homolog management") ||
(label == "protein, use minimal annotations") ||
......
......@@ -106,7 +106,7 @@
<item>
<widget class="QTabWidget" name="tabWidget">
<property name="currentIndex">
<number>2</number>
<number>5</number>
</property>
<widget class="QWidget" name="spectrum_tab">
<property name="sizePolicy">
......@@ -137,9 +137,9 @@
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<y>-199</y>
<width>992</width>
<height>680</height>
<height>655</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout_3">
......@@ -663,13 +663,6 @@
</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>
......@@ -690,49 +683,8 @@
</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>
<layout class="QHBoxLayout" name="horizontalLayout_37"/>
</item>
</layout>
</item>
......@@ -4310,22 +4262,6 @@
</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>
......@@ -4338,38 +4274,38 @@
<slot>doSelectDir()</slot>
</slots>
<buttongroups>
<buttongroup name="pqa_button_group"/>
<buttongroup name="buttonGroup_8"/>
<buttongroup name="pstpb_button_group"/>
<buttongroup name="szi_button_group"/>
<buttongroup name="pcsemi_button_group"/>
<buttongroup name="sir_button_group"/>
<buttongroup name="ospec_button_group"/>
<buttongroup name="rpm_button_group"/>
<buttongroup name="buttonGroup_2"/>
<buttongroup name="refine_button_group"/>
<buttongroup name="sbi_button_group"/>
<buttongroup name="sai_button_group"/>
<buttongroup name="buttonGroup_5"/>
<buttongroup name="rupmffr_button_group"/>
<buttongroup name="pcsemi_button_group"/>
<buttongroup name="spmmeu_button_group"/>
<buttongroup name="buttonGroup_7"/>
<buttongroup name="pstpb_button_group"/>
<buttongroup name="buttonGroup_4"/>
<buttongroup name="buttonGroup_3"/>
<buttongroup name="buttonGroup_6"/>
<buttongroup name="pqp_button_group"/>
<buttongroup name="buttonGroup"/>
<buttongroup name="pqa_button_group"/>
<buttongroup name="buttonGroup_7"/>
<buttongroup name="szi_button_group"/>
<buttongroup name="scp_button_group"/>
<buttongroup name="spmmie_button_group"/>
<buttongroup name="rss_button_group"/>
<buttongroup name="ruc_button_group"/>
<buttongroup name="buttonGroup_4"/>
<buttongroup name="rcsemi_button_group"/>
<buttongroup name="sci_button_group"/>
<buttongroup name="rupmffr_button_group"/>
<buttongroup name="sxi_button_group"/>
<buttongroup name="suca_button_group"/>
<buttongroup name="buttonGroup_3"/>
<buttongroup name="oresu_button_group"/>
<buttongroup name="pqp_button_group"/>
<buttongroup name="sir_button_group"/>
<buttongroup name="buttonGroup_8"/>
<buttongroup name="ospec_button_group"/>
<buttongroup name="sunlw_button_group"/>
<buttongroup name="scp_button_group"/>
<buttongroup name="refine_button_group"/>
<buttongroup name="buttonGroup"/>
<buttongroup name="sfmmeu_button_group"/>
<buttongroup name="spmmie_button_group"/>
<buttongroup name="rcsemi_button_group"/>
<buttongroup name="rpm_button_group"/>
<buttongroup name="suca_button_group"/>
<buttongroup name="buttonGroup_5"/>
<buttongroup name="syi_button_group"/>
<buttongroup name="sbi_button_group"/>
<buttongroup name="buttonGroup_2"/>
<buttongroup name="rss_button_group"/>
</buttongroups>
</ui>
......@@ -319,10 +319,6 @@ EditTandemPresetDialog::doHelp()
{
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");
......@@ -625,15 +621,6 @@ EditTandemPresetDialog::readUi()
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",
......@@ -943,15 +930,7 @@ EditTandemPresetDialog::populate()
{
ui->snlm_edit->setText("0.02");
}
//<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"));
......
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html>
<head>
<title>spectrum, use noise suppression</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css">
a {
color: blue;
cursor: pointer;
font-weight: normal;
font-family: Verdana, Arial, Helvetica,sans-serif;
text-decoration: none;
font-size: 10pt;
}
a:visited {
color: blue;
cursor: pointer;
font-weight: normal;
font-style: italic;
text-decoration: underline;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
}
h1 {
color: black;
font-weight: bold;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
h2 {
color: black;
font-weight: bold;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
p {
color: black;
font-weight: normal;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
.also {
color: black;
font-weight: normal;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
li {
color: black;
font-weight: normal;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
.e {
color: red;
font-style: italic;
font-weight: normal;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
.v {
color: red;
font-style: normal;
font-weight: bold;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
margin-bottom:10px;
}
PRE {
margin:0px;
display:inline
}
td {
color: black;
font-weight: normal;
font-family: Verdana, Arial, Helvetica,sans-serif;
font-size: 10pt;
}
</style>
</head>
<body bgcolor="#FFFFFF" text="#000000">
<table>
<tr>
<td align="left" valign="top"><h1>spectrum, use noise suppression</h1>
<h2>Syntax</h2>
<p>The parameter can have the values <span class="v">yes</span> or <span class="v">no</span>.</p>
<h2>Notes</h2>
<ol>
<li>No error message is generated when an uninterpretable value is entered for this parameter.</li>
<li>A default value of <span class="v">no</span> is substituted if the parameter cannot be interpreted or is absent.</li>
</ol>
<h2>Description</h2>
<p>X! TANDEM uses several mechanisms to attempt to reduce the number of spectra considered in a list
of spectra. When this parameter is set to <span class="v">yes</span>, spectra that fit the pattern
of "noise" - spectra caused by the fragmentation of chemical noise peaks - are rejected without
further analysis. This feature can be very useful when dealling with large amounts of data from
automated LC/MS experiments. Some experimentation may be required to determine what settings
are appropriate for the noise detection filters (see the links below). Setting the parameter to
<span class="v">no</span> skips the noise filters and allows all spectra to be modelled.</p>
<hr align="left" width="200">
<span class="also">see also:<a href="smpmh.html">spectrum, minimum parent m+h</a> |
<a href="smp.html">spectrum, minimum peaks</a>
</span>
<br><br><a href="index.html">X! TANDEM API description project</a>
</td></tr></table>
</body>
</html>
......@@ -11,7 +11,6 @@
<note type="input" label="spectrum, use neutral loss window">yes</note>
<note type="input" label="spectrum, neutral loss mass">18.01057</note>
<note type="input" label="spectrum, neutral loss window">0.02</note>
<note type="input" label="spectrum, use noise suppression">yes</note>
<note type="input" label="spectrum, dynamic range">100.0</note>
<note type="input" label="spectrum, total peaks">100</note>
<note type="input" label="spectrum, minimum peaks">15</note>
......
......@@ -2,6 +2,7 @@
<qresource prefix="/tandem">
<file>resources/html_doc/lpdp.html</file>
<file>resources/html_doc/lpti.html</file>
<file>resources/html_doc/mzid.html</file>
<file>resources/html_doc/ohcw.html</file>
<file>resources/html_doc/ohist.html</file>
<file>resources/html_doc/olp.html</file>
......@@ -81,7 +82,6 @@
<file>resources/html_doc/stp.html</file>
<file>resources/html_doc/suca.html</file>
<file>resources/html_doc/sunlw.html</file>
<file>resources/html_doc/suns.html</file>
<file>resources/html_doc/sxi.html</file>
<file>resources/html_doc/syi.html</file>
<file>resources/html_doc/szi.html</file>
......
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