From 135206c2dbc190a23a04574243e90e7eceb78258 Mon Sep 17 00:00:00 2001
From: Filippo Rusconi <lopippo@debian.org>
Date: Mon, 9 Nov 2020 13:46:00 +0100
Subject: [PATCH] Fix all typos as reported by lintian.
---
src/core/tandem_run/tandemcondorprocess.cpp | 2 +-
src/core/tandem_run/tandemcondorprocess.h | 2 +-
src/gui/about_dialog/about_dialog.ui | 2 +-
.../edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui | 2 +-
.../export_masschroq_dialog/masschroqfileparameters.cpp | 2 +-
.../export_masschroq_dialog/masschroqfileparameters.h | 2 +-
src/gui/tandem_run_dialog/tandem_run_dialog.ui | 2 +-
src/gui/tandem_run_dialog/tandemrundialog.cpp | 2 +-
src/gui/widgets/engines_view/xtandem_view_widget.ui | 2 +-
src/input/xtandemsaxhandler.cpp | 2 +-
src/output/ods/infosheet.cpp | 2 +-
src/output/proticdbml.cpp | 2 +-
src/resources/html_doc/refmm.html | 2 +-
src/resources/html_doc/refpmmotif.html | 2 +-
src/resources/html_doc/rmm.html | 2 +-
src/resources/html_doc/rpmm.html | 2 +-
src/resources/html_doc/rpmmotif.html | 2 +-
src/resources/html_doc/rsp.html | 2 +-
src/resources/html_doc/rtp.html | 2 +-
src/resources/html_doc/sfmt.html | 6 +++---
src/resources/html_doc/smic.html | 2 +-
src/resources/html_doc/smpc.html | 2 +-
src/resources/html_doc/smpmh.html | 2 +-
src/resources/html_doc/sp.html | 2 +-
src/resources/html_doc/spt.html | 2 +-
src/resources/html_doc/st.html | 2 +-
26 files changed, 28 insertions(+), 28 deletions(-)
diff --git a/src/core/tandem_run/tandemcondorprocess.cpp b/src/core/tandem_run/tandemcondorprocess.cpp
index 8c0fd97b..1462561a 100644
--- a/src/core/tandem_run/tandemcondorprocess.cpp
+++ b/src/core/tandem_run/tandemcondorprocess.cpp
@@ -2,7 +2,7 @@
* \file /core/tandem_run/tandemcondorprocess.cpp
* \date 5/9/2017
* \author Olivier Langella
- * \brief handles execution of a bunch of X!Tandem process throught condor job
+ * \brief handles execution of a bunch of X!Tandem process through condor job
*/
/*******************************************************************************
diff --git a/src/core/tandem_run/tandemcondorprocess.h b/src/core/tandem_run/tandemcondorprocess.h
index fd1c45d3..bb5c8ea6 100644
--- a/src/core/tandem_run/tandemcondorprocess.h
+++ b/src/core/tandem_run/tandemcondorprocess.h
@@ -2,7 +2,7 @@
* \file /core/tandem_run/tandemcondorprocess.h
* \date 5/9/2017
* \author Olivier Langella
- * \brief handles execution of a bunch of X!Tandem process throught condor job
+ * \brief handles execution of a bunch of X!Tandem process through condor job
*/
/*******************************************************************************
diff --git a/src/gui/about_dialog/about_dialog.ui b/src/gui/about_dialog/about_dialog.ui
index 5e05f8b2..17303e34 100644
--- a/src/gui/about_dialog/about_dialog.ui
+++ b/src/gui/about_dialog/about_dialog.ui
@@ -75,7 +75,7 @@
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Cantarell'; font-size:11pt; font-weight:400; font-style:normal;">
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">X!TandemPipeline C++ is developped by PAPPSO team (<a href="http://pappso.inra.fr"><span style=" text-decoration: underline; color:#0000ff;">http://pappso.inra.fr</span></a>).</p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">X!TandemPipeline C++ is developed by PAPPSO team (<a href="http://pappso.inra.fr"><span style=" text-decoration: underline; color:#0000ff;">http://pappso.inra.fr</span></a>).</p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This software is distributed under the terms of the GNU General Public License.</p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
diff --git a/src/gui/edit/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui b/src/gui/edit/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
index 14cc53ad..fce14fe4 100644
--- a/src/gui/edit/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
+++ b/src/gui/edit/edit_tandem_preset_dialog/edit_tandem_preset_dialog.ui
@@ -3479,7 +3479,7 @@
<item row="7" column="0">
<widget class="QLabel" name="label_71">
<property name="text">
- <string>Write spectrum informations</string>
+ <string>Write spectrum information</string>
</property>
</widget>
</item>
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
index 8fef08b5..56fe293b 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
@@ -2,7 +2,7 @@
* \file gui/export/export_masschroq_dialog/masschroqfileparameters.cpp
* \date 25/01/2019
* \author Olivier Langella
- * \brief all needed informations to write a MassChroqML file
+ * \brief all needed information to write a MassChroqML file
*/
/*******************************************************************************
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
index 9015506e..99c3716d 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
@@ -2,7 +2,7 @@
* \file gui/export/export_masschroq_dialog/masschroqfileparameters.h
* \date 25/01/2019
* \author Olivier Langella
- * \brief all needed informations to write a MassChroqML file
+ * \brief all needed information to write a MassChroqML file
*/
/*******************************************************************************
diff --git a/src/gui/tandem_run_dialog/tandem_run_dialog.ui b/src/gui/tandem_run_dialog/tandem_run_dialog.ui
index 4856d680..62ada811 100644
--- a/src/gui/tandem_run_dialog/tandem_run_dialog.ui
+++ b/src/gui/tandem_run_dialog/tandem_run_dialog.ui
@@ -103,7 +103,7 @@
<item>
<widget class="QGroupBox" name="use_htcondor_groupbox">
<property name="title">
- <string>&run X!Tandem throught HTCondor</string>
+ <string>&run X!Tandem through HTCondor</string>
</property>
<property name="checkable">
<bool>true</bool>
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index ee4d5c24..8a30342d 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -438,7 +438,7 @@ TandemRunDialog::selectTdfFolder()
{
throw pappso::PappsoException(
tr(
- "The directory %1/ dosent contain the mandatory analysis.tdf "
+ "The directory %1/ does not contain the mandatory analysis.tdf "
"file")
.arg(directory_name));
}
diff --git a/src/gui/widgets/engines_view/xtandem_view_widget.ui b/src/gui/widgets/engines_view/xtandem_view_widget.ui
index a89bb068..a1c852b4 100644
--- a/src/gui/widgets/engines_view/xtandem_view_widget.ui
+++ b/src/gui/widgets/engines_view/xtandem_view_widget.ui
@@ -3338,7 +3338,7 @@
<item row="7" column="0">
<widget class="QLabel" name="writeSpectrumInformationsLabel">
<property name="text">
- <string>Write spectrum informations</string>
+ <string>Write spectrum information</string>
</property>
</widget>
</item>
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 4508cec2..f6e3068b 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -392,7 +392,7 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
_p_peptide_evidence->setChecked(true);
- // missing informations
+ // missing information
// peptide.set_hypercorr(Float.valueOf(attrs.getValue("hyperscore")));
// peptide.set_pre(attrs.getValue("pre"));
// peptide.set_post(attrs.getValue("post"));
diff --git a/src/output/ods/infosheet.cpp b/src/output/ods/infosheet.cpp
index 16509051..790ffb2e 100644
--- a/src/output/ods/infosheet.cpp
+++ b/src/output/ods/infosheet.cpp
@@ -41,7 +41,7 @@ InfoSheet::InfoSheet(OdsExport *p_ods_export,
{
_p_ods_export = p_ods_export;
_p_writer = p_writer;
- p_writer->writeSheet("X!TandemPipeline informations");
+ p_writer->writeSheet("X!TandemPipeline information");
p_writer->writeCell("X!TandemPipeline version :");
p_writer->writeLine();
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index 3b0ffe73..0642df8a 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -412,7 +412,7 @@ ProticdbMl::writeIdentificationRun(IdentificationGroup *p_identification)
*/
_output_stream->writeEndElement(); // admin
- // if we can retrieve original informations in xml xtandem results
+ // if we can retrieve original information in xml xtandem results
//
for(IdentificationDataSource *p_identification_data_source :
p_identification->getIdentificationDataSourceList())
diff --git a/src/resources/html_doc/refmm.html b/src/resources/html_doc/refmm.html
index b937a0c3..a6f9c447 100644
--- a/src/resources/html_doc/refmm.html
+++ b/src/resources/html_doc/refmm.html
@@ -149,7 +149,7 @@ has been added. To specify additional sets of modifications, use the same parame
<p>The values for these parameters uses the same syntax as the normal command. Each of these modification sets is applied
one at a time to the peptides in a sequence file. Processing of these commands stops when a count value is missed (<i>e.g.</i>, if there is a "1"
but no "2" then processing stops at "1" even if there is a "3" in the command file).
-Processing is also stoped with a parameter has a zero length string value associated with it. Non-zero length strings that cannot be interpretted as modifications are interpretted as
+Processing is also stopped with a parameter has a zero length string value associated with it. Non-zero length strings that cannot be interpretted as modifications are interpretted as
no modifications, <i>i.e.</i>, the peptides with be tested for the case where no complete modifications are set.
<h2>Notes:</h2>
<ol>
diff --git a/src/resources/html_doc/refpmmotif.html b/src/resources/html_doc/refpmmotif.html
index a5b2a7cf..f55c5fec 100644
--- a/src/resources/html_doc/refpmmotif.html
+++ b/src/resources/html_doc/refpmmotif.html
@@ -130,7 +130,7 @@ below.</p>
</ol>
<h2>Description</h2>
<p>This parameter is used to modify residues selected by the residues surrounding the site of
-modification. Many biologically relavent modifications are performed by enzymes, which
+modification. Many biologically relevant modifications are performed by enzymes, which
are normally affected by the sequence surrounding a residue being modified. Finding sequence
motifs is fairly time consuming, so it is best done in the refinement process.</p>
diff --git a/src/resources/html_doc/rmm.html b/src/resources/html_doc/rmm.html
index b94545a6..34df8541 100644
--- a/src/resources/html_doc/rmm.html
+++ b/src/resources/html_doc/rmm.html
@@ -143,7 +143,7 @@ has been added. To specify additional sets of modifications, use the same parame
<p>The values for these parameters uses the same syntax as the normal command. Each of these modification sets is applied
one at a time to the peptides in a sequence file. Processing of these commands stops when a count value is missed (<i>e.g.</i>, if there is a "1"
but no "2" then processing stops at "1" even if there is a "3" in the command file).
-Processing is also stoped with a parameter has a zero length string value associated with it. Non-zero length strings that cannot be interpretted as modifications are interpretted as
+Processing is also stopped with a parameter has a zero length string value associated with it. Non-zero length strings that cannot be interpretted as modifications are interpretted as
no modifications, <i>i.e.</i>, the peptides with be tested for the case where no complete modifications are set.
<h2>Notes:</h2>
<ol>
diff --git a/src/resources/html_doc/rpmm.html b/src/resources/html_doc/rpmm.html
index 833be5c3..992991e0 100644
--- a/src/resources/html_doc/rpmm.html
+++ b/src/resources/html_doc/rpmm.html
@@ -116,7 +116,7 @@ X<sub>i</sub></span> is a single letter abbreviation for a type of amino acid re
<h2>Description</h2>
<p>In the course of isolating a protein and generating peptides for use in protein identification
experiments,some fraction of the residues of a particular type may be modified (<i>e.g.</i>, methionine
-residues are often oxidized). Additionally, other residues may be have been modified in the orginal
+residues are often oxidized). Additionally, other residues may be have been modified in the original
protein through a process commonly referred to as post-translational modification. These modifications
may be quite rare in a protein sample, but knowing which residues are modified in this way
may be very important biologically. These post-translational modifications are normally the
diff --git a/src/resources/html_doc/rpmmotif.html b/src/resources/html_doc/rpmmotif.html
index 0c063db5..fdfd9f74 100644
--- a/src/resources/html_doc/rpmmotif.html
+++ b/src/resources/html_doc/rpmmotif.html
@@ -129,7 +129,7 @@ below.</p>
</ol>
<h2>Description</h2>
<p>This parameter is used to modify residues selected by the residues surrounding the site of
-modification. Many biologically relavent modifications are performed by enzymes, which
+modification. Many biologically relevant modifications are performed by enzymes, which
are normally affected by the sequence surrounding a residue being modified. Finding sequence
motifs is fairly time consuming, so it is best done in the refinement process.</p>
diff --git a/src/resources/html_doc/rsp.html b/src/resources/html_doc/rsp.html
index c0e3f3cd..e32e53e7 100644
--- a/src/resources/html_doc/rsp.html
+++ b/src/resources/html_doc/rsp.html
@@ -116,7 +116,7 @@ sequence file, in valid BIOML format.</p>
<p>Just prior to executing the refinement steps of a search, a list of protein sequences to use
for the refinement steps is created. When this parameter is a valid input file path, that list of
proteins is altered by adding the sequences present in the input file. Repeated sequences are
-not included. The input file can either be an X! Tandem BIOML ouput file or a file generated by
+not included. The input file can either be an X! Tandem BIOML output file or a file generated by
the use of the <span class="e">output, sequence path</span> parameter. This sequence import step occurs
prior to the generation of a file by the use of the <span class="e">output, sequence path</span> parameter,
so using both parameters will generate an output file that is a composite of the sequences found
diff --git a/src/resources/html_doc/rtp.html b/src/resources/html_doc/rtp.html
index 4885fd40..310036b9 100644
--- a/src/resources/html_doc/rtp.html
+++ b/src/resources/html_doc/rtp.html
@@ -115,7 +115,7 @@ td {
<p>When X! Tandem is executing a refinement job, the number of protein sequences to be tested is
known. During the job, X! Tandem sends a dot "." character to the console (and log file, if desired)
when the fraction of the job corresponding to the value of this parameter has
-been finished. For exmaple, if this parameter is set to <span class="v">10</span>,
+been finished. For example, if this parameter is set to <span class="v">10</span>,
and 1000 protein sequences are being tested, then a character is sent to the
console every time <i>1000 x 10/100 = 100</i> sequences have been processed. The
total number of characters (tics) would be <i>10</i>.</p>
diff --git a/src/resources/html_doc/sfmt.html b/src/resources/html_doc/sfmt.html
index 2ef1f097..a96fbd2a 100644
--- a/src/resources/html_doc/sfmt.html
+++ b/src/resources/html_doc/sfmt.html
@@ -112,7 +112,7 @@ td {
<li>No error message is generated when a bad value is used for this parameter.</li>
</ol>
<h2>Description</h2>
-<p>Naturally occuring organic molecules do not have a single value corresponding to the "mass" of the molecule.
+<p>Naturally occurring organic molecules do not have a single value corresponding to the "mass" of the molecule.
Because organic molecules contain carbon, any collection of molecules will have some probability of containing one
or more <sup>13</sup>C atoms. In mass spectrometry, it is common to refer to the weighted average of all possible
<sup>13</sup>C-containing molecular masses as the "chemical" or "average" mass of the
@@ -120,8 +120,8 @@ molecule. When this parameter is set to <span class="v">average</span>, this wei
calculate the masses of the fragment ions in a tandem mass spectrum.</p>
<p>Most modern mass spectrometers have sufficient mass resolution so that the mass of each of the individual
<sup>13</sup>C-containing species can be measured separately. The lowest mass of these peaks will contain
-only <sup>12</sup>C atoms. This lowest mass peak in the isotopic distribution measured is commonly refered to
-as the "monoisotopic" mass for the molecule (also refered to as the A0 peak). When this parameter is
+only <sup>12</sup>C atoms. This lowest mass peak in the isotopic distribution measured is commonly referred to
+as the "monoisotopic" mass for the molecule (also referred to as the A0 peak). When this parameter is
set to <span class="v">monoisotopic</span>, this peak is used to define the mass of the fragment ions.</p>
<hr align="left" width="200">
<span class="also">see also: <a href="sfme.html">spectrum, fragment mass error</a> |
diff --git a/src/resources/html_doc/smic.html b/src/resources/html_doc/smic.html
index 36aa1521..636c9bdb 100644
--- a/src/resources/html_doc/smic.html
+++ b/src/resources/html_doc/smic.html
@@ -113,7 +113,7 @@ td {
<h2>Description</h2>
<p>Practically, there is some minimum number of assignable sequence-specific ions in a spectrum
that is necessary to consider the spectrum as a match to a peptide sequence. The value of this
-parameter sets the minumum number of total ions that must be assigned for a score to be calculated and stored
+parameter sets the minimum number of total ions that must be assigned for a score to be calculated and stored
in the scoring histogram structure used by TANDEM to track the statistical nature of the stochastic
distribution.</p>
diff --git a/src/resources/html_doc/smpc.html b/src/resources/html_doc/smpc.html
index d68d27cc..5d3029c7 100644
--- a/src/resources/html_doc/smpc.html
+++ b/src/resources/html_doc/smpc.html
@@ -112,7 +112,7 @@ td {
</ol>
<h2>Description</h2>
-<p>Each MS/MS spectrum whith a precursor charge higher than this thresold were not select for futher score calculation.</p>
+<p>Each MS/MS spectrum with a precursor charge higher than this thresold were not select for further score calculation.</p>
<hr align="left" width="200">
<span class="also">see also:
</span>
diff --git a/src/resources/html_doc/smpmh.html b/src/resources/html_doc/smpmh.html
index 52d50675..d970fad8 100644
--- a/src/resources/html_doc/smpmh.html
+++ b/src/resources/html_doc/smpmh.html
@@ -112,7 +112,7 @@ td {
<li>This parameter is not used if the value of <span class="e">spectrum, use noise suppression</span> = <span class="v">no</span>.
</ol>
<h2>Description</h2>
-<p>This parameter is used to supress the analysis of spectra that were generated by low
+<p>This parameter is used to suppress the analysis of spectra that were generated by low
mass parent ions. Depending on the instrumentation and excitation energy used to generate
fragment ions, there will be some low mass cutoff value, below which there is very little
chance of generating an interpretable MS/MS spectrum. In many experimental conditions, there
diff --git a/src/resources/html_doc/sp.html b/src/resources/html_doc/sp.html
index 7e816198..410f0fd7 100644
--- a/src/resources/html_doc/sp.html
+++ b/src/resources/html_doc/sp.html
@@ -128,7 +128,7 @@ data systems. Multiple spectra can be stored in a single file by concatenating s
DTA files together, leaving a blank line between spectra. Unlike DTA, the PKL format was originally
designed to be used to list multiple files.</li>
<li><b>MGF</b>: Mascot Generic Format is a multiple spectrum ASCII representation that was designed by
-Matrix Science as a replacment for platform-specific ASCII formats. It is well defined (
+Matrix Science as a replacement for platform-specific ASCII formats. It is well defined (
see the <a href="http://www.matrixscience.com">Matrix Science</a> web site) and it has a straightforward
syntax.</li>
<li><b>mzData</b>: mzData is an evolving XML standard for representing mass spectra. It is specified
diff --git a/src/resources/html_doc/spt.html b/src/resources/html_doc/spt.html
index 962877ca..099394a2 100644
--- a/src/resources/html_doc/spt.html
+++ b/src/resources/html_doc/spt.html
@@ -111,7 +111,7 @@ td {
<h2>Description</h2>
<p>When a spectrum listing file is imported into X! TANDEM, it is necessary to determine
the format of the file. The automatic routines in X! TANDEM should be able to discover if the
-format is acceptible, however it is possible that some files may be incorrectly typed. This
+format is acceptable, however it is possible that some files may be incorrectly typed. This
type of error can happen if the file is only near to the appropriate file format.
</p>
<p>The <span class="e">spectrum, path type</span> parameter can be used to override the format detection routines
diff --git a/src/resources/html_doc/st.html b/src/resources/html_doc/st.html
index 0f5d2ed7..51ef1952 100644
--- a/src/resources/html_doc/st.html
+++ b/src/resources/html_doc/st.html
@@ -103,7 +103,7 @@ td {
<tr>
<td align="left" valign="top"><h1>spectrum, threads</h1>
<h2>Syntax</h2>
-<p>The value of this paramter is a non-zero, positive integer in the range of
+<p>The value of this parameter is a non-zero, positive integer in the range of
<span class="v">1</span> to <span class="v">16</span>.</p>
<h2>Notes</h2>
<ol>
--
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