Fix all typos as reported by lintian.

135206c2 · Filippo Rusconi · 7380562b · 135206c2 · 135206c2 · 135206c2
Commit 135206c2 authored Nov 09, 2020 by Filippo Rusconi
--- 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
 */

 /*******************************************************************************

--- 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
 */

 /*******************************************************************************

--- a/src/gui/about_dialog/about_dialog.ui
+++ b/src/gui/about_dialog/about_dialog.ui
@@ -75,7 +75,7 @@
 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
 p, li { white-space: pre-wrap; }
 &lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'Cantarell'; font-size:11pt; font-weight:400; font-style:normal;&quot;&gt;
-&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;X!TandemPipeline C++ is developped by PAPPSO team (&lt;a href=&quot;http://pappso.inra.fr&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://pappso.inra.fr&lt;/span&gt;&lt;/a&gt;).&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;X!TandemPipeline C++ is developed by PAPPSO team (&lt;a href=&quot;http://pappso.inra.fr&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;http://pappso.inra.fr&lt;/span&gt;&lt;/a&gt;).&lt;/p&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;This software is distributed under the terms of the GNU General Public License.&lt;/p&gt;
 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;br /&gt;&lt;/p&gt;

--- 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>

--- 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
 */

 /*******************************************************************************

--- 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
 */

 /*******************************************************************************

--- 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>&amp;run X!Tandem throught HTCondor</string>
+                <string>&amp;run X!Tandem through HTCondor</string>
               </property>
               <property name="checkable">
                <bool>true</bool>

--- 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));
            }

--- 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>

--- 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"));

--- 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();

--- 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())

--- 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 &quot;1&quot;
 but no &quot;2&quot; then processing stops at &quot;1&quot; even if there is a &quot;3&quot; 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>

--- 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>


--- 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 &quot;1&quot;
 but no &quot;2&quot; then processing stops at &quot;1&quot; even if there is a &quot;3&quot; 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>

--- 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

--- 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>


--- 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

--- 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 &quot;.&quot; 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>

--- 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 &quot;mass&quot; of the molecule.
+<p>Naturally occurring organic molecules do not have a single value corresponding to the &quot;mass&quot; 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 &quot;chemical&quot; or &quot;average&quot; 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 &quot;monoisotopic&quot; 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 &quot;monoisotopic&quot; 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>  |