New upstream version 0.4.9

src/core/proteinmatch.h

@@ -33,8 +33,7 @@
 #include "../utils/groupstore.h"
 #include "../grouping/groupinggroup.h"
 
-#ifndef PROTEINMATCH_H
-#define PROTEINMATCH_H
+#pragma once
 
 class IdentificationGroup;
 
@@ -222,5 +221,3 @@ class ProteinMatch
    */
   bool _proxy_valid = false;
 };
-
-#endif // PROTEINMATCH_H

src/core/proteinxtp.cpp

@@ -39,6 +39,15 @@ DbXref::DbXref(const DbXref &other)
   : database(other.database), accession(other.accession)
 {
 }
+
+DbXref &
+DbXref::operator=(const DbXref &other)
+{
+  database  = other.database;
+  accession = other.accession;
+  return *this;
+}
+
 const QUrl
 DbXref::getUrl() const
 {

src/core/proteinxtp.h

@@ -38,6 +38,7 @@ struct DbXref
   DbXref();
   DbXref(const DbXref &other);
   DbXref(ExternalDatabase database_in, const QString &accession_in);
+  DbXref &operator=(const DbXref &);
   const QUrl getUrl() const;
   ExternalDatabase database;
   QString accession;

src/gui/peptide_list_view/peptidelistwindow.cpp

@@ -104,22 +104,15 @@ PeptideListWindow::PeptideListWindow(ProjectWindow *parent)
 
   QSettings settings;
   bool hide = settings.value("peptideview/hidenotvalid", "true").toBool();
-  if(hide)
-    {
-      ui->actionValid_peptides->setChecked(Qt::Checked);
-    }
+  ui->actionValid_peptides->setChecked(hide);
   _p_proxy_model->hideNotValid(hide);
   hide = settings.value("peptideview/hidenotchecked", "false").toBool();
-  if(hide)
-    {
-      ui->actionChecked_peptides->setChecked(Qt::Checked);
-    }
+  ui->actionChecked_peptides->setChecked(hide);
   _p_proxy_model->hideNotChecked(hide);
   hide = settings.value("peptideview/hidenotgrouped", "false").toBool();
-  if(hide)
-    {
-      ui->actionGrouped_peptides->setChecked(Qt::Checked);
-    }
+
+  ui->actionGrouped_peptides->setChecked(hide);
+
   _p_proxy_model->hideNotGrouped(hide);
 
   ui->scan_number_edit->setVisible(false);

src/gui/protein_list_view/proteinlistwindow.cpp

@@ -94,22 +94,13 @@ ProteinListWindow::ProteinListWindow(ProjectWindow *parent)
 
   QSettings settings;
   bool hide = settings.value("proteinview/hidenotvalid", "true").toBool();
-  if(hide)
-    {
-      ui->actionValid_proteins->setChecked(Qt::Checked);
-    }
+  ui->actionValid_proteins->setChecked(hide);
   _p_proxy_model->hideNotValid(hide);
   hide = settings.value("proteinview/hidenotchecked", "false").toBool();
-  if(hide)
-    {
-      ui->actionChecked_proteins->setChecked(Qt::Checked);
-    }
+  ui->actionChecked_proteins->setChecked(hide);
   _p_proxy_model->hideNotChecked(hide);
   hide = settings.value("proteinview/hidenotgrouped", "false").toBool();
-  if(hide)
-    {
-      ui->actionGrouped_proteins->setChecked(Qt::Checked);
-    }
+  ui->actionGrouped_proteins->setChecked(hide);
   _p_proxy_model->hideNotGrouped(hide);
 
 

src/output/proticdbml.cpp

@@ -11,7 +11,7 @@
  * This file is part of XTPcpp.
  *
  *     XTPcpp is free software: you can redistribute it and/or modify
- *     it under the terms of the GNU General Public License as published by
+ *     it under the terms of the GNU General Public License as published
  *     the Free Software Foundation, either version 3 of the License, or
  *     (at your option) any later version.
  *
@@ -513,6 +513,13 @@ getProticPeptideHitKey(const PeptideEvidence *p_peptide_evidence)
 
 struct ProticPeptideHit
 {
+  ProticPeptideHit(QString ikey, PeptideMatch ipeptide_match)
+    : key(ikey), peptide_match(ipeptide_match){};
+  ProticPeptideHit(const ProticPeptideHit &other)
+  {
+    key           = other.key;
+    peptide_match = other.peptide_match;
+  };
   bool
   operator==(const ProticPeptideHit &other) const
   {