update citation info to OpenMS 3 for GUI apps (OpenMS#7590)

* open idXML in same layer as underlying data, if raw mzML is detected in idXML meta data

* update citation info to OpenMS 3  for GUI apps

* better formatting

* Update OpenMSInfo.cpp

---------

Co-authored-by: Samuel Wein <sam@samwein.com>

src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h

@@ -188,6 +188,9 @@ namespace OpenMS
     /// Returns a link to the documentation of the tool (accessible on our servers and only after inclusion in the nightly branch or a release).
     String getDocumentationURL() const;
 
+    /// The latest and greatest OpenMS citation
+    static const Citation cite_openms;
+
   private:
     /// Tool name.  This is assigned once and for all in the constructor.
     String const tool_name_;
@@ -960,9 +963,6 @@ namespace OpenMS
     /// .TOPP.ini file for storing system default parameters
     static String topp_ini_file_;
 
-    /// The OpenMS citation
-    static const Citation cite_openms_;
-
     /// Debug level set by -debug
     Int debug_level_;
 private:

src/openms/source/APPLICATIONS/TOPPBase.cpp

@@ -69,7 +69,7 @@ namespace OpenMS
   using namespace Exception;
 
   String TOPPBase::topp_ini_file_ = String(QDir::homePath()) + "/.TOPP.ini";
-  const Citation TOPPBase::cite_openms_
+  const Citation TOPPBase::cite_openms
     = {"Pfeuffer, J., Bielow, C., Wein, S. et al.", "OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data",
        "Nat Methods (2024)", "10.1038/s41592-024-02197-7"};
 
@@ -571,7 +571,7 @@ namespace OpenMS
        << bright("Full documentation: ") << underline(docurl)  // the space is needed, otherwise the remaining line will be underlined on Windows..
        << "\n"
        << bright("Version: ") << verboseVersion_ << "\n"
-       << bright("To cite OpenMS:\n") << " + " << is.indent(3) << cite_openms_.toString() 
+       << bright("To cite OpenMS:\n") << " + " << is.indent(3) << cite_openms.toString() 
        << is.indent(0) << "\n";
     if (!citations_.empty())
     {
@@ -2402,7 +2402,7 @@ namespace OpenMS
       // collect citation information
       std::vector<std::string> citation_dois;
       citation_dois.reserve(citations_.size() + 1);
-      citation_dois.push_back(cite_openms_.doi);
+      citation_dois.push_back(cite_openms.doi);
       for (auto& citation : citations_)
       {
         citation_dois.push_back(citation.doi);

src/openms_gui/source/VISUAL/APPLICATIONS/MISC/QApplicationTOPP.cpp

@@ -9,6 +9,7 @@
 #include <cstdio>
 #include <cstdlib>
 
+#include <OpenMS/APPLICATIONS/TOPPBase.h>
 #include <OpenMS/CONCEPT/Exception.h>
 #include <OpenMS/CONCEPT/LogStream.h>
 #include <OpenMS/CONCEPT/VersionInfo.h>
@@ -116,24 +117,23 @@ namespace OpenMS
 
     // text
     QString text = QString("<BR>"
-      "<FONT size=+3>%1</font><BR>"
-      "<BR>"
-      "Version %2 %3"
-      "<BR>"
-      "OpenMS and TOPP is free software available under the<BR>"
-      "BSD 3-Clause License (BSD-new)<BR>"
-      "<BR>"
-      "<BR>"
-      "<BR>"
-      "<BR>"
-      "<BR>"
-      "Any published work based on TOPP and OpenMS shall cite these papers:<BR>"
-      "Roest, Sachsenberg, Aiche, Bielow, Weisser et al., Nat Methods (2016), 13(9):741-748<BR>"
-      "Kohlbacher et al., Bioinformatics (2007), 23:e191-e197<BR>")
+                           "<FONT size=+3>%1</font><BR>"
+                           "<BR>"
+                           "Version %2 %3"
+                           "<BR>"
+                           "OpenMS and TOPP is free software available under the<BR>"
+                           "BSD 3-Clause License (BSD-new)<BR>"
+                           "<BR>"
+                           "<BR>"
+                           "<BR>"
+                           "<BR>"
+                           "<BR>"
+                           "Any published work based on TOPP and OpenMS shall cite:<BR>%4")
     .arg(toolname)
     .arg(VersionInfo::getVersion().toQString())
     .arg( // if we have a revision, embed it also into the shown version number
-      VersionInfo::getRevision().empty() ? "" : QString(" (") + VersionInfo::getRevision().toQString() + ")");
+      VersionInfo::getRevision().empty() ? "" : QString(" (") + VersionInfo::getRevision().toQString() + ")")
+    .arg((TOPPBase::cite_openms.title + "<BR>" + TOPPBase::cite_openms.when_where + "<BR>doi:" + TOPPBase::cite_openms.doi).c_str());
 
     label = new QLabel(text, dlg);
 

src/topp/OpenMSInfo.cpp

@@ -111,7 +111,7 @@ class TOPPOpenMSInfo : public TOPPBase
        << underline(TOPPBase::getDocumentationURL()) << " " // the space is needed ...
        << '\n'
        << bright("To cite OpenMS:\n") << " + "
-       << is.indent(3) << cite_openms_.toString() << is.indent(0);
+       << is.indent(3) << cite_openms.toString() << is.indent(0);
 
     is << "\n\n"
        << green("<< OpenMS Version >>\n")