ClustalQtParams.h | 6 3 + 3 - 0 !
HelpDisplayWidget.cpp | 2 1 + 1 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-)

 hardcodes the location of help and color files to /usr/share/clustalx.
 When not patched, ClustalX will search for this files in the same
 directory as where the binary program is, but in Debian we do not
 distribute data in /usr/bin.
 .
 Alternatively, we could ship the XML files in /etc/clustal and treat them as
 configuration files. Please notify the Debian Med team if you think it is
 necessary.

clustalW/Help.cpp | 2 1 + 1 - 0 !
clustalW/alignment/Alignment.cpp | 2 1 + 1 - 0 !
clustalW/alignment/AlignmentOutput.cpp | 54 27 + 27 - 0 !
clustalW/alignment/Sequence.cpp | 2 1 + 1 - 0 !
clustalW/fileInput/ClustalFileParser.cpp | 6 3 + 3 - 0 !
clustalW/fileInput/EMBLFileParser.cpp | 8 4 + 4 - 0 !
clustalW/fileInput/GDEFileParser.cpp | 4 2 + 2 - 0 !
clustalW/fileInput/MSFFileParser.cpp | 6 3 + 3 - 0 !
clustalW/fileInput/PIRFileParser.cpp | 4 2 + 2 - 0 !
clustalW/fileInput/PearsonFileParser.cpp | 2 1 + 1 - 0 !
clustalW/fileInput/RSFFileParser.cpp | 6 3 + 3 - 0 !
clustalW/pairwise/FastPairwiseAlign.cpp | 2 1 + 1 - 0 !
clustalW/pairwise/FullPairwiseAlign.cpp | 2 1 + 1 - 0 !
clustalW/tree/ClusterTree.cpp | 2 1 + 1 - 0 !
clustalW/tree/RandomGenerator.cpp | 2 1 + 1 - 0 !
clustalW/tree/UPGMA/RootedClusterTree.cpp | 4 2 + 2 - 0 !
clustalW/tree/UnRootedClusterTree.cpp | 4 2 + 2 - 0 !
mainwindow.cpp | 2 1 + 1 - 0 !
18 files changed, 57 insertions(+), 57 deletions(-)

 fix spelling

AlignOutputFileNames.cpp | 2 1 + 1 - 0 !
AlignmentFormatOptions.cpp | 2 1 + 1 - 0 !
AlignmentParameters.cpp | 2 1 + 1 - 0 !
AlignmentViewerWidget.cpp | 2 1 + 1 - 0 !
AlignmentWidget.cpp | 2 1 + 1 - 0 !
BootstrapTreeDialog.cpp | 2 1 + 1 - 0 !
ColorFileXmlParser.cpp | 2 1 + 1 - 0 !
ColorParameters.cpp | 12 6 + 6 - 0 !
ColumnScoreParams.cpp | 2 1 + 1 - 0 !
HelpDisplayWidget.cpp | 2 1 + 1 - 0 !
HistogramWidget.cpp | 2 1 + 1 - 0 !
LowScoringSegParams.cpp | 2 1 + 1 - 0 !
PSPrinter.cpp | 4 2 + 2 - 0 !
PairwiseParams.cpp | 2 1 + 1 - 0 !
ProteinGapParameters.cpp | 2 1 + 1 - 0 !
SaveSeqFile.cpp | 2 1 + 1 - 0 !
SecStructOptions.cpp | 2 1 + 1 - 0 !
SeqNameWidget.cpp | 2 1 + 1 - 0 !
TreeFormatOptions.cpp | 2 1 + 1 - 0 !
TreeOutputFileNames.cpp | 2 1 + 1 - 0 !
WritePostscriptFile.cpp | 2 1 + 1 - 0 !
clustalx.pro | 1 1 + 0 - 0 !
mainwindow.cpp | 2 1 + 1 - 0 !
23 files changed, 29 insertions(+), 28 deletions(-)

 porting to qt5 following the hints at
   https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#QtWidgets_as_a_Separate_Module
   https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#toAscii.28.29_and_fromAscii.28.29_Methods_are_deprecated