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Merge pull request #1 from katrinleinweber/resolve-DOIs-securely
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Hyperlink DOIs to preferred resolver
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@novak-jiri
novak-jiri committed Nov 14, 2018
2 parents 0744d78 + dee0595 commit 8a7141b
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2 changes: 1 addition & 1 deletion CycloBranch/core/cSequence.cpp
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Expand Up @@ -204,7 +204,7 @@ string cSequence::getNameWithReferenceAsHTMLString() {
if (!correctreference) {
rx = "^DOI: ";
if (regex_search(reference, rx)) {
s += "<a href=\"http://dx.doi.org/" + reference.substr(5) + "\">";
s += "<a href=\"https://doi.org/" + reference.substr(5) + "\">";
s += name;
s += "</a>";
correctreference = true;
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6 changes: 3 additions & 3 deletions CycloBranch/gui/cAboutWidget.cpp
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Expand Up @@ -21,17 +21,17 @@ cAboutWidget::cAboutWidget(QWidget* parent) {
QString citations = "Any work based on CycloBranch shall cite any of the following references:<br/><br/>";
citations += "Jiri Novak, Karel Lemr, Kevin A. Schug, Vladimir Havlicek:<br/>";
citations += "CycloBranch: <i>De Novo</i> Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra,<br/>";
citations += "<i>J. Am. Soc. Mass Spectrom.</i>, vol. 26, no. 10, pp. 1780-1786, 2015. DOI: <a href=\"http://dx.doi.org/10.1007/s13361-015-1211-1\">10.1007/s13361-015-1211-1</a>.<br/>";
citations += "<i>J. Am. Soc. Mass Spectrom.</i>, vol. 26, no. 10, pp. 1780-1786, 2015. DOI: <a href=\"https://doi.org/10.1007/s13361-015-1211-1\">10.1007/s13361-015-1211-1</a>.<br/>";
citations += "Download citation: [ <a href=\"http://ms.biomed.cas.cz/cyclobranch/docs/cyclobranch_ris.txt\"><b>ris</b></a> ], [ <a href=\"http://ms.biomed.cas.cz/cyclobranch/docs/cyclobranch_bib.txt\"><b>bib</b></a> ]<br/><br/>";

citations += "Jiri Novak, Lucie Sokolova, Karel Lemr, Tomas Pluhacek, Andrea Palyzova, Vladimir Havlicek:<br/>";
citations += "Batch-processing of Imaging or Liquid-chromatography Mass Spectrometry Datasets and <i>De Novo</i> Sequencing of Polyketide Siderophores,<br/>";
citations += "<i>BBA - Proteins Proteom.</i>, vol. 1865, no. 7, pp. 768-775, 2017. DOI: <a href=\"http://dx.doi.org/10.1016/j.bbapap.2016.12.003\">10.1016/j.bbapap.2016.12.003</a>.<br/>";
citations += "<i>BBA - Proteins Proteom.</i>, vol. 1865, no. 7, pp. 768-775, 2017. DOI: <a href=\"https://doi.org/10.1016/j.bbapap.2016.12.003\">10.1016/j.bbapap.2016.12.003</a>.<br/>";
citations += "Download citation: [ <a href=\"http://ms.biomed.cas.cz/cyclobranch/docs/cyclobranch_bba_ris.txt\"><b>ris</b></a> ], [ <a href=\"http://ms.biomed.cas.cz/cyclobranch/docs/cyclobranch_bba_bib.txt\"><b>bib</b></a> ]<br/><br/>";

citations += "Jiri Novak, Anton Skriba, Jakub Zapal, Marek Kuzma, Vladimir Havlicek:<br/>";
citations += "CycloBranch: an Open Tool for Fine Isotope Structures in Conventional and Product Ion Mass Spectra,<br/>";
citations += "<i>J. Mass Spectrom.</i>, vol. 53, no. 11, pp. 1097-1103, 2018. DOI: <a href=\"http://dx.doi.org/10.1002/jms.4285\">10.1002/jms.4285</a>.<br/>";
citations += "<i>J. Mass Spectrom.</i>, vol. 53, no. 11, pp. 1097-1103, 2018. DOI: <a href=\"https://doi.org/10.1002/jms.4285\">10.1002/jms.4285</a>.<br/>";
citations += "Download citation: [ <a href=\"http://ms.biomed.cas.cz/cyclobranch/docs/cyclobranch_jms_ris.txt\"><b>ris</b></a> ], [ <a href=\"http://ms.biomed.cas.cz/cyclobranch/docs/cyclobranch_jms_bib.txt\"><b>bib</b></a> ]<br/><hr/><br/>";

QString licence = "Licence:<br/><br/> This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.<br/><br/>";
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8 changes: 4 additions & 4 deletions README.md
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Expand Up @@ -50,7 +50,7 @@ An open-source, cross-platform and stand-alone tool for mass spectrometry data a
http://ms.biomed.cas.cz/cyclobranch/

## Publications
* [1] *J. Am. Soc. Mass Spectrom.* (2015), 26(10):1780-1786. DOI: [10.1007/s13361-015-1211-1](http://dx.doi.org/10.1007/s13361-015-1211-1)
* [2] *BBA - Proteins Proteom.* (2017), 1865(7):768-775. DOI: [10.1016/j.bbapap.2016.12.003](http://dx.doi.org/10.1016/j.bbapap.2016.12.003)
* [3] *Sci. Rep.* (2017), 7:16523. DOI: [10.1038/s41598-017-16648-z](http://dx.doi.org/10.1038/s41598-017-16648-z)
* [4] *J. Mass Spectrom.* (2018), 53(11):1097-1103. DOI: [10.1002/jms.4285](http://dx.doi.org/10.1002/jms.4285)
* [1] *J. Am. Soc. Mass Spectrom.* (2015), 26(10):1780-1786. DOI: [10.1007/s13361-015-1211-1](https://doi.org/10.1007/s13361-015-1211-1)
* [2] *BBA - Proteins Proteom.* (2017), 1865(7):768-775. DOI: [10.1016/j.bbapap.2016.12.003](https://doi.org/10.1016/j.bbapap.2016.12.003)
* [3] *Sci. Rep.* (2017), 7:16523. DOI: [10.1038/s41598-017-16648-z](https://doi.org/10.1038/s41598-017-16648-z)
* [4] *J. Mass Spectrom.* (2018), 53(11):1097-1103. DOI: [10.1002/jms.4285](https://doi.org/10.1002/jms.4285)

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