<div dir="ltr">Ok thank you, I'll consider Biojava 1.9 if embl files are not supported in later versions. <div><br></div><div>By the way, I tried to compile biojava-legacy-1.9.2 and I got some tests failing:</div><div><br></div><div>----------------------</div><div>cd biojava-legacy-biojava-legacy-1.9.2</div><div>mvn package</div><div>....</div><div>....</div><div>







<p class="gmail-p1"><span class="gmail-s1">Results :</span></p>
<p class="gmail-p2"><span class="gmail-s1"></span><br></p>
<p class="gmail-p1"><span class="gmail-s1">Failed tests: </span></p>
<p class="gmail-p1"><span class="gmail-s1">  GenbankRichSequenceDBTest.testeFetch:24 Unexpected Bioexception: org.biojava.bio.BioException: Failed to read Genbank sequence</span></p>
<p class="gmail-p1"><span class="gmail-s1">  GenpeptRichSequenceDBTest.testeFetch:24 Unexpected BioException: org.biojava.bio.BioException: Failed to read Genbank sequence</span></p>
<p class="gmail-p2"><span class="gmail-s1"></span><br></p>
<p class="gmail-p1"><span class="gmail-s1">Tests run: 883, Failures: 2, Errors: 0, Skipped: 0</span></p>
<p class="gmail-p2"><span class="gmail-s1"></span><br></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] ------------------------------------------------------------------------</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] Reactor Summary:</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] </span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] biojava-legacy ..................................... SUCCESS [  0.725 s]</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] bytecode ........................................... SUCCESS [  1.505 s]</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] core ............................................... FAILURE [ 10.232 s]</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] alignment .......................................... SKIPPED</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] biosql ............................................. SKIPPED</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] blast .............................................. SKIPPED</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] sequencing ......................................... SKIPPED</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] gui ................................................ SKIPPED</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] phylo .............................................. SKIPPED</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] ------------------------------------------------------------------------</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] BUILD FAILURE</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] ------------------------------------------------------------------------</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] Total time: 12.692 s</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] Finished at: 2016-12-28T16:38:18+00:00</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] Final Memory: 11M/220M</span></p>
<p class="gmail-p1"><span class="gmail-s1">[INFO] ------------------------------------------------------------------------</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.17:test (default-test) on project core: There are test failures.</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] </span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] Please refer to /Users/berald01/Downloads/biojava-legacy-biojava-legacy-1.9.2/core/target/surefire-reports for the individual test results.</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] -> [Help 1]</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] </span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] Re-run Maven using the -X switch to enable full debug logging.</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] </span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] For more information about the errors and possible solutions, please read the following articles:</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] [Help 1] <a href="http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException">http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException</a></span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] </span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR] After correcting the problems, you can resume the build with the command</span></p>
<p class="gmail-p1"><span class="gmail-s1">[ERROR]   mvn <goals> -rf :core</span></p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 28 December 2016 at 15:45, Michael Heuer <span dir="ltr"><<a href="mailto:heuermh@gmail.com" target="_blank">heuermh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <span dir="ltr"><<a href="mailto:dario.beraldi@gmail.com" target="_blank">dario.beraldi@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>First, thanks for the great Biojava project!</div><div><br></div><div>Is it possible to parse embl files using (Bio)Java? </div><div><br></div><div>By Googling "biojava  embl format" I get some hits for the legacy Biojava 1.9 but I'm wondering weather I could (should?) use the more recent Biojava 4?</div></div></blockquote><div><br></div><div>If biojava-legacy works fine for you, feel confident using it.  It is actively maintained; there just won't be any new features.<br><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>A more general question... Which is the primary source of documentation for Biojava 4? Is it the tutorial at <a href="https://github.com/biojava/biojava-tutorial" target="_blank">https://github.com/biojava/bio<wbr>java-tutorial</a> together with the Javadocs (<a href="http://biojava.org/docs/api4.2.1/" target="_blank">http://biojava.org/docs/api4.<wbr>2.1/</a>)? </div><div><br></div><div>I find the home page Biojava.org a little confusing... The tutorial page <a href="http://biojava.org/wiki/BioJava:CookBook4.0/" target="_blank">http://biojava.org/wiki/B<wbr>ioJava:CookBook4.0/</a> gives me a 404 error. The wiki pages <a href="http://biojava.org/wiki.html" target="_blank">http://biojava.org/wiki.<wbr>html</a> seem a mixture of various topics.</div></div></blockquote><div><br></div><div>The <a href="http://biojava.org" target="_blank">biojava.org</a> website didn't survive a wiki migration to github without running into some problems.  If you find any, please file them as issues at<br><br><a href="https://github.com/biojava/biojava.github.io" target="_blank">https://github.com/biojava/<wbr>biojava.github.io<span class="HOEnZb"><font color="#888888"><br></font></span></a><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888">   michael<br></font></span></div></div></div>
</blockquote></div><br></div>