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ContentMine / phylotree

A repository for ami-phylotree development
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Unicode chars in NeXML output not good for some tree viewers #30

Open rossmounce opened 9 years ago

rossmounce commented 9 years ago

Dendroscope (phylogenetic tree viewing software) cannot view many of the output NeXML files because they contain Unicode characters.

Error log from Dendroscope:

Executing: open file='/home/ross/workspace/ami-plugin/all-output/all-input/ijs.0.000364-0-003.pbm.png/ijs.0.000364-0-003.pbm.nexml.xml';
[Fatal Error] :13:19: An invalid XML character (Unicode: 0x18) was found in the element content of the document.
org.xml.sax.SAXParseException; lineNumber: 13; columnNumber: 19; An invalid XML character (Unicode: 0x18) was found in the element content of the document.
    at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
    at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:347)
    at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
    at org.nexml.model.DocumentFactory.parse(DocumentFactory.java:52)
    at org.nexml.model.DocumentFactory.safeParse(DocumentFactory.java:62)
    at dendroscope.D.A.B.A(Unknown Source)
    at dendroscope.D.A.B(Unknown Source)
    at dendroscope.commands.OpenFileCommand.apply(Unknown Source)
    at jloda.C.A.F.A(Unknown Source)
    at jloda.C.A.F.D(Unknown Source)
    at dendroscope.N.B$2.run(Unknown Source)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Command usage: open file=<filename>; - Opens a file