[med-svn] [dazzle] 13/14: Update upstream source from tag 'upstream/1.0.1r3643'

[Andreas Tille]

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tille pushed a commit to branch master
in repository dazzle.

commit 36d982d438b65c55d0745b536f96a7f03cb5213d
Merge: 95ad4f7 79dee84
Author: Andreas Tille <tille at debian.org>
Date:   Tue Dec 5 14:26:59 2017 +0100

    Update upstream source from tag 'upstream/1.0.1r3643'
    
    Update to upstream version '1.0.1r3643'
    with Debian dir 80070e5f38cbf83b6fd6373ab0bc28a8b3dd893d

 build.xml                                          |  219 +++
 dazzle-webapp/WEB-INF/web.xml                      |   25 +
 dazzle-webapp/das.xsl                              |  914 ++++++++++
 dazzle-webapp/das_welcome.html                     |    6 +
 dazzle-webapp/dazzlecfg.xml                        |   56 +
 dazzle-webapp/example.up                           |  158 ++
 dazzle-webapp/fickett-tss.gff                      |   44 +
 dazzle-webapp/sources.xml                          |   26 +
 dazzle-webapp/test.embl                            | 1774 ++++++++++++++++++++
 dazzle-webapp/test.style                           |   17 +
 dazzle-webapp/tss.style                            |   17 +
 dazzle-webapp/welcome.html                         |    6 +
 docs/background.png                                |  Bin 0 -> 19517 bytes
 docs/deploy.html                                   |  312 ++++
 docs/docs.css                                      |   25 +
 manifest/dazzle.txt                                |    4 +
 .../org.biojava.servlets.dazzle.DazzleHandler      |   10 +
 resources/css/content.css                          |  475 ++++++
 resources/css/dazzle.css                           |  286 ++++
 resources/css/printer-styles.css                   |   18 +
 resources/css/screen-styles.css                    |   36 +
 resources/org/biodas/das1/dasdna.dtd               |    8 +
 resources/org/biodas/das1/dasdsn.dtd               |    8 +
 resources/org/biodas/das1/dasep.dtd                |   11 +
 resources/org/biodas/das1/dasgff.dtd               |   35 +
 resources/org/biodas/das1/dasres.dtd               |   11 +
 resources/org/biodas/das1/dassequence.dtd          |    7 +
 resources/org/biodas/das1/dasstyle.dtd             |   32 +
 resources/org/biodas/das1/dastypes.dtd             |   14 +
 src/META-INF/MANIFEST.MF                           |    3 +
 .../servlets/dazzle/AbstractDazzleHandler.java     |   53 +
 .../biojava/servlets/dazzle/AlignmentHandler.java  |  279 +++
 .../servlets/dazzle/DASQueryStringTranslator.java  |  121 ++
 src/org/biojava/servlets/dazzle/DASStatus.java     |   68 +
 .../biojava/servlets/dazzle/DazzleException.java   |   83 +
 src/org/biojava/servlets/dazzle/DazzleHandler.java |   48 +
 .../biojava/servlets/dazzle/DazzleResponse.java    |  109 ++
 src/org/biojava/servlets/dazzle/DazzleServlet.java |  720 ++++++++
 src/org/biojava/servlets/dazzle/DazzleTools.java   |  181 ++
 .../servlets/dazzle/EntryPointsHandler.java        |   98 ++
 .../biojava/servlets/dazzle/FeaturesHandler.java   |  902 ++++++++++
 .../servlets/dazzle/GFFFeaturesHandler.java        |  408 +++++
 .../servlets/dazzle/HydraGFFFeaturesHandler.java   |  352 ++++
 .../servlets/dazzle/InteractionHandler.java        |  318 ++++
 src/org/biojava/servlets/dazzle/LinkHandler.java   |   79 +
 .../biojava/servlets/dazzle/SangerProxyFilter.java |  116 ++
 src/org/biojava/servlets/dazzle/Segment.java       |  106 ++
 .../biojava/servlets/dazzle/SequenceHandler.java   |  244 +++
 .../biojava/servlets/dazzle/StructureHandler.java  |  403 +++++
 .../biojava/servlets/dazzle/StylesheetHandler.java |   75 +
 .../datasource/AbstractBiojavaFeatureSource.java   |  362 ++++
 .../dazzle/datasource/AbstractDataSource.java      |  366 ++++
 .../datasource/AbstractDazzleDataSource.java       |  136 ++
 .../datasource/AbstractGFFFeatureSource.java       |  273 +++
 .../dazzle/datasource/AlignmentSource.java         |   82 +
 .../servlets/dazzle/datasource/AlignmentTools.java |  126 ++
 .../dazzle/datasource/BasicDazzleInstallation.java |  321 ++++
 .../dazzle/datasource/BioSQLDataSource.java        |  225 +++
 .../dazzle/datasource/BiojavaFeatureSource.java    |  213 +++
 .../servlets/dazzle/datasource/DASGFFGroup.java    |   87 +
 .../dazzle/datasource/DataSourceException.java     |   44 +
 .../dazzle/datasource/DazzleDataSource.java        |  290 ++++
 .../dazzle/datasource/DazzleInstallation.java      |   47 +
 .../dazzle/datasource/DazzleReferenceSource.java   |   83 +
 .../servlets/dazzle/datasource/EmblDataSource.java |  163 ++
 .../dazzle/datasource/FastaDataSource.java         |  116 ++
 .../dazzle/datasource/GFFAnnotationSource.java     |  351 ++++
 .../servlets/dazzle/datasource/GFFFeature.java     |  138 ++
 .../dazzle/datasource/GFFFeatureSource.java        |   34 +
 .../dazzle/datasource/HydraGFFFeatureSource.java   |   58 +
 .../datasource/InteractionReferenceSource.java     |   42 +
 .../servlets/dazzle/datasource/LdasDataSource.java |  572 +++++++
 .../dazzle/datasource/PhobiusExampleSource.java    |  181 ++
 .../dazzle/datasource/ProxyDataSource.java         |  205 +++
 .../dazzle/datasource/ProxyReferenceSource.java    |  168 ++
 .../dazzle/datasource/SIFReferenceSource.java      |  480 ++++++
 .../dazzle/datasource/StructureSource.java         |  216 +++
 .../dazzle/datasource/TilingFeatureSource.java     |   27 +
 .../dazzle/datasource/TypeMetadataSource.java      |   19 +
 .../dazzle/datasource/UniProtDataSource.java       |  167 ++
 .../dazzle/datasource/db/GFFFeatureCache.java      |   34 +
 .../dazzle/datasource/db/MysqlFeatureCache.java    |  358 ++++
 82 files changed, 15304 insertions(+)

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