From: Patrick Plitzner
Date: Fri, 13 Jan 2017 14:32:31 +0000 (+0100)
Subject: Merge branch 'develop' into LibrAlign
X-Git-Tag: 4.5.0^2~18
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/1c69b0d01165dcae51f1f45667c202e0d15b960d
Merge branch 'develop' into LibrAlign
---
1c69b0d01165dcae51f1f45667c202e0d15b960d
diff --cc .gitignore
index 05274d7b9,ecfb4d5df..a8aaf71ff
--- a/.gitignore
+++ b/.gitignore
@@@ -31,4 -31,5 +31,6 @@@ eu.etaxonomy.taxeditor.webapp/lib/cdmli
/eu.etaxonomy.taxeditor.webapp/.settings/org.eclipse.m2e.core.prefs
/eu.etaxonomy.taxeditor.webapp/lib/
+/.ssh
+ eu.etaxonomy.taxeditor.test/src/test/resources/eu/etaxonomy/cdm/database/schema/dataset.xsd
+ eu.etaxonomy.taxeditor.test/src/test/resources/eu/etaxonomy/cdm/database/schema/PUBLIC.xsd
diff --cc eu.etaxonomy.taxeditor.cdmlib/.classpath
index d09ef07c6,658cb9c72..8f6c238b5
--- a/eu.etaxonomy.taxeditor.cdmlib/.classpath
+++ b/eu.etaxonomy.taxeditor.cdmlib/.classpath
@@@ -1,251 -1,251 +1,251 @@@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
++
++
++
++
++
++
++
++
++
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
diff --cc eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
index 29336904c,22f8923e1..543d4e02e
--- a/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.molecular.lib/META-INF/MANIFEST.MF
@@@ -2,25 -2,19 +2,25 @@@ Manifest-Version: 1.
Bundle-ManifestVersion: 2
Bundle-Name: eu.etaxonomy.taxeditor.molecular.lib
Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
- Bundle-Version: 4.4.0.qualifier
+ Bundle-Version: 4.5.0.qualifier
Bundle-ClassPath: .,
- lib/bioinfweb-commons-bio-2.0.0-preview-1.jar,
- lib/bioinfweb-commons-core-2.0.0-preview-1.jar,
- lib/bioinfweb-commons-swing-2.0.0-preview-1.jar,
- lib/bioinfweb-commons-swt-2.0.0-preview-1.jar,
- lib/core-1.9.2-SNAPSHOT.jar,
- lib/libralign-biojava1-0.4.0-preview-1.jar,
- lib/libralign-core-0.4.0-preview-1.jar,
- lib/libralign-swt-0.4.0-preview-1.jar,
- lib/sequencing-1.9.2-SNAPSHOT.jar,
- lib/tic-core-2.0.0-preview-1.jar,
- lib/tic-swt-2.0.0-preview-1.jar
+ lib/owlapi-xmlutils-4.1.4.jar,
+ lib/commons-collections4-4.1.jar,
+ lib/core-1.9.2.jar,
+ lib/sequencing-1.9.2.jar,
+ lib/commons-lang3-3.5.jar,
+ lib/commons-beanutils-1.9.2.jar,
+ lib/bioinfweb-commons-java-bio-2.0.0.jar,
+ lib/bioinfweb-commons-java-core-2.2.0.jar,
+ lib/bioinfweb-commons-java-swing-2.2.0.jar,
+ lib/bioinfweb-commons-java-swt-2.0.0.jar,
+ lib/jphyloio-core-0.3.0.jar,
+ lib/libralign-biojava1-0.4.0-preview-2.jar,
+ lib/libralign-core-0.4.0-preview-2.jar,
+ lib/libralign-io-0.4.0-preview-2.jar,
+ lib/libralign-swt-0.4.0-preview-2.jar,
+ lib/tic-core-2.0.0-preview-2.jar,
+ lib/tic-swt-2.0.0-preview-2.jar
Export-Package: info.bioinfweb.commons,
info.bioinfweb.commons.appversion,
info.bioinfweb.commons.beans,
diff --cc eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
index da122384a,c1023e1c6..41a6b82e1
--- a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java
@@@ -755,14 -761,4 +754,14 @@@ public class AlignmentEditor extends Ed
}
return id;
}
+
+
+ public static URI getPherogramURI(SingleRead pherogramInfo) {
+ if (pherogramInfo.getPherogram() != null) {
+ return MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
+ }
+ else {
+ return null;
+ }
+ }
- }
+ }
diff --cc eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
index 41c429529,e193176ec..fd6c1f29c
--- a/eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
+++ b/eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product
@@@ -1,58 -1,39 +1,39 @@@
-
-
-
-
-
- %productBlurb
-
-
-
-
- -data @user.home/.cdmLibrary -Dserver_port=58080
-
- -Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
-
- -XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
-
-
-
-
-
-
-
++
++
++
++
+ %productBlurb
+
-
-
-
-
-
-
- -data @user.home/.cdmLibrary -Dserver_port=58080
++
++
++
++ -data @user.home/.cdmLibrary -Dserver_port=58080
+
- -Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
++ -Xmx512M -XX:MaxPermSize=256M -Dorg.eclipse.update.reconcile=false -Declipse.p2.unsignedPolicy=allow
+
- -XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
++ -XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
+