Merge branch 'master' into patch-3

PathVisio · Aug 29, 2023 · 7a3053d · 7a3053d
2 parents 5c15ccd + 2ed1cb7
commit 7a3053d
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diff --git a/.travis.yml b/.travis.yml
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+title: PathVisio
+message: 'If you use this software, please cite it as below.'
+type: software
+identifiers:
+  - type: url
+    value: 'https://github.com/pathvisio/pathvisio'
+    description: Source code repository for PathVisio
+repository-code: 'https://github.com/pathvisio/pathvisio'
+url: 'https://pathvisio.org/'
+license: Apache-2
+preferred-citation:
+  type: article
+  authors:
+  - family-names: Summer-Kutmon
+    given-names: Martina
+  - family-names: Iersel
+    given-names: Martijn P
+    name-particle: van
+  - family-names: Bohler
+    given-names: Anwesha
+  - family-names: Kelder
+    given-names: Thomas
+  - family-names: Nunes
+    given-names: Nuno
+  - family-names: Pico
+    given-names: Alexander R.
+  - family-names: Evelo
+    given-names: Chris T.
+  doi: 10.1371/JOURNAL.PCBI.1004085
+  journal: 'PLoS Comput Biol'
+  title: 'PathVisio 3: an extendable pathway analysis toolbox'
+  issue: 2
+  volume: 11
+  year: 2015
diff --git a/CONTRIBUTORS.txt b/CONTRIBUTORS.txt
@@ -1,6 +1,5 @@
 # DEVELOPERS TEAM
 Martina Kutmon
-Nuno Nunes
 Alexander Pico
 Egon Willighagen
 Denise Slenter
@@ -9,9 +8,10 @@ Kristina Hanspers
 # FORMER DEVELOPERS
 Andra Waagmeester
 Anwesha Bohler
-Jonathan Melius
+Jonathan Mélius
 Martijn van Iersel
 Thomas Kelder
+Nuno Nunes
 
 # CONTRIBUTORS
 Adem Bilicna

diff --git a/build-common.xml b/build-common.xml
@@ -2,8 +2,8 @@
 <project name="PathVisio-common" basedir=".">
 
 	<property name="debug.mode" value="true"/>
-	<property name="ant.build.javac.target" value="1.6"/>
-	<property name="ant.build.javac.source" value="1.6"/>
+	<property name="ant.build.javac.target" value="1.8"/>
+	<property name="ant.build.javac.source" value="1.8"/>
 
 	<property name="pathvisio.version" value="3.4.0"/>
 	<property name="bundle.dest" value=".."/>

diff --git a/lib/commons-codec-1.5.jar b/lib/commons-codec-1.5.jar
diff --git a/lib/commons-codec-1.6.jar b/lib/commons-codec-1.6.jar
diff --git a/lib/org.bridgedb.bio.jar b/lib/org.bridgedb.bio.jar
diff --git a/lib/org.bridgedb.gui.jar b/lib/org.bridgedb.gui.jar
diff --git a/lib/org.bridgedb.jar b/lib/org.bridgedb.jar
diff --git a/lib/org.bridgedb.rdb.construct.jar b/lib/org.bridgedb.rdb.construct.jar
diff --git a/lib/org.bridgedb.rdb.jar b/lib/org.bridgedb.rdb.jar
diff --git a/lib/org.bridgedb.webservice.bridgerest.jar b/lib/org.bridgedb.webservice.bridgerest.jar
diff --git a/modules/org.pathvisio.gui/src/org/pathvisio/gui/DataSourceModel.java b/modules/org.pathvisio.gui/src/org/pathvisio/gui/DataSourceModel.java
@@ -115,25 +115,7 @@ private void initItems()
 	{
 		items = new ArrayList<DataSource>();
 		items.addAll(DataSourceHandler.getFilteredSetAlt(primary, type, organism, interaction));
-		items.remove(DataSource.getExistingBySystemCode("EnBs"));
-		items.remove(DataSource.getExistingBySystemCode("EnCe"));
-		items.remove(DataSource.getExistingBySystemCode("EnGg"));
-		items.remove(DataSource.getExistingBySystemCode("EnPt"));
-		items.remove(DataSource.getExistingBySystemCode("EnBt"));
-		items.remove(DataSource.getExistingBySystemCode("EnCf"));
-		items.remove(DataSource.getExistingBySystemCode("EnEc"));
-		items.remove(DataSource.getExistingBySystemCode("EnDm"));
-		items.remove(DataSource.getExistingBySystemCode("EnQc"));
-		items.remove(DataSource.getExistingBySystemCode("EnHs"));
-		items.remove(DataSource.getExistingBySystemCode("EnMx"));
-		items.remove(DataSource.getExistingBySystemCode("EnAg"));
-		items.remove(DataSource.getExistingBySystemCode("EnMm"));
-		items.remove(DataSource.getExistingBySystemCode("EnSs"));
-		items.remove(DataSource.getExistingBySystemCode("EP"));
-		items.remove(DataSource.getExistingBySystemCode("EnRn"));
-		items.remove(DataSource.getExistingBySystemCode("EnXt"));
-		items.remove(DataSource.getExistingBySystemCode("EnSc"));
-		items.remove(DataSource.getExistingBySystemCode("EnDr"));
+		items.remove(DataSource.getExistingBySystemCode("En"));
 
 		Collections.sort (items, new Comparator<DataSource>()
 		{