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refarctoring for HEADLESS

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commit 7e3c8f216b9219be7f39d0aec8f9de696e309ee0 1 parent d5a132b
@jonalv jonalv authored
Showing with 51 additions and 43 deletions.
  1. +2 −1  plugins/net.bioclipse.bioinformatics.rdf/META-INF/MANIFEST.MF
  2. +1 −1  plugins/net.bioclipse.bioinformatics.rdf/src/net/bioclipse/rdf/ui/RDFToSequenceFactory.java
  3. +2 −1  plugins/net.bioclipse.chemoinformatics.rdf/META-INF/MANIFEST.MF
  4. +2 −2 plugins/net.bioclipse.chemoinformatics.rdf/src/net/bioclipse/rdf/ui/RDFToCDKMoleculeFactory.java
  5. +2 −1  plugins/net.bioclipse.owl/META-INF/MANIFEST.MF
  6. +4 −4 plugins/net.bioclipse.owl/src/net/bioclipse/owl/business/IOWLManager.java
  7. +2 −2 plugins/net.bioclipse.owl/src/net/bioclipse/owl/business/OWLManager.java
  8. +2 −1  plugins/net.bioclipse.pellet.tests/META-INF/MANIFEST.MF
  9. +1 −1  plugins/net.bioclipse.pellet.tests/src/net/bioclipse/pellet/tests/APITest.java
  10. +1 −1  plugins/net.bioclipse.pellet.tests/src/net/bioclipse/pellet/tests/CoverageTest.java
  11. +2 −1  plugins/net.bioclipse.pellet/META-INF/MANIFEST.MF
  12. +7 −7 plugins/net.bioclipse.pellet/src/net/bioclipse/pellet/business/IPelletManager.java
  13. +2 −2 plugins/net.bioclipse.pellet/src/net/bioclipse/pellet/business/PelletManager.java
  14. +2 −1  plugins/net.bioclipse.rdf.tests/META-INF/MANIFEST.MF
  15. +1 −1  plugins/net.bioclipse.rdf.tests/src/net/bioclipse/rdf/tests/APITest.java
  16. +1 −1  plugins/net.bioclipse.rdf.tests/src/net/bioclipse/rdf/tests/AbstractRDFManagerPluginTest.java
  17. +1 −1  plugins/net.bioclipse.rdf.tests/src/net/bioclipse/rdf/tests/CoverageTest.java
  18. +2 −1  plugins/net.bioclipse.rdf.ui/META-INF/MANIFEST.MF
  19. +1 −1  plugins/net.bioclipse.rdf.ui/src/net/bioclipse/rdf/ui/IRDFToBioObjectFactory.java
  20. +1 −1  plugins/net.bioclipse.rdf.ui/src/net/bioclipse/rdf/ui/editors/RDFEditor.java
  21. +2 −1  plugins/net.bioclipse.rdf/META-INF/MANIFEST.MF
  22. +7 −7 plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/IRDFManager.java
  23. +3 −3 plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java
View
3  plugins/net.bioclipse.bioinformatics.rdf/META-INF/MANIFEST.MF
@@ -9,7 +9,8 @@ Require-Bundle: org.eclipse.core.runtime,
com.hp.hpl.jena;bundle-version="2.6.2",
net.bioclipse.rdf.ui;bundle-version="2.3.0",
org.eclipse.ui;bundle-version="3.5.1",
- net.bioclipse.biojava.business;bundle-version="2.2.0"
+ net.bioclipse.biojava.business;bundle-version="2.2.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ActivationPolicy: lazy
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Import-Package: org.apache.log4j
View
2  plugins/net.bioclipse.bioinformatics.rdf/src/net/bioclipse/rdf/ui/RDFToSequenceFactory.java
@@ -11,7 +11,7 @@
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*/
package net.bioclipse.rdf.ui;
-import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.core.api.domain.IBioObject;
import org.apache.log4j.Logger;
import org.eclipse.core.runtime.CoreException;
View
3  plugins/net.bioclipse.chemoinformatics.rdf/META-INF/MANIFEST.MF
@@ -9,7 +9,8 @@ Require-Bundle: org.eclipse.core.runtime,
net.bioclipse.core;bundle-version="2.2.0",
com.hp.hpl.jena;bundle-version="2.6.2",
net.bioclipse.rdf.ui;bundle-version="2.3.0",
- org.eclipse.ui;bundle-version="3.5.1"
+ org.eclipse.ui;bundle-version="3.5.1",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ActivationPolicy: lazy
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Import-Package: org.apache.log4j
View
4 .../net.bioclipse.chemoinformatics.rdf/src/net/bioclipse/rdf/ui/RDFToCDKMoleculeFactory.java
@@ -21,8 +21,8 @@
import org.eclipse.ui.plugin.AbstractUIPlugin;
import net.bioclipse.cdk.business.Activator;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IBioObject;
import net.bioclipse.core.util.LogUtils;
import com.hp.hpl.jena.rdf.model.Literal;
View
3  plugins/net.bioclipse.owl/META-INF/MANIFEST.MF
@@ -17,5 +17,6 @@ Require-Bundle: net.bioclipse.core,
net.bioclipse.scripting.ui,
net.bioclipse.rdf,
net.bioclipse.pellet;bundle-version="2.0.0",
- org.mindswap.pellet;bundle-version="2.0.0"
+ org.mindswap.pellet;bundle-version="2.0.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ClassPath: .
View
8 plugins/net.bioclipse.owl/src/net/bioclipse/owl/business/IOWLManager.java
@@ -15,10 +15,10 @@
import org.eclipse.core.runtime.CoreException;
-import net.bioclipse.core.PublishedClass;
-import net.bioclipse.core.PublishedMethod;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.managers.IBioclipseManager;
+import net.bioclipse.core.api.managers.PublishedClass;
+import net.bioclipse.core.api.managers.PublishedMethod;
import net.bioclipse.rdf.business.IRDFStore;
@PublishedClass("Contains OWL related methods")
View
4 plugins/net.bioclipse.owl/src/net/bioclipse/owl/business/OWLManager.java
@@ -21,8 +21,8 @@
import java.io.IOException;
import java.util.List;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.pellet.business.IPelletManager;
import net.bioclipse.pellet.business.PelletManager;
import net.bioclipse.rdf.business.IRDFStore;
View
3  plugins/net.bioclipse.pellet.tests/META-INF/MANIFEST.MF
@@ -17,7 +17,8 @@ Require-Bundle: org.eclipse.ui,
com.hp.hpl.jena;bundle-version="2.6.0",
com.hp.hpl.jena.arq;bundle-version="2.8.2",
org.mindswap.pellet;bundle-version="2.0.0",
- com.hp.hpl.jena.tdb;bundle-version="0.8.4"
+ com.hp.hpl.jena.tdb;bundle-version="0.8.4",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ActivationPolicy: lazy
Export-Package: net.bioclipse.pellet.tests
Import-Package: org.apache.log4j
View
2  plugins/net.bioclipse.pellet.tests/src/net/bioclipse/pellet/tests/APITest.java
@@ -10,8 +10,8 @@
******************************************************************************/
package net.bioclipse.pellet.tests;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.core.tests.AbstractManagerTest;
-import net.bioclipse.managers.business.IBioclipseManager;
import net.bioclipse.pellet.business.IPelletManager;
import net.bioclipse.pellet.business.PelletManager;
View
2  plugins/net.bioclipse.pellet.tests/src/net/bioclipse/pellet/tests/CoverageTest.java
@@ -10,8 +10,8 @@
******************************************************************************/
package net.bioclipse.pellet.tests;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.core.tests.coverage.AbstractCoverageTest;
-import net.bioclipse.managers.business.IBioclipseManager;
import net.bioclipse.pellet.business.IPelletManager;
import net.bioclipse.pellet.business.PelletManager;
View
3  plugins/net.bioclipse.pellet/META-INF/MANIFEST.MF
@@ -18,5 +18,6 @@ Require-Bundle: net.bioclipse.core,
org.mindswap.pellet;bundle-version="2.0.0",
net.bioclipse.rdf,
com.hp.hpl.jena.arq;bundle-version="2.8.2",
- com.hp.hpl.jena.tdb;bundle-version="0.8.4"
+ com.hp.hpl.jena.tdb;bundle-version="0.8.4",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ClassPath: .
View
14 plugins/net.bioclipse.pellet/src/net/bioclipse/pellet/business/IPelletManager.java
@@ -13,13 +13,13 @@
import java.io.IOException;
import java.util.List;
-import net.bioclipse.core.PublishedClass;
-import net.bioclipse.core.PublishedMethod;
-import net.bioclipse.core.Recorded;
-import net.bioclipse.core.TestClasses;
-import net.bioclipse.core.TestMethods;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.Recorded;
+import net.bioclipse.core.api.managers.IBioclipseManager;
+import net.bioclipse.core.api.managers.PublishedClass;
+import net.bioclipse.core.api.managers.PublishedMethod;
+import net.bioclipse.core.api.managers.TestClasses;
+import net.bioclipse.core.api.managers.TestMethods;
import net.bioclipse.rdf.business.IRDFStore;
import org.eclipse.core.runtime.CoreException;
View
4 plugins/net.bioclipse.pellet/src/net/bioclipse/pellet/business/PelletManager.java
@@ -23,8 +23,8 @@
import java.util.Iterator;
import java.util.List;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.rdf.business.IJenaStore;
import net.bioclipse.rdf.business.IRDFStore;
import net.bioclipse.rdf.business.RDFManager;
View
3  plugins/net.bioclipse.rdf.tests/META-INF/MANIFEST.MF
@@ -12,6 +12,7 @@ Require-Bundle: org.eclipse.ui,
org.eclipse.core.resources,
net.bioclipse.core.tests;bundle-version="0.1.0",
net.bioclipse.rdf,
- net.bioclipse.ui;bundle-version="2.0.0"
+ net.bioclipse.ui;bundle-version="2.0.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ActivationPolicy: lazy
Export-Package: net.bioclipse.rdf.tests
View
2  plugins/net.bioclipse.rdf.tests/src/net/bioclipse/rdf/tests/APITest.java
@@ -10,8 +10,8 @@
******************************************************************************/
package net.bioclipse.rdf.tests;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.core.tests.AbstractManagerTest;
-import net.bioclipse.managers.business.IBioclipseManager;
import net.bioclipse.rdf.business.IRDFManager;
import net.bioclipse.rdf.business.RDFManager;
View
2  ...ins/net.bioclipse.rdf.tests/src/net/bioclipse/rdf/tests/AbstractRDFManagerPluginTest.java
@@ -16,7 +16,7 @@
import java.net.URL;
import java.util.List;
-import net.bioclipse.core.ResourcePathTransformer;
+import net.bioclipse.core.api.ResourcePathTransformer;
import net.bioclipse.rdf.business.IRDFManager;
import net.bioclipse.rdf.business.IRDFStore;
import net.bioclipse.rdf.model.IStringMatrix;
View
2  plugins/net.bioclipse.rdf.tests/src/net/bioclipse/rdf/tests/CoverageTest.java
@@ -10,8 +10,8 @@
******************************************************************************/
package net.bioclipse.rdf.tests;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.core.tests.coverage.AbstractCoverageTest;
-import net.bioclipse.managers.business.IBioclipseManager;
import net.bioclipse.rdf.business.IRDFManager;
import net.bioclipse.rdf.business.RDFManager;
View
3  plugins/net.bioclipse.rdf.ui/META-INF/MANIFEST.MF
@@ -15,7 +15,8 @@ Require-Bundle: org.eclipse.ui,
net.bioclipse.rdf,
com.hp.hpl.jena;bundle-version="2.6.2",
net.bioclipse.core,
- net.bioclipse.ui.business;bundle-version="2.2.0"
+ net.bioclipse.ui.business;bundle-version="2.2.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ActivationPolicy: lazy
Import-Package: org.apache.log4j
View
2  plugins/net.bioclipse.rdf.ui/src/net/bioclipse/rdf/ui/IRDFToBioObjectFactory.java
@@ -10,7 +10,7 @@
******************************************************************************/
package net.bioclipse.rdf.ui;
-import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.core.api.domain.IBioObject;
import org.eclipse.core.resources.IFile;
import org.eclipse.jface.resource.ImageDescriptor;
View
2  plugins/net.bioclipse.rdf.ui/src/net/bioclipse/rdf/ui/editors/RDFEditor.java
@@ -10,7 +10,7 @@
import java.io.ByteArrayInputStream;
-import net.bioclipse.core.domain.IBioObject;
+import net.bioclipse.core.api.domain.IBioObject;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.rdf.business.IRDFStore;
import net.bioclipse.rdf.business.JenaModel;
View
3  plugins/net.bioclipse.rdf/META-INF/MANIFEST.MF
@@ -18,5 +18,6 @@ Require-Bundle: net.bioclipse.core,
net.bioclipse.scripting.ui,
com.hp.hpl.jena.arq;bundle-version="2.8.2",
com.hp.hpl.jena.tdb;bundle-version="0.8.4",
- org.eclipse.ui.views;bundle-version="3.4.1"
+ org.eclipse.ui.views;bundle-version="3.4.1",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ClassPath: .
View
14 plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/IRDFManager.java
@@ -14,13 +14,13 @@
import java.io.InputStream;
import java.util.List;
-import net.bioclipse.core.PublishedClass;
-import net.bioclipse.core.PublishedMethod;
-import net.bioclipse.core.Recorded;
-import net.bioclipse.core.TestClasses;
-import net.bioclipse.core.TestMethods;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.Recorded;
+import net.bioclipse.core.api.managers.IBioclipseManager;
+import net.bioclipse.core.api.managers.PublishedClass;
+import net.bioclipse.core.api.managers.PublishedMethod;
+import net.bioclipse.core.api.managers.TestClasses;
+import net.bioclipse.core.api.managers.TestMethods;
import net.bioclipse.rdf.model.IStringMatrix;
import org.eclipse.core.resources.IFile;
View
6 plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java
@@ -32,9 +32,9 @@
import java.util.Map;
import java.util.Set;
-import net.bioclipse.core.ResourcePathTransformer;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.ResourcePathTransformer;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import net.bioclipse.rdf.model.StringMatrix;
import org.eclipse.core.resources.IFile;
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