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refarctoring for HEADLESS

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1 parent 52a9162 commit 3d369d7b071977d88e5462c2d5e9f619cb94ebb0 @jonalv jonalv committed Oct 26, 2010
Showing with 100 additions and 93 deletions.
  1. +2 −1 plugins/net.bioclipse.align.kalign.ws.tests/META-INF/MANIFEST.MF
  2. +3 −3 ...ipse.align.kalign.ws.tests/src/net/bioclipse/align/kalign/ws/tests/PluginTestKalignwsManager.java
  3. +2 −1 plugins/net.bioclipse.align.kalign.ws/META-INF/MANIFEST.MF
  4. +1 −1 ...ns/net.bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/business/IKalignJSManager.java
  5. +7 −7 plugins/net.bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/business/IKalignManager.java
  6. +6 −6 plugins/net.bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/business/KalignManager.java
  7. +3 −3 plugins/net.bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/handlers/AlignHandler.java
  8. +3 −3 .../net.bioclipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/handlers/KalignPopupHandler.java
  9. +1 −1 ...ipse.align.kalign.ws/src/net/bioclipse/align/kalign/ws/util/SequenceCollectionContentHandler.java
  10. +2 −1 plugins/net.bioclipse.biojava.business.tests/META-INF/MANIFEST.MF
  11. +3 −3 ...net.bioclipse.biojava.business.tests/tests/net/bioclipse/biojava/business/BiojavaManagerTest.java
  12. +2 −1 plugins/net.bioclipse.biojava.business/META-INF/MANIFEST.MF
  13. +7 −7 plugins/net.bioclipse.biojava.business/src/net/bioclipse/biojava/business/BiojavaManager.java
  14. +9 −9 plugins/net.bioclipse.biojava.business/src/net/bioclipse/biojava/business/IBiojavaManager.java
  15. +1 −1 .../net.bioclipse.biojava.business/src/net/bioclipse/biojava/business/IJavaScriptBiojavaManager.java
  16. +1 −1 plugins/net.bioclipse.biojava.business/src/net/bioclipse/biojava/domain/BiojavaDNA.java
  17. +1 −1 plugins/net.bioclipse.biojava.business/src/net/bioclipse/biojava/domain/BiojavaProtein.java
  18. +1 −1 plugins/net.bioclipse.biojava.business/src/net/bioclipse/biojava/domain/BiojavaRNA.java
  19. +3 −3 plugins/net.bioclipse.biojava.business/src/net/bioclipse/biojava/domain/BiojavaSequence.java
  20. +2 −1 plugins/net.bioclipse.biojava.ui/META-INF/MANIFEST.MF
  21. +2 −2 plugins/net.bioclipse.biojava.ui/plugin.xml
  22. +1 −1 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/actions/TranslateAction.java
  23. +2 −2 ...ns/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/actions/TranslateDNAToProteinAction.java
  24. +2 −2 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/actions/TranslateDNAToRNAAction.java
  25. +1 −1 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/actions/TranslateRNAToDNAAction.java
  26. +1 −1 ...ns/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/actions/TranslateRNAToProteinAction.java
  27. +4 −4 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/describer/SequenceEditorDescriber.java
  28. +1 −1 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/editors/Aligner.java
  29. +2 −2 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/editors/SequenceEditor.java
  30. +2 −2 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/views/SequenceContentProvider.java
  31. +2 −2 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/views/SequenceLabelProvider.java
  32. +1 −1 plugins/net.bioclipse.biojava.ui/src/net/bioclipse/biojava/ui/views/outline/SequenceOutlinePage.java
  33. +2 −1 plugins/net.bioclipse.biows.tests/META-INF/MANIFEST.MF
  34. +3 −3 plugins/net.bioclipse.biows.tests/src/net/bioclipse/biows/tests/PluginTestBiowsManager.java
  35. +2 −1 plugins/net.bioclipse.biows/META-INF/MANIFEST.MF
  36. +4 −4 plugins/net.bioclipse.biows/src/net/bioclipse/biows/business/BiowsManager.java
  37. +1 −1 plugins/net.bioclipse.biows/src/net/bioclipse/biows/business/IBiowsJSManager.java
  38. +7 −7 plugins/net.bioclipse.biows/src/net/bioclipse/biows/business/IBiowsManager.java
@@ -11,6 +11,7 @@ Require-Bundle: org.eclipse.ui,
net.bioclipse.core.tests;bundle-version="0.1.0",
net.bioclipse.biojava.business;bundle-version="0.1.0",
org.junit4;bundle-version="4.3.1",
- net.bioclipse.align.kalign.ws;bundle-version="1.0.0"
+ net.bioclipse.align.kalign.ws;bundle-version="1.0.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ActivationPolicy: lazy
@@ -18,9 +18,9 @@
import net.bioclipse.align.kalign.ws.Activator;
import net.bioclipse.align.kalign.ws.business.IKalignManager;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.IProtein;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.IProtein;
import org.junit.Test;
@@ -13,7 +13,8 @@ Require-Bundle: org.eclipse.ui,
net.bioclipse.biojava,
net.bioclipse.biojava.ui,
org.eclipse.core.resources,
- net.bioclipse.ui.business;bundle-version="2.1.1"
+ net.bioclipse.ui.business;bundle-version="2.1.1",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ActivationPolicy: lazy
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ClassPath: .,
@@ -10,7 +10,7 @@
******************************************************************************/
package net.bioclipse.align.kalign.ws.business;
-import net.bioclipse.managers.business.IBioclipseJSManager;
+import net.bioclipse.core.api.managers.IBioclipseJSManager;
/**
*
@@ -12,13 +12,13 @@
import java.util.List;
-import net.bioclipse.core.PublishedClass;
-import net.bioclipse.core.PublishedMethod;
-import net.bioclipse.core.Recorded;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.Recorded;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.managers.IBioclipseManager;
+import net.bioclipse.core.api.managers.PublishedClass;
+import net.bioclipse.core.api.managers.PublishedMethod;
@PublishedClass(value = "Controls access to KAlign Webservice at EBI.")
/**
@@ -35,12 +35,12 @@
import net.bioclipse.align.kalign.ws.util.SequenceCollectionContentHandler;
import net.bioclipse.biojava.business.Activator;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.core.domain.ISequence;
-import net.bioclipse.core.domain.RecordableList;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.domain.ISequence;
+import net.bioclipse.core.api.domain.RecordableList;
+import net.bioclipse.core.api.managers.IBioclipseManager;
/**
@@ -17,9 +17,9 @@
import net.bioclipse.align.kalign.ws.Activator;
import net.bioclipse.align.kalign.ws.business.IKalignManager;
import net.bioclipse.biojava.ui.editors.SequenceEditor;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.domain.ISequence;
import org.eclipse.core.commands.AbstractHandler;
import org.eclipse.core.commands.ExecutionEvent;
@@ -17,9 +17,9 @@
import net.bioclipse.align.kalign.ws.Activator;
import net.bioclipse.align.kalign.ws.business.IKalignManager;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.domain.ISequence;
import net.bioclipse.ui.business.IUIManager;
import org.apache.log4j.Logger;
@@ -14,7 +14,7 @@
import net.bioclipse.biojava.business.Activator;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.ISequence;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
@@ -8,7 +8,8 @@ Require-Bundle: org.eclipse.core.runtime,
net.bioclipse.biojava.business,
net.bioclipse.core,
net.bioclipse.biojava,
- net.bioclipse.scripting
+ net.bioclipse.scripting,
+ net.bioclipse.core.api;bundle-version="1.0.0"
Eclipse-LazyStart: true
Bundle-ClassPath: .
Export-Package: net.bioclipse.biojava.business,
@@ -15,9 +15,9 @@
import net.bioclipse.biojava.domain.BiojavaDNA;
import net.bioclipse.biojava.domain.BiojavaProtein;
import net.bioclipse.biojava.domain.BiojavaRNA;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.core.domain.IRNA;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.domain.IRNA;
import org.junit.Test;
@@ -16,7 +16,8 @@ Require-Bundle: org.eclipse.core.runtime,
org.eclipse.core.resources,
org.springframework.bundle.spring.aop,
net.sf.cglib,
- org.springframework.osgi.aopalliance.osgi;bundle-version="1.0.0"
+ org.springframework.osgi.aopalliance.osgi;bundle-version="1.0.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Export-Package: net.bioclipse.biojava.business,
net.bioclipse.biojava.domain
Bundle-Vendor: The Bioclipse Team
@@ -42,13 +42,13 @@
import net.bioclipse.biojava.domain.BiojavaProtein;
import net.bioclipse.biojava.domain.BiojavaRNA;
import net.bioclipse.biojava.domain.IFeature;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.core.domain.IRNA;
-import net.bioclipse.core.domain.ISequence;
-import net.bioclipse.core.domain.RecordableList;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.domain.IRNA;
+import net.bioclipse.core.api.domain.ISequence;
+import net.bioclipse.core.api.domain.RecordableList;
+import net.bioclipse.core.api.managers.IBioclipseManager;
import org.apache.log4j.Logger;
import org.biojava.bio.BioException;
@@ -21,15 +21,15 @@
import org.eclipse.core.runtime.IProgressMonitor;
import net.bioclipse.biojava.domain.IFeature;
-import net.bioclipse.core.PublishedClass;
-import net.bioclipse.core.PublishedMethod;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.IProtein;
-import net.bioclipse.core.domain.IRNA;
-import net.bioclipse.core.domain.ISequence;
-import net.bioclipse.core.domain.RecordableList;
-import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.IProtein;
+import net.bioclipse.core.api.domain.IRNA;
+import net.bioclipse.core.api.domain.ISequence;
+import net.bioclipse.core.api.domain.RecordableList;
+import net.bioclipse.core.api.managers.IBioclipseManager;
+import net.bioclipse.core.api.managers.PublishedClass;
+import net.bioclipse.core.api.managers.PublishedMethod;
/**
* @author jonalv, ola
@@ -10,7 +10,7 @@
******************************************************************************/
package net.bioclipse.biojava.business;
-import net.bioclipse.managers.business.IBioclipseJSManager;
+import net.bioclipse.core.api.managers.IBioclipseJSManager;
public interface IJavaScriptBiojavaManager
extends IBiojavaManager, IBioclipseJSManager {
@@ -14,7 +14,7 @@
import org.biojava.bio.seq.Sequence;
-import net.bioclipse.core.domain.IDNA;
+import net.bioclipse.core.api.domain.IDNA;
public class BiojavaDNA extends BiojavaSequence
implements IDNA {
@@ -12,7 +12,7 @@
******************************************************************************/
package net.bioclipse.biojava.domain;
-import net.bioclipse.core.domain.IProtein;
+import net.bioclipse.core.api.domain.IProtein;
import org.biojava.bio.seq.Sequence;
@@ -14,7 +14,7 @@
import org.biojava.bio.seq.Sequence;
-import net.bioclipse.core.domain.IRNA;
+import net.bioclipse.core.api.domain.IRNA;
public class BiojavaRNA extends BiojavaSequence
implements IRNA {
@@ -15,9 +15,9 @@
import java.io.ByteArrayOutputStream;
import java.io.IOException;
-import net.bioclipse.core.Recorded;
-import net.bioclipse.core.domain.BioObject;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.Recorded;
+import net.bioclipse.core.api.domain.BioObject;
+import net.bioclipse.core.api.domain.ISequence;
import org.biojava.bio.seq.Sequence;
import org.biojavax.Namespace;
@@ -17,7 +17,8 @@ Require-Bundle: org.eclipse.ui,
org.eclipse.ui.forms,
org.eclipse.ui.ide,
org.eclipse.ui.views;bundle-version="3.3.0",
- net.bioclipse.ui.business;bundle-version="2.0.0"
+ net.bioclipse.ui.business;bundle-version="2.0.0",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-ActivationPolicy: lazy
Export-Package: net.bioclipse.biojava.ui,
net.bioclipse.biojava.ui.actions,
@@ -30,12 +30,12 @@
<BioObject
describer="net.bioclipse.biojava.ui.describer.SequenceEditorDescriber"
id="net.bioclipse.cdk.sequenceditor.describer"
- objectClass="net.bioclipse.core.domain.RecordableList">
+ objectClass="net.bioclipse.core.api.domain.RecordableList">
</BioObject>
<BioObject
describer="net.bioclipse.biojava.ui.describer.SequenceEditorDescriber"
id="net.bioclipse.cdk.sequenceditor.describer"
- objectClass="net.bioclipse.core.domain.ISequence">
+ objectClass="net.bioclipse.core.api.domain.ISequence">
</BioObject>
</extension>
@@ -15,7 +15,7 @@
import net.bioclipse.biojava.business.Activator;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.ISequence;
import org.eclipse.jface.action.IAction;
import org.eclipse.jface.dialogs.MessageDialog;
@@ -14,8 +14,8 @@
import java.io.IOException;
import net.bioclipse.biojava.domain.BiojavaDNA;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.ISequence;
public class TranslateDNAToProteinAction extends TranslateAction{
@@ -14,8 +14,8 @@
import java.io.IOException;
import net.bioclipse.biojava.domain.BiojavaDNA;
-import net.bioclipse.core.domain.IDNA;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.IDNA;
+import net.bioclipse.core.api.domain.ISequence;
public class TranslateDNAToRNAAction extends TranslateAction{
@@ -15,7 +15,7 @@
import org.apache.log4j.Logger;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.ISequence;
/**
@@ -15,7 +15,7 @@
import org.apache.log4j.Logger;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.ISequence;
/**
@@ -1,10 +1,10 @@
package net.bioclipse.biojava.ui.describer;
import net.bioclipse.biojava.ui.editors.SequenceEditor;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.IBioObject;
-import net.bioclipse.core.domain.ISequence;
-import net.bioclipse.core.domain.RecordableList;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.IBioObject;
+import net.bioclipse.core.api.domain.ISequence;
+import net.bioclipse.core.api.domain.RecordableList;
import net.bioclipse.ui.business.describer.IBioObjectDescriber;
@@ -19,7 +19,7 @@
import net.bioclipse.biojava.business.Activator;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.ISequence;
import net.bioclipse.ui.editors.ColorManager;
import org.eclipse.core.resources.IFile;
@@ -14,8 +14,8 @@
import net.bioclipse.biojava.business.Activator;
import net.bioclipse.biojava.business.IBiojavaManager;
import net.bioclipse.biojava.ui.views.outline.SequenceOutlinePage;
-import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.BioclipseException;
+import net.bioclipse.core.api.domain.ISequence;
import net.bioclipse.core.util.LogUtils;
import org.apache.log4j.Logger;
@@ -28,8 +28,8 @@
import net.bioclipse.biojava.business.Activator;
import net.bioclipse.biojava.business.IBiojavaManager;
-import net.bioclipse.core.domain.IBioObject;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.IBioObject;
+import net.bioclipse.core.api.domain.ISequence;
import net.bioclipse.core.util.LogUtils;
import org.apache.log4j.Logger;
@@ -24,8 +24,8 @@
import java.util.List;
import net.bioclipse.biojava.ui.Activator;
-import net.bioclipse.core.domain.ISequence;
-import net.bioclipse.core.domain.RecordableList;
+import net.bioclipse.core.api.domain.ISequence;
+import net.bioclipse.core.api.domain.RecordableList;
import org.eclipse.jface.resource.ImageDescriptor;
import org.eclipse.jface.viewers.ILabelProvider;
@@ -11,7 +11,7 @@
import net.bioclipse.biojava.business.IBiojavaManager;
import net.bioclipse.biojava.ui.editors.Aligner;
import net.bioclipse.biojava.ui.editors.SequenceEditor;
-import net.bioclipse.core.domain.ISequence;
+import net.bioclipse.core.api.domain.ISequence;
import org.eclipse.core.resources.IFile;
import org.eclipse.core.runtime.IAdaptable;
@@ -11,7 +11,8 @@ Require-Bundle: org.eclipse.ui,
net.bioclipse.core.tests;bundle-version="0.1.0",
net.bioclipse.biojava.business;bundle-version="0.1.0",
net.bioclipse.biows;bundle-version="0.1.1",
- org.junit4;bundle-version="4.3.1"
+ org.junit4;bundle-version="4.3.1",
+ net.bioclipse.core.api;bundle-version="1.0.0"
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Bundle-ActivationPolicy: lazy
Import-Package: org.apache.log4j
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