Back to org.biojava

diff --git a/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java b/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java
index cdfc493..b65a847 100644 (file)
--- a/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java
+++ b/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java
@@ -21,7 +21,7 @@
  * @author Andreas Prlic
  *
  */
-package jalview.biojava.dasobert.das;
+package org.biojava.dasobert.das;
 
 
 import java.net.URL                         ;

diff --git a/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java b/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java
index 957d511..fa42fe4 100644 (file)
--- a/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java
+++ b/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java
@@ -21,7 +21,7 @@
  * @author Andreas Prlic
  *
  */
-package jalview.biojava.dasobert.das;
+package org.biojava.dasobert.das;
 
 import org.xml.sax.helpers.DefaultHandler;
 import org.xml.sax.Attributes;

diff --git a/src/jalview/biojava/dasobert/das/FeatureThread.java b/src/jalview/biojava/dasobert/das/FeatureThread.java
index 5446789..4d07c89 100644 (file)
--- a/src/jalview/biojava/dasobert/das/FeatureThread.java
+++ b/src/jalview/biojava/dasobert/das/FeatureThread.java
@@ -22,14 +22,14 @@
  *
  */
 
-package jalview.biojava.dasobert.das ;
+package org.biojava.dasobert.das ;
 
 import java.util.*;
 import java.net.*;
 import java.util.logging.* ;
-import jalview.biojava.dasobert.eventmodel.FeatureListener;
-import jalview.biojava.dasobert.eventmodel.FeatureEvent;
-import jalview.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.eventmodel.FeatureListener;
+import org.biojava.dasobert.eventmodel.FeatureEvent;
+import org.biojava.dasobert.dasregistry.Das1Source;
 
 /** a thread that connects to a DAS - Feature service and gets the features
  *

diff --git a/src/jalview/biojava/dasobert/das2/Das2Capability.java b/src/jalview/biojava/dasobert/das2/Das2Capability.java
index 12ad52b..5cff3f5 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/Das2Capability.java
+++ b/src/jalview/biojava/dasobert/das2/Das2Capability.java
@@ -20,7 +20,7 @@
  * Created on Feb 9, 2006
  *
  */
-package jalview.biojava.dasobert.das2;
+package org.biojava.dasobert.das2;
 
 public interface Das2Capability {
 

diff --git a/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java b/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java
index a30b2fa..507a2d3 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java
+++ b/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java
@@ -20,7 +20,7 @@
  * Created on Feb 9, 2006
  *
  */
-package jalview.biojava.dasobert.das2;
+package org.biojava.dasobert.das2;
 
 public class Das2CapabilityImpl
 implements Das2Capability{

diff --git a/src/jalview/biojava/dasobert/das2/Das2Source.java b/src/jalview/biojava/dasobert/das2/Das2Source.java
index 882f0fd..c370de9 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/Das2Source.java
+++ b/src/jalview/biojava/dasobert/das2/Das2Source.java
@@ -20,9 +20,9 @@
  * Created on Feb 9, 2006
  *
  */
-package jalview.biojava.dasobert.das2;
+package org.biojava.dasobert.das2;
 
-import jalview.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.DasSource;
 
 public interface Das2Source
 extends DasSource {

diff --git a/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java b/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java
index 5c49366..bb5325d 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java
+++ b/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java
@@ -20,10 +20,10 @@
  * Created on Feb 9, 2006
  *
  */
-package jalview.biojava.dasobert.das2;
+package org.biojava.dasobert.das2;
 
-import jalview.biojava.dasobert.dasregistry.Das1Source;
-import jalview.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasSource;
 
 public class Das2SourceImpl
 extends Das1Source

diff --git a/src/jalview/biojava/dasobert/das2/DasSourceConverter.java b/src/jalview/biojava/dasobert/das2/DasSourceConverter.java
index ca7cd9f..513ba3f 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/DasSourceConverter.java
+++ b/src/jalview/biojava/dasobert/das2/DasSourceConverter.java
@@ -20,10 +20,10 @@
  * Created on Mar 23, 2006
  *
  */
-package jalview.biojava.dasobert.das2;
+package org.biojava.dasobert.das2;
 
-//import jalview.biojava.bio.program.das.dasalignment.DASException;
-import jalview.biojava.dasobert.dasregistry.Das1Source;
+//import org.biojava.bio.program.das.dasalignment.DASException;
+import org.biojava.dasobert.dasregistry.Das1Source;
 
 public class DasSourceConverter {
 

diff --git a/src/jalview/biojava/dasobert/das2/io/DAS2SourceHandler.java b/src/jalview/biojava/dasobert/das2/io/DAS2SourceHandler.java
index fe2889e..a9c0af3 100755 (executable)
--- a/src/jalview/biojava/dasobert/das2/io/DAS2SourceHandler.java
+++ b/src/jalview/biojava/dasobert/das2/io/DAS2SourceHandler.java
@@ -20,17 +20,17 @@
  * Created on Mar 15, 2006
  *
  */
-package jalview.biojava.dasobert.das2.io;
+package org.biojava.dasobert.das2.io;
 
 import java.util.ArrayList;
 import java.util.List;
 
-import jalview.biojava.dasobert.das2.Das2Capability;
-import jalview.biojava.dasobert.das2.Das2CapabilityImpl;
-import jalview.biojava.dasobert.das2.Das2Source;
-import jalview.biojava.dasobert.das2.Das2SourceImpl;
-import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import jalview.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.das2.Das2Capability;
+import org.biojava.dasobert.das2.Das2CapabilityImpl;
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.Das2SourceImpl;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
 import org.xml.sax.Attributes;
 import org.xml.sax.helpers.DefaultHandler;
 

diff --git a/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java b/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java
index 547c968..8044fb7 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java
+++ b/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java
@@ -20,11 +20,11 @@
  * Created on Feb 24, 2006
  *
  */
-package jalview.biojava.dasobert.das2.io;
+package org.biojava.dasobert.das2.io;
 
 import java.io.InputStream;
 
-import jalview.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.DasSource;
 
 public interface DasSourceReader {
 

diff --git a/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java
index 03b23ff..3f0a07a 100644 (file)
--- a/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java
+++ b/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java
@@ -20,7 +20,7 @@
  * Created on Feb 24, 2006
  *
  */
-package jalview.biojava.dasobert.das2.io;
+package org.biojava.dasobert.das2.io;
 
 import java.io.InputStream;
 import java.net.HttpURLConnection;
@@ -31,9 +31,9 @@ import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
 
-//import jalview.biojava.dasobert.das.AlignmentThread;
-import jalview.biojava.dasobert.das.DAS_FeatureRetrieve;
-import jalview.biojava.dasobert.dasregistry.DasSource;
+//import org.biojava.dasobert.das.AlignmentThread;
+import org.biojava.dasobert.das.DAS_FeatureRetrieve;
+import org.biojava.dasobert.dasregistry.DasSource;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 import org.xml.sax.SAXNotRecognizedException;

diff --git a/src/jalview/biojava/dasobert/dasregistry/Das1Source.java b/src/jalview/biojava/dasobert/dasregistry/Das1Source.java
index 4a54353..de007d6 100644 (file)
--- a/src/jalview/biojava/dasobert/dasregistry/Das1Source.java
+++ b/src/jalview/biojava/dasobert/dasregistry/Das1Source.java
@@ -21,7 +21,7 @@
  * @author Andreas Prlic
  *
  */
-package jalview.biojava.dasobert.dasregistry;
+package org.biojava.dasobert.dasregistry;
 
 import java.util.Date ;
 import java.io.IOException;
@@ -29,9 +29,9 @@ import java.io.PrintWriter;
 import java.io.StringWriter;
 
 
-//import jalview.biojava.dasobert.das2.io.DasSourceWriter;
-//import jalview.biojava.dasobert.das2.io.DasSourceWriterImpl;
-//import jalview.biojava.utils.xml.PrettyXMLWriter;
+//import org.biojava.dasobert.das2.io.DasSourceWriter;
+//import org.biojava.dasobert.das2.io.DasSourceWriterImpl;
+//import org.biojava.utils.xml.PrettyXMLWriter;
 
 
 /** a simple Bean class to be returned via SOAP

diff --git a/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java b/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java
index 2a9e8d0..48cb4f0 100755 (executable)
--- a/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java
+++ b/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java
@@ -20,9 +20,9 @@
  * Created on Mar 20, 2006
  *
  */
-package jalview.biojava.dasobert.dasregistry;
+package org.biojava.dasobert.dasregistry;
 
-import jalview.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.das2.Das2Source;
 
 public class Das2Validator {
 

diff --git a/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java b/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java
index ce9ddc5..621fbc8 100644 (file)
--- a/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java
+++ b/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java
@@ -23,13 +23,13 @@
  */
 
 
-package jalview.biojava.dasobert.dasregistry ;
+package org.biojava.dasobert.dasregistry ;
 
 import java.util.Comparator ;
 import java.util.Map ;
 import java.util.HashMap ;
 
-import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
 /** a comparator to sort DasSources
  * @author Andreas Prlic

diff --git a/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java
index 58fa023..8fc4ccb 100644 (file)
--- a/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java
+++ b/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java
@@ -21,7 +21,7 @@
  * @author Andreas Prlic
  *
  */
-package jalview.biojava.dasobert.dasregistry;
+package org.biojava.dasobert.dasregistry;
 
 
 /** a Bean to be returned via SOAP. It takes care of the DAS -  coordinate Systems

diff --git a/src/jalview/biojava/dasobert/dasregistry/DasSource.java b/src/jalview/biojava/dasobert/dasregistry/DasSource.java
index a6e0096..6dd49e5 100644 (file)
--- a/src/jalview/biojava/dasobert/dasregistry/DasSource.java
+++ b/src/jalview/biojava/dasobert/dasregistry/DasSource.java
@@ -20,7 +20,7 @@
  * Created on Feb 8, 2006
  *
  */
-package jalview.biojava.dasobert.dasregistry;
+package org.biojava.dasobert.dasregistry;
 
 import java.util.Date;
 
@@ -102,4 +102,4 @@ public interface DasSource {
 
     public  boolean getAlertAdmin();
 
-}
\ No newline at end of file
+}

diff --git a/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java b/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java
index fb6b249..ddbad1a 100644 (file)
--- a/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java
+++ b/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java
@@ -23,7 +23,7 @@
  */
 
 
-package jalview.biojava.dasobert.dasregistry ;
+package org.biojava.dasobert.dasregistry ;
 
 import java.util.Comparator ;
 import java.util.Map ;

diff --git a/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java b/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java
index 0df2358..63b5da4 100644 (file)
--- a/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java
+++ b/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java
@@ -20,11 +20,11 @@
  * Created on Oct 28, 2005
  *
  */
-package jalview.biojava.dasobert.eventmodel;
+package org.biojava.dasobert.eventmodel;
 
 import java.util.Map;
 
-import jalview.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.Das1Source;
 public class FeatureEvent {
 
     Map[] features;

diff --git a/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java b/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java
index fb58345..299a6bf 100644 (file)
--- a/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java
+++ b/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java
@@ -20,9 +20,9 @@
  * Created on Oct 28, 2005
  *
  */
-package jalview.biojava.dasobert.eventmodel;
+package org.biojava.dasobert.eventmodel;
 
-//import jalview.biojava.spice.multipanel.eventmodel.FeatureEvent;
+//import org.biojava.spice.multipanel.eventmodel.FeatureEvent;
 
 /**  a feature listener that returns the raw features as returned by a DAS source.
  *

diff --git a/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java b/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java
index 497d382..640b413 100644 (file)
--- a/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java
+++ b/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java
@@ -20,7 +20,7 @@
  * Created on Nov 1, 2005
  *
  */
-package jalview.biojava.dasobert.eventmodel;
+package org.biojava.dasobert.eventmodel;
 
 /** an interface for the listeners of new PDB code requested / new Uniprot code requested
  *

diff --git a/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java b/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java
index 14038c9..7798da1 100644 (file)
--- a/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java
+++ b/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java
@@ -20,7 +20,7 @@
  * Created on Nov 20, 2005
  *
  */
-package jalview.biojava.dasobert.eventmodel;
+package org.biojava.dasobert.eventmodel;
 
 
 public class SequenceEvent {

diff --git a/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java b/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java
index 0f6d724..37779bd 100644 (file)
--- a/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java
+++ b/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java
@@ -20,7 +20,7 @@
  * Created on Jun 10, 2005
  *
  */
-package jalview.biojava.dasobert.eventmodel;
+package org.biojava.dasobert.eventmodel;
 
 /** An interface fore events related to selections of sequence
  * position, sequence range and locking of the selection.