From: amwaterhouse Date: Wed, 26 Jul 2006 10:43:06 +0000 (+0000) Subject: Back to org.biojava X-Git-Tag: Release_2_1~203 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=74fee91ef567d4637911a9c20834c9fb1de8c64a;p=jalview.git 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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.