From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 10:49:55 +0000 (+0000)
Subject: jalview.biojava
X-Git-Tag: Release_2_1~218
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f759d39bf8d95e5657eccda618b65ad31171fcf;p=jalview.git

jalview.biojava
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5036a0b..155e7ee 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -35,7 +35,7 @@ import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
 import java.awt.dnd.*;
-import org.biojava.dasobert.eventmodel.*;
+import jalview.biojava.dasobert.eventmodel.*;
 
 /**
  * DOCUMENT ME!
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 7875d7b..bdb3b57 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -27,9 +27,9 @@ import javax.swing.*;
 import java.util.*;
 
 
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.dasregistry.Das1Source;
+import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import jalview.biojava.dasobert.dasregistry.DasSource;
+import jalview.biojava.dasobert.dasregistry.Das1Source;
 import java.awt.BorderLayout;
 
 public class DasSourceBrowser extends GDasSourceBrowser
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index ad9ad1d..ce88b90 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -31,8 +31,8 @@ import jalview.io.JalviewFileChooser;
 import java.awt.BorderLayout;
 import java.awt.Font;
 import java.awt.Color;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import jalview.biojava.dasobert.dasregistry.DasSource;
+import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
 public class FeatureSettings extends JPanel
 {
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index f8bd7e0..3ccbbc5 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -26,21 +26,20 @@ import java.util.*;
 
 import java.net.URL;
 
-import org.biojava.dasobert.das.FeatureThread;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.eventmodel.FeatureEvent;
-import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.dasobert.dasregistry.DasSource;
+import jalview.biojava.dasobert.das.FeatureThread;
+import jalview.biojava.dasobert.eventmodel.FeatureEvent;
+import jalview.biojava.dasobert.eventmodel.FeatureListener;
+import jalview.biojava.dasobert.dasregistry.DasSource;
 
-import org.biojava.dasobert.das2.io.DasSourceReaderImpl;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.das2.DasSourceConverter;
+import jalview.biojava.dasobert.das2.io.DasSourceReaderImpl;
+import jalview.biojava.dasobert.dasregistry.Das1Source;
+import jalview.biojava.dasobert.dasregistry.DasSource;
+import jalview.biojava.dasobert.das2.Das2Source;
+import jalview.biojava.dasobert.das2.DasSourceConverter;
 
 
 import jalview.bin.Cache;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
 import javax.swing.*;
 
@@ -373,7 +372,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               {
 
                 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
-                org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
                 for (int l=0; l<cs.length; l++)
                 {
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))