X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=36e51647c1e4491ff79221cdfb717d48a89b5d29;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=bdb3b572ff7d28c0c8b03342a68a95f38bca13f5;hpb=8f759d39bf8d95e5657eccda618b65ad31171fcf;p=jalview.git

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index bdb3b57..36e5164 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -27,9 +27,9 @@ import javax.swing.*;
 import java.util.*;
 
 
-import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import jalview.biojava.dasobert.dasregistry.DasSource;
-import jalview.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
+import org.biojava.dasobert.dasregistry.Das1Source;
 import java.awt.BorderLayout;
 
 public class DasSourceBrowser extends GDasSourceBrowser
@@ -41,10 +41,13 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   Vector selectedSources;
 
+  String DEFAULT_REGISTRY = "http://das.sanger.ac.uk/registry/das1/sources/";
+
+
   public DasSourceBrowser()
   {
     registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://das.sanger.ac.uk/registry/das1/sources/") );
+        DEFAULT_REGISTRY) );
 
     setSelectedFromProperties();
 
@@ -61,10 +64,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     {
       public void valueChanged(ListSelectionEvent e)
       {
-        //Ignore extra messages.
-        if (e.getValueIsAdjusting())
-          return;
-
         ListSelectionModel lsm = (ListSelectionModel) e.getSource();
         if (!lsm.isSelectionEmpty())
         {
@@ -240,7 +239,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   public void run()
   {
-
     addLocal.setVisible(false);
     refresh.setVisible(false);
     progressBar.setVisible(true);
@@ -251,6 +249,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
     appendLocalSources();
 
     init();
+
   }
 
   public Vector getSelectedSources()
@@ -549,23 +548,26 @@ public class DasSourceBrowser extends GDasSourceBrowser
         index++;
       }
 
-         dasSources = tmp;
+      dasSources = tmp;
 
-         refreshTableData(data);
+      refreshTableData(data);
   }
 
   public void valueChanged(ListSelectionEvent evt)
   {
     //Called when the MainTable selection changes
-    if (evt.getValueIsAdjusting())
+    if (evt.getValueIsAdjusting() )
     {
       return;
     }
 
+
     displayFullDetails(null);
 
     // Filter the displayed data sources
     int dSize = dasSources.length;
+
+
     ArrayList names = new ArrayList();
     ArrayList selected = new ArrayList();
     DasSource ds;
@@ -575,10 +577,25 @@ public class DasSourceBrowser extends GDasSourceBrowser
     //July 2006 - only 6 sources fo not serve features
     Object [] dummyFeatureList = new Object[]{"features"};
 
-    // capabilities.get
     for (int i = 0; i < dSize; i++)
     {
       ds = dasSources[i];
+      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
+
+      if (dcs.length == 0 && ds.getCapabilities().length == 0
+          && filter1.getSelectedIndex() == 0
+          && filter2.getSelectedIndex() == 0
+          && filter3.getSelectedIndex() == 0)
+      {
+        //THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
+        //HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
+        //IS ADDED FROM THE REGISTRY
+        names.add(ds.getNickname());
+        selected.add(new Boolean(
+              selectedSources.contains(ds.getNickname())));
+        continue;
+      }
+
 
       if (!selectedInList(dummyFeatureList, ds.getCapabilities())
       ||  !selectedInList(filter3.getSelectedValues(),
@@ -587,12 +604,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
         continue;
       }
 
-      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
       for (int j = 0; j < dcs.length; j++)
       {
-        if (selectedInList(dummyFeatureList,ds.getCapabilities())
-        &&
-            selectedInList(filter1.getSelectedValues(),
+        if (   selectedInList(filter1.getSelectedValues(),
                            new String[]
                            {dcs[j].getName()})
             && selectedInList(filter2.getSelectedValues(),
@@ -622,7 +636,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
   {
     for (int i = 0; i < selection.length; i++)
     {
-      if (selection[i].equals("Any"))
+      if (selection[i].equals("Any") )
         return true;
 
       for (int j = 0; j < items.length; j++)
@@ -666,9 +680,17 @@ public class DasSourceBrowser extends GDasSourceBrowser
      }
   }
 
+  public void reset_actionPerformed(ActionEvent e)
+  {
+    registryURL.setText(DEFAULT_REGISTRY);
+  }
+
   public void saveProperties(Properties properties)
   {
-    properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
+    if (registryURL.getText() == null || registryURL.getText().length() < 1)
+      properties.remove("DAS_REGISTRY_URL");
+    else
+      properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
 
     StringBuffer sb = new StringBuffer();
     for(int r=0; r<table.getModel().getRowCount(); r++)