X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=b58ce95ecbb02e88b1d3e4bd859310a0ea437fac;hb=6834a636a0b72693041e2f1090c1123f215c9ec1;hp=01aa532f3c78638230593bc6bca98f387b709bdc;hpb=d2735d899ea977b635ca89378daa9ae16c5f55b9;p=jalview.git

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index 01aa532..b58ce95 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -25,10 +25,11 @@ import jalview.util.TableSorter;
 import java.awt.event.*;
 import javax.swing.*;
 import java.util.*;
-import java.net.*;
 
-import org.biojava.services.das.registry.DasCoordinateSystem;
-import org.biojava.services.das.registry.DasSource;
+
+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
@@ -40,19 +41,32 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   Vector selectedSources;
 
+  String DEFAULT_REGISTRY = "http://www.dasregistry.org/registry/das1/sources/";
+
+  boolean loadingDasSources = false;
+
+
   public DasSourceBrowser()
   {
-    registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://servlet.sanger.ac.uk/dasregistry/services/das_registry") );
+    String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+        DEFAULT_REGISTRY);
+
+    if(registry.equals("http://das.sanger.ac.uk/registry/das1/sources/"))
+    {
+      jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);
+      registry = DEFAULT_REGISTRY;
+    }
+
+    registryURL.setText( registry );
 
     setSelectedFromProperties();
 
     displayFullDetails(null);
     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 
-    capabilities.addListSelectionListener(this);
-    coords1.addListSelectionListener(this);
-    coords2.addListSelectionListener(this);
+    filter1.addListSelectionListener(this);
+    filter2.addListSelectionListener(this);
+    filter3.addListSelectionListener(this);
 
     //Ask to be notified of selection changes.
     ListSelectionModel rowSM = table.getSelectionModel();
@@ -60,10 +74,6 @@ 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())
         {
@@ -83,15 +93,19 @@ public class DasSourceBrowser extends GDasSourceBrowser
           }
         });
 
-    if(dasSources==null)
+    if(dasSources!=null)
     {
-    Thread worker = new Thread(this);
-    worker.start();
-    }
-    else
-     {
        init();
-     }
+    }
+  }
+
+  public void paintComponent(java.awt.Graphics g)
+  {
+    if (dasSources == null && !loadingDasSources)
+    {
+      Thread worker = new Thread(this);
+      worker.start();
+    }
   }
 
   void init()
@@ -212,7 +226,9 @@ public class DasSourceBrowser extends GDasSourceBrowser
       text.append("<font color=\"#0000FF\">Description:</font> " +
                   dasSources[i].getDescription() + "<br>");
 
-      if (dasSources[i].getHelperurl().length() > 0)
+
+      if (dasSources[i].getHelperurl()!=null
+          && dasSources[i].getHelperurl().length() > 0)
       {
         text.append("<font color=\"#0000FF\"><a href=\"" +
                     dasSources[i].getHelperurl()
@@ -237,6 +253,8 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   public void run()
   {
+    loadingDasSources = true;
+
     addLocal.setVisible(false);
     refresh.setVisible(false);
     progressBar.setVisible(true);
@@ -247,6 +265,28 @@ public class DasSourceBrowser extends GDasSourceBrowser
     appendLocalSources();
 
     init();
+
+    loadingDasSources = false;
+
+  }
+
+  public Vector getSelectedSources()
+  {
+    Vector selected = new Vector();
+    for (int r = 0; r < selectedSources.size(); r++)
+    {
+        for (int i = 0; i < dasSources.length; i++)
+        {
+          if (dasSources[i].getNickname().equals(
+              selectedSources.elementAt(r)))
+          {
+            selected.addElement(dasSources[i]);
+            break;
+          }
+        }
+    }
+
+    return selected;
   }
 
   public DasSource[] getDASSource()
@@ -270,49 +310,51 @@ public class DasSourceBrowser extends GDasSourceBrowser
 
   private void setCapabilities(DasSource[] sources)
   {
-    Vector vcapabilities = new Vector();
-    Vector vcoords = new Vector();
-    Vector vcoords2 = new Vector();
+    Vector authority = new Vector();
+    Vector type = new Vector();
+    Vector label = new Vector();
 
-    vcapabilities.addElement("All");
-    vcoords.addElement("All");
-    vcoords2.addElement("All");
+    authority.addElement("Any");
+    type.addElement("Any");
+    label.addElement("Any");
 
     for (int i = 0; i < sources.length; i++)
     {
       DasSource ds = sources[i];
-      String[] scap = ds.getCapabilities();
-      for (int s = 0; s < scap.length; s++)
-      {
-        if (!vcapabilities.contains(scap[s]))
-        {
-          vcapabilities.addElement(scap[s]);
-        }
-      }
 
       DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
 
       for (int j = 0; j < dcs.length; j++)
       {
-        if (!vcoords.contains(dcs[j].getCategory()))
-          vcoords.addElement(dcs[j].getCategory());
+        if (!type.contains(dcs[j].getCategory()))
+          type.addElement(dcs[j].getCategory());
 
-        if (!vcoords2.contains(dcs[j].getName()))
-          vcoords2.addElement(dcs[j].getName());
+        if (!authority.contains(dcs[j].getName()))
+          authority.addElement(dcs[j].getName());
       }
+
+      String[] slabels = ds.getLabels();
+      for (int s = 0; s < slabels.length; s++)
+      {
+        if (!label.contains(slabels[s]))
+        {
+          label.addElement(slabels[s]);
+        }
+      }
+
     }
 
-    capabilities.setListData(vcapabilities);
-    coords1.setListData(vcoords);
-    coords2.setListData(vcoords2);
+    filter1.setListData(authority);
+    filter2.setListData(type);
+    filter3.setListData(label);
 
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
       public void run()
       {
-        capabilities.setSelectedIndex(0);
-        coords1.setSelectedIndex(0);
-        coords2.setSelectedIndex(0);
+        filter1.setSelectedIndex(0);
+        filter2.setSelectedIndex(0);
+        filter3.setSelectedIndex(0);
       }
     });
   }
@@ -354,7 +396,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
        if(!urltf.getText().endsWith("/"))
          urltf.setText(urltf.getText()+"/");
 
-       DasSource local = new DasSource();
+       Das1Source local = new Das1Source();
 
        local.setUrl(urltf.getText());
        local.setNickname(nametf.getText());
@@ -490,77 +532,104 @@ public class DasSourceBrowser extends GDasSourceBrowser
       }
     }
 
-  void appendLocalSources()
-  {
-    if(localSources==null)
-      return;
+    void appendLocalSources()
+    {
+      if(localSources==null)
+        return;
 
-    int size = dasSources.length;
-    int lsize = localSources.size();
+      int size = dasSources!=null ? dasSources.length : 0;
+      int lsize = localSources.size();
 
-    Object[][] data = new Object[size+lsize][2];
-    for (int i = 0; i < size; i++)
-    {
-      data[i][0] = dasSources[i].getNickname();
-      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
-          getNickname()));
-    }
+      Object[][] data = new Object[size+lsize][2];
+      for (int i = 0; i < size; i++)
+      {
+        data[i][0] = dasSources[i].getNickname();
+        data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
+            getNickname()));
+      }
 
-    DasSource [] tmp = new DasSource[size+lsize];
-    System.arraycopy(dasSources, 0, tmp, 0, size);
+      DasSource [] tmp = new DasSource[size+lsize];
+      if(dasSources!=null)
+        System.arraycopy(dasSources, 0, tmp, 0, size);
 
-    Enumeration en = localSources.keys();
-    int index = size;
-    while(en.hasMoreElements())
-    {
-      String key = en.nextElement().toString();
-      data[index][0] = key;
-      data[index][1] = new Boolean(false);
-      tmp[index] = new DasSource();
-      tmp[index].setNickname(key);
-      tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
-
-      index++;
-    }
+      Enumeration en = localSources.keys();
+      int index = size;
+      while(en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        data[index][0] = key;
+        data[index][1] = new Boolean(false);
+        tmp[index] = new Das1Source();
+        tmp[index].setNickname(key);
+        tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
+
+        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;
 
-    // capabilities.get
+    //The features filter is not visible, but we must still
+    //filter the das source list here.
+    //July 2006 - only 6 sources fo not serve features
+    Object [] dummyFeatureList = new Object[]{"features"};
+
     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(capabilities, ds.getCapabilities()))
+      if (!selectedInList(dummyFeatureList, ds.getCapabilities())
+      ||  !selectedInList(filter3.getSelectedValues(),
+                          ds.getLabels()))
       {
         continue;
       }
 
-      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
       for (int j = 0; j < dcs.length; j++)
       {
-        if (selectedInList(coords1, new String[]
-                           {dcs[j].getCategory()})
-            && selectedInList(coords2, new String[]
-                              {dcs[j].getName()}))
+        if (   selectedInList(filter1.getSelectedValues(),
+                           new String[]
+                           {dcs[j].getName()})
+            && selectedInList(filter2.getSelectedValues(),
+                              new String[]
+                              {dcs[j].getCategory()}))
         {
           names.add(ds.getNickname());
           selected.add(new Boolean(
@@ -581,12 +650,11 @@ public class DasSourceBrowser extends GDasSourceBrowser
     refreshTableData(data);
   }
 
-  boolean selectedInList(JList list, String[] items)
+  boolean selectedInList(Object [] selection, String[] items)
   {
-    Object[] selection = list.getSelectedValues();
     for (int i = 0; i < selection.length; i++)
     {
-      if (selection[i].equals("All"))
+      if (selection[i].equals("Any") )
         return true;
 
       for (int j = 0; j < items.length; j++)
@@ -620,7 +688,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
        {
          String token = st.nextToken();
          int bar = token.indexOf("|");
-         DasSource source = new DasSource();
+         Das1Source source = new Das1Source();
 
          source.setUrl(token.substring(bar + 1));
          source.setNickname(token.substring(0, bar));
@@ -630,9 +698,17 @@ public class DasSourceBrowser extends GDasSourceBrowser
      }
   }
 
-  void saveProperties(Properties properties)
+  public void reset_actionPerformed(ActionEvent e)
   {
-    properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
+    registryURL.setText(DEFAULT_REGISTRY);
+  }
+
+  public void saveProperties(Properties properties)
+  {
+    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++)