From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 17 Jul 2006 10:02:34 +0000 (+0000)
Subject: Towards an auto dbref fetcher
X-Git-Tag: Release_2_1~282
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3bff9f93376444b36ca6b69d30193e10ea3c07ab;p=jalview.git

Towards an auto dbref fetcher
---

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index bacb383..065fcdf 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -44,7 +44,7 @@ public class DasSourceBrowser extends GDasSourceBrowser
   public DasSourceBrowser()
   {
     registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://www.spice-3d.org/dasregistry/das1/sources") );
+        "http://das.sanger.ac.uk/registry/das1/sources/") );
 
     setSelectedFromProperties();
 
@@ -300,8 +300,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
     authority.addElement("Any");
     type.addElement("Any");
     label.addElement("Any");
-    label.addElement("NOT IMPLEMENTED YET");
-    filter3.setEnabled(false);
 
     for (int i = 0; i < sources.length; i++)
     {
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index b720008..ad9ad1d 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -558,28 +558,34 @@ public class FeatureSettings extends JPanel
   {
     Vector selectedSources = dassourceBrowser.getSelectedSources();
 
-    int uniprotCount = 0;
-    for(int i=0; i<selectedSources.size(); i++)
+    SequenceI [] dataset, seqs ;
+    int iSize;
+
+    if(af.getViewport().getSelectionGroup()!=null
+      && af.getViewport().getSelectionGroup().getSize(false)>0)
     {
-     DasSource source = (DasSource)selectedSources.elementAt(i);
-     DasCoordinateSystem [] coords = source.getCoordinateSystem();
-     for(int c=0; c<coords.length; c++)
-     {
-       if (coords[c].getName().equalsIgnoreCase("UniProt"))
-       {
-         uniprotCount++;
-         break;
-       }
-     }
+      iSize = af.getViewport().getSelectionGroup().getSize(false);
+      dataset = new SequenceI[iSize];
+      seqs = af.getViewport().getSelectionGroup().
+          getSequencesInOrder(
+              af.getViewport().getAlignment());
+    }
+    else
+    {
+       iSize = af.getViewport().getAlignment().getHeight();
+       seqs = af.getViewport().getAlignment().getSequencesArray();
     }
 
-    System.out.println("User selection is "
-                       + (((float)uniprotCount/(float)selectedSources.size())*100)
-                       +" % Uniprot");
+    dataset = new SequenceI[iSize];
+    for (int i = 0; i < iSize; i++)
+    {
+      dataset[i] = seqs[i].getDatasetSequence();
+    }
 
-   new jalview.io.DasSequenceFeatureFetcher(af.getViewport().getAlignment(),
-                                             af,
-                                            selectedSources);
+    new jalview.io.DasSequenceFeatureFetcher(
+        dataset,
+        af,
+        selectedSources);
 
     af.getViewport().setShowSequenceFeatures(true);
     af.showSeqFeatures.setSelected(true);
diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/io/DBRefFetcher.java
index c11910b..4488d02 100644
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/io/DBRefFetcher.java
@@ -48,6 +48,7 @@ public class DBRefFetcher implements Runnable
   CutAndPasteTransfer output = new CutAndPasteTransfer();
   StringBuffer sbuffer = new StringBuffer();
   boolean uniprotFlag = false;
+  boolean running = false;
 
   public DBRefFetcher()
   {}
@@ -91,9 +92,25 @@ public class DBRefFetcher implements Runnable
     unknownSequences = new ArrayList();
     this.align = align;
     this.dataset = align.getDataset();
+  }
 
+  public boolean fetchDBRefs(boolean waitTillFinished)
+  {
     Thread thread = new Thread(this);
     thread.start();
+    running = true;
+
+    if(waitTillFinished)
+    {
+      while(running)
+      {
+        try{
+          Thread.sleep(500);
+        }catch(Exception ex){}
+      }
+    }
+
+    return true;
   }
 
   /**
@@ -103,6 +120,7 @@ public class DBRefFetcher implements Runnable
   {
     long startTime = System.currentTimeMillis();
     af.setProgressBar("Fetching db refs", startTime);
+    running = true;
 
     try
     {
@@ -187,6 +205,8 @@ public class DBRefFetcher implements Runnable
     af.setProgressBar("DBRef search completed", startTime);
    // promptBeforeBlast();
 
+   running = false;
+
   }
 
 
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 1295520..70af276 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -40,7 +40,9 @@ import org.biojava.dasobert.das2.DasSourceConverter;
 
 
 import jalview.bin.Cache;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
+import javax.swing.*;
 
 /**
  * DOCUMENT ME!
@@ -67,13 +69,73 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param ap DOCUMENT ME!
    */
   public DasSequenceFeatureFetcher(SequenceI [] sequences,
-                                   AlignFrame af,
+                                   final AlignFrame af,
                                    Vector selectedSources)
   {
     this.selectedSources = selectedSources;
     this.sequences = sequences;
     this.af = af;
 
+    int uniprotCount = 0;
+    for (int i = 0; i < selectedSources.size(); i++)
+    {
+      DasSource source = (DasSource) selectedSources.elementAt(i);
+      DasCoordinateSystem[] coords = source.getCoordinateSystem();
+      for (int c = 0; c < coords.length; c++)
+      {
+        if (coords[c].getName().equalsIgnoreCase("UniProt"))
+        {
+          uniprotCount++;
+          break;
+        }
+      }
+    }
+
+    int refCount = 0;
+    for(int i=0; i<sequences.length; i++)
+    {
+      if(sequences[i].getDBRef()!=null)
+      {
+        for(int j=0; j<sequences[i].getDBRef().size(); j++)
+        {
+          System.out.println(sequences[i].getDBRef().elementAt(j)
+                             +" "+jalview.datamodel.DBRefSource.UNIPROT);
+          if(sequences[i].getDBRef().elementAt(j)
+             .equals(jalview.datamodel.DBRefSource.UNIPROT))
+          {
+            System.out.println("got a match");
+            refCount++;
+            break;
+          }
+        }
+      }
+    }
+
+   System.out.println(refCount+" "+uniprotCount+" "+sequences.length);
+    if(refCount<sequences.length && uniprotCount>0)
+    {
+
+     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "Do you want Jalview to find\n"
+         +"Uniprot Accession ids for given sequence names?",
+         "Find Uniprot Accession Ids",
+         JOptionPane.YES_NO_OPTION,
+         JOptionPane.QUESTION_MESSAGE);
+
+     if(reply == JOptionPane.YES_OPTION)
+     {
+       new DBRefFetcher(
+             af.getViewport().getAlignment(), af).fetchDBRefs(true);
+
+     }
+    }
+
+   System.out.println("User selection is "
+                      +
+                       ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)
+                      + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");
+
+
     Thread thread = new Thread(this);
     thread.start();
   }
@@ -338,7 +400,7 @@ public class DasSequenceFeatureFetcher implements Runnable
     DasSourceReaderImpl reader = new DasSourceReaderImpl();
 
     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
-        "http://www.spice-3d.org/dasregistry/das1/sources"
+        "http://das.sanger.ac.uk/registry/das1/sources/"
       );
 
     try