Towards an auto dbref fetcher

[jalview.git] / src / jalview / io / DasSequenceFeatureFetcher.java

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index dc51617..70af276 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -40,7 +40,9 @@ import org.biojava.dasobert.das2.DasSourceConverter;
 \r
 \r
 import jalview.bin.Cache;\r
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
 \r
+import javax.swing.*;\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -50,8 +52,8 @@ import jalview.bin.Cache;
  */\r
 public class DasSequenceFeatureFetcher implements Runnable\r
 {\r
-  final AlignmentI dataset;\r
-  final AlignFrame af;\r
+  SequenceI [] sequences;\r
+  AlignFrame af;\r
   StringBuffer sbuffer = new StringBuffer();\r
   Vector selectedSources;\r
 \r
@@ -66,14 +68,74 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param align DOCUMENT ME!\r
    * @param ap DOCUMENT ME!\r
    */\r
-  public DasSequenceFeatureFetcher(AlignmentI align,\r
-                                   AlignFrame af,\r
+  public DasSequenceFeatureFetcher(SequenceI [] sequences,\r
+                                   final AlignFrame af,\r
                                    Vector selectedSources)\r
   {\r
     this.selectedSources = selectedSources;\r
-    this.dataset = align.getDataset();\r
+    this.sequences = sequences;\r
     this.af = af;\r
 \r
+    int uniprotCount = 0;\r
+    for (int i = 0; i < selectedSources.size(); i++)\r
+    {\r
+      DasSource source = (DasSource) selectedSources.elementAt(i);\r
+      DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
+      for (int c = 0; c < coords.length; c++)\r
+      {\r
+        if (coords[c].getName().equalsIgnoreCase("UniProt"))\r
+        {\r
+          uniprotCount++;\r
+          break;\r
+        }\r
+      }\r
+    }\r
+\r
+    int refCount = 0;\r
+    for(int i=0; i<sequences.length; i++)\r
+    {\r
+      if(sequences[i].getDBRef()!=null)\r
+      {\r
+        for(int j=0; j<sequences[i].getDBRef().size(); j++)\r
+        {\r
+          System.out.println(sequences[i].getDBRef().elementAt(j)\r
+                             +" "+jalview.datamodel.DBRefSource.UNIPROT);\r
+          if(sequences[i].getDBRef().elementAt(j)\r
+             .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
+          {\r
+            System.out.println("got a match");\r
+            refCount++;\r
+            break;\r
+          }\r
+        }\r
+      }\r
+    }\r
+\r
+   System.out.println(refCount+" "+uniprotCount+" "+sequences.length);\r
+    if(refCount<sequences.length && uniprotCount>0)\r
+    {\r
+\r
+     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+          "Do you want Jalview to find\n"\r
+         +"Uniprot Accession ids for given sequence names?",\r
+         "Find Uniprot Accession Ids",\r
+         JOptionPane.YES_NO_OPTION,\r
+         JOptionPane.QUESTION_MESSAGE);\r
+\r
+     if(reply == JOptionPane.YES_OPTION)\r
+     {\r
+       new DBRefFetcher(\r
+             af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
+\r
+     }\r
+    }\r
+\r
+   System.out.println("User selection is "\r
+                      +\r
+                       ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)\r
+                      + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");\r
+\r
+\r
     Thread thread = new Thread(this);\r
     thread.start();\r
   }\r
@@ -145,7 +207,7 @@ public class DasSequenceFeatureFetcher implements Runnable
    * @param SourceUrl\r
    * @param id\r
    */\r
-  protected void createFeatureFetcher(final Sequence seq,\r
+  protected void createFeatureFetcher(final SequenceI seq,\r
                                       final String sourceUrl,\r
                                       String id,\r
                                       String nickname)  {\r
@@ -262,11 +324,9 @@ public class DasSequenceFeatureFetcher implements Runnable
     try\r
     {\r
       int seqIndex = 0;\r
-      Vector sequences = dataset.getSequences();\r
-      while (seqIndex < sequences.size())\r
+      while (seqIndex < sequences.length)\r
       {\r
-          Sequence sequence = (Sequence) sequences.get(seqIndex);\r
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
               new String[]  {\r
               jalview.datamodel.DBRefSource.PDB,\r
               jalview.datamodel.DBRefSource.UNIPROT});\r
@@ -292,7 +352,7 @@ public class DasSequenceFeatureFetcher implements Runnable
                                     cs[l].getName());\r
 \r
 \r
-                    createFeatureFetcher(sequence,\r
+                    createFeatureFetcher(sequences[seqIndex],\r
                                          dasSource.getUrl(),\r
                                          ( (DBRefEntry) uprefs.get(j)).\r
                                          getAccessionId(),\r
@@ -305,19 +365,19 @@ public class DasSequenceFeatureFetcher implements Runnable
             {\r
               String id = null;\r
               // try and use the name as the sequence id\r
-              if (sequence.getName().indexOf("|") > -1)\r
+              if (sequences[seqIndex].getName().indexOf("|") > -1)\r
               {\r
-                id = sequence.getName().substring(\r
-                    sequence.getName().lastIndexOf("|") + 1);\r
+                id = sequences[seqIndex].getName().substring(\r
+                    sequences[seqIndex].getName().lastIndexOf("|") + 1);\r
               }\r
               else\r
               {\r
-                id = sequence.getName();\r
+                id = sequences[seqIndex].getName();\r
               }\r
               if (id != null)\r
               {\r
                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
-                createFeatureFetcher(sequence,\r
+                createFeatureFetcher(sequences[seqIndex],\r
                                      dasSource.getUrl(),\r
                                      id,\r
                                      dasSource.getNickname());\r
@@ -340,7 +400,7 @@ public class DasSequenceFeatureFetcher implements Runnable
     DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
 \r
     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
-        "http://www.spice-3d.org/dasregistry/das1/sources"\r
+        "http://das.sanger.ac.uk/registry/das1/sources/"\r
       );\r
 \r
     try\r