moved visible sub-alignment extraction and update from MsaWSThread to

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

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 1e07c49..7a001a9 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -27,7 +27,6 @@ import java.util.*;
 import java.net.URL;\r
 \r
 import org.biojava.dasobert.das.FeatureThread;\r
-import org.biojava.dasobert.dasregistry.Das1Source;\r
 import org.biojava.dasobert.eventmodel.FeatureEvent;\r
 import org.biojava.dasobert.eventmodel.FeatureListener;\r
 import org.biojava.dasobert.dasregistry.DasSource;\r
@@ -83,7 +82,6 @@ public class DasSequenceFeatureFetcher implements Runnable
       DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
       for (int c = 0; c < coords.length; c++)\r
       {\r
-        System.out.println(coords[c].getName());\r
         if (coords[c].getName().indexOf("UniProt")>-1)\r
         {\r
           uniprotCount++;\r
@@ -100,12 +98,9 @@ public class DasSequenceFeatureFetcher implements Runnable
       {\r
         for(int j=0; j<dbref.length; j++)\r
         {\r
-          System.out.println(dbref[j].getSource()\r
-                             +" "+jalview.datamodel.DBRefSource.UNIPROT);\r
           if(dbref[j].getSource()\r
              .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
           {\r
-            System.out.println("got a match");\r
             refCount++;\r
             break;\r
           }\r
@@ -113,7 +108,6 @@ public class DasSequenceFeatureFetcher implements Runnable
       }\r
     }\r
 \r
-   System.out.println(refCount+" "+uniprotCount+" "+sequences.length);\r
     if(refCount<sequences.length && uniprotCount>0)\r
     {\r
 \r
@@ -126,21 +120,38 @@ public class DasSequenceFeatureFetcher implements Runnable
 \r
      if(reply == JOptionPane.YES_OPTION)\r
      {\r
-       new DBRefFetcher(\r
-             af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
-\r
+       Thread thread = new Thread(new FetchDBRefs());\r
+       thread.start();\r
      }\r
+     else\r
+      startFetching();\r
     }\r
+    else\r
+      startFetching();\r
 \r
-   System.out.println("User selection is "\r
-                      +\r
+  /* System.out.println("User selection is "   +\r
                        ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)\r
                       + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");\r
+*/\r
+  }\r
 \r
-\r
+  void startFetching()\r
+  {\r
     Thread thread = new Thread(this);\r
     thread.start();\r
   }\r
+\r
+  class FetchDBRefs implements Runnable\r
+  {\r
+    public void run()\r
+    {\r
+      new DBRefFetcher(\r
+             af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
+      startFetching();\r
+    }\r
+  }\r
+\r
+\r
   /**\r
    * creates a jalview sequence feature from a das feature document\r
    * @param dasfeature\r
@@ -194,7 +205,6 @@ public class DasSequenceFeatureFetcher implements Runnable
                                //  null\r
                        // );\r
 \r
-                     // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
          return f;\r
          }\r
          catch (Exception e) {\r
@@ -228,9 +238,8 @@ public class DasSequenceFeatureFetcher implements Runnable
           {\r
             setThreadsRunning(+1);\r
 \r
-            int start=seq.getStart(), end = seq.getEnd();\r
-\r
-            if(af.getViewport().getSelectionGroup()!=null)\r
+          //  int start=seq.getStart(), end = seq.getEnd();\r
+          /*  if(af.getViewport().getSelectionGroup()!=null)\r
             {\r
               SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());\r
               start = tmp.findPosition(\r
@@ -240,7 +249,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               end = tmp.findPosition(\r
                  af.getViewport().getSelectionGroup().getEndRes()\r
                  );\r
-            }\r
+            }*/\r
 \r
             FeatureThread fetcher = new FeatureThread(id\r
                                                    //  +  ":" + start + "," + end,\r
@@ -300,7 +309,12 @@ public class DasSequenceFeatureFetcher implements Runnable
   {\r
     threadsRunning += i;\r
     if(threadsRunning<1)\r
+    {\r
       af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
+\r
+      if(af.featureSettings!=null)\r
+        af.featureSettings.setTableData();\r
+    }\r
   }\r
 \r
   /**\r
@@ -361,7 +375,7 @@ public class DasSequenceFeatureFetcher implements Runnable
               {\r
 \r
                 // 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\r
-                org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
+                DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
                 for (int l=0; l<cs.length; l++)\r
                 {\r
                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r