Dont use gold colouring for highlight

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

diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 33791ad..2f94d64 100755 (executable)
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -130,8 +130,7 @@ public class DasSequenceFeatureFetcher
   {\r
     public void run()\r
     {\r
-      new DBRefFetcher(\r
-          af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
+      new DBRefFetcher(sequences, af).fetchDBRefs(true);\r
       startFetching();\r
     }\r
   }\r
@@ -173,6 +172,8 @@ public class DasSequenceFeatureFetcher
      {\r
        System.out.println("No DAS Sources active");\r
        af.setProgressBar("No DAS Sources Active", startTime);\r
+       cancelled = true;\r
+       fsettings.noDasSourceActive();\r
        return;\r
      }\r
 \r
@@ -250,7 +251,9 @@ public class DasSequenceFeatureFetcher
 \r
   void nextSequence(DasSource dasSource, SequenceI seq)\r
   {\r
-      DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),\r
+    if (cancelled)\r
+      return;\r
+    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),\r
           new String[]\r
           {\r
         //  jalview.datamodel.DBRefSource.PDB,\r
@@ -264,11 +267,11 @@ public class DasSequenceFeatureFetcher
       if (uprefs != null)\r
         {\r
           // do any of these ids match the source's coordinate system ?\r
-          for (int j = 0; j < uprefs.length; j++)\r
+          for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)\r
           {\r
             DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 \r
-            for(int csIndex=0; csIndex<cs.length; csIndex++)\r
+            for(int csIndex=0; csIndex<cs.length && !dasCoordSysFound; csIndex++)\r
             {\r
               if (cs.length > 0 && jalview.util.DBRefUtils\r
                   .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))\r
@@ -281,11 +284,10 @@ public class DasSequenceFeatureFetcher
                 System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)\r
                                    + " " + dasSource.getUrl());\r
 \r
-                dasCoordSysFound = false;\r
+                dasCoordSysFound = true; // break's out of the loop\r
                 createFeatureFetcher(seq,\r
                                      dasSource,\r
                                      uprefs[j]);\r
-                break; // only do this for one reference - assume same source will send same features for all IDs\r
               }\r
               else\r
                 System.out.println("IGNORE " + cs[csIndex].getName());\r
@@ -372,7 +374,19 @@ public class DasSequenceFeatureFetcher
                   source.getNickname());\r
               if (dbref.getMap()!=null && f.getBegin()>0 && f.getEnd()>0) {\r
                 Cache.log.debug("mapping from "+f.getBegin()+" - "+f.getEnd());\r
-                SequenceFeature vf[] = dbref.getMap().locateFeature(f);\r
+                SequenceFeature vf[]=null;\r
+                \r
+                try {\r
+                  vf = dbref.getMap().locateFeature(f);\r
+                }\r
+                catch (Exception ex)\r
+                {\r
+                  Cache.log.info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");\r
+                  Cache.log.info("Mapping feature from "+f.getBegin()+" to "+f.getEnd()+" in dbref "+dbref.getAccessionId()+" in "+dbref.getSource());\r
+                  Cache.log.info("using das Source "+ds.getUrl());\r
+                  Cache.log.info(ex);\r
+                }\r
+                \r
                 if (vf!=null) {\r
                   for (int v=0;v<vf.length;v++)\r
                   {\r
@@ -475,6 +489,10 @@ public class DasSequenceFeatureFetcher
    */\r
   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
   {\r
+    if (dasfeature==null)\r
+    {\r
+      return null;\r
+    }\r
     try\r
     {\r
       /**\r