updated jalview version of dasobert 1.53e client and added Das Sequence Source discov...

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

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 1e7ea06..137bdb8 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -51,7 +51,23 @@ public class DasSequenceFeatureFetcher
   Vector selectedSources;\r
 \r
   boolean cancelled = false;\r
-\r
+  private void debug(String mesg)\r
+  {\r
+    debug(mesg, null);\r
+  }\r
+  private void debug(String mesg, Exception e)\r
+  {\r
+    if (Cache.log!=null)\r
+    {\r
+      debug(mesg, e);\r
+    } else {\r
+      System.err.println(mesg);\r
+      if (e!=null)\r
+      { \r
+        e.printStackTrace(); \r
+      }\r
+    }\r
+  }\r
   long startTime;\r
 \r
   /**\r
@@ -157,7 +173,10 @@ public class DasSequenceFeatureFetcher
   {\r
     cancelled = false;\r
     startTime = System.currentTimeMillis();\r
-    af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
+    if (af!=null)\r
+    {\r
+      af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
+    }\r
 \r
     DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 \r
@@ -336,7 +355,7 @@ public class DasSequenceFeatureFetcher
                   && jalview.util.DBRefUtils.isDasCoordinateSystem(\r
                           cs[csIndex].getName(), uprefs[j]))\r
           {\r
-            Cache.log.debug("Launched fetcher for coordinate system "\r
+            debug("Launched fetcher for coordinate system "\r
                     + cs[0].getName());\r
             //  Will have to pass any mapping information to the fetcher\r
             //- the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
@@ -407,7 +426,7 @@ public class DasSequenceFeatureFetcher
       responseComplete(dasSource, seq); // reduce thread count anyhow\r
       return;\r
     }\r
-    Cache.log.debug("new Das Feature Fetcher for " + dbref.getSource()\r
+    debug("new Das Feature Fetcher for " + dbref.getSource()\r
             + ":" + dbref.getAccessionId() + " querying "\r
             + dasSource.getUrl());\r
     FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()\r
@@ -419,7 +438,7 @@ public class DasSequenceFeatureFetcher
       public void comeBackLater(FeatureEvent e)\r
       {\r
         responseComplete(dasSource, seq);\r
-        Cache.log.debug("das source " + e.getDasSource().getNickname()\r
+        debug("das source " + e.getSource().getNickname()\r
                 + " asked us to come back in " + e.getComeBackLater()\r
                 + " secs.");\r
       }\r
@@ -427,11 +446,11 @@ public class DasSequenceFeatureFetcher
       public void newFeatures(FeatureEvent e)\r
       {\r
 \r
-        Das1Source ds = e.getDasSource();\r
+        Das1Source ds = e.getSource();\r
 \r
         Map[] features = e.getFeatures();\r
         // add features to sequence\r
-        Cache.log.debug("das source " + ds.getUrl() + " returned "\r
+        debug("das source " + ds.getUrl() + " returned "\r
                 + features.length + " features");\r
 \r
         if (features.length > 0)\r
@@ -443,7 +462,7 @@ public class DasSequenceFeatureFetcher
             if (dbref.getMap() != null && f.getBegin() > 0\r
                     && f.getEnd() > 0)\r
             {\r
-              Cache.log.debug("mapping from " + f.getBegin() + " - "\r
+              debug("mapping from " + f.getBegin() + " - "\r
                       + f.getEnd());\r
               SequenceFeature vf[] = null;\r
 \r
@@ -466,7 +485,7 @@ public class DasSequenceFeatureFetcher
               {\r
                 for (int v = 0; v < vf.length; v++)\r
                 {\r
-                  Cache.log.debug("mapping to " + v + ": "\r
+                  debug("mapping to " + v + ": "\r
                           + vf[v].getBegin() + " - " + vf[v].getEnd());\r
                   seq.addSequenceFeature(vf[v]);\r
                 }\r
@@ -510,7 +529,7 @@ public class DasSequenceFeatureFetcher
     }\r
     if (id != null && id.length() > 0)\r
     {\r
-      Cache.log.debug("new Das Feature Fetcher for " + id + " querying "\r
+      debug("new Das Feature Fetcher for " + id + " querying "\r
               + dasSource.getUrl());\r
       FeatureThread fetcher = new FeatureThread(id\r
       //  +  ":" + start + "," + end,\r
@@ -521,7 +540,7 @@ public class DasSequenceFeatureFetcher
         public void comeBackLater(FeatureEvent e)\r
         {\r
           responseComplete(dasSource, seq);\r
-          Cache.log.debug("das source " + e.getDasSource().getNickname()\r
+          debug("das source " + e.getSource().getNickname()\r
                   + " asked us to come back in " + e.getComeBackLater()\r
                   + " secs.");\r
         }\r
@@ -529,11 +548,11 @@ public class DasSequenceFeatureFetcher
         public void newFeatures(FeatureEvent e)\r
         {\r
 \r
-          Das1Source ds = e.getDasSource();\r
+          Das1Source ds = e.getSource();\r
 \r
           Map[] features = e.getFeatures();\r
           // add features to sequence\r
-          Cache.log.debug("das source " + ds.getUrl() + " returned "\r
+          debug("das source " + ds.getUrl() + " returned "\r
                   + features.length + " features");\r
 \r
           if (features.length > 0)\r
@@ -563,7 +582,7 @@ public class DasSequenceFeatureFetcher
       fetcher.start();\r
     } else {\r
       // invalid fetch - indicate it is finished.\r
-      Cache.log.debug("Skipping empty ID for querying "\r
+      debug("Skipping empty ID for querying "\r
               + dasSource.getUrl());\r
       responseComplete(dasSource, seq);\r
     }\r
@@ -635,7 +654,7 @@ public class DasSequenceFeatureFetcher
       System.out.println("ERRR " + e);\r
       e.printStackTrace();\r
       System.out.println("############");\r
-      Cache.log.debug("Failed to parse " + dasfeature.toString(), e);\r
+      debug("Failed to parse " + dasfeature.toString(), e);\r
       return null;\r
     }\r
   }\r