JAL-4090 JAL-1551 spotlessApply

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

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 6e7df71..8170801 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -32,6 +32,7 @@ import jalview.util.MessageManager;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -83,7 +84,7 @@ public class WSWUBlastClient
     for (int i = 0; i < ids.size(); i++)
     {
       Sequence sequence = (Sequence) ids.get(i);
-      System.out.println(sequence.getName());
+      jalview.bin.Console.outPrintln(sequence.getName());
 
       BlastThread thread = new BlastThread(sequence);
       thread.start();
@@ -175,16 +176,17 @@ public class WSWUBlastClient
           }
         }
 
-        DBRefEntry[] entries = oldseq.getDBRefs();
-        if (entries != null)
+        List<DBRefEntry> entries = oldseq.getDBRefs();
+        // BH 2019.01.25 check for 0-length was missing here
+        if (entries != null && entries.size() > 0)
         {
           oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
                   jalview.datamodel.DBRefSource.UNIPROT, "0",
-                  entries[0].getAccessionId()));
+                  entries.get(0).getAccessionId()));
         }
       }
     }
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, false);
 
   }
 
@@ -247,7 +249,7 @@ public class WSWUBlastClient
 
     BlastThread(Sequence sequence)
     {
-      System.out.println("blasting for: " + sequence.getName());
+      jalview.bin.Console.outPrintln("blasting for: " + sequence.getName());
       this.sequence = sequence;
     }
 
@@ -274,7 +276,7 @@ public class WSWUBlastClient
           else
           {
             Thread.sleep(10000);
-            System.out.println("WSWuBlastClient: I'm alive "
+            jalview.bin.Console.outPrintln("WSWuBlastClient: I'm alive "
                     + sequence.getName() + " " + jobid); // log.debug
           }
         } catch (Exception ex)
@@ -313,7 +315,8 @@ public class WSWUBlastClient
       {
         jobComplete = true;
         jobsRunning--;
-        System.err.println("WSWUBlastClient error:\n" + exp.toString());
+        jalview.bin.Console
+                .errPrintln("WSWUBlastClient error:\n" + exp.toString());
         exp.printStackTrace();
       }
     }