X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws2%2Foperations%2FAlignmentOperation.java;h=f836c91a2600054bd1d11814ccb3a121276e23a2;hb=bc7c6b545d858f698f4e60f782b354e59430dddb;hp=f72978a1e6d97c7aa968b6261bc346793aba44ac;hpb=5989790542b20a5ceb228edc7ef6c158974ea8a3;p=jalview.git

diff --git a/src/jalview/ws2/operations/AlignmentOperation.java b/src/jalview/ws2/operations/AlignmentOperation.java
index f72978a..f836c91 100644
--- a/src/jalview/ws2/operations/AlignmentOperation.java
+++ b/src/jalview/ws2/operations/AlignmentOperation.java
@@ -366,6 +366,7 @@ public class AlignmentOperation implements Operation
     @Override
     public void startJobs() throws IOException
     {
+      Cache.log.info(format("Starting new %s job.", service.getName()));
       String outputHeader = String.format("%s of %s%nJob details%n",
               submitGaps ? "Re-alignment" : "Alignment", alnTitle);
       SequenceI[][] conmsa = msa.getVisibleContigs('-');
@@ -382,7 +383,7 @@ public class AlignmentOperation implements Operation
         WSJob job = new WSJob(service.getProviderName(), service.getName(),
                 service.getHostName());
         job.setJobNum(wsInfo.addJobPane());
-        if (conmsa.length > 0)
+        if (conmsa.length > 1)
         {
           wsInfo.setProgressName(String.format("region %d", i),
                   job.getJobNum());
@@ -448,7 +449,7 @@ public class AlignmentOperation implements Operation
       boolean done = true;
       for (WSJob job : getJobs())
       {
-        if (!job.getStatus().isDone())
+        if (!job.getStatus().isDone() && !job.getStatus().isFailed())
         {
           Cache.log.debug(format("Polling job %s.", job));
           try
@@ -479,7 +480,7 @@ public class AlignmentOperation implements Operation
           Cache.log.debug(
                   format("Job %s status is %s", job, job.getStatus()));
         }
-        done &= job.getStatus().isDone();
+        done &= job.getStatus().isDone() || job.getStatus().isFailed();
       }
       updateWSInfoGlobalStatus();
       return done;