X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=4fcba3177a5249aa967062537c690dfab78386df;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=5d734c10cfb3319d40d2d80db5bdc4acdb380adf;hpb=9659f01c9954d78d03e47aaedb89f6122f2b7142;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 5d734c1..4fcba31 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws1;
 
@@ -197,7 +198,8 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alcsel = ColumnSelection.propagateInsertions(profileseq, al, input);
+            alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+                    input);
           }
         }
       }
@@ -255,7 +257,6 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
     }
 
-
     public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
     {
       super();
@@ -269,6 +270,10 @@ class JPredThread extends JWS1Thread implements WSClientI
         sequence.setId(seq.getName());
         sequence.setSeq(sq);
       }
+      else
+      {
+        errorMessage = "Sequence is too short to predict with JPred - need at least 20 amino acids.";
+      }
     }
 
     public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
@@ -284,6 +289,13 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
       }
     }
+
+    String errorMessage = "";
+
+    public String getValidationMessages()
+    {
+      return errorMessage + "\n";
+    }
   }
 
   ext.vamsas.Jpred server;
@@ -313,6 +325,10 @@ class JPredThread extends JWS1Thread implements WSClientI
       { job };
       job.setJobnum(0);
     }
+    else
+    {
+      wsInfo.appendProgressText(job.getValidationMessages());
+    }
   }
 
   JPredThread(WebserviceInfo wsinfo, String altitle,
@@ -329,6 +345,10 @@ class JPredThread extends JWS1Thread implements WSClientI
       OutputHeader = wsInfo.getProgressText();
       job.setJobnum(0);
     }
+    else
+    {
+      wsInfo.appendProgressText(job.getValidationMessages());
+    }
   }
 
   public void StartJob(AWsJob j)
@@ -451,6 +471,8 @@ class JPredThread extends JWS1Thread implements WSClientI
     }
     else
     {
+      wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
+      wsInfo.appendInfoText("No jobs ran.");
       wsInfo.setFinishedNoResults();
     }
   }