X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=863e80e2c166f7de7471fa331ac92207239bcb02;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=a4d8b1fa0d133432e4da53ee6c9b5bf134145848;hpb=a5481d6e853a962af603f4a21b171ba6fc9c200d;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index a4d8b1f..863e80e 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -60,7 +60,7 @@ public class JPredClient
    * @param title String
    * @param msa boolean
    * @param alview AlignmentView
-   * @param viewonly if true then the prediction will be made just on the concatenated visible regions 
+   * @param viewonly if true then the prediction will be made just on the concatenated visible regions
    */
   private void startJPredClient(String title, boolean msa,
                                 jalview.datamodel.AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
@@ -89,13 +89,13 @@ public class JPredClient
       int spos=0;
       int i=0;
       if (viscontigs!=null) {
-        // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence  
-        
+        // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence
+
         delMap = new int[seq.getEnd()-seq.getStart()+1];
         int gapMap[] = seq.gapMap();
         for (int contig = 0; contig<viscontigs.length; contig += 2)
         {
-           
+
           while (spos<gapMap.length && gapMap[spos]<viscontigs[contig]) {
             spos++;
           }
@@ -106,11 +106,11 @@ public class JPredClient
         int tmap[] = new int[i];
         System.arraycopy(delMap, 0, tmap, 0, i);
         delMap=tmap;
-      } 
+      }
     }
     if (msa && msf.length > 1)
     {
-      
+
       String altitle = "JNet prediction on "+(viewonly?"visible ":"") + seq.getName() +
           " using alignment from " + title;
 
@@ -119,22 +119,22 @@ public class JPredClient
       {
         aln[i] = msf[i].getSeq('-');
       }
-      
-      
+
+
       Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
       if (viewonly) {
         // Remove hidden regions from sequence objects.
         String seqs[] = alview.getSequenceStrings('-');
         for (int i = 0, j = msf.length; i < j; i++)
-        { 
+        {
           aln[i].setSequence(seqs[i]);
-        } 
+        }
         seq.setSequence(seqs[0]);
-      }  
+      }
       wsInfo.setProgressText("Job details for "+(viewonly?"visible ":"")+"MSA based prediction (" +
           title + ") on sequence :\n>" + seq.getName() +
           "\n" +
-          AlignSeq.extractGaps("-. ", seq.getSequence()) +
+          AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
           "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server,
                                             SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
@@ -155,10 +155,10 @@ public class JPredClient
         // Remove hidden regions from input sequence
         String seqs[] = alview.getSequenceStrings('-');
         seq.setSequence(seqs[0]);
-      } 
+      }
       wsInfo.setProgressText("Job details for prediction on "+(viewonly?"visible ":"")+"sequence :\n>" +
           seqname + "\n" +
-          AlignSeq.extractGaps("-. ", seq.getSequence()) +
+          AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
           "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
                                             SequenceInfo, seq, delMap, alview, parentFrame);
@@ -203,7 +203,7 @@ public class JPredClient
 
     wsInfo.setProgressText("Job details for MSA based prediction (" +
                            title + ") on sequence :\n>" + seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
                            "\n");
     SequenceI aln[] = new SequenceI[msf.length];
     for (int i = 0, j = msf.length; i < j; i++)
@@ -232,7 +232,7 @@ public class JPredClient
     }
     wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
                            seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
                            "\n");
     String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
         title;