JAL-1432 updated copyright notices

[jalview.git] / src / jalview / ws / jws1 / JPredClient.java

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index eab47d7..dccaf4a 100644 (file)
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
 
@@ -99,33 +100,7 @@ public class JPredClient extends WS1Client
 
     if (viewonly)
     {
-      int[] viscontigs = alview.getVisibleContigs();
-      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
-
-        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++;
-          }
-          while (spos < gapMap.length
-                  && gapMap[spos] <= viscontigs[contig + 1])
-          {
-            delMap[i++] = spos++;
-          }
-        }
-        int tmap[] = new int[i];
-        System.arraycopy(delMap, 0, tmap, 0, i);
-        delMap = tmap;
-      }
+      delMap = alview.getVisibleContigMapFor(seq.gapMap());
     }
     if (msa && msf.length > 1)
     {
@@ -252,15 +227,9 @@ public class JPredClient extends WS1Client
     String altitle = "JNet prediction on " + seq.getName()
             + " using alignment from " + title;
 
-    wsInfo
-            .setProgressText("Job details for MSA based prediction ("
-                    + title
-                    + ") on sequence :\n>"
-                    + seq.getName()
-                    + "\n"
-                    + AlignSeq
-                            .extractGaps("-. ", seq.getSequenceAsString())
-                    + "\n");
+    wsInfo.setProgressText("Job details for MSA based prediction (" + title
+            + ") on sequence :\n>" + seq.getName() + "\n"
+            + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
     SequenceI aln[] = new SequenceI[msf.length];
     for (int i = 0, j = msf.length; i < j; i++)
     {
@@ -289,13 +258,9 @@ public class JPredClient extends WS1Client
     {
       wsInfo = setWebService();
     }
-    wsInfo
-            .setProgressText("Job details for prediction on sequence :\n>"
-                    + seq.getName()
-                    + "\n"
-                    + AlignSeq
-                            .extractGaps("-. ", seq.getSequenceAsString())
-                    + "\n");
+    wsInfo.setProgressText("Job details for prediction on sequence :\n>"
+            + seq.getName() + "\n"
+            + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
     String altitle = "JNet prediction for sequence " + seq.getName()
             + " from " + title;
 
@@ -371,16 +336,16 @@ public class JPredClient extends WS1Client
         if (msa.getSequences().length == 1)
         {
           // Single Sequence prediction
-          new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
-                  true);
+          new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa,
+                  af, true);
         }
         else
         {
           if (msa.getSequences().length > 1)
           {
             // Sequence profile based prediction
-            new jalview.ws.jws1.JPredClient(sh, af.getTitle(), true, msa, af,
-                    true);
+            new jalview.ws.jws1.JPredClient(sh, af.getTitle(), true, msa,
+                    af, true);
           }
         }
       }