X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FRNAalifoldClient.java;h=253a7976dd6e1d6d2ad25b1f80303742d715bf41;hb=7e8241cdc284ef2586e36a3abbe3bd385dad10dc;hp=c7d8efdc611dbd97a46ad3cf1865e96c17f2dc60;hpb=b920a3c8476e5f43399393d580d4e3d8b79c15b6;p=jalview.git

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index c7d8efd..253a797 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -1,3 +1,23 @@
+/*
+ * 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.jws2;
 
 import jalview.api.AlignCalcWorkerI;
@@ -17,6 +37,7 @@ import java.util.TreeSet;
 import java.util.regex.Pattern;
 
 import compbio.data.sequence.RNAStructReader.AlifoldResult;
+import compbio.data.sequence.FastaSequence;
 import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
@@ -24,11 +45,12 @@ import compbio.metadata.Argument;
 
 /**
  * Client for the JABA RNA Alifold Service
+ * 
  * @author daluke - Daniel Barton
- *
+ * 
  */
 
-public class RNAalifoldClient extends JabawsAlignCalcWorker implements
+public class RNAalifoldClient extends JabawsCalcWorker implements
         AlignCalcWorkerI
 {
 
@@ -44,24 +66,21 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
           WsParamSetI preset, List<Argument> paramset)
   {
     super(sh, alignFrame, preset, paramset);
-
-    //if (arguments == null)
-    //  arguments = new ArrayList<Argument>();
-
     af = alignFrame;
     methodName = sh.serviceType;
-    alignedSeqs=true;
-    submitGaps=true;
+    alignedSeqs = true;
+    submitGaps = true;
     nucleotidesAllowed = true;
     proteinAllowed = false;
     initViewportParams();
   }
-  
+
   public String getCalcId()
   {
     return CALC_ID;
   }
-  private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient";
+
+  private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
 
   public static AlignAnalysisUIText getAlignAnalysisUITest()
   {
@@ -87,6 +106,12 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   }
 
   @Override
+  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+  {
+    return (seqs.size() > 1);
+  }
+
+  @Override
   public void updateResultAnnotation(boolean immediate)
   {
 
@@ -198,7 +223,8 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   private AlignmentAnnotation constructAnnotationFromScoreHolder(
           AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
   {
-    Annotation[] anns = new Annotation[gapMap!= null ? gapMap.length+1 : struct.length()];
+    Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
+            : struct.length()];
 
     if (data != null
             && data.size() > 1
@@ -216,10 +242,10 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
         basePairs.put(score.getRanges().first(), new Float(score
                 .getScores().get(0)));
       }
-      
-      for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+
+      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
       {
-        if (gapMap!=null)
+        if (gapMap != null)
         {
           // skip any gapped columns in the input data
           while (!gapMap[ri])
@@ -256,16 +282,16 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
     }
     else if (data == null || data.size() == 1)
     {
-      for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
       {
-        if (gapMap!=null)
+        if (gapMap != null)
         {
           // skip any gapped columns in the input data
-          while (!gapMap[ri] && ri<gapMap.length)
+          while (!gapMap[ri] && ri < gapMap.length)
           {
             ri++;
           }
-          if (ri==gapMap.length)
+          if (ri == gapMap.length)
           {
             break;
           }