JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / jws2 / RNAalifoldClient.java

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index 2779732..b3000b3 100644 (file)
--- 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 2.8.2b1)
+ * 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[struct.length()];
+    Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
+            : struct.length()];
 
     if (data != null
             && data.size() > 1
@@ -216,9 +242,17 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
         basePairs.put(score.getRanges().first(), new Float(score
                 .getScores().get(0)));
       }
-      for (int i = 0; i < struct.length(); i++)
-      {
 
+      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
+      {
+        if (gapMap != null)
+        {
+          // skip any gapped columns in the input data
+          while (!gapMap[ri])
+          {
+            ri++;
+          }
+        }
         // Return all the contacts associated with position i
         LinkedHashMap<Range, Float> contacts = isContact(basePairs, i + 1);
 
@@ -242,16 +276,27 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
           }
         }
 
-        anns[i] = new Annotation(struct.substring(i, i + 1), description,
+        anns[ri] = new Annotation(struct.substring(i, i + 1), description,
                 isSS(struct.charAt(i)), prob);
       }
     }
     else if (data == null || data.size() == 1)
     {
-      for (int i = 0; i < struct.length(); i++)
+      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
       {
-
-        anns[i] = new Annotation(struct.substring(i, i + 1), "",
+        if (gapMap != null)
+        {
+          // skip any gapped columns in the input data
+          while (!gapMap[ri] && ri < gapMap.length)
+          {
+            ri++;
+          }
+          if (ri == gapMap.length)
+          {
+            break;
+          }
+        }
+        anns[ri] = new Annotation(struct.substring(i, i + 1), "",
                 isSS(struct.charAt(i)), Float.NaN);
       }