X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FRNAalifoldClient.java;h=fac08570bb7d4e2dff56e9f475c98560a3779ebe;hb=2b8cf92a2483d206d9e574bbe8306ad845a308d8;hp=ec40552b38048fe6b6a390c2c816fd6121c4550e;hpb=54da3e753588d95f08dd66ca2d111f16475b061c;p=jalview.git
diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index ec40552..fac0857 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 .
+ * 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
{
@@ -45,23 +67,24 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
{
super(sh, alignFrame, preset, paramset);
- //if (arguments == null)
- // arguments = new ArrayList();
+ // if (arguments == null)
+ // arguments = new ArrayList();
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 +110,12 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public void updateResultAnnotation(boolean immediate)
{
@@ -198,7 +227,8 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
private AlignmentAnnotation constructAnnotationFromScoreHolder(
AlignmentAnnotation annotation, String struct, TreeSet data)
{
- Annotation[] anns = new Annotation[struct.length()];
+ Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
+ : struct.length()];
if (data != null
&& data.size() > 1
@@ -216,10 +246,10 @@ 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