/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
-import jalview.ws.jws2.dm.AAConSettings;
+import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.TreeSet;
import java.util.regex.Pattern;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
*
*/
-public class RNAalifoldClient extends JabawsAlignCalcWorker implements
- AlignCalcWorkerI
+public class RNAalifoldClient extends JabawsCalcWorker
{
String methodName;
WsParamSetI preset, List<Argument> paramset)
{
super(sh, alignFrame, preset, paramset);
-
- // if (arguments == null)
- // arguments = new ArrayList<Argument>();
-
af = alignFrame;
methodName = sh.serviceType;
alignedSeqs = true;
initViewportParams();
}
+ @Override
public String getCalcId()
{
return CALC_ID;
{
return new AlignAnalysisUIText(
compbio.ws.client.Services.RNAalifoldWS.toString(),
- jalview.ws.jws2.RNAalifoldClient.class,
- CALC_ID,
- true,
- false,
- true,
- "RNAAliFold Prediction",
- "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.",
- "Change RNAAliFold settings...",
- "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters");
-
+ jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false,
+ true, MessageManager.getString("label.rnalifold_calculations"),
+ MessageManager.getString("tooltip.rnalifold_calculations"),
+ MessageManager.getString("label.rnalifold_settings"),
+ MessageManager.getString("tooltip.rnalifold_settings"));
}
@Override
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public void updateResultAnnotation(boolean immediate)
{
* same data object as was overwritten with the contact probabilites data.
*/
if (data == null)
+ {
data = compbio.data.sequence.RNAStructReader
.newEmptyScore(AlifoldResult.consensusAlignment);
+ }
if (descriptionData == null)
+ {
descriptionData = data;
+ }
String[] typenameAndDescription = constructTypenameAndDescription(descriptionData
.first());
{
float t = contacts.get(contact);
if (t > prob)
+ {
prob = t;
+ }
description += Integer.toString(contact.from) + "->"
+ Integer.toString(contact.to) + ": "
+ Float.toString(t) + "% | ";
score.getScores().get(0), score.getScores().get(1));
}
else
+ {
description = "Stochastic Backtrack Structure";
+ }
}
else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
{
description = typename;
}
- return new String[]
- { typename, description };
+ return new String[] { typename, description };
}
// Check whether, at position i there is a base contact and return all the
// ordering of the Scores TreeSet in ScoreManager which is, descending
// probability
if (contact.from == i || contact.to == i)
+ {
contacts.put(contact, basePairs.get(contact));
+ }
}
return contacts;