/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
/**
* Client for the JABA RNA Alifold Service
+ *
* @author daluke - Daniel Barton
- *
+ *
*/
-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;
- submitGaps=true;
+ alignedSeqs = true;
+ submitGaps = true;
nucleotidesAllowed = true;
proteinAllowed = false;
initViewportParams();
}
-
+
+ @Override
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()
{
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());
+ String[] typenameAndDescription = constructTypenameAndDescription(
+ descriptionData.first());
String typename = typenameAndDescription[0];
String description = typenameAndDescription[1];
}
private AlignmentAnnotation constructAnnotationFromScoreHolder(
- AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
+ 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
- && data.first().getMethod()
- .equals(AlifoldResult.contactProbabilities.toString()))
+ if (data != null && data.size() > 1 && data.first().getMethod()
+ .equals(AlifoldResult.contactProbabilities.toString()))
{
// The base pair probabilities are stored in a set in scoreholder. we want
{
// The Score objects contain a set of size one containing the range and
// an ArrayList<float> of size one containing the probabilty
- basePairs.put(score.getRanges().first(), new Float(score
- .getScores().get(0)));
+ 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])
{
float t = contacts.get(contact);
if (t > prob)
+ {
prob = t;
+ }
description += Integer.toString(contact.from) + "->"
+ Integer.toString(contact.to) + ": "
+ Float.toString(t) + "% | ";
}
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;
}
description = MessageFormat.format(
"Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
- score.getScores().get(0), score.getScores().get(1), score
- .getScores().get(2));
+ score.getScores().get(0), score.getScores().get(1),
+ score.getScores().get(2));
typename = "MFE Structure";
}
- else if (datatype.equals(AlifoldResult.contactProbabilityStructure
- .toString()))
+ else if (datatype
+ .equals(AlifoldResult.contactProbabilityStructure.toString()))
{
- description = MessageFormat
- .format("Base Pair Contact Probabilities. "
- + "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
- score.getScores().get(0), score.getScores().get(1));
+ description = MessageFormat.format("Base Pair Contact Probabilities. "
+ + "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
+ score.getScores().get(0), score.getScores().get(1));
typename = "Contact Probabilities";
}
else if (datatype.equals(AlifoldResult.centroidStructure.toString()))
{
description = MessageFormat.format(
- "Centroid Structure. Energy: {0} = {1} + {2}", score
- .getScores().get(0), score.getScores().get(1), score
- .getScores().get(2));
+ "Centroid Structure. Energy: {0} = {1} + {2}",
+ score.getScores().get(0), score.getScores().get(1),
+ score.getScores().get(2));
typename = "Centroid Structure";
}
else if (datatype.equals(AlifoldResult.stochBTStructure.toString()))
score.getScores().get(0), score.getScores().get(1));
}
else
+ {
description = "Stochastic Backtrack Structure";
+ }
}
else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
{
description = MessageFormat.format(
- "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}", score
- .getScores().get(0), score.getScores().get(1));
+ "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}",
+ score.getScores().get(0), score.getScores().get(1));
typename = "MEA Structure";
}
else if (datatype.equals(AlifoldResult.consensusAlignment.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;
git://source.jalview.org / jalview.git / blobdiff