import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
-import jalview.schemes.NucleotideColourScheme;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import java.text.MessageFormat;
import java.util.ArrayList;
-import java.util.Iterator;
+import java.util.Arrays;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import java.util.TreeSet;
-import compbio.data.msa.jaxws.Align;
+import compbio.data.sequence.RNAStructReader.AlifoldResult;
+import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
-import compbio.data.sequence.RNAStructScoreManager;
-import compbio.data.sequence.ScoreManager;
import compbio.metadata.Argument;
public class RNAalifoldClient extends JabawsAlignCalcWorker implements
AlignFrame af;
+ // keeps track of whether the RNAalifold result includes base contact probabilities
+ boolean bpScores;
+
public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
WsParamSetI preset, List<Argument> paramset)
{
arguments.add(sh.getRunnerConfig().getArgumentByOptionName("-p"));
}
- @Override
- public String getServiceActionText()
- {
- return "Submitting RNA alignment for Secondary Structure prediction using "
- + "RNAalifold Service";
- }
-
+ @Override
+ public String getServiceActionText()
+ {
+ return "Submitting RNA alignment for Secondary Structure prediction using "
+ + "RNAalifold Service";
+ }
+
+
@Override
public void updateResultAnnotation(boolean immediate)
{
-
if (immediate || !calcMan.isWorking(this) && scoremanager != null)
{
List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
- // ourAnnots = new ArrayList<AlignmentAnnotation>();
- // So I don't have to do any more casting
+ // Unpack the ScoreManager
List<String> structs = ((RNAStructScoreManager) scoremanager).getStructs();
List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager).getData();
-
- // I think this will never find an annotation at the moment. It will always create...
- AlignmentAnnotation annotation = alignViewport.getAlignment()
- .findOrCreateAnnotation("Consensus Structure", getCalcId(), false, null , null);
-
- // construct Annotation from scoremanager
-
- // Deal with the consensus structure and (?)BasePair Probabilities
- Annotation[] anns = new Annotation[structs.get(1).length()];
-
- // check if the first Score object is populated with base pair probabilities
+ // test to see if this data object contains base pair contacts
Score fscore = data.get(0).first();
- boolean BPScores = (fscore.getScores().size() > 0
- && fscore.getRanges() != null);
-
- TreeMap<Range, Float> basePairs = null;
- if (BPScores) {
- // The base pair probabilities are stored in a set in scoremanager... we want a map
- basePairs = new TreeMap<Range, Float>();
- for (Score score : data.get(0)) {
- // 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)));
- }
- }
-
- // ignoring the Consensus alignemnt for now, get the Structure and make an AlignmentAnnotation
- String struct = structs.get(1); // get(1)
- for (int i = 0; i < struct.length(); i++) {
-
- if (BPScores) {
- // Return all the contacts associated with position i
- List<Range> contacts = isContact(basePairs, i+1);
+ this.bpScores = (fscore.getMethod().equals(
+ AlifoldResult.contactProbabilities.toString()));
- if (contacts.size() == 0) {
- anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
- }
- else if (contacts.size() == 1) {
- // There is only one contact associated with this base
- float prob = basePairs.get(contacts.get(0));
- anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), prob);
- }
- else if (contacts.size() > 1) {
- // For now we will simply deal with alternate contact information by mentioning its
- // existance in the description
- float prob = basePairs.get(contacts.get(0));
- anns[i] = new Annotation(struct.substring(i, i+1), "This base has alternate contacts",
- struct.charAt(i), prob);
+ // Add annotations for the mfe Structure
+ if (bpScores)
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(1),
+ data.get(0), data.get(1));
+ else
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(1),
+ data.get(1));
+
+ // add annotation for the consensus sequence alignment
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(0), null);
+
+ // Not loop for the rest of the Annotations
+ if (structs.size() > 2) {
+ for (int i = 2; i < structs.size(); i++) {
+ // I can't think of a nice way of presenting the ensembleValues data
+ // so I wont for now.
+ if (!data.get(i).first().getMethod().equals(
+ AlifoldResult.ensembleValues.toString())) {
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(i),
+ data.get(i));
}
}
- else {
- // Same as the first if from the previous block
- anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
- }
- }
-
- System.out.println("size of anns: " + anns.length);
-
- // Set the annotation to the AlignmentAnnotation object
- annotation.annotations = anns;
-
- // Set the probability
- annotation.setScore(data.get(1).first().getScores().get(0));
-
-
-
- // old
-// AlignmentAnnotation annot = new AlignmentAnnotation("Consensus Structure", "Free Energy", anns);
-
-
-
-
- System.out.println("RNAalifoldClient - annotation:\n");
- for (Annotation ann : annotation.annotations) {
- System.out.print(ann.toString()+"|");
}
- System.out.println();
-
- // Instead of this look at existing methods for creating annotations
- ourAnnot.add(annotation);
if (ourAnnot.size() > 0) {
// Modify the visible annotation on the alignment viewport with the
// new alignment annotation rows created.
updateOurAnnots(ourAnnot);
- ap.adjustAnnotationHeight();
+ // ap.adjustAnnotationHeight();
}
-
}
}
+ // just for the base pair contact annotation. It uses a second score object.
+ protected void createAnnotationRowforScoreHolder(
+ List<AlignmentAnnotation> ourAnnot, String calcId,
+ String struct, TreeSet<Score> data, TreeSet<Score> descriptionData) {
+
+ String typename = data.first().getMethod().toString();
+
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(typename, calcId, false, null, null);
+
+ constructAnnotationFromContactProbabilities(annotation, struct, data);
+
+ String description = constructAlignmentAnnotationDescription(descriptionData.first());
+ if (description.length() == 0) description = typename;
+ annotation.description = description;
+
+ // dan test
+ annotation.belowAlignment = false;
+
+ annotation.validateRangeAndDisplay();
+
+ ourAnnot.add(annotation);
+ }
+
+ protected void createAnnotationRowforScoreHolder(
+ List<AlignmentAnnotation> ourAnnot, String calcId,
+ String struct, TreeSet<Score> data)
+ {
+ /* If contactProbability information is returned from RNAalifold it is stored
+ * in the first TreeSet<Score> object corresponding to the String Id which
+ * holds the consensus alignment. The method enumeration is then updated to
+ * AlifoldResult.contactProbabilties. This line (hack) recreates the same
+ * data object as was overwritten with the contact probabilites data.
+ */
+ if (data == null) data = compbio.data.sequence.RNAStructReader
+ .newEmptyScore(AlifoldResult.consensusAlignment);
+
+ String typename = data.first().getMethod().toString();
+
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(typename, calcId, false, null, null);
+
+ // construct annotation from ScoreHolder (unpacked into struct and data)
+ if (bpScores && data.first().getMethod().equals(
+ AlifoldResult.contactProbabilities.toString()))
+ constructAnnotationFromContactProbabilities(annotation, struct, data);
+
+ else
+ // if bpScores is false the TreeSet<Score> data should always contain
+ // a single Score object
+ constructAnnotationFromStructureString(annotation, struct, data.first());
+
+ /* update annotation description with the free Energy, frequency in ensemble
+ * or other data where appropriate.
+ *
+ * Doesnt deal with AlifoldResult.ensembleValues, the free energy of ensemble
+ * and frequency of mfe structure in ensemble. How to deal with these?
+ */
+ String description = constructAlignmentAnnotationDescription(data.first());
+ if (description.length() == 0) description = typename;
+ annotation.description = description;
+
+ // dan test
+ annotation.belowAlignment = false;
+
+ annotation.validateRangeAndDisplay();
+
+ ourAnnot.add(annotation);
+ }
+
+
+
+ private AlignmentAnnotation constructAnnotationFromStructureString(
+ AlignmentAnnotation annotation, String struct, Score score)
+ {
+
+ Annotation[] anns = new Annotation[struct.length()];
+
+ for (int i = 0; i < struct.length(); i++) {
+ anns[i] = new Annotation(struct.substring(i, i+1), "",
+ struct.charAt(i), Float.NaN);
+ }
+
+ annotation.graph = 0; // No graph
+ annotation.annotations = anns;
+
+
+ return annotation;
+
+ }
+
+ private String constructAlignmentAnnotationDescription(Score score) {
+ String description = "";
+ String datatype = score.getMethod();
+
+ if (datatype.equals(AlifoldResult.mfeStructure.toString()) ||
+ datatype.equals(AlifoldResult.centroidStructure.toString())) {
+ description = MessageFormat.format("Energy: {0} = {1} + {2}",
+ score.getScores().get(0), score.getScores().get(1), score.getScores().get(2));
+ }
+ else if (datatype.equals(AlifoldResult.contactProbabilityStructure.toString())) {
+ description = MessageFormat.format("Energy: {0} Frequency: {1}",
+ score.getScores().get(0), score.getScores().get(1));
+ }
+ else if (datatype.equals(AlifoldResult.stochBTStructure.toString())) {
+ if (score.getScores().size() > 0) {
+ description = MessageFormat.format("Probability: {0} Energy: {1}",
+ 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));
+ }
+
+ return description;
+ }
+
+
+ private AlignmentAnnotation constructAnnotationFromContactProbabilities(
+ AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
+ {
+ Annotation[] anns = new Annotation[struct.length()];
+
+ TreeMap<Range, Float> basePairs = null;
+ // The base pair probabilities are stored in a set in scoreholder. we want a map
+ basePairs = new TreeMap<Range, Float>();
+ for (Score score : data) {
+ // 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)));
+ }
+ for (int i = 0; i < struct.length(); i++) {
+
+ // Return all the contacts associated with position i
+ List<Range> contacts = isContact(basePairs, i+1);
+
+ if (contacts.size() == 0) {
+ anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
+ }
+ else if (contacts.size() == 1) {
+ // There is only one contact associated with this base
+ float prob = basePairs.get(contacts.get(0));
+ anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), prob);
+ }
+ else if (contacts.size() > 1) {
+ // For now we will simply deal with alternate contact information by mentioning its
+ // existance in the description
+ float prob = basePairs.get(contacts.get(0));
+ anns[i] = new Annotation(struct.substring(i, i+1), "This base has alternate contacts",
+ struct.charAt(i), prob);
+ }
+ }
+
+ annotation.annotations = anns;
+
+ return annotation;
+ }
+
+
// Check whether, at position i there is a base contact and return all the
// contacts at this position. Should be in order of descending probability.
private List<Range> isContact(TreeMap<Range, Float> basePairs, int i) {
return contacts;
}
+
public String getCalcId()
{
return SequenceAnnotationWSClient.AAConCalcId;
git://source.jalview.org / jalview.git / commitdiff