import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.TreeMap;
+import java.util.LinkedHashMap;
import java.util.TreeSet;
+import java.util.regex.Pattern;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
import compbio.data.sequence.RNAStructScoreManager;
AlignCalcWorkerI
{
- // test
-
String methodName;
AlignFrame af;
super(sh, alignFrame, preset, paramset);
if (arguments == null) arguments = new ArrayList<Argument>();
- arguments.add(sh.getRunnerConfig().getArgumentByOptionName("-p"));
af = alignFrame;
methodName = sh.serviceType;
- // defult false. Which one here?
- // submitGaps = true;
nucleotidesAllowed = true;
proteinAllowed = false;
- arguments.add(sh.getRunnerConfig().getArgumentByOptionName("-p"));
}
@Override
List<String> structs = ((RNAStructScoreManager) scoremanager).getStructs();
List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager).getData();
+ System.out.println("Length of RNAStructScoreManager is: " + structs.size());
+
// test to see if this data object contains base pair contacts
Score fscore = data.get(0).first();
this.bpScores = (fscore.getMethod().equals(
AlifoldResult.contactProbabilities.toString()));
- // 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));
- }
- }
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(0),
+ null, null);
+
+ // Add annotations for the mfe Structure
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(1),
+ data.get(1), null);
+
+ // decide whether to add base pair contact probability histogram
+ int count = 2;
+ if (bpScores) {
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(2),
+ data.get(0), data.get(2));
+ count++;
+ }
+
+
+ // Now loop for the rest of the Annotations (if there it isn't stochastic output
+ // only the centroid and MEA structures remain anyway)
+ for (int i = count; i < structs.size(); i++) {
+ // The ensemble values should be displayed in the description of the
+ // first (or all?) Stochastic Backtrack Structures.
+ if (!data.get(i).first().getMethod().equals(
+ AlifoldResult.ensembleValues.toString())) {
+
+ createAnnotationRowforScoreHolder(ourAnnot, getCalcId(), structs.get(i),
+ data.get(i), null);
+ }
}
-
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)
+ String struct, TreeSet<Score> data, TreeSet<Score> descriptionData)
{
/* 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
+ * AlifoldResult.contactProbabilties. This line 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();
+ if (descriptionData == null) descriptionData = data;
+
+ String[] typenameAndDescription = constructTypenameAndDescription(
+ descriptionData.first());
+ String typename = typenameAndDescription[0];
+ String description = typenameAndDescription[1];
+
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());
+ constructAnnotationFromScoreHolder(annotation, struct, data);
/* 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.showAllColLabels = true;
annotation.validateRangeAndDisplay();
ourAnnot.add(annotation);
}
-
-
- private AlignmentAnnotation constructAnnotationFromStructureString(
- AlignmentAnnotation annotation, String struct, Score score)
+
+
+ private AlignmentAnnotation constructAnnotationFromScoreHolder(
+ AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
{
-
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);
+
+ 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 a map
+ LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<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
+ LinkedHashMap<Range, Float> contacts = isContact(basePairs, i+1);
+
+ String description = "";
+ float prob = 0f;
+
+ if (contacts.size() == 0) {
+ description = "No Data";
+ }
+ else {
+ for (Range contact : contacts.keySet()) {
+ float t = contacts.get(contact);
+ if (t > prob) prob = t;
+ description += Integer.toString(contact.from) + "->"
+ + Integer.toString(contact.to) + ": " + Float.toString(t) + "% | ";
+ }
+ }
+
+ anns[i] = 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++) {
+
+ anns[i] = new Annotation(struct.substring(i, i+1), "",
+ isSS(struct.charAt(i)), Float.NaN);
+ }
+
+ annotation.graph = 0; // No graph
}
- annotation.graph = 0; // No graph
annotation.annotations = anns;
-
return annotation;
-
}
-
- private String constructAlignmentAnnotationDescription(Score score) {
+
+ private String[] constructTypenameAndDescription(Score score) {
String description = "";
+ String typename = "";
String datatype = score.getMethod();
- if (datatype.equals(AlifoldResult.mfeStructure.toString()) ||
- datatype.equals(AlifoldResult.centroidStructure.toString())) {
- description = MessageFormat.format("Energy: {0} = {1} + {2}",
+ if (datatype.equals(AlifoldResult.mfeStructure.toString())) {
+
+ description = MessageFormat.format("Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
score.getScores().get(0), score.getScores().get(1), score.getScores().get(2));
+ typename = "MFE Structure";
}
else if (datatype.equals(AlifoldResult.contactProbabilityStructure.toString())) {
- description = MessageFormat.format("Energy: {0} Frequency: {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));
+ typename = "Centroid Structure";
}
else if (datatype.equals(AlifoldResult.stochBTStructure.toString())) {
if (score.getScores().size() > 0) {
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));
+ typename = "MEA Structure";
}
-
- 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)));
+ else if (datatype.equals(AlifoldResult.consensusAlignment.toString())) {
+ typename = "RNAalifold Consensus";
+ description = "Consensus Alignment Produced by RNAalifold";
}
- 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);
- }
+ else {
+ typename = datatype;
+ description = typename;
}
- annotation.annotations = anns;
-
- return annotation;
+ return new String[] {typename, description};
}
-
// 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) {
-
- List<Range> contacts = new ArrayList<Range>();
+ private LinkedHashMap<Range, Float> isContact(LinkedHashMap<Range,
+ Float> basePairs, int i)
+ {
+ LinkedHashMap<Range, Float> contacts = new LinkedHashMap<Range, Float>();
for (Range contact : basePairs.keySet()) {
// finds the contacts associtated with position i ordered by the natural
// ordering of the Scores TreeSet in ScoreManager which is, descending probability
- if (contact.from == i || contact.to == i) contacts.add(contact);
+ if (contact.from == i || contact.to == i)
+ contacts.put(contact, basePairs.get(contact));
}
return contacts;
}
+ private char isSS (char chr) {
+ String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
+ char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S': ' ';
+ return ss;
+ }
public String getCalcId()
{
git://source.jalview.org / jalview.git / commitdiff