*/
package jalview.ws.jws2.jabaws2;
-import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.util.MessageManager;
-import jalview.ws.gui.AnnotationWsJob;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
import java.util.TreeSet;
import java.util.regex.Pattern;
private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
-
public static AlignAnalysisUIText getAlignAnalysisUIText()
{
return new AlignAnalysisUIText(
compbio.ws.client.Services.RNAalifoldWS.toString(),
jalview.ws.jws2.jabaws2.RNAalifoldClient.class, CALC_ID, true,
- false,
- true, true, false, 2,
+ false, true, true, false, 2,
MessageManager.getString("label.rnalifold_calculations"),
MessageManager.getString("tooltip.rnalifold_calculations"),
MessageManager.getString("label.rnalifold_settings"),
+ "RNAalifold Service";
}
-
// instance
public RNAalifoldClient(Jws2Instance handle)
}
@Override
- List<AlignmentAnnotation> annotationFromScoreManager(
- AnnotationWsJob running, AlignViewportI alignViewport,
- boolean[] gapMap)
+ List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
+ Map<String, FeatureColourI> featureColours,
+ Map<String, FeatureMatcherSetI> featureFilters)
{
List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
.equals(AlifoldResult.contactProbabilities.toString()));
// add annotation for the consensus sequence alignment
- createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ createAnnotationRowforScoreHolder(seqs, null,
+ ourAnnot,
getCalcId(), structs.get(0), null, null);
// Add annotations for the mfe Structure
- createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ createAnnotationRowforScoreHolder(seqs, null,
+ ourAnnot,
getCalcId(), structs.get(1), data.get(1), null);
// decide whether to add base pair contact probability histogram
int count = 2;
if (bpScores)
{
- createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ createAnnotationRowforScoreHolder(seqs, null,
+ ourAnnot,
getCalcId(), structs.get(2), data.get(0), data.get(2));
count++;
}
.equals(AlifoldResult.ensembleValues.toString()))
{
- createAnnotationRowforScoreHolder(alignViewport, gapMap, ourAnnot,
+ createAnnotationRowforScoreHolder(seqs, null, ourAnnot,
getCalcId(), structs.get(i), data.get(i), null);
}
}
}
private static void createAnnotationRowforScoreHolder(
- AlignViewportI alignViewport, boolean[] gapMap,
+ AlignmentI alignment, boolean[] gapMap,
List<AlignmentAnnotation> ourAnnot, String calcId, String struct,
TreeSet<Score> data, TreeSet<Score> descriptionData)
{
String typename = typenameAndDescription[0];
String description = typenameAndDescription[1];
- AlignmentAnnotation annotation = alignViewport.getAlignment()
+ AlignmentAnnotation annotation = alignment
.findOrCreateAnnotation(typename, calcId, false, null, null);
constructAnnotationFromScoreHolder(gapMap, annotation, struct, data);
annotation.belowAlignment = false;
// annotation.showAllColLabels = true;
-
+ annotation.validateRangeAndDisplay();
ourAnnot.add(annotation);
}
return ss;
}
- }
+}