* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.ws.jws2;
+package jalview.ws.jws2.jabaws2;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.gui.AlignFrame;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
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;
-import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
-import compbio.metadata.Argument;
/**
* Client for the JABA RNA Alifold Service
*
*/
-public class RNAalifoldClient extends JabawsCalcWorker
+public class RNAalifoldClient extends JabawsAnnotationInstance
{
- String methodName;
-
- 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)
- {
- super(sh, alignFrame, preset, paramset);
- af = alignFrame;
- methodName = sh.serviceType;
- alignedSeqs = true;
- submitGaps = true;
- nucleotidesAllowed = true;
- proteinAllowed = false;
- initViewportParams();
- }
+ // configuration
@Override
public String getCalcId()
private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
- public static AlignAnalysisUIText getAlignAnalysisUITest()
+ public static AlignAnalysisUIText getAlignAnalysisUIText()
{
return new AlignAnalysisUIText(
compbio.ws.client.Services.RNAalifoldWS.toString(),
- jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false,
- true, MessageManager.getString("label.rnalifold_calculations"),
+ jalview.ws.jws2.jabaws2.RNAalifoldClient.class, CALC_ID, true,
+ false, true, true, false, 2,
+ MessageManager.getString("label.rnalifold_calculations"),
MessageManager.getString("tooltip.rnalifold_calculations"),
MessageManager.getString("label.rnalifold_settings"),
MessageManager.getString("tooltip.rnalifold_settings"));
}
- @Override
- public String getServiceActionText()
+ public static String getServiceActionText()
{
return "Submitting RNA alignment for Secondary Structure prediction using "
+ "RNAalifold Service";
}
- @Override
- boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ // instance
+
+ public RNAalifoldClient(Jws2Instance handle)
{
- return (seqs.size() > 1);
+ super(handle);
}
@Override
- public void updateResultAnnotation(boolean immediate)
+ List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
+ Map<String, FeatureColourI> featureColours,
+ Map<String, FeatureMatcherSetI> featureFilters)
{
-
- if (immediate || !calcMan.isWorking(this) && scoremanager != null)
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
+
+ // Unpack the ScoreManager
+ List<String> structs = ((RNAStructScoreManager) scoremanager)
+ .getStructs();
+ List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
+ .getData();
+
+ // test to see if this data object contains base pair contacts
+ Score fscore = data.get(0).first();
+ boolean bpScores = (fscore.getMethod()
+ .equals(AlifoldResult.contactProbabilities.toString()));
+
+ // add annotation for the consensus sequence alignment
+ createAnnotationRowforScoreHolder(seqs, null,
+ ourAnnot,
+ getCalcId(), structs.get(0), null, null);
+
+ // Add annotations for the mfe Structure
+ 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(seqs, null,
+ ourAnnot,
+ getCalcId(), structs.get(2), data.get(0), data.get(2));
+ count++;
+ }
- List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
-
- // Unpack the ScoreManager
- List<String> structs = ((RNAStructScoreManager) scoremanager)
- .getStructs();
- List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
- .getData();
-
- // 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 annotation for the consensus sequence alignment
- 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)
+ // 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()))
{
- updateOurAnnots(ourAnnot);
- ap.adjustAnnotationHeight();
+ createAnnotationRowforScoreHolder(seqs, null, ourAnnot,
+ getCalcId(), structs.get(i), data.get(i), null);
}
}
+ return ourAnnot;
}
- protected void createAnnotationRowforScoreHolder(
+ private static void createAnnotationRowforScoreHolder(
+ 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(annotation, struct, data);
+ constructAnnotationFromScoreHolder(gapMap, annotation, struct, data);
/*
* update annotation description with the free Energy, frequency in ensemble
annotation.belowAlignment = false;
// annotation.showAllColLabels = true;
-
- alignViewport.getAlignment().validateAnnotation(annotation);
- af.setMenusForViewport();
-
+ annotation.validateRangeAndDisplay();
ourAnnot.add(annotation);
}
- private AlignmentAnnotation constructAnnotationFromScoreHolder(
- AlignmentAnnotation annotation, String struct,
+ private static AlignmentAnnotation constructAnnotationFromScoreHolder(
+ boolean[] gapMap, AlignmentAnnotation annotation, String struct,
TreeSet<Score> data)
{
Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
// The base pair probabilities are stored in a set in scoreholder. we want
// a map
- LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<Range, Float>();
+ LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<>();
for (Score score : data)
{
// The Score objects contain a set of size one containing the range and
return annotation;
}
- private String[] constructTypenameAndDescription(Score score)
+ private static String[] constructTypenameAndDescription(Score score)
{
String description = "";
String typename = "";
// 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 LinkedHashMap<Range, Float> isContact(
+ private static LinkedHashMap<Range, Float> isContact(
LinkedHashMap<Range, Float> basePairs, int i)
{
- LinkedHashMap<Range, Float> contacts = new LinkedHashMap<Range, Float>();
+ LinkedHashMap<Range, Float> contacts = new LinkedHashMap<>();
for (Range contact : basePairs.keySet())
{
return contacts;
}
- private char isSS(char chr)
+ private static char isSS(char chr)
{
String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
return ss;
}
+
}
git://source.jalview.org / jalview.git / blobdiff