+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws.jws2;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.gui.AlignFrame;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.WsParamSetI;
-import jalview.ws.uimodel.AlignAnalysisUIText;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.JpredAlignment;
-import compbio.metadata.Argument;
-
-public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
-{
- /**
- *
- * @return default args for this service when run as dynamic web service
- */
- public List<Argument> selectDefaultArgs()
- {
- List<ArgumentI> rgs = new ArrayList<ArgumentI>();
- for (ArgumentI argi : service.getParamStore().getServiceParameters())
- {
- if (argi instanceof OptionI)
- {
- List<String> o = ((OptionI) argi).getPossibleValues();
- if (o.contains("-pred-nohits"))
- {
- OptionI cpy = ((OptionI) argi).copy();
- cpy.setValue("-pred-nohits");
- rgs.add(cpy);
- }
- }
- }
- return JabaParamStore.getJabafromJwsArgs(rgs);
- }
-
- public JPred301Client(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
- {
- super(service, alignFrame, preset, paramset);
- submitGaps = true;
- alignedSeqs = true;
- nucleotidesAllowed = false;
- proteinAllowed = true;
- gapMap = new boolean[0];
- updateParameters(null, selectDefaultArgs());
- }
-
- @Override
- boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
- {
- return (seqs.size() > 1);
- }
-
- @Override
- public String getServiceActionText()
- {
- return "calculating consensus secondary structure prediction using JPred service";
- }
-
- private static Map<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
-
- private static final Set<String> jpredRes_graph;
-
- private static final Set<String> jpredRes_ssonly;
- static
- {
- jpredRes_ssonly = new HashSet<String>();
- jpredRes_ssonly.add("jnetpred".toLowerCase());
- jpredRes_ssonly.add("jnetpssm".toLowerCase());
- jpredRes_ssonly.add("jnethmm".toLowerCase());
- jpredRes_graph = new HashSet<String>();
- jpredRes_graph.add("jnetconf".toLowerCase());
- jpredRes_graph.add("jnet burial".toLowerCase());
- }
-
- /**
- * update the consensus annotation from the sequence profile data using
- * current visualization settings.
- */
- @Override
- public void updateResultAnnotation(boolean immediate)
- {
- if (immediate || !calcMan.isWorking(this) && msascoreset != null)
- {
- if (msascoreset instanceof compbio.data.sequence.JpredAlignment)
- {
- JpredAlignment jpres = (JpredAlignment) msascoreset;
- int alWidth = alignViewport.getAlignment().getWidth();
- ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
- char[] sol = new char[jpres.getJpredSequences().get(0).getLength()];
- boolean firstsol = true;
- for (FastaSequence fsq : jpres.getJpredSequences())
- {
- String[] k = jpredRowLabels.get(fsq.getId());
- if (k == null)
- {
- k = new String[] { fsq.getId(), "JNet Output" };
- }
- if (fsq.getId().startsWith("JNETSOL"))
- {
- char amnt = (fsq.getId().endsWith("25") ? "3" : fsq.getId()
- .endsWith("5") ? "6" : "9").charAt(0);
- char[] vseq = fsq.getSequence().toCharArray();
- for (int spos = 0, sposL = fsq.getLength(); spos < sposL; spos++)
- {
- if (firstsol)
- {
- sol[spos] = '0';
- }
- if (vseq[spos] == 'B'
- && (sol[spos] == '0' || sol[spos] < amnt))
- {
- sol[spos] = amnt;
- }
- }
- firstsol = false;
- }
- else
- {
- createAnnotationRowFromString(
- ourAnnot,
- getCalcId(),
- alWidth,
- k[0],
- k[1],
- jpredRes_graph.contains(fsq.getId()) ? AlignmentAnnotation.BAR_GRAPH
- : AlignmentAnnotation.NO_GRAPH, 0f, 9f,
- fsq.getSequence());
- }
-
- }
- createAnnotationRowFromString(
- ourAnnot,
- getCalcId(),
- alWidth,
- "Jnet Burial",
- "<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>",
- AlignmentAnnotation.BAR_GRAPH, 0f, 9f, new String(sol));
- for (FastaSequence fsq : jpres.getSequences())
- {
- if (fsq.getId().equalsIgnoreCase("QUERY"))
- {
- createAnnotationRowFromString(ourAnnot, getCalcId(), alWidth,
- "Query", "JPred Reference Sequence",
- AlignmentAnnotation.NO_GRAPH, 0f, 0f, fsq.getSequence());
- }
- }
- if (ourAnnot.size() > 0)
- {
- updateOurAnnots(ourAnnot);
- }
- }
- }
- }
-
- private void createAnnotationRowFromString(
- ArrayList<AlignmentAnnotation> ourAnnot, String calcId,
- int alWidth, String label, String descr, int rowType, float min,
- float max, String jpredPrediction)
- {
- // simple annotation row
- AlignmentAnnotation annotation = alignViewport.getAlignment()
- .findOrCreateAnnotation(label, calcId, true, null, null);
- if (alWidth == gapMap.length) // scr.getScores().size())
- {
- annotation.label = new String(label);
- annotation.description = new String(descr);
- annotation.graph = rowType;
- annotation.graphMin = min;
- annotation.graphMax = max;
- if (constructAnnotationFromString(annotation, jpredPrediction,
- alWidth, rowType))
- {
- // created a valid annotation from the data
- ourAnnot.add(annotation);
- // annotation.validateRangeAndDisplay();
- }
- }
- }
-
- private boolean constructAnnotationFromString(
- AlignmentAnnotation annotation, String sourceData, int alWidth,
- int rowType)
- {
- if (sourceData.length() == 0 && alWidth > 0)
- {
- return false;
- }
- Annotation[] elm = new Annotation[alWidth];
- boolean ssOnly = jpredRes_ssonly.contains(annotation.label
- .toLowerCase());
- boolean graphOnly = rowType != AlignmentAnnotation.NO_GRAPH;
- if (!ssOnly && !graphOnly)
- {
- // for burial 'B'
- annotation.showAllColLabels = true;
- }
-
- for (int i = 0, iSize = sourceData.length(); i < iSize; i++)
- {
- char annot = sourceData.charAt(i);
- // if we're at a gapped column then skip to next ungapped position
- if (gapMap != null && gapMap.length > 0)
- {
- while (!gapMap[i])
- {
- elm[i++] = new Annotation("", "", ' ', Float.NaN);
- }
- }
- switch (rowType)
- {
- case AlignmentAnnotation.NO_GRAPH:
- elm[i] = ssOnly ? new Annotation("", "", annot, Float.NaN,
- colourSS(annot)) : new Annotation("" + annot, "" + annot,
- '\0', Float.NaN);
- break;
- default:
- try
- {
- elm[i] = new Annotation("" + annot, "" + annot, annot,
- Integer.valueOf("" + annot));
- } catch (Exception x)
- {
- System.err.println("Expected numeric value in character '"
- + annot + "'");
- }
- }
- }
-
- annotation.annotations = elm;
- annotation.belowAlignment = true;
- annotation.validateRangeAndDisplay();
- return true;
- }
-
- private Color colourSS(char annot)
- {
- switch (annot)
- {
- case 'H':
- return jalview.renderer.AnnotationRenderer.HELIX_COLOUR;
- case 'E':
- return jalview.renderer.AnnotationRenderer.SHEET_COLOUR;
- }
- return jalview.renderer.AnnotationRenderer.GLYPHLINE_COLOR;
- }
-
- @Override
- public String getCalcId()
- {
- return CALC_ID;
- }
-
- private static String CALC_ID = "jabaws21.JPred3Cons";
-
- public static AlignAnalysisUIText getAlignAnalysisUITest()
- {
- return new AlignAnalysisUIText(
- compbio.ws.client.Services.JpredWS.toString(),
- jalview.ws.jws2.JPred301Client.class, CALC_ID, false, true,
- true, "JPred Consensus",
- "When checked, JPred consensus is updated automatically.",
- "Change JPred Settings...",
- "Modify settings for JPred calculations.");
- }
-}
git://source.jalview.org / jalview.git / blobdiff