X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FRNAalifoldClient.java;h=f9e597f4e549d0ad664e7d98fa8144836e27c161;hb=0aa7f6fab658c9a203b410d4bead72217da5c9a0;hp=277973241f04401bae6d30edcac185b80eee7e88;hpb=6c54f6a2f72b57aa1f803d68241549e050ae68e8;p=jalview.git diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java index 2779732..f9e597f 100644 --- a/src/jalview/ws/jws2/RNAalifoldClient.java +++ b/src/jalview/ws/jws2/RNAalifoldClient.java @@ -1,10 +1,29 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.jws2; -import jalview.api.AlignCalcWorkerI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.gui.AlignFrame; -import jalview.ws.jws2.dm.AAConSettings; +import jalview.util.MessageManager; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.WsParamSetI; import jalview.ws.uimodel.AlignAnalysisUIText; @@ -16,6 +35,7 @@ import java.util.List; 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; @@ -24,12 +44,12 @@ import compbio.metadata.Argument; /** * Client for the JABA RNA Alifold Service + * * @author daluke - Daniel Barton - * + * */ -public class RNAalifoldClient extends JabawsAlignCalcWorker implements - AlignCalcWorkerI +public class RNAalifoldClient extends JabawsCalcWorker { String methodName; @@ -44,39 +64,32 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements WsParamSetI preset, List paramset) { super(sh, alignFrame, preset, paramset); - - //if (arguments == null) - // arguments = new ArrayList(); - af = alignFrame; methodName = sh.serviceType; - alignedSeqs=true; - submitGaps=true; + alignedSeqs = true; + submitGaps = true; nucleotidesAllowed = true; proteinAllowed = false; initViewportParams(); } - + + @Override public String getCalcId() { return CALC_ID; } - private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient"; + + private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient"; public static AlignAnalysisUIText getAlignAnalysisUITest() { return new AlignAnalysisUIText( compbio.ws.client.Services.RNAalifoldWS.toString(), - jalview.ws.jws2.RNAalifoldClient.class, - CALC_ID, - true, - false, - true, - "RNAAliFold Prediction", - "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.", - "Change RNAAliFold settings...", - "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters"); - + jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false, + true, MessageManager.getString("label.rnalifold_calculations"), + MessageManager.getString("tooltip.rnalifold_calculations"), + MessageManager.getString("label.rnalifold_settings"), + MessageManager.getString("tooltip.rnalifold_settings")); } @Override @@ -87,6 +100,12 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements } @Override + boolean checkValidInputSeqs(boolean dynamic, List seqs) + { + return (seqs.size() > 1); + } + + @Override public void updateResultAnnotation(boolean immediate) { @@ -160,14 +179,18 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements * same data object as was overwritten with the contact probabilites data. */ if (data == null) + { data = compbio.data.sequence.RNAStructReader .newEmptyScore(AlifoldResult.consensusAlignment); + } if (descriptionData == null) + { descriptionData = data; + } - String[] typenameAndDescription = constructTypenameAndDescription(descriptionData - .first()); + String[] typenameAndDescription = constructTypenameAndDescription( + descriptionData.first()); String typename = typenameAndDescription[0]; String description = typenameAndDescription[1]; @@ -196,14 +219,14 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements } private AlignmentAnnotation constructAnnotationFromScoreHolder( - AlignmentAnnotation annotation, String struct, TreeSet data) + AlignmentAnnotation annotation, String struct, + TreeSet data) { - Annotation[] anns = new Annotation[struct.length()]; + Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1 + : struct.length()]; - if (data != null - && data.size() > 1 - && data.first().getMethod() - .equals(AlifoldResult.contactProbabilities.toString())) + 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 @@ -213,12 +236,20 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements { // The Score objects contain a set of size one containing the range and // an ArrayList of size one containing the probabilty - basePairs.put(score.getRanges().first(), new Float(score - .getScores().get(0))); + basePairs.put(score.getRanges().first(), + Float.valueOf(score.getScores().get(0))); } - for (int i = 0; i < struct.length(); i++) - { + for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++) + { + if (gapMap != null) + { + // skip any gapped columns in the input data + while (!gapMap[ri]) + { + ri++; + } + } // Return all the contacts associated with position i LinkedHashMap contacts = isContact(basePairs, i + 1); @@ -235,23 +266,36 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements { 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, + anns[ri] = 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++) + for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++) { - - anns[i] = new Annotation(struct.substring(i, i + 1), "", + if (gapMap != null) + { + // skip any gapped columns in the input data + while (!gapMap[ri] && ri < gapMap.length) + { + ri++; + } + if (ri == gapMap.length) + { + break; + } + } + anns[ri] = new Annotation(struct.substring(i, i + 1), "", isSS(struct.charAt(i)), Float.NaN); } @@ -275,25 +319,24 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements description = MessageFormat.format( "Minimum Free Energy Structure. Energy: {0} = {1} + {2}", - score.getScores().get(0), score.getScores().get(1), score - .getScores().get(2)); + score.getScores().get(0), score.getScores().get(1), + score.getScores().get(2)); typename = "MFE Structure"; } - else if (datatype.equals(AlifoldResult.contactProbabilityStructure - .toString())) + else if (datatype + .equals(AlifoldResult.contactProbabilityStructure.toString())) { - description = MessageFormat - .format("Base Pair Contact Probabilities. " - + "Energy of Ensemble: {0} Frequency of Ensemble: {1}", - score.getScores().get(0), score.getScores().get(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)); + "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())) @@ -304,13 +347,15 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements 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)); + "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}", + score.getScores().get(0), score.getScores().get(1)); typename = "MEA Structure"; } else if (datatype.equals(AlifoldResult.consensusAlignment.toString())) @@ -324,8 +369,7 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements description = typename; } - return new String[] - { typename, description }; + return new String[] { typename, description }; } // Check whether, at position i there is a base contact and return all the @@ -341,7 +385,9 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements // ordering of the Scores TreeSet in ScoreManager which is, descending // probability if (contact.from == i || contact.to == i) + { contacts.put(contact, basePairs.get(contact)); + } } return contacts;