X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=d5593e38ba1c92de0b224433949d3effa987c042;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=07a0068d2f17bd110164cd91c1e20d50fb6d4793;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index 07a0068..d5593e3 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -1,41 +1,58 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/package jalview.io; - -import jalview.datamodel.*; + * 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.io; + +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; public class JnetAnnotationMaker { public static void add_annotation(JPredFile prediction, AlignmentI al, - int firstSeq, boolean noMsa) throws Exception { - JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[]) null); + int firstSeq, boolean noMsa) throws Exception + { + JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, + (int[]) null); } + /** * adds the annotation parsed by prediction to al. - * @param prediction JPredFile - * @param al AlignmentI - * @param firstSeq int - - * @param noMsa boolean - * @param delMap mapping from columns in JPredFile prediction to residue number in al.getSequence(firstSeq) + * + * @param prediction + * JPredFile + * @param al + * AlignmentI + * @param firstSeq + * int the index of the sequence to attach the annotation to (usually + * zero) + * @param noMsa + * boolean + * @param delMap + * mapping from columns in JPredFile prediction to residue number in + * al.getSequence(firstSeq) */ public static void add_annotation(JPredFile prediction, AlignmentI al, - int firstSeq, boolean noMsa, int[] delMap) - throws Exception + int firstSeq, boolean noMsa, int[] delMap) throws Exception { int i = 0; SequenceI[] preds = prediction.getSeqsAsArray(); @@ -44,118 +61,156 @@ public class JnetAnnotationMaker SequenceI seqRef = al.getSequenceAt(firstSeq); int width = preds[0].getSequence().length; int[] gapmap = al.getSequenceAt(firstSeq).gapMap(); - if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width)) + if ((delMap != null && delMap.length > width) + || (delMap == null && gapmap.length != width)) { throw (new Exception( - "Number of residues in "+(delMap==null ? "" : " mapped ")+"supposed query sequence ('" + - al.getSequenceAt(firstSeq).getName() + "'\n" + - al.getSequenceAt(firstSeq).getSequence() + - ")\ndiffer from number of prediction sites in prediction (" + width + - ")")); + MessageManager + .formatMessage( + "exception.number_of_residues_in_query_sequence_differ_from_prediction", + new String[] { + (delMap == null ? "" : MessageManager + .getString("label.mapped")), + al.getSequenceAt(firstSeq).getName(), + al.getSequenceAt(firstSeq) + .getSequenceAsString(), + Integer.valueOf(width).toString() }))); } AlignmentAnnotation annot; Annotation[] annotations = null; int existingAnnotations = 0; - if(al.getAlignmentAnnotation()!=null) - existingAnnotations = al.getAlignmentAnnotation().length; + if (al.getAlignmentAnnotation() != null) + { + existingAnnotations = al.getAlignmentAnnotation().length; + } + Annotation[] sol = new Annotation[al.getWidth()]; + boolean firstsol = true; while (i < preds.length) { String id = preds[i].getName().toUpperCase(); - if (id.startsWith("LUPAS") || id.startsWith("JNET") || - id.startsWith("JPRED")) + if (id.startsWith("LUPAS") || id.startsWith("JNET") + || id.startsWith("JPRED")) { - annotations = new Annotation[al.getWidth()]; - /* if (delMap!=null) { - for (int j=0; jPrediction of Solvent Accessibility
levels are", + sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH); + + annot.validateRangeAndDisplay(); + if (seqRef != null) + { + annot.createSequenceMapping(seqRef, 1, true); + seqRef.addAlignmentAnnotation(annot); + } + al.addAnnotation(annot); + al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length + - existingAnnotations - 1); + } + // Hashtable scores = prediction.getScores(); + + /* + * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"), + * "JnetpropH", "Jnet Helix Propensity", 0f,1f,1); + * + * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"), + * "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1); + * + * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"), + * "JnetpropC", "Jnet Coil Propensity", 0f,1f,1); */ }