X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=8c841a885423a6d5fb69f90c15de07bfb83f3cdf;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=61f0ce1b26fcb676e20a1e3606d0a1bbe04f5c2c;hpb=7f88b4e40175e3f47d35786ba1cb44d1ae79cce8;p=jalview.git diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index 61f0ce1..8c841a8 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -1,145 +1,202 @@ -/* -* 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.*; - -public class JnetAnnotationMaker -{ - /** - * adds the annotation parsed by prediction to al. - * @param prediction JPredFile - * @param al AlignmentI - * @param FirstSeq int - - * @param noMsa boolean - */ - public static void add_annotation(JPredFile prediction, AlignmentI al, - int FirstSeq, boolean noMsa) - throws Exception - { - int i = 0; - SequenceI[] preds = prediction.getSeqsAsArray(); - // in the future we could search for the query - // sequence in the alignment before calling this function. - SequenceI seqRef = al.getSequenceAt(FirstSeq); - int width = preds[0].getSequence().length(); - int[] gapmap = al.getSequenceAt(FirstSeq).gapMap(); - if (gapmap.length != width) - { - throw (new Exception( - "Number of residues in supposed query sequence ('" + - al.getSequenceAt(FirstSeq).getName() + "'\n" + - al.getSequenceAt(FirstSeq).getSequence() + - ")\ndiffer from number of prediction sites in prediction (" + width + - ")")); - } - - AlignmentAnnotation annot; - Annotation[] annotations = null; - - int existingAnnotations = 0; - if(al.getAlignmentAnnotation()!=null) - existingAnnotations = al.getAlignmentAnnotation().length; - - - while (i < preds.length) - { - String id = preds[i].getName().toUpperCase(); - - if (id.startsWith("LUPAS") || id.startsWith("JNET") || - id.startsWith("JPRED")) - { - annotations = new Annotation[al.getWidth()]; - - if (id.equals("JNETPRED") || id.equals("JNETPSSM") || - id.equals("JNETFREQ") || id.equals("JNETHMM") || - id.equals("JNETALIGN") || id.equals("JPRED")) - { - for (int j = 0; j < width; j++) - { - annotations[gapmap[j]] = new Annotation("", "", - preds[i].getCharAt(j), 0); - } - } - else if (id.equals("JNETCONF")) - { - for (int j = 0; j < width; j++) - { - float value = new Float(preds[i].getCharAt( - j) + "").floatValue(); - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt( - j) + "", "", preds[i].getCharAt(j), - value); - } - } - else - { - for (int j = 0; j < width; j++) - { - annotations[gapmap[j]] = new Annotation(preds[i].getCharAt( - j) + "", "", ' ', 0); - } - } - - if (id.equals("JNETCONF")) - { - annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", annotations, 0f, - 10f, - AlignmentAnnotation.BAR_GRAPH); - } - else - { - annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", annotations); - } - - if (seqRef != null) - { - annot.createSequenceMapping(seqRef, 1, true); - seqRef.addAlignmentAnnotation(annot); - } - - al.addAnnotation(annot); - al.setAnnotationIndex(annot, - al.getAlignmentAnnotation(). - length - existingAnnotations - 1); - - if (noMsa) - { - al.deleteSequence(preds[i]); - } - } - - i++; - } - - //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); - */ - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 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.*; + +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); + } + + /** + * adds the annotation parsed by prediction to al. + * + * @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 i = 0; + SequenceI[] preds = prediction.getSeqsAsArray(); + // in the future we could search for the query + // sequence in the alignment before calling this function. + 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)) + { + throw (new Exception("Number of residues in " + + (delMap == null ? "" : " mapped ") + + "supposed query sequence ('" + + al.getSequenceAt(firstSeq).getName() + "'\n" + + al.getSequenceAt(firstSeq).getSequenceAsString() + + ")\ndiffer from number of prediction sites in prediction (" + + width + ")")); + } + + AlignmentAnnotation annot; + Annotation[] annotations = null; + + int existingAnnotations = 0; + if (al.getAlignmentAnnotation() != null) + { + existingAnnotations = al.getAlignmentAnnotation().length; + } + + while (i < preds.length) + { + String id = preds[i].getName().toUpperCase(); + + if (id.startsWith("LUPAS") || id.startsWith("JNET") + || id.startsWith("JPRED")) + { + annotations = new Annotation[al.getWidth()]; + /* + * if (delMap!=null) { for (int j=0; j