X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=7c96d45633119940b87e21a5f06ed23d4e09e5ff;hb=70f9c4700f20a8fa57ed7eb974277d8bad0723c2;hp=497e4c920df0b04fef00bf0f84fb0a5ab5540437;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 497e4c9..7c96d45 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -1,31 +1,36 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * 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. + * 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 . + * 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 java.util.ArrayList; -import java.util.Hashtable; -import java.util.Vector; import jalview.datamodel.DBRefEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.util.UrlLink; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; + + /** * generate HTML reports for a sequence * @@ -51,30 +56,30 @@ public class SequenceAnnotationReport * TODO refactor to Jalview 'utilities' somehow. */ public void appendFeatures(final StringBuffer tooltipText2, int rpos, - SequenceFeature[] features) + List features) { appendFeatures(tooltipText2, rpos, features, null); } public void appendFeatures(final StringBuffer tooltipText2, int rpos, - SequenceFeature[] features, Hashtable minmax) + List features, Hashtable minmax) { String tmpString; if (features != null) { - for (int i = 0; i < features.length; i++) + for (SequenceFeature feature:features) { - if (features[i].getType().equals("disulfide bond")) + if (feature.getType().equals("disulfide bond")) { - if (features[i].getBegin() == rpos - || features[i].getEnd() == rpos) + if (feature.getBegin() == rpos + || feature.getEnd() == rpos) { if (tooltipText2.length() > 6) { tooltipText2.append("
"); } - tooltipText2.append("disulfide bond " + features[i].getBegin() - + ":" + features[i].getEnd()); + tooltipText2.append("disulfide bond " + feature.getBegin() + + ":" + feature.getEnd()); } } else @@ -84,25 +89,25 @@ public class SequenceAnnotationReport tooltipText2.append("
"); } // TODO: remove this hack to display link only features - boolean linkOnly = features[i].getValue("linkonly") != null; + boolean linkOnly = feature.getValue("linkonly") != null; if (!linkOnly) { - tooltipText2.append(features[i].getType() + " "); + tooltipText2.append(feature.getType() + " "); if (rpos != 0) { // we are marking a positional feature - tooltipText2.append(features[i].begin); + tooltipText2.append(feature.begin); } - if (features[i].begin != features[i].end) + if (feature.begin != feature.end) { - tooltipText2.append(" " + features[i].end); + tooltipText2.append(" " + feature.end); } - if (features[i].getDescription() != null - && !features[i].description.equals(features[i] + if (feature.getDescription() != null + && !feature.description.equals(feature .getType())) { - tmpString = features[i].getDescription(); + tmpString = feature.getDescription(); String tmp2up = tmpString.toUpperCase(); int startTag = tmp2up.indexOf(""); if (startTag > -1) @@ -147,27 +152,27 @@ public class SequenceAnnotationReport } } // check score should be shown - if (features[i].getScore() != Float.NaN) + if (feature.getScore() != Float.NaN) { float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(features[i].getType())); + .get(feature.getType())); if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { - tooltipText2.append(" Score=" + features[i].getScore()); + tooltipText2.append(" Score=" + feature.getScore()); } } - if (features[i].getValue("status") != null) + if (feature.getValue("status") != null) { - String status = features[i].getValue("status").toString(); + String status = feature.getValue("status").toString(); if (status.length() > 0) { - tooltipText2.append("; (" + features[i].getValue("status") + tooltipText2.append("; (" + feature.getValue("status") + ")"); } } } } - if (features[i].links != null) + if (feature.links != null) { if (linkImageURL != null) { @@ -175,7 +180,7 @@ public class SequenceAnnotationReport } else { - for (String urlstring : (Vector) features[i].links) + for (String urlstring : feature.links) { try { @@ -360,8 +365,7 @@ public class SequenceAnnotationReport } // ADD NON POSITIONAL SEQUENCE INFO - SequenceFeature[] features = ds.getSequenceFeatures(); - SequenceFeature[] tfeat = new SequenceFeature[1]; + SequenceFeature[] features = sequence.getSequenceFeatures(); if (showNpFeats && features != null) { for (int i = 0; i < features.length; i++) @@ -369,7 +373,8 @@ public class SequenceAnnotationReport if (features[i].begin == 0 && features[i].end == 0) { int sz = -tip.length(); - tfeat[0] = features[i]; + List tfeat = new ArrayList(); + tfeat.add(features[i]); appendFeatures(tip, 0, tfeat, minmax); sz += tip.length(); maxWidth = Math.max(maxWidth, sz);