X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=6b826712db05ff9503209a7999a09128cf6a6cf2;hb=6d35ae6c809d36b2e2fa984436134dbff712a377;hp=59daa8756a7d3f01c8cfcf1d4ddc7ad391bca610;hpb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;p=jalview.git diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 59daa87..6b82671 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -20,18 +20,20 @@ */ package jalview.io; +import jalview.api.FeatureColourI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.io.gff.GffConstants; -import jalview.util.DBRefUtils; import jalview.util.MessageManager; +import jalview.util.StringUtils; import jalview.util.UrlLink; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; -import java.util.ArrayList; import java.util.Arrays; +import java.util.Collection; import java.util.Comparator; +import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -57,7 +59,8 @@ public class SequenceAnnotationReport final String linkImageURL; /* - * Comparator to order DBRefEntry by Source + accession id (case-insensitive) + * Comparator to order DBRefEntry by Source + accession id (case-insensitive), + * with 'Primary' sources placed before others, and 'chromosome' first of all */ private static Comparator comparator = new Comparator() { @@ -65,6 +68,14 @@ public class SequenceAnnotationReport @Override public int compare(DBRefEntry ref1, DBRefEntry ref2) { + if (ref1.isChromosome()) + { + return -1; + } + if (ref2.isChromosome()) + { + return 1; + } String s1 = ref1.getSource(); String s2 = ref2.getSource(); boolean s1Primary = isPrimarySource(s1); @@ -105,9 +116,9 @@ public class SequenceAnnotationReport } }; - public SequenceAnnotationReport(String linkImageURL) + public SequenceAnnotationReport(String linkURL) { - this.linkImageURL = linkImageURL; + this.linkImageURL = linkURL; } /** @@ -119,13 +130,13 @@ public class SequenceAnnotationReport * @param minmax */ public void appendFeatures(final StringBuilder sb, int rpos, - List features, Map minmax) + List features, FeatureRendererModel fr) { if (features != null) { for (SequenceFeature feature : features) { - appendFeature(sb, rpos, minmax, feature); + appendFeature(sb, rpos, fr, feature); } } } @@ -139,10 +150,9 @@ public class SequenceAnnotationReport * @param feature */ void appendFeature(final StringBuilder sb, int rpos, - Map minmax, SequenceFeature feature) + FeatureRendererModel fr, SequenceFeature feature) { - String tmpString; - if (feature.getType().equals("disulfide bond")) + if (feature.isContactFeature()) { if (feature.getBegin() == rpos || feature.getEnd() == rpos) { @@ -150,102 +160,95 @@ public class SequenceAnnotationReport { sb.append("
"); } - sb.append("disulfide bond ").append(feature.getBegin()).append(":") - .append(feature.getEnd()); + sb.append(feature.getType()).append(" ").append(feature.getBegin()) + .append(":").append(feature.getEnd()); } + return; } - else + + if (sb.length() > 6) + { + sb.append("
"); + } + // TODO: remove this hack to display link only features + boolean linkOnly = feature.getValue("linkonly") != null; + if (!linkOnly) { - if (sb.length() > 6) + sb.append(feature.getType()).append(" "); + if (rpos != 0) { - sb.append("
"); + // we are marking a positional feature + sb.append(feature.begin); } - // TODO: remove this hack to display link only features - boolean linkOnly = feature.getValue("linkonly") != null; - if (!linkOnly) + if (feature.begin != feature.end) { - sb.append(feature.getType()).append(" "); - if (rpos != 0) - { - // we are marking a positional feature - sb.append(feature.begin); - } - if (feature.begin != feature.end) - { - sb.append(" ").append(feature.end); - } + sb.append(" ").append(feature.end); + } - if (feature.getDescription() != null - && !feature.description.equals(feature.getType())) - { - tmpString = feature.getDescription(); - String tmp2up = tmpString.toUpperCase(); - int startTag = tmp2up.indexOf(""); - if (startTag > -1) - { - tmpString = tmpString.substring(startTag + 6); - tmp2up = tmp2up.substring(startTag + 6); - } - int endTag = tmp2up.indexOf(""); - if (endTag > -1) - { - tmpString = tmpString.substring(0, endTag); - tmp2up = tmp2up.substring(0, endTag); - } - endTag = tmp2up.indexOf(""); - if (endTag > -1) - { - tmpString = tmpString.substring(0, endTag); - } + String description = feature.getDescription(); + if (description != null && !description.equals(feature.getType())) + { + description = StringUtils.stripHtmlTags(description); + sb.append("; ").append(description); + } - if (startTag > -1) - { - sb.append("; ").append(tmpString); - } - else - { - if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1) - { - // The description does not specify html is to - // be used, so we must remove < > symbols - tmpString = tmpString.replaceAll("<", "<"); - tmpString = tmpString.replaceAll(">", ">"); + if (showScore(feature, fr)) + { + sb.append(" Score=").append(String.valueOf(feature.getScore())); + } + String status = (String) feature.getValue("status"); + if (status != null && status.length() > 0) + { + sb.append("; (").append(status).append(")"); + } - sb.append("; "); - sb.append(tmpString); - } - else - { - sb.append("; ").append(tmpString); - } - } - } - // check score should be shown - if (!Float.isNaN(feature.getScore())) + /* + * add attribute value if coloured by attribute + */ + if (fr != null) + { + FeatureColourI fc = fr.getFeatureColours().get(feature.getType()); + if (fc != null && fc.isColourByAttribute()) { - float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(feature.getType())); - if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) + String[] attName = fc.getAttributeName(); + String attVal = feature.getValueAsString(attName); + if (attVal != null) { - sb.append(" Score=" + feature.getScore()); + sb.append("; ").append(String.join(":", attName)).append("=") + .append(attVal); } } - String status = (String) feature.getValue("status"); - if (status != null && status.length() > 0) - { - sb.append("; (").append(status).append(")"); - } - String clinSig = (String) feature - .getValue(GffConstants.CLINICAL_SIGNIFICANCE); - if (clinSig != null) - { - sb.append("; ").append(clinSig); - } } } } /** + * Answers true if score should be shown, else false. Score is shown if it is + * not NaN, and the feature type has a non-trivial min-max score range + */ + boolean showScore(SequenceFeature feature, FeatureRendererModel fr) + { + if (Float.isNaN(feature.getScore())) + { + return false; + } + if (fr == null) + { + return true; + } + float[][] minMax = fr.getMinMax().get(feature.getType()); + + /* + * minMax[0] is the [min, max] score range for positional features + */ + if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1]) + { + return false; + } + return true; + } + + /** * Format and appends any hyperlinks for the sequence feature to the string * buffer * @@ -266,17 +269,17 @@ public class SequenceAnnotationReport { try { - for (String[] urllink : createLinksFrom(null, urlstring)) + for (List urllink : createLinksFrom(null, urlstring)) { sb.append("
" - + (urllink[0].toLowerCase().equals( - urllink[1].toLowerCase()) ? urllink[0] - : (urllink[0] + ":" + urllink[1])) - + "
"); + + (urllink.get(0).toLowerCase() + .equals(urllink.get(1).toLowerCase()) ? urllink + .get(0) : (urllink.get(0) + ":" + urllink + .get(1))) + "
"); } } catch (Exception x) { @@ -294,133 +297,30 @@ public class SequenceAnnotationReport * * @param seq * @param link - * @return String[][] { String[] { link target, link label, dynamic component - * inserted (if any), url }} + * @return Collection< List > { List { link target, link + * label, dynamic component inserted (if any), url }} */ - String[][] createLinksFrom(SequenceI seq, String link) + Collection> createLinksFrom(SequenceI seq, String link) { - List urlSets = new ArrayList(); - List uniques = new ArrayList(); + Map> urlSets = new LinkedHashMap<>(); UrlLink urlLink = new UrlLink(link); if (!urlLink.isValid()) { System.err.println(urlLink.getInvalidMessage()); return null; } - final String target = urlLink.getTarget(); // link.substring(0, - // link.indexOf("|")); - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { - urlSets.addAll(createDynamicLinks(seq, urlLink, uniques)); - } - else - { - String unq = label + "|" + urlLink.getUrl_prefix(); - if (!uniques.contains(unq)) - { - uniques.add(unq); - urlSets.add(new String[] { target, label, null, - urlLink.getUrl_prefix() }); - } - } - return urlSets.toArray(new String[][] {}); - } + urlLink.createLinksFromSeq(seq, urlSets); - /** - * Formats and returns a list of dynamic href links - * - * @param seq - * @param urlLink - * @param uniques - */ - List createDynamicLinks(SequenceI seq, UrlLink urlLink, - List uniques) - { - List result = new ArrayList(); - final String target = urlLink.getTarget(); - final String label = urlLink.getLabel(); - - // collect matching db-refs - DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(), - new String[] { target }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } - if (dbr != null) - { - for (int r = 0; r < dbr.length; r++) - { - if (id != null && dbr[r].getAccessionId().equals(id)) - { - // suppress duplicate link creation for the bare sequence ID - // string with this link - id = null; - } - // create Bare ID link for this URL - String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - String unq = urls[u] + "|" + urls[u + 1]; - if (!uniques.contains(unq)) - { - result.add(new String[] { target, label, urls[u], urls[u + 1] }); - uniques.add(unq); - } - } - } - } - } - if (id != null) - { - // create Bare ID link for this URL - String[] urls = urlLink.makeUrls(id, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - String unq = urls[u] + "|" + urls[u + 1]; - if (!uniques.contains(unq)) - { - result.add(new String[] { target, label, urls[u], urls[u + 1] }); - uniques.add(unq); - } - } - } - } - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description only if regex matches - String[] urls = urlLink.makeUrls(descr, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - String unq = urls[u] + "|" + urls[u + 1]; - if (!uniques.contains(unq)) - { - result.add(new String[] { target, label, urls[u], urls[u + 1] }); - uniques.add(unq); - } - } - } - } - return result; + return urlSets.values(); } public void createSequenceAnnotationReport(final StringBuilder tip, SequenceI sequence, boolean showDbRefs, boolean showNpFeats, - Map minmax) + FeatureRendererModel fr) { createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats, - minmax, false); + fr, false); } /** @@ -435,13 +335,13 @@ public class SequenceAnnotationReport * whether to include database references for the sequence * @param showNpFeats * whether to include non-positional sequence features - * @param minmax + * @param fr * @param summary * @return */ int createSequenceAnnotationReport(final StringBuilder sb, SequenceI sequence, boolean showDbRefs, boolean showNpFeats, - Map minmax, boolean summary) + FeatureRendererModel fr, boolean summary) { String tmp; sb.append(""); @@ -458,108 +358,128 @@ public class SequenceAnnotationReport { ds = ds.getDatasetSequence(); } + + if (showDbRefs) + { + maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary)); + } + + /* + * add non-positional features if wanted + */ + if (showNpFeats) + { + for (SequenceFeature sf : sequence.getFeatures() + .getNonPositionalFeatures()) + { + int sz = -sb.length(); + appendFeature(sb, 0, fr, sf); + sz += sb.length(); + maxWidth = Math.max(maxWidth, sz); + } + } + sb.append(""); + return maxWidth; + } + + /** + * A helper method that appends any DBRefs, returning the maximum line length + * added + * + * @param sb + * @param ds + * @param summary + * @return + */ + protected int appendDbRefs(final StringBuilder sb, SequenceI ds, + boolean summary) + { DBRefEntry[] dbrefs = ds.getDBRefs(); - if (showDbRefs && dbrefs != null) + if (dbrefs == null) { - // note this sorts the refs held on the sequence! - Arrays.sort(dbrefs, comparator); - boolean ellipsis = false; - String source = null; - String lastSource = null; - int countForSource = 0; - int sourceCount = 0; - boolean moreSources = false; - int lineLength = 0; - - for (DBRefEntry ref : dbrefs) + return 0; + } + + // note this sorts the refs held on the sequence! + Arrays.sort(dbrefs, comparator); + boolean ellipsis = false; + String source = null; + String lastSource = null; + int countForSource = 0; + int sourceCount = 0; + boolean moreSources = false; + int maxLineLength = 0; + int lineLength = 0; + + for (DBRefEntry ref : dbrefs) + { + source = ref.getSource(); + if (source == null) { - source = ref.getSource(); - if (source == null) - { - // shouldn't happen - continue; - } - boolean sourceChanged = !source.equals(lastSource); - if (sourceChanged) - { - lineLength = 0; - countForSource = 0; - sourceCount++; - } - if (sourceCount > MAX_SOURCES && summary) - { - ellipsis = true; - moreSources = true; - break; - } - lastSource = source; - countForSource++; - if (countForSource == 1 || !summary) - { - sb.append("
"); - } - if (countForSource <= MAX_REFS_PER_SOURCE || !summary) - { - String accessionId = ref.getAccessionId(); - lineLength += accessionId.length() + 1; - if (countForSource > 1 && summary) - { - sb.append(", ").append(accessionId); - lineLength++; - } - else - { - sb.append(source).append(" ").append(accessionId); - lineLength += source.length(); - } - maxWidth = Math.max(maxWidth, lineLength); - } - if (countForSource == MAX_REFS_PER_SOURCE && summary) - { - sb.append(COMMA).append(ELLIPSIS); - ellipsis = true; - } + // shouldn't happen + continue; } - if (moreSources) + boolean sourceChanged = !source.equals(lastSource); + if (sourceChanged) { - sb.append("
").append(ELLIPSIS).append(COMMA).append(source) - .append(COMMA).append(ELLIPSIS); + lineLength = 0; + countForSource = 0; + sourceCount++; } - if (ellipsis) + if (sourceCount > MAX_SOURCES && summary) { - sb.append("
("); - sb.append(MessageManager.getString("label.output_seq_details")); - sb.append(")"); + ellipsis = true; + moreSources = true; + break; } - } - - /* - * add non-positional features if wanted - */ - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (showNpFeats && features != null) - { - for (int i = 0; i < features.length; i++) + lastSource = source; + countForSource++; + if (countForSource == 1 || !summary) { - if (features[i].begin == 0 && features[i].end == 0) + sb.append("
"); + } + if (countForSource <= MAX_REFS_PER_SOURCE || !summary) + { + String accessionId = ref.getAccessionId(); + lineLength += accessionId.length() + 1; + if (countForSource > 1 && summary) + { + sb.append(", ").append(accessionId); + lineLength++; + } + else { - int sz = -sb.length(); - appendFeature(sb, 0, minmax, features[i]); - sz += sb.length(); - maxWidth = Math.max(maxWidth, sz); + sb.append(source).append(" ").append(accessionId); + lineLength += source.length(); } + maxLineLength = Math.max(maxLineLength, lineLength); + } + if (countForSource == MAX_REFS_PER_SOURCE && summary) + { + sb.append(COMMA).append(ELLIPSIS); + ellipsis = true; } } - sb.append(""); - return maxWidth; + if (moreSources) + { + sb.append("
").append(source).append(COMMA).append(ELLIPSIS); + } + if (ellipsis) + { + sb.append("
("); + sb.append(MessageManager.getString("label.output_seq_details")); + sb.append(")"); + } + + return maxLineLength; } public void createTooltipAnnotationReport(final StringBuilder tip, SequenceI sequence, boolean showDbRefs, boolean showNpFeats, - Map minmax) + FeatureRendererModel fr) { int maxWidth = createSequenceAnnotationReport(tip, sequence, - showDbRefs, showNpFeats, minmax, true); + showDbRefs, showNpFeats, fr, true); if (maxWidth > 60) {