X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=f1ebcac17ed05eabeb937fdf410f18cc897e91fd;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=59daa8756a7d3f01c8cfcf1d4ddc7ad391bca610;hpb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;p=jalview.git diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 59daa87..f1ebcac 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -25,13 +25,13 @@ 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.UrlLink; -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 +57,8 @@ 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 */ private static Comparator comparator = new Comparator() { @@ -77,14 +78,14 @@ public class SequenceAnnotationReport { return 1; } - int comp = s1 == null ? -1 : (s2 == null ? 1 : s1 - .compareToIgnoreCase(s2)); + int comp = s1 == null ? -1 + : (s2 == null ? 1 : s1.compareToIgnoreCase(s2)); if (comp == 0) { String a1 = ref1.getAccessionId(); String a2 = ref2.getAccessionId(); - comp = a1 == null ? -1 : (a2 == null ? 1 : a1 - .compareToIgnoreCase(a2)); + comp = a1 == null ? -1 + : (a2 == null ? 1 : a1.compareToIgnoreCase(a2)); } return comp; } @@ -141,8 +142,7 @@ public class SequenceAnnotationReport void appendFeature(final StringBuilder sb, int rpos, Map minmax, SequenceFeature feature) { - String tmpString; - if (feature.getType().equals("disulfide bond")) + if (feature.isContactFeature()) { if (feature.getBegin() == rpos || feature.getEnd() == rpos) { @@ -150,8 +150,8 @@ 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()); } } else @@ -178,7 +178,7 @@ public class SequenceAnnotationReport if (feature.getDescription() != null && !feature.description.equals(feature.getType())) { - tmpString = feature.getDescription(); + String tmpString = feature.getDescription(); String tmp2up = tmpString.toUpperCase(); int startTag = tmp2up.indexOf(""); if (startTag > -1) @@ -223,11 +223,11 @@ public class SequenceAnnotationReport // check score should be shown if (!Float.isNaN(feature.getScore())) { - float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(feature.getType())); + float[][] rng = (minmax == null) ? null + : minmax.get(feature.getType()); if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { - sb.append(" Score=" + feature.getScore()); + sb.append(" Score=").append(String.valueOf(feature.getScore())); } } String status = (String) feature.getValue("status"); @@ -266,22 +266,21 @@ 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])) + sb.append("
" + + (urllink.get(0).toLowerCase() + .equals(urllink.get(1).toLowerCase()) + ? urllink.get(0) + : (urllink.get(0) + ":" + + urllink.get(1))) + "
"); } } catch (Exception x) { - System.err.println("problem when creating links from " - + urlstring); + System.err.println( + "problem when creating links from " + urlstring); x.printStackTrace(); } } @@ -294,125 +293,22 @@ 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, @@ -458,108 +354,129 @@ 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, minmax, 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) + { + sb.append("
"); + } + if (countForSource <= MAX_REFS_PER_SOURCE || !summary) { - if (features[i].begin == 0 && features[i].end == 0) + 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) { - int maxWidth = createSequenceAnnotationReport(tip, sequence, - showDbRefs, showNpFeats, minmax, true); + int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs, + showNpFeats, minmax, true); if (maxWidth > 60) {