X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=c8313664c86b70d07679fb7655dab9dd7d0bc019;hp=6d819d39a88092a7f285d0e954e583bf82292db6;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hpb=14193747f3831242bc7dfac12394eb20eb0ba480 diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 6d819d3..c831366 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -20,21 +20,28 @@ */ package jalview.io; +import java.util.Locale; +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; + +import com.google.common.collect.Lists; + +import jalview.api.FeatureColourI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; +import jalview.datamodel.GeneLociI; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.io.gff.GffConstants; import jalview.util.MessageManager; import jalview.util.StringUtils; import jalview.util.UrlLink; - -import java.util.Arrays; -import java.util.Collection; -import java.util.Comparator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; /** * generate HTML reports for a sequence @@ -43,6 +50,8 @@ import java.util.Map; */ public class SequenceAnnotationReport { + private static final int MAX_DESCRIPTION_LENGTH = 40; + private static final String COMMA = ","; private static final String ELLIPSIS = "..."; @@ -51,11 +60,9 @@ public class SequenceAnnotationReport private static final int MAX_SOURCES = 40; - private static final String[][] PRIMARY_SOURCES = new String[][] { - DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS, - DBRefSource.PROTEINDBS }; + private static String linkImageURL; - final String linkImageURL; + // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java /* * Comparator to order DBRefEntry by Source + accession id (case-insensitive), @@ -67,18 +74,18 @@ public class SequenceAnnotationReport @Override public int compare(DBRefEntry ref1, DBRefEntry ref2) { - if (ref1.isChromosome()) + if (ref1 instanceof GeneLociI) { return -1; } - if (ref2.isChromosome()) + if (ref2 instanceof GeneLociI) { return 1; } String s1 = ref1.getSource(); String s2 = ref2.getSource(); - boolean s1Primary = isPrimarySource(s1); - boolean s2Primary = isPrimarySource(s2); + boolean s1Primary = DBRefSource.isPrimarySource(s1); + boolean s2Primary = DBRefSource.isPrimarySource(s2); if (s1Primary && !s2Primary) { return -1; @@ -99,45 +106,91 @@ public class SequenceAnnotationReport return comp; } - private boolean isPrimarySource(String source) - { - for (String[] primary : PRIMARY_SOURCES) - { - for (String s : primary) - { - if (source.equals(s)) - { - return true; - } - } - } - return false; - } + // private boolean isPrimarySource(String source) + // { + // for (String[] primary : DBRefSource.PRIMARY_SOURCES) + // { + // for (String s : primary) + // { + // if (source.equals(s)) + // { + // return true; + // } + // } + // } + // return false; + // } }; - public SequenceAnnotationReport(String linkImageURL) + private boolean forTooltip; + + /** + * Constructor given a flag which affects behaviour + * + * + * @param isForTooltip + */ + public SequenceAnnotationReport(boolean isForTooltip) { - this.linkImageURL = linkImageURL; + this.forTooltip = isForTooltip; + if (linkImageURL == null) + { + linkImageURL = getClass().getResource("/images/link.gif").toString(); + } } /** - * Append text for the list of features to the tooltip + * Append text for the list of features to the tooltip. Returns the number of + * features not added if maxlength limit is (or would have been) reached. * * @param sb - * @param rpos + * @param residuePos * @param features * @param minmax + * @param maxlength + */ + public int appendFeatures(final StringBuilder sb, int residuePos, + List features, FeatureRendererModel fr, + int maxlength) + { + for (int i = 0; i < features.size(); i++) + { + SequenceFeature feature = features.get(i); + if (appendFeature(sb, residuePos, fr, feature, null, maxlength)) + { + return features.size() - i; + } + } + return 0; + } + + /** + * Appends text for mapped features (e.g. CDS feature for peptide or vice + * versa) Returns number of features left if maxlength limit is (or would have + * been) reached. + * + * @param sb + * @param residuePos + * @param mf + * @param fr + * @param maxlength */ - public void appendFeatures(final StringBuilder sb, int rpos, - List features, Map minmax) + public int appendFeatures(StringBuilder sb, int residuePos, + MappedFeatures mf, FeatureRendererModel fr, int maxlength) { - if (features != null) + for (int i = 0; i < mf.features.size(); i++) { - for (SequenceFeature feature : features) + SequenceFeature feature = mf.features.get(i); + if (appendFeature(sb, residuePos, fr, feature, mf, maxlength)) { - appendFeature(sb, rpos, minmax, feature); + return mf.features.size() - i; } } + return 0; } /** @@ -148,71 +201,195 @@ public class SequenceAnnotationReport * @param minmax * @param feature */ - void appendFeature(final StringBuilder sb, int rpos, - Map minmax, SequenceFeature feature) + boolean appendFeature(final StringBuilder sb0, int rpos, + FeatureRendererModel fr, SequenceFeature feature, + MappedFeatures mf, int maxlength) { + int begin = feature.getBegin(); + int end = feature.getEnd(); + + /* + * if this is a virtual features, convert begin/end to the + * coordinates of the sequence it is mapped to + */ + int[] beginRange = null; // feature start in local coordinates + int[] endRange = null; // feature end in local coordinates + if (mf != null) + { + if (feature.isContactFeature()) + { + /* + * map start and end points individually + */ + beginRange = mf.getMappedPositions(begin, begin); + endRange = begin == end ? beginRange + : mf.getMappedPositions(end, end); + } + else + { + /* + * map the feature extent + */ + beginRange = mf.getMappedPositions(begin, end); + endRange = beginRange; + } + if (beginRange == null || endRange == null) + { + // something went wrong + return false; + } + begin = beginRange[0]; + end = endRange[endRange.length - 1]; + } + + StringBuilder sb = new StringBuilder(); if (feature.isContactFeature()) { - if (feature.getBegin() == rpos || feature.getEnd() == rpos) + /* + * include if rpos is at start or end position of [mapped] feature + */ + boolean showContact = (mf == null) && (rpos == begin || rpos == end); + boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0] + && rpos <= beginRange[beginRange.length - 1]) + || (rpos >= endRange[0] + && rpos <= endRange[endRange.length - 1])); + if (showContact || showMappedContact) { - if (sb.length() > 6) + if (sb0.length() > 6) { - sb.append("
"); + sb.append("
"); } - sb.append(feature.getType()).append(" ").append(feature.getBegin()) - .append(":").append(feature.getEnd()); + sb.append(feature.getType()).append(" ").append(begin).append(":") + .append(end); } + return appendText(sb0, sb, maxlength); } - else + + if (sb0.length() > 6) { - if (sb.length() > 6) - { - sb.append("
"); - } - // TODO: remove this hack to display link only features - boolean linkOnly = feature.getValue("linkonly") != null; - if (!linkOnly) + sb.append("
"); + } + // TODO: remove this hack to display link only features + boolean linkOnly = feature.getValue("linkonly") != null; + if (!linkOnly) + { + sb.append(feature.getType()).append(" "); + if (rpos != 0) { - sb.append(feature.getType()).append(" "); - if (rpos != 0) + // we are marking a positional feature + sb.append(begin); + if (begin != end) { - // we are marking a positional feature - sb.append(feature.begin); - } - if (feature.begin != feature.end) - { - sb.append(" ").append(feature.end); + sb.append(" ").append(end); } + } - String description = feature.getDescription(); - if (description != null && !description.equals(feature.getType())) + String description = feature.getDescription(); + if (description != null && !description.equals(feature.getType())) + { + description = StringUtils.stripHtmlTags(description); + + /* + * truncate overlong descriptions unless they contain an href + * before the truncation point (as truncation could leave corrupted html) + */ + int linkindex = description.toLowerCase(Locale.ROOT).indexOf(" -1 + && linkindex < MAX_DESCRIPTION_LENGTH; + if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink) { - description = StringUtils.stripHtmlTags(description); - sb.append("; ").append(description); + description = description.substring(0, MAX_DESCRIPTION_LENGTH) + + ELLIPSIS; } - // check score should be shown - if (!Float.isNaN(feature.getScore())) + + sb.append("; ").append(description); + } + + 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(")"); + } + + /* + * 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 - : 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=").append(String.valueOf(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) + } + + if (mf != null) + { + String variants = mf.findProteinVariants(feature); + if (!variants.isEmpty()) { - sb.append("; ").append(clinSig); + sb.append(" ").append(variants); } } } + return appendText(sb0, sb, maxlength); + } + + /** + * Appends sb to sb0, and returns false, unless maxlength is not zero and + * appending would make the result longer than or equal to maxlength, in which + * case the append is not done and returns true + * + * @param sb0 + * @param sb + * @param maxlength + * @return + */ + private static boolean appendText(StringBuilder sb0, StringBuilder sb, + int maxlength) + { + if (maxlength == 0 || sb0.length() + sb.length() < maxlength) + { + sb0.append(sb); + return false; + } + return true; + } + + /** + * 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; } /** @@ -240,12 +417,12 @@ public class SequenceAnnotationReport { sb.append("
" - + (urllink.get(0).toLowerCase() - .equals(urllink.get(1).toLowerCase()) + + (urllink.get(0).toLowerCase(Locale.ROOT).equals( + urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink.get(0) : (urllink.get(0) + ":" + urllink.get(1))) - + "
"); + + "
"); } } catch (Exception x) { @@ -268,7 +445,7 @@ public class SequenceAnnotationReport */ Collection> createLinksFrom(SequenceI seq, String link) { - Map> urlSets = new LinkedHashMap>(); + Map> urlSets = new LinkedHashMap<>(); UrlLink urlLink = new UrlLink(link); if (!urlLink.isValid()) { @@ -283,10 +460,10 @@ public class SequenceAnnotationReport 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); } /** @@ -301,13 +478,13 @@ 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(""); @@ -316,19 +493,21 @@ public class SequenceAnnotationReport if (sequence.getDescription() != null) { tmp = sequence.getDescription(); - sb.append("
").append(tmp); + sb.append(tmp); maxWidth = Math.max(maxWidth, tmp.length()); } + sb.append("\n"); SequenceI ds = sequence; while (ds.getDatasetSequence() != null) { ds = ds.getDatasetSequence(); } - + if (showDbRefs) { maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary)); } + sb.append("\n"); /* * add non-positional features if wanted @@ -339,7 +518,7 @@ public class SequenceAnnotationReport .getNonPositionalFeatures()) { int sz = -sb.length(); - appendFeature(sb, 0, minmax, sf); + appendFeature(sb, 0, fr, sf, null, 0); sz += sb.length(); maxWidth = Math.max(maxWidth, sz); } @@ -360,14 +539,21 @@ public class SequenceAnnotationReport protected int appendDbRefs(final StringBuilder sb, SequenceI ds, boolean summary) { - DBRefEntry[] dbrefs = ds.getDBRefs(); - if (dbrefs == null) + List dbrefs, dbrefset = ds.getDBRefs(); + + if (dbrefset == null) { return 0; } + // PATCH for JAL-3980 defensive copy + + dbrefs = new ArrayList(); + + dbrefs.addAll(dbrefset); + // note this sorts the refs held on the sequence! - Arrays.sort(dbrefs, comparator); + dbrefs.sort(comparator); boolean ellipsis = false; String source = null; String lastSource = null; @@ -402,7 +588,7 @@ public class SequenceAnnotationReport countForSource++; if (countForSource == 1 || !summary) { - sb.append("
"); + sb.append("
\n"); } if (countForSource <= MAX_REFS_PER_SOURCE || !summary) { @@ -410,7 +596,7 @@ public class SequenceAnnotationReport lineLength += accessionId.length() + 1; if (countForSource > 1 && summary) { - sb.append(", ").append(accessionId); + sb.append(",\n ").append(accessionId); lineLength++; } else @@ -428,12 +614,11 @@ public class SequenceAnnotationReport } if (moreSources) { - sb.append("
").append(source) - .append(COMMA).append(ELLIPSIS); + sb.append("
\n").append(source).append(COMMA).append(ELLIPSIS); } if (ellipsis) { - sb.append("
("); + sb.append("
\n("); sb.append(MessageManager.getString("label.output_seq_details")); sb.append(")"); } @@ -443,10 +628,10 @@ public class SequenceAnnotationReport 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); + showNpFeats, fr, true); if (maxWidth > 60) {