*/
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.DBRefUtils;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.util.UrlLink;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
/**
* generate HTML reports for a sequence
*/
public class SequenceAnnotationReport
{
+ private static final int MAX_DESCRIPTION_LENGTH = 40;
+
private static final String COMMA = ",";
private static final String ELLIPSIS = "...";
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)
+ * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
+ * with 'Primary' sources placed before others, and 'chromosome' first of all
*/
private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
{
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
+ if (ref1 instanceof GeneLociI)
+ {
+ return -1;
+ }
+ 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;
{
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;
}
- 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
+ * <ul>
+ * <li>if true, generates feature details suitable to show in a tooltip</li>
+ * <li>if false, generates feature details in a form suitable for the sequence
+ * details report</li>
+ * </ul>
+ *
+ * @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 void appendFeatures(final StringBuilder sb, int rpos,
- List<SequenceFeature> features, Map<String, float[][]> minmax)
+ public int appendFeatures(final StringBuilder sb, int residuePos,
+ List<SequenceFeature> features, FeatureRendererModel fr,
+ int maxlength)
{
- if (features != null)
+ for (int i = 0; i < features.size(); i++)
{
- for (SequenceFeature feature : features)
+ SequenceFeature feature = features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
{
- appendFeature(sb, rpos, minmax, feature);
+ 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 int appendFeatures(StringBuilder sb, int residuePos,
+ MappedFeatures mf, FeatureRendererModel fr, int maxlength)
+ {
+ for (int i = 0; i < mf.features.size(); i++)
+ {
+ SequenceFeature feature = mf.features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
+ {
+ return mf.features.size() - i;
+ }
+ }
+ return 0;
}
/**
* @param minmax
* @param feature
*/
- void appendFeature(final StringBuilder sb, int rpos,
- Map<String, float[][]> minmax, SequenceFeature feature)
+ boolean appendFeature(final StringBuilder sb0, int rpos,
+ FeatureRendererModel fr, SequenceFeature feature,
+ MappedFeatures mf, int maxlength)
{
- String tmpString;
- if (feature.getType().equals("disulfide bond"))
+ 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.getBegin() == rpos || feature.getEnd() == rpos)
+ if (feature.isContactFeature())
{
- if (sb.length() > 6)
- {
- sb.append("<br>");
- }
- sb.append("disulfide bond ").append(feature.getBegin()).append(":")
- .append(feature.getEnd());
+ /*
+ * 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];
}
- else
+
+ StringBuilder sb = new StringBuilder();
+ if (feature.isContactFeature())
{
- if (sb.length() > 6)
+ /*
+ * 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)
{
- sb.append("<br>");
+ if (sb0.length() > 6)
+ {
+ sb.append("<br/>");
+ }
+ sb.append(feature.getType()).append(" ").append(begin).append(":")
+ .append(end);
}
- // TODO: remove this hack to display link only features
- boolean linkOnly = feature.getValue("linkonly") != null;
- if (!linkOnly)
+ return appendText(sb0, sb, maxlength);
+ }
+
+ if (sb0.length() > 6)
+ {
+ sb.append("<br/>");
+ }
+ // 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);
+ sb.append(" ").append(end);
}
- if (feature.begin != feature.end)
+ }
+
+ 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("<a ");
+ boolean hasLink = linkindex > -1
+ && linkindex < MAX_DESCRIPTION_LENGTH;
+ if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
{
- sb.append(" ").append(feature.end);
+ description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ + ELLIPSIS;
}
- if (feature.getDescription() != null
- && !feature.description.equals(feature.getType()))
- {
- tmpString = feature.getDescription();
- String tmp2up = tmpString.toUpperCase();
- int startTag = tmp2up.indexOf("<HTML>");
- if (startTag > -1)
- {
- tmpString = tmpString.substring(startTag + 6);
- tmp2up = tmp2up.substring(startTag + 6);
- }
- int endTag = tmp2up.indexOf("</BODY>");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- tmp2up = tmp2up.substring(0, endTag);
- }
- endTag = tmp2up.indexOf("</HTML>");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- }
+ 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)
+ }
+
+ 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;
}
/**
{
try
{
- for (String[] urllink : createLinksFrom(null, urlstring))
+ for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\""
- + urllink[3]
- + "\" target=\""
- + urllink[0]
- + "\">"
- + (urllink[0].toLowerCase().equals(
- urllink[1].toLowerCase()) ? urllink[0]
- : (urllink[0] + ":" + urllink[1]))
- + "</a></br>");
+ sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
+ + urllink.get(0) + "\">"
+ + (urllink.get(0).toLowerCase(Locale.ROOT).equals(
+ urllink.get(1).toLowerCase(Locale.ROOT))
+ ? urllink.get(0)
+ : (urllink.get(0) + ":"
+ + urllink.get(1)))
+ + "</a><br/>");
}
} catch (Exception x)
{
- System.err.println("problem when creating links from "
- + urlstring);
+ System.err.println(
+ "problem when creating links from " + urlstring);
x.printStackTrace();
}
}
*
* @param seq
* @param link
- * @return String[][] { String[] { link target, link label, dynamic component
- * inserted (if any), url }}
+ * @return Collection< List<String> > { List<String> { link target, link
+ * label, dynamic component inserted (if any), url }}
*/
- String[][] createLinksFrom(SequenceI seq, String link)
+ Collection<List<String>> createLinksFrom(SequenceI seq, String link)
{
- List<String[]> urlSets = new ArrayList<String[]>();
- List<String> uniques = new ArrayList<String>();
+ Map<String, List<String>> 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<String[]> createDynamicLinks(SequenceI seq, UrlLink urlLink,
- List<String> uniques)
- {
- List<String[]> result = new ArrayList<String[]>();
- 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<String, float[][]> minmax)
+ FeatureRendererModel fr)
{
createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
- minmax, false);
+ fr, false);
}
/**
* 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<String, float[][]> minmax, boolean summary)
+ FeatureRendererModel fr, boolean summary)
{
String tmp;
sb.append("<i>");
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("<br>").append(tmp);
+ sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
+ sb.append("\n");
SequenceI ds = sequence;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
- DBRefEntry[] dbrefs = ds.getDBRefs();
- if (showDbRefs && dbrefs != null)
+
+ if (showDbRefs)
{
- // 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)
- {
- 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("<br>");
- }
- 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;
- }
- }
- if (moreSources)
- {
- sb.append("<br>").append(ELLIPSIS).append(COMMA).append(source)
- .append(COMMA).append(ELLIPSIS);
- }
- if (ellipsis)
- {
- sb.append("<br>(");
- sb.append(MessageManager.getString("label.output_seq_details"));
- sb.append(")");
- }
+ maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
}
+ sb.append("\n");
/*
* add non-positional features if wanted
*/
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (showNpFeats && features != null)
+ if (showNpFeats)
{
- for (int i = 0; i < features.length; i++)
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
{
- if (features[i].begin == 0 && features[i].end == 0)
- {
- int sz = -sb.length();
- appendFeature(sb, 0, minmax, features[i]);
- sz += sb.length();
- maxWidth = Math.max(maxWidth, sz);
- }
+ int sz = -sb.length();
+ appendFeature(sb, 0, fr, sf, null, 0);
+ sz += sb.length();
+ maxWidth = Math.max(maxWidth, sz);
}
}
sb.append("</i>");
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)
+ {
+ List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
+
+ if (dbrefset == null)
+ {
+ return 0;
+ }
+
+ // PATCH for JAL-3980 defensive copy
+
+ dbrefs = new ArrayList<DBRefEntry>();
+
+ dbrefs.addAll(dbrefset);
+
+ // note this sorts the refs held on the sequence!
+ dbrefs.sort(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)
+ {
+ // 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("<br/>\n");
+ }
+ if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
+ {
+ String accessionId = ref.getAccessionId();
+ lineLength += accessionId.length() + 1;
+ if (countForSource > 1 && summary)
+ {
+ sb.append(",\n ").append(accessionId);
+ lineLength++;
+ }
+ else
+ {
+ 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;
+ }
+ }
+ if (moreSources)
+ {
+ sb.append("<br/>\n").append(source).append(COMMA).append(ELLIPSIS);
+ }
+ if (ellipsis)
+ {
+ sb.append("<br/>\n(");
+ 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<String, float[][]> minmax)
+ FeatureRendererModel fr)
{
- int maxWidth = createSequenceAnnotationReport(tip, sequence,
- showDbRefs, showNpFeats, minmax, true);
+ int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+ showNpFeats, fr, true);
if (maxWidth > 60)
{
git://source.jalview.org / jalview.git / blobdiff