*/
package jalview.io;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+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
*/
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 };
+ // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
final String linkImageURL;
/*
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
- * with 'Primary' sources placed before others
+ * 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)
+// 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 linkURL)
+ {
+ this.linkImageURL = linkURL;
+ }
+
+ /**
+ * Append text for the list of features to the tooltip Returns number of
+ * features left if maxlength limit is (or would have been) reached
+ *
+ * @param sb
+ * @param residuePos
+ * @param features
+ * @param minmax
+ * @param maxlength
+ */
+ public int appendFeaturesLengthLimit(final StringBuilder sb,
+ int residuePos, List<SequenceFeature> features,
+ FeatureRendererModel fr, int maxlength)
+ {
+ for (int i = 0; i < features.size(); i++)
{
- for (String[] primary : PRIMARY_SOURCES)
+ SequenceFeature feature = features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
{
- for (String s : primary)
- {
- if (source.equals(s))
- {
- return true;
- }
- }
+ return features.size() - i;
}
- return false;
}
- };
+ return 0;
+ }
- public SequenceAnnotationReport(String linkImageURL)
+ public void appendFeatures(final StringBuilder sb, int residuePos,
+ List<SequenceFeature> features, FeatureRendererModel fr)
{
- this.linkImageURL = linkImageURL;
+ appendFeaturesLengthLimit(sb, residuePos, features, fr, 0);
}
/**
- * Append text for the list of features to the tooltip
+ * 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 rpos
- * @param features
- * @param minmax
+ * @param residuePos
+ * @param mf
+ * @param fr
+ * @param maxlength
*/
- public void appendFeatures(final StringBuilder sb, int rpos,
- List<SequenceFeature> features, Map<String, float[][]> minmax)
+ public int appendFeaturesLengthLimit(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;
+ }
+
+ public void appendFeatures(StringBuilder sb, int residuePos,
+ MappedFeatures mf, FeatureRendererModel fr)
+ {
+ appendFeaturesLengthLimit(sb, residuePos, mf, fr, 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)
{
+ StringBuilder sb = new StringBuilder();
if (feature.isContactFeature())
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
- if (sb.length() > 6)
+ if (sb0.length() > 6)
{
- sb.append("<br>");
+ sb.append("<br/>");
}
sb.append(feature.getType()).append(" ").append(feature.getBegin())
.append(":").append(feature.getEnd());
}
+ return appendTextMaxLengthReached(sb0, sb, maxlength);
}
- else
+
+ if (sb0.length() > 6)
{
- if (sb.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("<br>");
+ // 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);
+ }
+
+ 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().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()))
- {
- String 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
- : 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 appendTextMaxLengthReached(sb0, sb, maxlength);
+ }
+
+ void appendFeature(final StringBuilder sb, int rpos,
+ FeatureRendererModel fr, SequenceFeature feature,
+ MappedFeatures mf)
+ {
+ appendFeature(sb, rpos, fr, feature, mf, 0);
+ }
+
+ /**
+ * Appends {@code sb} to {@code sb0}, and returns false, unless
+ * {@code maxlength} is not zero and appending would make the total length
+ * greater than {@code maxlength}, in which case the text is not appended, and
+ * the method returns true.
+ *
+ * @param sb0
+ * @param sb
+ * @param maxlength
+ * @return
+ */
+ private static boolean appendTextMaxLengthReached(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;
}
/**
{
for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
- + urllink.get(0) + "\">"
+ sb.append("<br/> <a href=\""
+ + urllink.get(3)
+ + "\" target=\""
+ + urllink.get(0)
+ + "\">"
+ (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase())
- ? urllink.get(0)
- : (urllink.get(0) + ":"
- + urllink.get(1)))
- + "</a></br>");
+ .equals(urllink.get(1).toLowerCase()) ? 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();
}
}
*/
Collection<List<String>> createLinksFrom(SequenceI seq, String link)
{
- Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
+ Map<String, List<String>> urlSets = new LinkedHashMap<>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
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());
}
SequenceI ds = sequence;
{
ds = ds.getDatasetSequence();
}
-
+
if (showDbRefs)
{
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
.getNonPositionalFeatures())
{
int sz = -sb.length();
- appendFeature(sb, 0, minmax, sf);
+ appendFeature(sb, 0, fr, sf, null);
sz += sb.length();
maxWidth = Math.max(maxWidth, sz);
}
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- DBRefEntry[] dbrefs = ds.getDBRefs();
+ List<DBRefEntry> dbrefs = ds.getDBRefs();
if (dbrefs == null)
{
return 0;
}
// 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;
countForSource++;
if (countForSource == 1 || !summary)
{
- sb.append("<br>");
+ sb.append("<br/>");
}
if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
}
if (moreSources)
{
- sb.append("<br>").append(source)
- .append(COMMA).append(ELLIPSIS);
+ sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
}
if (ellipsis)
{
- sb.append("<br>(");
+ sb.append("<br/>(");
sb.append(MessageManager.getString("label.output_seq_details"));
sb.append(")");
}
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)
{