*/
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.util.UrlLink;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
/**
* 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, and 'chromosome' first of all
*/
- private static Comparator<DBRefEntry> comparator = new Comparator<>()
+ private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
{
@Override
}
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 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 linkURL)
}
/**
- * Append text for the list of features to the tooltip
+ * 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 void appendFeatures(final StringBuilder sb, int residuePos,
- List<SequenceFeature> features, FeatureRendererModel fr)
+ public int appendFeaturesLengthLimit(final StringBuilder sb,
+ int residuePos, List<SequenceFeature> features,
+ FeatureRendererModel fr, int maxlength)
{
- for (SequenceFeature feature : features)
+ for (int i = 0; i < features.size(); i++)
{
- appendFeature(sb, residuePos, fr, feature, null);
+ SequenceFeature feature = features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
+ {
+ return features.size() - i;
+ }
}
+ return 0;
+ }
+
+ public void appendFeatures(final StringBuilder sb, int residuePos,
+ List<SequenceFeature> features, FeatureRendererModel fr)
+ {
+ appendFeaturesLengthLimit(sb, residuePos, features, fr, 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(StringBuilder sb, int residuePos,
- MappedFeatures mf, FeatureRendererModel fr)
+ public int appendFeaturesLengthLimit(StringBuilder sb, int residuePos,
+ MappedFeatures mf, FeatureRendererModel fr, int maxlength)
{
- for (SequenceFeature feature : mf.features)
+ for (int i = 0; i < mf.features.size(); i++)
{
- appendFeature(sb, residuePos, fr, feature, mf);
+ SequenceFeature feature = mf.features.get(i);
+ if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
+ {
+ 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,
+ boolean appendFeature(final StringBuilder sb0, int rpos,
FeatureRendererModel fr, SequenceFeature feature,
- MappedFeatures mf)
+ 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;
+ return appendTextMaxLengthReached(sb0, sb, maxlength);
}
- if (sb.length() > 6)
+ if (sb0.length() > 6)
{
- sb.append("<br>");
+ sb.append("<br/>");
}
// TODO: remove this hack to display link only features
boolean linkOnly = feature.getValue("linkonly") != null;
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)
+ {
+ description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+ + ELLIPSIS;
+ }
+
sb.append("; ").append(description);
}
}
}
}
+ 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;
}
/**
+ (urllink.get(0).toLowerCase()
.equals(urllink.get(1).toLowerCase()) ? urllink
.get(0) : (urllink.get(0) + ":" + urllink
- .get(1))) + "</a></br>");
+ .get(1)))
+ + "</a><br/>");
}
} catch (Exception x)
{
if (sequence.getDescription() != null)
{
tmp = sequence.getDescription();
- sb.append("<br>").append(tmp);
+ sb.append(tmp);
maxWidth = Math.max(maxWidth, tmp.length());
}
SequenceI ds = sequence;
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(")");
}
git://source.jalview.org / jalview.git / blobdiff