package jalview.io;
import jalview.datamodel.DBRefEntry;
+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.Collections;
import java.util.Comparator;
-import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
/**
* generate HTML reports for a sequence
*/
public class SequenceAnnotationReport
{
+ private static final String COMMA = ",";
+
+ private static final String ELLIPSIS = "...";
+
+ private static final int MAX_REFS_PER_SOURCE = 4;
+
+ private static final int MAX_SOURCES = 40;
+
+ private static final String[][] PRIMARY_SOURCES = new String[][] {
+ DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
+ DBRefSource.PROTEINDBS };
+
final String linkImageURL;
/*
*/
private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
{
+
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
String s1 = ref1.getSource();
String s2 = ref2.getSource();
+ boolean s1Primary = isPrimarySource(s1);
+ boolean s2Primary = isPrimarySource(s2);
+ if (s1Primary && !s2Primary)
+ {
+ return -1;
+ }
+ if (!s1Primary && s2Primary)
+ {
+ return 1;
+ }
int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
.compareToIgnoreCase(s2));
if (comp == 0)
}
return comp;
}
+
+ private boolean isPrimarySource(String source)
+ {
+ for (String[] primary : PRIMARY_SOURCES)
+ {
+ for (String s : primary)
+ {
+ if (source.equals(s))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
};
public SequenceAnnotationReport(String linkImageURL)
}
/**
- * appends the features at rpos to the given stringbuffer ready for display in
- * a tooltip
+ * Append text for the list of features to the tooltip
*
- * @param tooltipText
- * @param linkImageURL
+ * @param sb
* @param rpos
* @param features
* @param minmax
- * TODO refactor to Jalview 'utilities' somehow.
*/
- public void appendFeatures(final StringBuilder tooltipText, int rpos,
- List<SequenceFeature> features, Hashtable minmax)
+ public void appendFeatures(final StringBuilder sb, int rpos,
+ List<SequenceFeature> features, Map<String, float[][]> minmax)
{
- String tmpString;
if (features != null)
{
for (SequenceFeature feature : features)
{
- if (feature.getType().equals("disulfide bond"))
+ appendFeature(sb, rpos, minmax, feature);
+ }
+ }
+ }
+
+ /**
+ * Appends the feature at rpos to the given buffer
+ *
+ * @param sb
+ * @param rpos
+ * @param minmax
+ * @param feature
+ */
+ void appendFeature(final StringBuilder sb, int rpos,
+ Map<String, float[][]> minmax, SequenceFeature feature)
+ {
+ String tmpString;
+ if (feature.getType().equals("disulfide bond"))
+ {
+ if (feature.getBegin() == rpos || feature.getEnd() == rpos)
+ {
+ if (sb.length() > 6)
{
- if (feature.getBegin() == rpos || feature.getEnd() == rpos)
- {
- if (tooltipText.length() > 6)
- {
- tooltipText.append("<br>");
- }
- tooltipText.append("disulfide bond " + feature.getBegin()
- + ":" + feature.getEnd());
- }
+ sb.append("<br>");
}
- else
+ sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+ .append(feature.getEnd());
+ }
+ }
+ else
+ {
+ 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)
{
- if (tooltipText.length() > 6)
+ // we are marking a positional feature
+ sb.append(feature.begin);
+ }
+ if (feature.begin != feature.end)
+ {
+ sb.append(" ").append(feature.end);
+ }
+
+ if (feature.getDescription() != null
+ && !feature.description.equals(feature.getType()))
+ {
+ tmpString = feature.getDescription();
+ String tmp2up = tmpString.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -1)
{
- tooltipText.append("<br>");
+ tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag + 6);
}
- // TODO: remove this hack to display link only features
- boolean linkOnly = feature.getValue("linkonly") != null;
- if (!linkOnly)
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
{
- tooltipText.append(feature.getType() + " ");
- if (rpos != 0)
- {
- // we are marking a positional feature
- tooltipText.append(feature.begin);
- }
- if (feature.begin != feature.end)
- {
- tooltipText.append(" " + feature.end);
- }
+ tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
- if (feature.getDescription() != null
- && !feature.description.equals(feature.getType()))
+ if (startTag > -1)
+ {
+ sb.append("; ").append(tmpString);
+ }
+ else
+ {
+ if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
{
- 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);
- }
-
- if (startTag > -1)
- {
- tooltipText.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(">", ">");
+ // The description does not specify html is to
+ // be used, so we must remove < > symbols
+ tmpString = tmpString.replaceAll("<", "<");
+ tmpString = tmpString.replaceAll(">", ">");
- tooltipText.append("; ");
- tooltipText.append(tmpString);
-
- }
- else
- {
- tooltipText.append("; " + tmpString);
- }
- }
+ sb.append("; ");
+ sb.append(tmpString);
}
- // check score should be shown
- if (!Float.isNaN(feature.getScore()))
+ else
{
- float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(feature.getType()));
- if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
- {
- tooltipText.append(" Score=" + feature.getScore());
- }
- }
- if (feature.getValue("status") != null)
- {
- String status = feature.getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText.append("; (" + feature.getValue("status")
- + ")");
- }
+ sb.append("; ").append(tmpString);
}
}
}
- if (feature.links != null)
+ // check score should be shown
+ if (!Float.isNaN(feature.getScore()))
{
- if (linkImageURL != null)
+ float[][] rng = (minmax == null) ? null : ((float[][]) minmax
+ .get(feature.getType()));
+ if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- tooltipText.append(" <img src=\"" + linkImageURL + "\">");
+ sb.append(" Score=" + feature.getScore());
}
- else
+ }
+ 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)
+ {
+ sb.append("; ").append(clinSig);
+ }
+ }
+ }
+ }
+
+ /**
+ * Format and appends any hyperlinks for the sequence feature to the string
+ * buffer
+ *
+ * @param sb
+ * @param feature
+ */
+ void appendLinks(final StringBuffer sb, SequenceFeature feature)
+ {
+ if (feature.links != null)
+ {
+ if (linkImageURL != null)
+ {
+ sb.append(" <img src=\"" + linkImageURL + "\">");
+ }
+ else
+ {
+ for (String urlstring : feature.links)
+ {
+ try
{
- for (String urlstring : feature.links)
+ for (String[] urllink : createLinksFrom(null, urlstring))
{
- try
- {
- for (String[] urllink : createLinksFrom(null, urlstring))
- {
- tooltipText.append("<br/> <a href=\""
- + urllink[3]
- + "\" target=\""
- + urllink[0]
- + "\">"
- + (urllink[0].toLowerCase().equals(
- urllink[1].toLowerCase()) ? urllink[0]
- : (urllink[0] + ":" + urllink[1]))
- + "</a></br>");
- }
- } catch (Exception x)
- {
- System.err.println("problem when creating links from "
- + urlstring);
- x.printStackTrace();
- }
+ 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>");
}
+ } catch (Exception x)
+ {
+ System.err.println("problem when creating links from "
+ + urlstring);
+ x.printStackTrace();
}
-
}
}
+
}
}
* @return String[][] { String[] { link target, link label, dynamic component
* inserted (if any), url }}
*/
- public String[][] createLinksFrom(SequenceI seq, String link)
+ String[][] createLinksFrom(SequenceI seq, String link)
{
- ArrayList<String[]> urlSets = new ArrayList<String[]>();
- ArrayList<String> uniques = new ArrayList<String>();
+ List<String[]> urlSets = new ArrayList<String[]>();
+ List<String> uniques = new ArrayList<String>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
final String label = urlLink.getLabel();
if (seq != null && urlLink.isDynamic())
{
-
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.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)
+ urlSets.addAll(createDynamicLinks(seq, urlLink, uniques));
+ }
+ else
+ {
+ String unq = label + "|" + urlLink.getUrl_prefix();
+ if (!uniques.contains(unq))
{
- descr = null;
+ uniques.add(unq);
+ urlSets.add(new String[] { target, label, null,
+ urlLink.getUrl_prefix() });
}
- if (dbr != null)
+ }
+
+ return urlSets.toArray(new String[][] {});
+ }
+
+ /**
+ * 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++)
{
- for (int r = 0; r < dbr.length; r++)
+ if (id != null && dbr[r].getAccessionId().equals(id))
{
- 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 RUL
- 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))
- {
- urlSets.add(new String[] { target, label, urls[u],
- urls[u + 1] });
- uniques.add(unq);
- }
- }
- }
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
+ id = null;
}
- }
- if (id != null)
- {
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(id, true);
+ // 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))
{
- urlSets.add(new String[] { target, label, urls[u],
- urls[u + 1] });
+ result.add(new String[] { target, label, urls[u], urls[u + 1] });
uniques.add(unq);
}
}
}
}
- if (descr != null && urlLink.getRegexReplace() != null)
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this URL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls != 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)
{
- for (int u = 0; u < urls.length; u += 2)
+ String unq = urls[u] + "|" + urls[u + 1];
+ if (!uniques.contains(unq))
{
- String unq = urls[u] + "|" + urls[u + 1];
- if (!uniques.contains(unq))
- {
- urlSets.add(new String[] { target, label, urls[u],
- urls[u + 1] });
- uniques.add(unq);
- }
+ result.add(new String[] { target, label, urls[u], urls[u + 1] });
+ uniques.add(unq);
}
}
}
-
}
- else
+ if (descr != null && urlLink.getRegexReplace() != null)
{
- String unq = label + "|" + urlLink.getUrl_prefix();
- if (!uniques.contains(unq))
+ // create link for this URL from description only if regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
{
- uniques.add(unq);
- // Add a non-dynamic link
- urlSets.add(new String[] { target, label, null,
- urlLink.getUrl_prefix() });
+ 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 urlSets.toArray(new String[][] {});
+ return result;
}
- public void createTooltipAnnotationReport(final StringBuilder tip,
+ public void createSequenceAnnotationReport(final StringBuilder tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
- Hashtable minmax)
+ Map<String, float[][]> minmax)
{
- int maxWidth = createSequenceAnnotationReport(tip, sequence,
- showDbRefs, showNpFeats, minmax, true);
-
- if (maxWidth > 60)
- {
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
- }
- }
-
- public int createSequenceAnnotationReport(final StringBuilder tip,
- SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
- Hashtable minmax)
- {
- return createSequenceAnnotationReport(tip, sequence, showDbRefs,
- showNpFeats, minmax, false);
+ createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
+ minmax, false);
}
/**
- * Adds an html-formatted sequence annotation report to the provided string
- * buffer, and returns the longest line length added
+ * Builds an html formatted report of sequence details and appends it to the
+ * provided buffer.
*
* @param sb
+ * buffer to append report to
* @param sequence
+ * the sequence the report is for
* @param showDbRefs
- * if true, include database references
+ * whether to include database references for the sequence
* @param showNpFeats
- * if true, include non-positional sequence features
+ * whether to include non-positional sequence features
* @param minmax
* @param summary
- * if true, build a shortened summary report (for tooltip)
* @return
*/
int createSequenceAnnotationReport(final StringBuilder sb,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
- Hashtable minmax, boolean summary)
+ Map<String, float[][]> minmax, boolean summary)
{
String tmp;
sb.append("<i>");
ds = ds.getDatasetSequence();
}
DBRefEntry[] dbrefs = ds.getDBRefs();
- Arrays.sort(dbrefs, comparator);
if (showDbRefs && 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)
{
- String source = ref.getSource();
+ source = ref.getSource();
if (source == null)
{
// shouldn't happen
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++;
{
sb.append("<br>");
}
- if (countForSource < 3 || !summary)
+ if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
{
String accessionId = ref.getAccessionId();
- int len = accessionId.length() + 1;
+ lineLength += accessionId.length() + 1;
if (countForSource > 1 && summary)
{
sb.append(", ").append(accessionId);
- len++;
+ lineLength++;
}
else
{
sb.append(source).append(" ").append(accessionId);
- len += source.length();
+ lineLength += source.length();
}
- maxWidth = Math.max(maxWidth, len);
+ maxWidth = Math.max(maxWidth, lineLength);
}
- if (countForSource == 3 && summary)
+ if (countForSource == MAX_REFS_PER_SOURCE && summary)
{
- sb.append(", ...");
+ sb.append(COMMA).append(ELLIPSIS);
ellipsis = true;
}
}
- if (ellipsis) {
- sb.append("<br>(Output Sequence Details to list all database references)");
+ 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(")");
}
}
- // ADD NON POSITIONAL SEQUENCE INFO
+ /*
+ * add non-positional features if wanted
+ */
SequenceFeature[] features = sequence.getSequenceFeatures();
if (showNpFeats && features != null)
{
if (features[i].begin == 0 && features[i].end == 0)
{
int sz = -sb.length();
- List<SequenceFeature> tfeat = Collections
- .singletonList(features[i]);
- appendFeatures(sb, 0, tfeat, minmax);
+ appendFeature(sb, 0, minmax, features[i]);
sz += sb.length();
maxWidth = Math.max(maxWidth, sz);
}
}
}
+ sb.append("</i>");
return maxWidth;
}
+
+ public void createTooltipAnnotationReport(final StringBuilder tip,
+ SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
+ Map<String, float[][]> minmax)
+ {
+ int maxWidth = createSequenceAnnotationReport(tip, sequence,
+ showDbRefs, showNpFeats, minmax, true);
+
+ if (maxWidth > 60)
+ {
+ // ? not sure this serves any useful purpose
+ // tip.insert(0, "<table width=350 border=0><tr><td>");
+ // tip.append("</td></tr></table>");
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff