import javax.swing.*;
import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
import jalview.util.UrlLink;
/**
int lastid = -1;
boolean mouseDragging = false;
+ private final SequenceAnnotationReport seqAnnotReport;
/**
* Creates a new IdPanel object.
alignPanel = parent;
idCanvas = new IdCanvas(av);
linkImageURL = getClass().getResource("/images/link.gif").toString();
+ seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
addMouseListener(this);
addMouseWheelListener(this);
ToolTipManager.sharedInstance().registerComponent(this);
}
-
/**
* DOCUMENT ME!
*
{
SeqPanel sp = alignPanel.seqPanel;
int seq = Math.max(0, sp.findSeq(e));
- String tmp;
if (seq > -1 && seq < av.getAlignment().getHeight())
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
StringBuffer tip = new StringBuffer();
- tip.append("<i>");
-
- int maxWidth = 0;
- if (sequence.getDescription() != null)
- {
- tmp = sequence.getDescription();
- tip.append("<br>" + tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
-
- DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
- if (av.isShowDbRefs() && dbrefs != null)
- {
- for (int i = 0; i < dbrefs.length; i++)
- {
- tip.append("<br>");
- tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
- tip.append(tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
- }
-
- // ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = sequence.getDatasetSequence()
- .getSequenceFeatures();
- SequenceFeature[] tfeat = new SequenceFeature[1];
- if (av.isShowNpFeats() && features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].begin == 0 && features[i].end == 0)
- {
- int sz = -tip.length();
- tfeat[0] = features[i];
- sp.appendFeatures(tip, linkImageURL, 0, tfeat,
- sp.seqCanvas.fr.minmax);
- sz += tip.length();
- maxWidth = Math.max(maxWidth, sz);
- }
- }
- }
-
- if (maxWidth > 60)
- {
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
- }
-
- tip.append("</html>");
-
+ seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+ av.isShowDbRefs(), av.isShowNpFeats(),
+ sp.seqCanvas.fr.minmax);
setToolTipText("<html>" + sequence.getDisplayId(true) + " "
- + tip.toString());
+ + tip.toString()+"</html>");
}
}
import jalview.commands.*;
import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
import jalview.schemes.*;
import jalview.structure.*;
StringBuffer keyboardNo2;
java.net.URL linkImageURL;
-
+ private final SequenceAnnotationReport seqARep;
StringBuffer tooltipText = new StringBuffer("<html>");
String tmpString;
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
linkImageURL = getClass().getResource("/images/link.gif");
+ seqARep=new SequenceAnnotationReport(linkImageURL.toString());
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
SequenceFeature[] features = findFeaturesAtRes(
sequence.getDatasetSequence(),
rpos = sequence.findPosition(res));
- appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
+ seqARep.appendFeatures(tooltipText, rpos, features,
this.ap.seqPanel.seqCanvas.fr.minmax);
}
if (tooltipText.length() == 6) // <html></html>
return lastp = p;
}
- /**
- * appends the features at rpos to the given stringbuffer ready for display in
- * a tooltip
- *
- * @param tooltipText2
- * @param linkImageURL
- * @param rpos
- * @param features
- * TODO refactor to Jalview 'utilities' somehow.
- */
- public void appendFeatures(StringBuffer tooltipText2,
- String linkImageURL, int rpos, SequenceFeature[] features)
- {
- appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
- }
-
- public void appendFeatures(StringBuffer tooltipText2, String string,
- int rpos, SequenceFeature[] features, Hashtable minmax)
- {
- String tmpString;
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].getType().equals("disulfide bond"))
- {
- if (features[i].getBegin() == rpos
- || features[i].getEnd() == rpos)
- {
- if (tooltipText2.length() > 6)
- {
- tooltipText2.append("<br>");
- }
- tooltipText2.append("disulfide bond " + features[i].getBegin()
- + ":" + features[i].getEnd());
- if (features[i].links != null)
- {
- tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
- }
- }
- }
- else
- {
- if (tooltipText2.length() > 6)
- {
- tooltipText2.append("<br>");
- }
- // TODO: remove this hack to display link only features
- boolean linkOnly = features[i].getValue("linkonly") != null;
- if (!linkOnly)
- {
- tooltipText2.append(features[i].getType() + " ");
- if (rpos != 0)
- {
- // we are marking a positional feature
- tooltipText2.append(features[i].begin);
- }
- if (features[i].begin != features[i].end)
- {
- tooltipText2.append(" " + features[i].end);
- }
-
- if (features[i].getDescription() != null
- && !features[i].description.equals(features[i]
- .getType()))
- {
- tmpString = features[i].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)
- {
- tooltipText2.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(">", ">");
-
- tooltipText2.append("; ");
- tooltipText2.append(tmpString);
-
- }
- else
- {
- tooltipText2.append("; " + tmpString);
- }
- }
- }
- // check score should be shown
- if (features[i].getScore() != Float.NaN)
- {
- float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(features[i].getType()));
- if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
- {
- tooltipText2.append(" Score=" + features[i].getScore());
- }
- }
- if (features[i].getValue("status") != null)
- {
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText2.append("; (" + features[i].getValue("status")
- + ")");
- }
- }
- }
- if (features[i].links != null)
- {
- tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
- }
-
- }
- }
- }
- }
String lastTooltip;
--- /dev/null
+package jalview.io;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.UrlLink;
+
+/**
+ * generate HTML reports for a sequence
+ *
+ * @author jimp
+ */
+public class SequenceAnnotationReport
+{
+ final String linkImageURL;
+
+ public SequenceAnnotationReport(String linkImageURL)
+ {
+ this.linkImageURL = linkImageURL;
+ }
+
+ /**
+ * appends the features at rpos to the given stringbuffer ready for display in
+ * a tooltip
+ *
+ * @param tooltipText2
+ * @param linkImageURL
+ * @param rpos
+ * @param features
+ * TODO refactor to Jalview 'utilities' somehow.
+ */
+ public void appendFeatures(final StringBuffer tooltipText2, int rpos,
+ SequenceFeature[] features)
+ {
+ appendFeatures(tooltipText2, rpos, features, null);
+ }
+
+ public void appendFeatures(final StringBuffer tooltipText2, int rpos,
+ SequenceFeature[] features, Hashtable minmax)
+ {
+ String tmpString;
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (features[i].getType().equals("disulfide bond"))
+ {
+ if (features[i].getBegin() == rpos
+ || features[i].getEnd() == rpos)
+ {
+ if (tooltipText2.length() > 6)
+ {
+ tooltipText2.append("<br>");
+ }
+ tooltipText2.append("disulfide bond " + features[i].getBegin()
+ + ":" + features[i].getEnd());
+ }
+ }
+ else
+ {
+ if (tooltipText2.length() > 6)
+ {
+ tooltipText2.append("<br>");
+ }
+ // TODO: remove this hack to display link only features
+ boolean linkOnly = features[i].getValue("linkonly") != null;
+ if (!linkOnly)
+ {
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
+ {
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
+ }
+ if (features[i].begin != features[i].end)
+ {
+ tooltipText2.append(" " + features[i].end);
+ }
+
+ if (features[i].getDescription() != null
+ && !features[i].description.equals(features[i]
+ .getType()))
+ {
+ tmpString = features[i].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)
+ {
+ tooltipText2.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(">", ">");
+
+ tooltipText2.append("; ");
+ tooltipText2.append(tmpString);
+
+ }
+ else
+ {
+ tooltipText2.append("; " + tmpString);
+ }
+ }
+ }
+ // check score should be shown
+ if (features[i].getScore() != Float.NaN)
+ {
+ float[][] rng = (minmax == null) ? null : ((float[][]) minmax
+ .get(features[i].getType()));
+ if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
+ {
+ tooltipText2.append(" Score=" + features[i].getScore());
+ }
+ }
+ if (features[i].getValue("status") != null)
+ {
+ String status = features[i].getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText2.append("; (" + features[i].getValue("status")
+ + ")");
+ }
+ }
+ }
+ }
+ if (features[i].links != null)
+ {
+ if (linkImageURL != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+ }
+ else
+ {
+ for (String urlstring : (Vector<String>) features[i].links)
+ {
+ try
+ {
+ for (String[] urllink : createLinksFrom(null, urlstring))
+ {
+ tooltipText2.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();
+ }
+ }
+ }
+
+ }
+ }
+ }
+ }
+
+ /**
+ *
+ * @param seq
+ * @param link
+ * @return String[][] { String[] { link target, link label, dynamic component
+ * inserted (if any), url }}
+ */
+ public String[][] createLinksFrom(SequenceI seq, String link)
+ {
+ ArrayList<String[]> urlSets = new ArrayList<String[]>();
+ ArrayList<String> uniques=new ArrayList<String>();
+ 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())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
+ 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 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);
+ }
+ }
+ }
+ }
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this RUL
+ 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))
+ {
+ urlSets.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))
+ {
+ urlSets.add(new String[]
+ { target, label, urls[u], urls[u + 1] });
+ uniques.add(unq);
+ }
+ }
+ }
+ }
+
+ } else {
+ String unq=label + "|" + urlLink.getUrl_prefix();
+ if (!uniques.contains(unq)){
+ uniques.add(unq);
+ // Add a non-dynamic link
+ urlSets.add(new String[] {target, label, null, urlLink.getUrl_prefix()});
+ }
+ }
+
+ return urlSets.toArray(new String[][]
+ {});
+ }
+
+
+ public void createSequenceAnnotationReport(final StringBuffer tip,
+ SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
+ Hashtable minmax)
+ {
+ createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats, true, minmax);
+ }
+
+ public void createSequenceAnnotationReport(final StringBuffer tip,
+ SequenceI sequence, boolean showDbRefs, boolean showNpFeats, boolean tableWrap,
+ Hashtable minmax)
+ {
+ String tmp;
+ tip.append("<i>");
+
+ int maxWidth = 0;
+ if (sequence.getDescription() != null)
+ {
+ tmp = sequence.getDescription();
+ tip.append("<br>" + tmp);
+ maxWidth = Math.max(maxWidth, tmp.length());
+ }
+
+ DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
+ if (showDbRefs && dbrefs != null)
+ {
+ for (int i = 0; i < dbrefs.length; i++)
+ {
+ tip.append("<br>");
+ tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
+ tip.append(tmp);
+ maxWidth = Math.max(maxWidth, tmp.length());
+ }
+ }
+
+ // ADD NON POSITIONAL SEQUENCE INFO
+ SequenceFeature[] features = sequence.getDatasetSequence()
+ .getSequenceFeatures();
+ SequenceFeature[] tfeat = new SequenceFeature[1];
+ if (showNpFeats && features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (features[i].begin == 0 && features[i].end == 0)
+ {
+ int sz = -tip.length();
+ tfeat[0] = features[i];
+ appendFeatures(tip, 0, tfeat, minmax);
+ sz += tip.length();
+ maxWidth = Math.max(maxWidth, sz);
+ }
+ }
+ }
+
+ if (tableWrap && maxWidth > 60)
+ {
+ tip.insert(0, "<table width=350 border=0><tr><td><i>");
+ tip.append("</i></td></tr></table>");
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / commitdiff