package jalview.datamodel;
import jalview.datamodel.features.FeatureLocationI;
+import jalview.util.StringUtils;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * A class that models a single contiguous feature on a sequence. If flag
+ * 'contactFeature' is true, the start and end positions are interpreted instead
+ * as two contact points.
*/
public class SequenceFeature implements FeatureLocationI
{
// private key for ENA location designed not to conflict with real GFF data
private static final String LOCATION = "!Location";
+ private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td></tr>";
+
/*
* map of otherDetails special keys, and their value fields' delimiter
*/
}
/**
- * Answers a formatted text report of feature details
+ * Answers an html-formatted report of feature details
*
* @return
*/
public String getDetailsReport()
{
StringBuilder sb = new StringBuilder(128);
- if (begin == end)
- {
- sb.append(String.format("%s %d %s", type, begin, description));
- }
- else
- {
- sb.append(String.format("%s %d-%d %s", type, begin, end, description));
- }
+ sb.append("<br>");
+ sb.append("<table>");
+ sb.append(String.format(ROW_DATA, "Type", type));
+ sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
+ String desc = StringUtils.stripHtmlTags(description);
+ sb.append(String.format(ROW_DATA, "Description", desc));
if (!Float.isNaN(score) && score != 0f)
{
- sb.append(" score=").append(score);
+ sb.append(String.format(ROW_DATA, "Score", score));
}
if (featureGroup != null)
{
- sb.append(" (").append(featureGroup).append(")");
+ sb.append(String.format(ROW_DATA, "Group", featureGroup));
}
- sb.append("\n\n");
if (otherDetails != null)
{
{
continue; // to avoid double reporting
}
+ sb.append("<tr><td>").append(key).append("</td><td>");
if (INFO_KEYS.containsKey(key))
{
/*
* split selected INFO data by delimiter over multiple lines
*/
- sb.append(key).append("=\n ");
+ sb.append("</td></tr>");
String delimiter = INFO_KEYS.get(key);
- String value = entry.getValue().toString();
- sb.append(value.replace(delimiter, "\n "));
+ String[] values = entry.getValue().toString().split(delimiter);
+ for (String value : values)
+ {
+ sb.append("<tr><td> </td><td>").append(value)
+ .append("</td></tr>");
+ }
}
else
{
- sb.append(key + "=" + entry.getValue().toString() + "\n");
+ sb.append(entry.getValue().toString()).append("</td></tr>");
}
}
}
+ sb.append("</table>");
+
String text = sb.toString();
return text;
}
*/
public void setText(String text)
{
+ textarea.setDocument(textarea.getEditorKit().createDefaultDocument());
textarea.setText(text);
}
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.util.UrlLink;
import java.awt.Color;
String description = sf.getDescription();
if (description != null)
{
+ description = StringUtils.stripHtmlTags(description);
if (description.length() <= 6)
{
desc = desc + " " + description;
*/
protected void showFeatureDetails(SequenceFeature sf)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ // it appears Java's CSS does not support border-collaps :-(
+ cap.addStylesheetRule("table { border-collapse: collapse;}");
+ cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
cap.setText(sf.getDetailsReport());
+
Desktop.addInternalFrame(cap,
MessageManager.getString("label.feature_details"), 500, 500);
}
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;
sb.append(" ").append(feature.end);
}
- if (feature.getDescription() != null
- && !feature.description.equals(feature.getType()))
+ String description = feature.getDescription();
+ if (description != null && !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);
- }
-
- 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(">", ">");
-
- sb.append("; ");
- sb.append(tmpString);
- }
- else
- {
- sb.append("; ").append(tmpString);
- }
- }
+ description = StringUtils.stripHtmlTags(description);
+ sb.append("; ").append(description);
}
// check score should be shown
if (!Float.isNaN(feature.getScore()))
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.text.EditorKit;
+import javax.swing.text.html.HTMLEditorKit;
/**
* DOCUMENT ME!
{
try
{
+ textarea.setEditorKit(new HTMLEditorKit());
setJMenuBar(editMenubar);
jbInit();
} catch (Exception e)
{
}
+
+ /**
+ * Adds the given stylesheet rule to the Html editor. However note that CSS
+ * support is limited.
+ *
+ * @param rule
+ * @see javax.swing.text.html.CSS
+ */
+ public void addStylesheetRule(String rule)
+ {
+ EditorKit editorKit = textarea.getEditorKit();
+ if (editorKit != null)
+ {
+ ((HTMLEditorKit) editorKit).getStyleSheet().addRule(rule);
+ }
+ }
}
}
return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
}
+
+ /**
+ * A helper method that strips off any leading or trailing html and body tags.
+ * If no html tag is found, then also html-encodes angle bracket characters.
+ *
+ * @param text
+ * @return
+ */
+ public static String stripHtmlTags(String text)
+ {
+ if (text == null)
+ {
+ return null;
+ }
+ String tmp2up = text.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -1)
+ {
+ text = text.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag + 6);
+ }
+ // is omission of "<BODY>" intentional here??
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
+ {
+ text = text.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ text = text.substring(0, endTag);
+ }
+
+ if (startTag == -1 && (text.contains("<") || text.contains(">")))
+ {
+ text = text.replaceAll("<", "<");
+ text = text.replaceAll(">", ">");
+ }
+ return text;
+ }
}
"group");
assertTrue(sf.isContactFeature());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport()
+ {
+ // single locus, no group, no score
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
+ String expected = "<br><table><tr><td>Type</td><td>variant</td></tr>"
+ + "<tr><td>Start/end</td><td>22</td></tr>"
+ + "<tr><td>Description</td><td>G,C</td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport());
+
+ // contact feature
+ sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+ null);
+ expected = "<br><table><tr><td>Type</td><td>Disulphide Bond</td></tr>"
+ + "<tr><td>Start/end</td><td>28:31</td></tr>"
+ + "<tr><td>Description</td><td>a description</td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport());
+
+ sf = new SequenceFeature("variant", "G,C", 22, 33,
+ 12.5f, "group");
+ sf.setValue("Parent", "ENSG001");
+ sf.setValue("Child", "ENSP002");
+ expected = "<br><table><tr><td>Type</td><td>variant</td></tr>"
+ + "<tr><td>Start/end</td><td>22-33</td></tr>"
+ + "<tr><td>Description</td><td>G,C</td></tr>"
+ + "<tr><td>Score</td><td>12.5</td></tr>"
+ + "<tr><td>Group</td><td>group</td></tr>"
+ + "<tr><td>Child</td><td>ENSP002</td></tr>"
+ + "<tr><td>Parent</td><td>ENSG001</td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport());
+
+ /*
+ * feature with embedded html link in description
+ */
+ String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>";
+ sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot");
+ expected = "<br><table><tr><td>Type</td><td>Pfam</td></tr>"
+ + "<tr><td>Start/end</td><td>8-83</td></tr>"
+ + "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td></tr>"
+ + "<tr><td>Group</td><td>Uniprot</td></tr></table>";
+ assertEquals(expected, sf.getDetailsReport());
+ }
}
assertEquals("", StringUtils.toSentenceCase(""));
assertNull(StringUtils.toSentenceCase(null));
}
+
+ @Test(groups = { "Functional" })
+ public void testStripHtmlTags()
+ {
+ assertNull(StringUtils.stripHtmlTags(null));
+ assertEquals("", StringUtils.stripHtmlTags(""));
+ assertEquals(
+ "<a href=\"something\">label</href>",
+ StringUtils
+ .stripHtmlTags("<html><a href=\"something\">label</href></html>"));
+
+ // if no "<html>" tag, < and > get html-encoded (not sure why)
+ assertEquals("<a href=\"something\">label</href>",
+ StringUtils.stripHtmlTags("<a href=\"something\">label</href>"));
+
+ // </body> gets removed but not <body> (is this intentional?)
+ assertEquals("<body><p>hello",
+ StringUtils.stripHtmlTags("<html><body><p>hello</body></html>"));
+
+ assertEquals("kdHydro < 12.53",
+ StringUtils.stripHtmlTags("kdHydro < 12.53"));
+ }
}
git://source.jalview.org / jalview.git / commitdiff