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;
+ /*
+ * Comparator to order DBRefEntry by Source + accession id (case-insensitive)
+ */
+ 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)
+ {
+ String a1 = ref1.getAccessionId();
+ String a2 = ref2.getAccessionId();
+ comp = a1 == null ? -1 : (a2 == null ? 1 : a1
+ .compareToIgnoreCase(a2));
+ }
+ 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)
{
this.linkImageURL = 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 tooltipText2
++ * @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 StringBuffer tooltipText2, int rpos,
++ 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(tooltipText2, rpos, minmax, feature);
++ appendFeature(sb, rpos, minmax, feature);
+ }
+ }
+ }
+
+ /**
- * Appends text for one sequence feature to the string buffer
++ * Appends the feature at rpos to the given buffer
+ *
+ * @param sb
+ * @param rpos
+ * @param minmax
- * {{min, max}, {min, max}} positional and non-positional feature
- * scores for this type
+ * @param feature
+ */
- void appendFeature(final StringBuffer sb, int rpos,
++ void appendFeature(final StringBuilder sb, int rpos,
+ Map<String, float[][]> minmax, SequenceFeature feature)
+ {
- if ("disulfide bond".equals(feature.getType()))
++ 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(" " + feature.end);
++ sb.append(" ").append(feature.end);
+ }
+
+ if (feature.getDescription() != null
+ && !feature.description.equals(feature.getType()))
+ {
- String tmpString = feature.getDescription();
++ tmpString = feature.getDescription();
+ String tmp2up = tmpString.toUpperCase();
- final int startTag = tmp2up.indexOf("<HTML>");
++ 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)
- // TODO strips off </body> but not <body> - is that intended?
+ 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(">", ">");
- sb.append("; ").append(tmpString);
+
- 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)
-
- /*
- * score should be shown if there is one, and min != max
- * for this feature type (e.g. not all 0)
- */
++ // check score should be shown
+ if (!Float.isNaN(feature.getScore()))
{
- if (linkImageURL != null)
- float[][] rng = (minmax == null) ? null : minmax.get(feature
- .getType());
++ 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=").append(String.valueOf(feature.getScore()));
++ 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);
+ }
+ }
+ }
- appendLinks(sb, feature);
+ }
+
+ /**
+ * 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();
}
-
}
}
+
}
}
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.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 target = urlLink.getTarget();
- String label = urlLink.getLabel();
+ 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)
}
}
}
-
}
- 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 StringBuffer 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,
- true, minmax);
++ minmax, false);
}
- public void createSequenceAnnotationReport(final StringBuffer tip,
+ /**
- * 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)
- boolean tableWrap, Map<String, float[][]> minmax)
++ Map<String, float[][]> minmax, boolean summary)
{
String tmp;
- tip.append("<i>");
+ sb.append("<i>");
int maxWidth = 0;
if (sequence.getDescription() != null)
ds = ds.getDatasetSequence();
}
DBRefEntry[] dbrefs = ds.getDBRefs();
- Arrays.sort(dbrefs, comparator);
if (showDbRefs && dbrefs != null)
{
- for (int i = 0; i < dbrefs.length; i++)
++ // 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
+ continue;
+ }
+ 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++;
+ if (countForSource == 1 || !summary)
+ {
+ 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)
+ {
- tip.append("<br>");
- tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
- tip.append(tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
++ 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 = -tip.length();
- List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
- tfeat.add(features[i]);
- appendFeatures(tip, 0, tfeat, minmax);
- sz += tip.length();
+ 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 (tableWrap && maxWidth > 60)
++ if (maxWidth > 60)
+ {
- tip.insert(0, "<table width=350 border=0><tr><td><i>");
- tip.append("</i></td></tr></table>");
++ // ? not sure this serves any useful purpose
++ // tip.insert(0, "<table width=350 border=0><tr><td>");
++ // tip.append("</td></tr></table>");
+ }
-
+ }
}
--- /dev/null
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+ package jalview.io;
+
+ import static org.testng.AssertJUnit.assertEquals;
+
+ import jalview.datamodel.SequenceFeature;
+
+ import java.util.Hashtable;
+ import java.util.Map;
+
+ import org.testng.annotations.Test;
+
+ public class SequenceAnnotationReportTest
+ {
+ @Test(groups = "Functional")
+ public void testAppendFeature_disulfideBond()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ sb.append("123456");
+ SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
+ 3, 1.2f, "group");
+
+ // residuePos == 2 does not match start or end of feature, nothing done:
+ sar.appendFeature(sb, 2, null, sf);
+ assertEquals("123456", sb.toString());
+
+ // residuePos == 1 matches start of feature, text appended (but no <br>)
+ // feature score is not included
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("123456disulfide bond 1:3", sb.toString());
+
+ // residuePos == 3 matches end of feature, text appended
+ // <br> is prefixed once sb.length() > 6
+ sar.appendFeature(sb, 3, null, sf);
+ assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
+ sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_status()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
+ Float.NaN, "group");
+ sf.setStatus("Confirmed");
+
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_withScore()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
+ "group");
+
+ Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+ sar.appendFeature(sb, 1, minmax, sf);
+ /*
+ * map has no entry for this feature type - score is not shown:
+ */
+ assertEquals("METAL 1 3; Fe2-S", sb.toString());
+
+ /*
+ * map has entry for this feature type - score is shown:
+ */
+ minmax.put("METAL", new float[][] { { 0f, 1f }, null });
+ sar.appendFeature(sb, 1, minmax, sf);
+ // <br> is appended to a buffer > 6 in length
+ assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
+ sb.toString());
+
+ /*
+ * map has min == max for this feature type - score is not shown:
+ */
+ minmax.put("METAL", new float[][] { { 2f, 2f }, null });
+ sb.setLength(0);
+ sar.appendFeature(sb, 1, minmax, sf);
+ assertEquals("METAL 1 3; Fe2-S", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_noScore()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
+ Float.NaN, "group");
+
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3; Fe2-S", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_clinicalSignificance()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
+ Float.NaN, "group");
+ sf.setValue("clinical_significance", "Benign");
+
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_withScoreStatusClinicalSignificance()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
+ "group");
+ sf.setStatus("Confirmed");
+ sf.setValue("clinical_significance", "Benign");
+ Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+ minmax.put("METAL", new float[][] { { 0f, 1f }, null });
+ sar.appendFeature(sb, 1, minmax, sf);
+
+ assertEquals("METAL 1 3; Fe2-S Score=1.3; (Confirmed); Benign",
+ sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_DescEqualsType()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
+ Float.NaN, "group");
+
+ // description is not included if it duplicates type:
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3", sb.toString());
+
+ sb.setLength(0);
+ sf.setDescription("Metal");
+ // test is case-sensitive:
+ sar.appendFeature(sb, 1, null, sf);
+ assertEquals("METAL 1 3; Metal", sb.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testAppendFeature_stripHtml()
+ {
+ SequenceAnnotationReport sar = new SequenceAnnotationReport(null);
- StringBuffer sb = new StringBuffer();
++ StringBuilder sb = new StringBuilder();
+ SequenceFeature sf = new SequenceFeature("METAL",
+ "<html><body>hello<em>world</em></body></html>", 1, 3,
+ Float.NaN, "group");
+
+ sar.appendFeature(sb, 1, null, sf);
+ // !! strips off </body> but not <body> ??
+ assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
+
+ sb.setLength(0);
+ sf.setDescription("<br>&kHD>6");
+ sar.appendFeature(sb, 1, null, sf);
+ // if no <html> tag, html-encodes > and < (only):
+ assertEquals("METAL 1 3; <br>&kHD>6", sb.toString());
+ }
+ }
git://source.jalview.org / jalview.git / commitdiff