/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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 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.io.gff.GffConstants;
+import jalview.util.DBRefUtils;
import jalview.util.UrlLink;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
/**
* generate HTML reports for a sequence
*
}
/**
- * 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 tooltipText2
- * @param linkImageURL
* @param rpos
* @param features
- * TODO refactor to Jalview 'utilities' somehow.
+ * @param minmax
*/
public void appendFeatures(final StringBuffer tooltipText2, int rpos,
- SequenceFeature[] features)
+ List<SequenceFeature> features, Map<String, float[][]> minmax)
{
- appendFeatures(tooltipText2, rpos, features, null);
+ if (features != null)
+ {
+ for (SequenceFeature feature : features)
+ {
+ appendFeature(tooltipText2, rpos, minmax, feature);
+ }
+ }
}
- public void appendFeatures(final StringBuffer tooltipText2, int rpos,
- SequenceFeature[] features, Hashtable minmax)
+ /**
+ * Appends text for one sequence feature to the string 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,
+ Map<String, float[][]> minmax, SequenceFeature feature)
{
- String tmpString;
- if (features != null)
+ if ("disulfide bond".equals(feature.getType()))
{
- for (int i = 0; i < features.length; i++)
+ if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
- if (features[i].getType().equals("disulfide bond"))
+ if (sb.length() > 6)
{
- 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());
- }
+ sb.append("<br>");
+ }
+ 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)
+ {
+ // we are marking a positional feature
+ sb.append(feature.begin);
+ }
+ if (feature.begin != feature.end)
+ {
+ sb.append(" " + feature.end);
}
- else
+
+ if (feature.getDescription() != null
+ && !feature.description.equals(feature.getType()))
{
- if (tooltipText2.length() > 6)
+ String tmpString = feature.getDescription();
+ String tmp2up = tmpString.toUpperCase();
+ final int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -1)
{
- tooltipText2.append("<br>");
+ tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag + 6);
}
- // TODO: remove this hack to display link only features
- boolean linkOnly = features[i].getValue("linkonly") != null;
- if (!linkOnly)
+ // TODO strips off </body> but not <body> - is that intended?
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
{
- 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);
+ tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
- }
- else
- {
- tooltipText2.append("; " + tmpString);
- }
- }
- }
- // check score should be shown
- if (features[i].getScore() != Float.NaN)
+ if (startTag > -1)
+ {
+ sb.append("; ").append(tmpString);
+ }
+ else
+ {
+ if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
{
- 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());
- }
+ // 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);
}
- if (features[i].getValue("status") != null)
+ else
{
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText2.append("; (" + features[i].getValue("status")
- + ")");
- }
+ sb.append("; ").append(tmpString);
}
}
}
- if (features[i].links != null)
+
+ /*
+ * score should be shown if there is one, and min != max
+ * for this feature type (e.g. not all 0)
+ */
+ if (!Float.isNaN(feature.getScore()))
{
- if (linkImageURL != null)
+ float[][] rng = (minmax == null) ? null : minmax.get(feature
+ .getType());
+ if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+ sb.append(" Score=").append(String.valueOf(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 : (Vector<String>) features[i].links)
+ for (String[] urllink : createLinksFrom(null, urlstring))
{
- 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();
- }
+ 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())
{
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)
+ 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)
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 createSequenceAnnotationReport(final StringBuffer tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
- Hashtable minmax)
+ Map<String, float[][]> minmax)
{
createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
true, minmax);
public void createSequenceAnnotationReport(final StringBuffer tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
- boolean tableWrap, Hashtable minmax)
+ boolean tableWrap, Map<String, float[][]> minmax)
{
String tmp;
tip.append("<i>");
{
ds = ds.getDatasetSequence();
}
- DBRefEntry[] dbrefs = ds.getDBRef();
+ DBRefEntry[] dbrefs = ds.getDBRefs();
if (showDbRefs && dbrefs != null)
{
for (int i = 0; i < dbrefs.length; i++)
}
// ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = ds.getSequenceFeatures();
- SequenceFeature[] tfeat = new SequenceFeature[1];
+ SequenceFeature[] features = sequence.getSequenceFeatures();
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];
+ List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
+ tfeat.add(features[i]);
appendFeatures(tip, 0, tfeat, minmax);
sz += tip.length();
maxWidth = Math.max(maxWidth, sz);
git://source.jalview.org / jalview.git / blobdiff