and the desktop application are able to open URLs as 'popups' in
your web browser. <br> Double-clicking on the ID of a sequence
will open the first URL that can be generated from its sequence ID.
- This is often the SRS site, but you can easily configure your own <a
+ This is by default the EMBL-EBI site, but you can easily configure your own <a
href="#urllinks">sequence URL links</a>.
</p>
<p>
<p>
<strong><a name="urllinks">Configuring URL Links</a></strong> <br>URL
links are defined in the "Connections" tab of the <a
- href="../features/preferences.html">Jalview desktop
- preferences</a>, or specified as <a
- href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
- parameters</a>. <br> By default the item "SRS" is added
+ href="../features/preferences.html">Jalview desktop
+ preferences</a>, or specified as <a
+ href="http://www.jalview.org/examples/appletParameters.html#parameters">applet
+ parameters</a>. <br> By default the item "EMBL-EBI Search" is added
to this link menu. This link will show a web page in your default
browser with the selected sequence id as part of the URL.<br>
In the preferences dialog box, click <strong>new</strong> to add a
to remove it.<br> You can name the link, this will be displayed
on a new menu item under the "Link" menu when you right
click on a sequence id. <br> The URL string must contain a
- token that can be replaced with a sequence ID. The simplest token is
+ token that can be replaced with a sequence ID or DB accession ID. The simplest token is
"$SEQUENCE_ID$", which will be replaced by the chosen
- sequence id when you click on it.
+ sequence id when you click on it.
</p>
<p>
eg.<br> UniRef100 =
Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$ <br> <br>
Links will also be made for any database cross references associated
with the sequence where the database name exactly matches a URL link
- name. In this case, the $SEQUENCE_ID$ string will be replaced with
+ name. In this case, the $DB_ACCESSION$ string will be replaced with
the accession string for the database cross-reference, rather than
- the sequence ID for the sequence (<em>since Jalview 2.4</em>).
+ the sequence ID for the sequence (<em>since Jalview 2.10.1</em>).
</p>
<p>
<strong>Regular Expression Substitution</strong><br> A url may
contain a string of the form $SEQUENCE_ID=/<em>regular
- expression</em>/=$. In this case, the regular expression will be
- applied to the full sequence ID string and the resulting match will
+ expression</em>/=$ or $DB_ACCESSION=/<em>regular expression</em>/=$.
+ In this case, the regular expression will be
+ applied to the full sequence ID or DB accession ID string and the resulting match will
be inserted into the URL. Groups of parentheses can be used to
specify which regions of the regular expression will be used to
generate the URL:
label.hide_columns_not_containing = Hide columns that do not contain
option.trim_retrieved_seqs = Trim retrieved sequences
label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences.
-label.use_sequence_id_1 = Use $SEQUENCE_ID$ or $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = to embed sequence id in URL
-label.use_sequence_id_3 = Use $SEQUENCE_NAME$ similarly to embed sequence name
+label.use_sequence_id_1 = Use $DB_ACCESSION$ or $DB_ACCESSION=/<regex>/=$
+label.use_sequence_id_2 = to embed accession id in URL
+label.use_sequence_id_3 = Use $SEQUENCE_ID$ similarly to embed sequence id
label.use_sequence_id_4 =
label.ws_parameters_for = Parameters for {0}
label.switch_server = Switch server
label.column = Column
label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
label.operation_failed = Operation failed
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB accessions
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
+label.do_not_display_again = Do not display this message again
label.select_columns_not_containing = Seleccione las columnas que no contengan
option.trim_retrieved_seqs = Ajustar las secuencias recuperadas
label.trim_retrieved_sequences = Cuando la secuencia de referencia es más larga que la secuencia con la que está trabajando, sólo se mantienen las subsecuencias relevantes.
-label.use_sequence_id_1 = Utilice $SEQUENCE_ID$ o $SEQUENCE_ID=/<regex>/=$
-label.use_sequence_id_2 = para embeber el id de la secuencia en una URL
-label.use_sequence_id_3 = Utilice $SEQUENCE_NAME$ de manera similar para embeber
-label.use_sequence_id_4 = el nombre de la secuencia
+label.use_sequence_id_1 = Utilice $DB_ACCESSION$ o $DB_ACCESSION=/<regex>/=$
+label.use_sequence_id_2 = para embeber el ID de accesión en una URL
+label.use_sequence_id_3 = Utilice $SEQUENCE_ID$ de manera similar para embeber
+label.use_sequence_id_4 = el ID de la secuencia
label.ws_parameters_for = Parámetros para {0}
label.switch_server = Cambiar servidor
label.open_jabaws_web_page = Abra el página principal del servidor JABAWS en un navegador web
label.column = Columna
label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos
label.operation_failed = Operación fallada
+label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ no se utiliza más para accesiones DB
+label.SEQUENCE_ID_for_DB_ACCESSION1 = Por favor, revise sus URLs en la pestaña 'Conexiones' de la ventana de Preferencias:
+label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'.
+label.do_not_display_again = No mostrar este mensaje de nuevo
\ No newline at end of file
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
+import jalview.bin.Cache;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- for (int i = 0; i < links.size(); i++)
- {
- String link = links.elementAt(i);
- UrlLink urlLink = new UrlLink(link);
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- continue;
- }
- 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)
- {
- 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)
- {
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- }
- }
- }
- 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)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- // addshowLink(linkMenu, target, url_pref + id + url_suff);
- }
- // Now construct URLs from description but only try to do it for regex
- // URL links
- 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)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- else
- {
- addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
- }
- /*
- * final String url;
- *
- * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
- * string and any matching database reference accessions String url_pref
- * = link.substring(link.indexOf("|") + 1,
- * link.indexOf("$SEQUENCE_ID$"));
- *
- * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
- * // collect matching db-refs DBRefEntry[] dbr =
- * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
- * String[]{target}); // collect id string too String id =
- * seq.getName(); if (id.indexOf("|") > -1) { id =
- * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
- * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
- * suppress duplicate link creation for the bare sequence ID string with
- * this link id = null; } addshowLink(linkMenu,
- * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
- * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
- * create Bare ID link for this RUL addshowLink(linkMenu, target,
- * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
- * link.substring(link.lastIndexOf("|")+1)); }
- */
- }
- if (linkMenu.getItemCount() > 0)
- {
- if (seq != null)
- {
- seqMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
- }
- }
+ addFeatureLinks(seq, links);
}
+
// TODO: add group link menu entry here
if (seq != null)
{
}
/**
+ * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ *
+ * @param seq
+ * @param links
+ */
+ void addFeatureLinks(final SequenceI seq, List<String> links)
+ {
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
+ for (String link : links)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ addshowLinks(linkMenu, linkset.values());
+
+ if (linkMenu.getItemCount() > 0)
+ {
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
+ /**
* Build menus for annotation types that may be shown or hidden, and for
* 'reference annotations' that may be added to the alignment.
*/
url = null;
continue;
}
- ;
+
+ if (urlLink.usesDBAccession())
+ {
+ // this URL requires an accession id, not the name of a sequence
+ url = null;
+ continue;
+ }
+
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
import java.util.concurrent.Semaphore;
import javax.swing.AbstractAction;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
showNews.setVisible(false);
+ checkURLLinks();
+
this.addWindowListener(new WindowAdapter()
{
@Override
new Thread(jvq).start();
}
+ public void checkURLLinks()
+ {
+ // Thread off the URL link checker
+ addDialogThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (Cache.getDefault("CHECKURLLINKS", true))
+ {
+ // check in case URL links use old style tokens ($SEQUENCE_ID$ for
+ // sequence id _or_ accession id)
+ JPanel msgPanel = new JPanel();
+ msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
+ msgPanel.add(Box.createVerticalGlue());
+ JLabel msg = new JLabel(
+ MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(
+ MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ msgPanel.add(msg);
+ msgPanel.add(msg2);
+
+ final JCheckBox jcb = new JCheckBox(
+ MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // update Cache settings if checkbox is selected
+ if (jcb.isSelected())
+ {
+ Cache.setProperty("CHECKURLLINKS", "false");
+ }
+ }
+ });
+ msgPanel.add(jcb);
+
+ JOptionPane.showMessageDialog(null, msgPanel, MessageManager
+ .getString("label.SEQUENCE_ID_no_longer_used"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ }
+
/**
* Proxy class for JDesktopPane which optionally displays the current memory
* usage and highlights the desktop area with a red bar if free memory runs
url = null;
continue;
}
- ;
+
+ if (urlLink.usesDBAccession())
+ {
+ // this URL requires an accession id, not the name of a sequence
+ url = null;
+ continue;
+ }
+
if (!urlLink.isValid())
{
jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.util.DBRefUtils;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
void addFeatureLinks(final SequenceI seq, List<String> links)
{
JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- List<String> linkset = new ArrayList<String>();
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
for (String link : links)
{
UrlLink urlLink = null;
Cache.log.error("Exception for URLLink '" + link + "'", foo);
continue;
}
- ;
+
if (!urlLink.isValid())
{
Cache.log.error(urlLink.getInvalidMessage());
continue;
}
- final String label = urlLink.getLabel();
-
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
-
- if (seq != null && urlLink.usesSeqId()) // link is ID
- {
- // collect matching db-refs
- DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { urlLink.getTarget() });
-
- // if there are any dbrefs which match up with the link
- 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 URL
- createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset,
- linkMenu, label, true);
- }
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
- }
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
- }
- else if (seq != null && !urlLink.usesSeqId()) // link is name
- {
- if (id != null)
- {
- // create Bare ID link for this URL
- createBareURLLink(urlLink, id, linkset, linkMenu, label, false);
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
- }
- }
- else
- {
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
- {
- linkset.add(label + "|" + urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
- }
- }
+ addshowLinks(linkMenu, linkset.values());
- }
if (sequence != null)
{
sequenceMenu.add(linkMenu);
}
}
- /*
- * Create a bare URL Link
- */
- private void createBareURLLink(UrlLink urlLink, String id,
- List<String> linkset, JMenu linkMenu, String label,
- Boolean addSepToLabel)
- {
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.add(urls[u] + "|" + urls[u + 1]);
- if (addSepToLabel)
- {
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- else
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- }
+
/**
* Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
}
}
+ private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
/**
* add a show URL menu item to the given linkMenu
*
package jalview.gui;
import static jalview.util.UrlConstants.EMBLEBI_STRING;
-import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
+import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
import static jalview.util.UrlConstants.SRS_STRING;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
String name = st.nextToken();
String url = st.nextToken();
// check for '|' within a regex
- int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+ int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
if (rxstart == -1)
{
- rxstart = url.indexOf("$" + SEQUENCE_NAME + "$");
+ rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
}
while (rxstart == -1 && url.indexOf("/=$") == -1)
{
{
sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
}
- // upgrade old EMBL-EBI link
- int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
- if (emblPos > -1)
- {
- sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
- }
}
/**
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.Collection;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
{
try
{
- for (String[] urllink : createLinksFrom(null, urlstring))
+ for (List<String> urllink : createLinksFrom(null, urlstring))
{
sb.append("<br/> <a href=\""
- + urllink[3]
+ + urllink.get(3)
+ "\" target=\""
- + urllink[0]
+ + urllink.get(0)
+ "\">"
- + (urllink[0].toLowerCase().equals(
- urllink[1].toLowerCase()) ? urllink[0]
- : (urllink[0] + ":" + urllink[1]))
+ + (urllink.get(0).toLowerCase()
+ .equals(urllink.get(1).toLowerCase()) ? urllink
+ .get(0) : (urllink.get(0) + ":" + urllink
+ .get(1)))
+ "</a></br>");
}
} catch (Exception x)
*
* @param seq
* @param link
- * @return String[][] { String[] { link target, link label, dynamic component
- * inserted (if any), url }}
+ * @return Collection< List<String> > { List<String> { link target, link
+ * label, dynamic component inserted (if any), url }}
*/
- String[][] createLinksFrom(SequenceI seq, String link)
+ Collection<List<String>> createLinksFrom(SequenceI seq, String link)
{
- List<String[]> urlSets = new ArrayList<String[]>();
- List<String> uniques = new ArrayList<String>();
+ Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
return null;
}
- if (seq != null && urlLink.isDynamic())
- {
- 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))
- {
- uniques.add(unq);
- urlSets.add(new String[] { target, label, null,
- urlLink.getUrl_prefix() });
- }
- }
-
- 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();
+ urlLink.createLinksFromSeq(seq, urlSets);
- // 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++)
- {
- 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 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))
- {
- result.add(new String[] { target, label, urls[u], urls[u + 1] });
- uniques.add(unq);
- }
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this URL
- 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))
- {
- result.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))
- {
- result.add(new String[] { target, label, urls[u], urls[u + 1] });
- uniques.add(unq);
- }
- }
- }
- }
- return result;
+ return urlSets.values();
}
public void createSequenceAnnotationReport(final StringBuffer tip,
HashSet<String> srcs = new HashSet<String>();
for (String src : sources)
{
- srcs.add(src);
+ srcs.add(src.toUpperCase());
}
List<DBRefEntry> res = new ArrayList<DBRefEntry>();
for (DBRefEntry dbr : dbrefs)
{
String source = getCanonicalName(dbr.getSource());
- if (srcs.contains(source))
+ if (srcs.contains(source.toUpperCase()))
{
res.add(dbr);
}
/*
* Sequence ID string
*/
- public static final String SEQUENCE_ID = "SEQUENCE_ID";
+ public static final String DB_ACCESSION = "DB_ACCESSION";
/*
* Sequence Name string
*/
- public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
-
- /*
- * Default sequence URL link string for EMBL-EBI search
- */
- public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$";
+ public static final String SEQUENCE_ID = "SEQUENCE_ID";
/*
* Default sequence URL link string for EMBL-EBI search
*/
- public static final String OLD_EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
+ public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
/*
* Default sequence URL link string for SRS
*/
package jalview.util;
+import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
import java.util.Vector;
public class UrlLink
* Jalview 2.4 extension allows regular expressions to be used to parse ID
* strings and replace the result in the URL. Regex's operate on the whole ID
* string given to the matchURL method, if no regex is supplied, then only
- * text following the first pipe symbol will be susbstituted. Usage
+ * text following the first pipe symbol will be substituted. Usage
* documentation todo.
*/
- private String url_suffix, url_prefix, target, label, regexReplace;
+
+ // Internal constants
+ private static final String SEP = "|";
+
+ private static final String DELIM = "$";
+
+ private String urlSuffix;
+
+ private String urlPrefix;
+
+ private String target;
+
+ private String label;
+
+ private String regexReplace;
private boolean dynamic = false;
- private boolean uses_seq_id = false;
+ private boolean usesDBaccession = false;
private String invalidMessage = null;
/**
- * parse the given linkString of the form '<label>|<url>' into parts url may
+ * parse the given linkString of the form '<label>SEP<url>' into parts url may
* contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
* must be of the form =/<perl style regex>/=$
*
*/
public UrlLink(String link)
{
- int sep = link.indexOf("|");
- int psqid = link.indexOf("$" + SEQUENCE_ID);
- int nsqid = link.indexOf("$" + SEQUENCE_NAME);
+ int sep = link.indexOf(SEP);
+ int psqid = link.indexOf(DELIM + DB_ACCESSION);
+ int nsqid = link.indexOf(DELIM + SEQUENCE_ID);
if (psqid > -1)
{
dynamic = true;
- uses_seq_id = true;
+ usesDBaccession = true;
sep = parseTargetAndLabel(sep, psqid, link);
- parseUrl(link, SEQUENCE_ID, psqid, sep);
+ parseUrl(link, DB_ACCESSION, psqid, sep);
}
else if (nsqid > -1)
{
dynamic = true;
sep = parseTargetAndLabel(sep, nsqid, link);
- parseUrl(link, SEQUENCE_NAME, nsqid, sep);
+ parseUrl(link, SEQUENCE_ID, nsqid, sep);
}
else
{
target = link.substring(0, sep);
- sep = link.lastIndexOf("|");
+ sep = link.lastIndexOf(SEP);
label = link.substring(0, sep);
- url_prefix = link.substring(sep + 1);
+ urlPrefix = link.substring(sep + 1).trim();
regexReplace = null; // implies we trim any prefix if necessary //
- // regexReplace=".*\\|?(.*)";
- url_suffix = null;
+ urlSuffix = null;
}
label = label.trim();
target = target.trim();
- target = target.toUpperCase(); // DBRefEntry uppercases DB names
- // NB getCanonicalName might be better but does not currently change case
}
/**
*/
public String getUrl_suffix()
{
- return url_suffix;
+ return urlSuffix;
}
/**
*/
public String getUrl_prefix()
{
- return url_prefix;
+ return urlPrefix;
}
/**
}
/**
+ *
+ * @return whether link is dynamic
+ */
+ public boolean isDynamic()
+ {
+ return dynamic;
+ }
+
+ /**
+ *
+ * @return whether link uses DB Accession id
+ */
+ public boolean usesDBAccession()
+ {
+ return usesDBaccession;
+ }
+
+ /**
+ * Set the label
+ *
+ * @param newlabel
+ */
+ public void setLabel(String newlabel)
+ {
+ this.label = newlabel;
+ }
+
+ /**
* return one or more URL strings by applying regex to the given idstring
*
* @param idstring
{
// take whole regex
return new String[] { rg.stringMatched(),
- url_prefix + rg.stringMatched() + url_suffix };
+ urlPrefix + rg.stringMatched() + urlSuffix };
} /*
* else if (ns==1) { // take only subgroup match return new String[]
* { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
if (mtch.length() > 0)
{
subs.addElement(mtch);
- subs.addElement(url_prefix + mtch + url_suffix);
+ subs.addElement(urlPrefix + mtch + urlSuffix);
}
s = r;
}
if (rg.matchedFrom(s) > -1)
{
subs.addElement(rg.stringMatched(s));
- subs.addElement(url_prefix + rg.stringMatched(s)
- + url_suffix);
+ subs.addElement(urlPrefix + rg.stringMatched(s)
+ + urlSuffix);
}
s++;
}
}
}
/* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
- if (idstring.indexOf("|") > -1)
+ if (idstring.indexOf(SEP) > -1)
{
- idstring = idstring.substring(idstring.lastIndexOf("|") + 1);
+ idstring = idstring.substring(idstring.lastIndexOf(SEP) + 1);
}
// just return simple url substitution.
- return new String[] { idstring, url_prefix + idstring + url_suffix };
+ return new String[] { idstring, urlPrefix + idstring + urlSuffix };
}
else
{
- return new String[] { "", url_prefix };
+ return new String[] { "", urlPrefix };
}
}
@Override
public String toString()
{
- String var = (uses_seq_id ? SEQUENCE_ID : SEQUENCE_NAME);
+ String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
return label
- + "|"
- + url_prefix
- + (dynamic ? ("$" + var + ((regexReplace != null) ? "="
- + regexReplace + "=$" : "$")) : "")
- + ((url_suffix == null) ? "" : url_suffix);
+ + SEP
+ + urlPrefix
+ + (dynamic ? (DELIM + var + ((regexReplace != null) ? "="
+ + regexReplace + "=" + DELIM : DELIM)) : "")
+ + ((urlSuffix == null) ? "" : urlSuffix);
}
/**
do
{
sep = p;
- p = link.indexOf("|", sep + 1);
+ p = link.indexOf(SEP, sep + 1);
} while (p > sep && p < psqid);
- // Assuming that the URL itself does not contain any '|' symbols
+ // Assuming that the URL itself does not contain any SEP symbols
// sep now contains last pipe symbol position prior to any regex symbols
label = link.substring(0, sep);
- if (label.indexOf("|") > -1)
+ if (label.indexOf(SEP) > -1)
{
- // | terminated database name / www target at start of Label
- target = label.substring(0, label.indexOf("|"));
+ // SEP terminated database name / www target at start of Label
+ target = label.substring(0, label.indexOf(SEP));
}
else if (label.indexOf(" ") > 2)
{
*/
protected void parseUrl(String link, String varName, int sqidPos, int sep)
{
- url_prefix = link.substring(sep + 1, sqidPos);
+ urlPrefix = link.substring(sep + 1, sqidPos).trim();
// delimiter at start of regex: e.g. $SEQUENCE_ID=/
- String startDelimiter = "$" + varName + "=/";
+ String startDelimiter = DELIM + varName + "=/";
// delimiter at end of regex: /=$
- String endDelimiter = "/=$";
+ String endDelimiter = "/=" + DELIM;
int startLength = startDelimiter.length();
&& (p > sqidPos + startLength))
{
// Extract Regex and suffix
- url_suffix = link.substring(p + endDelimiter.length());
+ urlSuffix = link.substring(p + endDelimiter.length());
regexReplace = link.substring(sqidPos + startLength, p);
try
{
// no regex
regexReplace = null;
// verify format is really correct.
- if (link.indexOf("$" + varName + "$") == sqidPos)
+ if (link.indexOf(DELIM + varName + DELIM) == sqidPos)
{
- url_suffix = link.substring(sqidPos + startLength - 1);
+ urlSuffix = link.substring(sqidPos + startLength - 1);
regexReplace = null;
}
else
}
}
+ /**
+ * Create a set of URL links for a sequence
+ *
+ * @param seq
+ * The sequence to create links for
+ * @param linkset
+ * Map of links: key = id + SEP + link, value = [target, label, id,
+ * link]
+ */
+ public void createLinksFromSeq(final SequenceI seq,
+ Map<String, List<String>> linkset)
+ {
+ if (seq != null && dynamic)
+ {
+ createDynamicLinks(seq, linkset);
+ }
+ else
+ {
+ createStaticLink(linkset);
+ }
+ }
+
+ /**
+ * Create a static URL link
+ *
+ * @param linkset
+ * Map of links: key = id + SEP + link, value = [target, label, id,
+ * link]
+ */
+ protected void createStaticLink(Map<String, List<String>> linkset)
+ {
+ if (!linkset.containsKey(label + SEP + getUrl_prefix()))
+ {
+ // Add a non-dynamic link
+ linkset.put(label + SEP + getUrl_prefix(),
+ Arrays.asList(target, label, null, getUrl_prefix()));
+ }
+ }
+
+ /**
+ * Create dynamic URL links
+ *
+ * @param seq
+ * The sequence to create links for
+ * @param linkset
+ * Map of links: key = id + SEP + link, value = [target, label, id,
+ * link]
+ */
+ protected void createDynamicLinks(final SequenceI seq,
+ Map<String, List<String>> linkset)
+ {
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+
+ if (usesDBAccession()) // link is ID
+ {
+ // collect matching db-refs
+ DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[] { target });
+
+ // if there are any dbrefs which match up with the link
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ // create Bare ID link for this URL
+ createBareURLLink(dbr[r].getAccessionId(), true, linkset);
+ }
+ }
+ }
+ else if (!usesDBAccession() && id != null) // link is name
+ {
+ // create Bare ID link for this URL
+ createBareURLLink(id, false, linkset);
+ }
+
+ // Create urls from description but only for URL links which are regex
+ // links
+ if (descr != null && getRegexReplace() != null)
+ {
+ // create link for this URL from description where regex matches
+ createBareURLLink(descr, false, linkset);
+ }
+ }
+
+ /*
+ * Create a bare URL Link
+ * Returns map where key = id + SEP + link, and value = [target, label, id, link]
+ */
+ protected void createBareURLLink(String id, Boolean combineLabel,
+ Map<String, List<String>> linkset)
+ {
+ String[] urls = makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.containsKey(urls[u] + SEP + urls[u + 1]))
+ {
+ String thisLabel = label;
+ if (combineLabel)
+ {
+ // incorporate label with idstring
+ thisLabel = label + SEP + urls[u];
+ }
+
+ linkset.put(urls[u] + SEP + urls[u + 1],
+ Arrays.asList(target, thisLabel, urls[u], urls[u + 1]));
+ }
+ }
+ }
+ }
+
private static void testUrls(UrlLink ul, String idstring, String[] urls)
{
* "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
* , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
*/
- "NESTED|http://nested/$" + SEQUENCE_ID
+ "NESTED|http://nested/$" + DB_ACCESSION
+ "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
String[] idstrings = new String[] {
/*
}
}
}
-
- public boolean isDynamic()
- {
- // TODO Auto-generated method stub
- return dynamic;
- }
-
- public boolean usesSeqId()
- {
- return uses_seq_id;
- }
-
- public void setLabel(String newlabel)
- {
- this.label = newlabel;
- }
}
*/
package jalview.gui;
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
// links as might be added into Preferences | Connections dialog
- links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$");
- links.add("UNIPROT | http://www.uniprot.org/uniprot/$SEQUENCE_ID$");
- links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$SEQUENCE_ID$");
+ links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ + SEQUENCE_ID + "$");
+ links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
+ + "$");
+ links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+ + DB_ACCESSION + "$");
// Gene3D entry tests for case (in)sensitivity
- links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$SEQUENCE_ID$&mode=protein");
+ links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+ + DB_ACCESSION + "$&mode=protein");
// make seq0 dbrefs
refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
*/
package jalview.util;
+import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Sequence;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
import org.testng.annotations.Test;
public class UrlLinkTest
@Test(groups = { "Functional" })
public void testUrlLinkCreationNoRegex()
{
- // SEQUENCE_NAME
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+ // SEQUENCE_ID
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ DELIM + URL_SUFFIX);
assertEquals(DB.toUpperCase(), ul.getTarget());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
- assertFalse(ul.usesSeqId());
+ assertFalse(ul.usesDBAccession());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
- // SEQUENCE_ID
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+ // DB_ACCESSION
+ ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
+ URL_SUFFIX);
assertEquals(DB.toUpperCase(), ul.getTarget());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
- assertTrue(ul.usesSeqId());
+ assertTrue(ul.usesDBAccession());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
assertFalse(ul.isDynamic());
- assertFalse(ul.usesSeqId());
+ assertFalse(ul.usesDBAccession());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
@Test(groups = { "Functional" })
public void testUrlLinkCreationWithRegex()
{
- // SEQUENCE_NAME
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+ // SEQUENCE_ID
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ REGEX_NESTED + DELIM + URL_SUFFIX);
assertEquals(DB.toUpperCase(), ul.getTarget());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
- assertFalse(ul.usesSeqId());
+ assertFalse(ul.usesDBAccession());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
- // SEQUENCE_ID
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ // DB_ACCESSION
+ ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
+ REGEX_NESTED + DELIM + URL_SUFFIX);
assertEquals(DB.toUpperCase(), ul.getTarget());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
- assertTrue(ul.usesSeqId());
+ assertTrue(ul.usesDBAccession());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
// invalid regex
- ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
+ REGEX_RUBBISH + DELIM + URL_SUFFIX);
assertEquals(DB.toUpperCase(), ul.getTarget());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
- assertTrue(ul.usesSeqId());
+ assertTrue(ul.usesDBAccession());
assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
ul.getRegexReplace());
assertFalse(ul.isValid());
public void testMakeUrlNoRegex()
{
// Single non-regex
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ DELIM + URL_SUFFIX);
String idstring = "FER_CAPAA";
String[] urls = ul.makeUrls(idstring, true);
}
/**
- * Test construction of link by substituting sequence id or name
+ * Test construction of link by substituting sequence id or name using regular
+ * expression
*/
@Test(groups = { "Functional" })
public void testMakeUrlWithRegex()
{
// Unused regex
- UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
+ REGEX_NESTED + DELIM + URL_SUFFIX);
String idstring = "FER_CAPAA";
String[] urls = ul.makeUrls(idstring, true);
assertNull(ul.getInvalidMessage());
}
+ /**
+ * Test creating links with null sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateLinksFromNullSequence()
+ {
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ + DELIM + URL_SUFFIX);
+
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(null, linkset);
+
+ String key = DB + SEP + URL_PREFIX;
+ assertEquals(1, linkset.size());
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), DB.toUpperCase());
+ assertEquals(linkset.get(key).get(1), DB);
+ assertEquals(linkset.get(key).get(2), null);
+ assertEquals(linkset.get(key).get(3), URL_PREFIX);
+ }
+
+ /**
+ * Test creating links with non-dynamic urlLink
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateLinksForNonDynamic()
+ {
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX);
+
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(null, linkset);
+
+ String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
+ assertEquals(1, linkset.size());
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), DB.toUpperCase());
+ assertEquals(linkset.get(key).get(1), DB);
+ assertEquals(linkset.get(key).get(2), null);
+ assertEquals(linkset.get(key).get(3), URL_PREFIX + URL_SUFFIX);
+ }
+
+ /**
+ * Test creating links
+ */
+ @Test(groups = { "Functional" })
+ public void testCreateLinksFromSequence()
+ {
+
+ // create list of links and list of DBRefs
+ List<String> links = new ArrayList<String>();
+ List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+
+ // links as might be added into Preferences | Connections dialog
+ links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ + SEQUENCE_ID + "$");
+ links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
+ + "$");
+ links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+ + DB_ACCESSION + "$");
+
+ // make seq0 dbrefs
+ refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058"));
+ refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675"));
+
+ Sequence seq0 = new Sequence("FER1", "AKPNGVL");
+
+ // add all the dbrefs to the sequence
+ seq0.addDBRef(refs.get(0));
+ seq0.addDBRef(refs.get(1));
+ seq0.addDBRef(refs.get(2));
+ seq0.addDBRef(refs.get(3));
+ seq0.createDatasetSequence();
+
+ // Test where link takes a sequence id as replacement
+ UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+ + DELIM + URL_SUFFIX);
+
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+
+ String key = seq0.getName() + SEP + URL_PREFIX + seq0.getName()
+ + URL_SUFFIX;
+ assertEquals(1, linkset.size());
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), DB.toUpperCase());
+ assertEquals(linkset.get(key).get(1), DB);
+ assertEquals(linkset.get(key).get(2), seq0.getName());
+ assertEquals(linkset.get(key).get(3), URL_PREFIX + seq0.getName()
+ + URL_SUFFIX);
+
+ // Test where link takes a db annotation id and only has one dbref
+ ul = new UrlLink(links.get(1));
+ linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+
+ key = "P83527|http://www.uniprot.org/uniprot/P83527";
+ assertEquals(1, linkset.size());
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), DBRefSource.UNIPROT);
+ assertEquals(linkset.get(key).get(1), DBRefSource.UNIPROT + SEP
+ + "P83527");
+ assertEquals(linkset.get(key).get(2), "P83527");
+ assertEquals(linkset.get(key).get(3),
+ "http://www.uniprot.org/uniprot/P83527");
+
+ // Test where link takes a db annotation id and has multiple dbrefs
+ ul = new UrlLink(links.get(2));
+ linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+ assertEquals(3, linkset.size());
+
+ // check each link made it in correctly
+ key = "IPR001041|http://www.ebi.ac.uk/interpro/entry/IPR001041";
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), "INTERPRO");
+ assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR001041");
+ assertEquals(linkset.get(key).get(2), "IPR001041");
+ assertEquals(linkset.get(key).get(3),
+ "http://www.ebi.ac.uk/interpro/entry/IPR001041");
+
+ key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058";
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), "INTERPRO");
+ assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR006058");
+ assertEquals(linkset.get(key).get(2), "IPR006058");
+ assertEquals(linkset.get(key).get(3),
+ "http://www.ebi.ac.uk/interpro/entry/IPR006058");
+
+ key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675";
+ assertTrue(linkset.containsKey(key));
+ assertEquals(linkset.get(key).get(0), "INTERPRO");
+ assertEquals(linkset.get(key).get(1), "INTERPRO" + SEP + "IPR012675");
+ assertEquals(linkset.get(key).get(2), "IPR012675");
+ assertEquals(linkset.get(key).get(3),
+ "http://www.ebi.ac.uk/interpro/entry/IPR012675");
+
+ // Test where there are no matching dbrefs for the link
+ ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
+ + URL_SUFFIX);
+ linkset = new LinkedHashMap<String, List<String>>();
+ ul.createLinksFromSeq(seq0, linkset);
+ assertTrue(linkset.isEmpty());
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff