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
+exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
\ No newline at end of file
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
+label.do_not_display_again = No mostrar este mensaje de nuevo
+exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
+exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
\ No newline at end of file
*/
package jalview.appletgui;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
-import static jalview.util.UrlConstants.SRS_STRING;
-
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.util.UrlLink;
+import jalview.util.UrlProvider;
+import jalview.util.UrlProviderI;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+import java.util.HashMap;
import java.util.List;
import java.util.Vector;
boolean mouseDragging = false;
- java.util.Vector links = new java.util.Vector();
+ UrlProviderI urlProvider = null;
public IdPanel(AlignViewport av, AlignmentPanel parent)
{
String label, url;
// TODO: add in group link parameter
+
+ // make a list of label,url pairs
+ HashMap<String, String> urlList = new HashMap<String, String>();
if (av.applet != null)
{
for (int i = 1; i < 10; i++)
label = av.applet.getParameter("linkLabel_" + i);
url = av.applet.getParameter("linkURL_" + i);
- if (label != null && url != null)
- {
- links.addElement(label + "|" + url);
- }
-
+ urlList.put(label, url);
}
- }
- {
- // upgrade old SRS link
- int srsPos = links.indexOf(SRS_STRING);
- if (srsPos > -1)
+
+ if (!urlList.isEmpty())
{
- links.setElementAt(EMBLEBI_STRING, srsPos);
+ // set default as first entry in list
+ String defaultUrl = av.applet.getParameter("linkLabel_1");
+ urlProvider = new UrlProvider(defaultUrl, urlList);
}
}
- if (links.size() < 1)
- {
- links = new java.util.Vector();
- links.addElement(EMBLEBI_STRING);
- }
}
Tooltip tooltip;
return;
}
String id = sq.getName();
+ String url = urlProvider.getDefaultUrl(id);
+ String target = urlProvider.getDefaultTarget(id);
- String target = null;
- String url = null;
- int i = 0;
- while (url == null && i < links.size())
- {
- // DEFAULT LINK IS FIRST IN THE LINK LIST
- // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
- url = links.elementAt(i++).toString();
- jalview.util.UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(url);
- target = urlLink.getTarget();
- } catch (Exception foo)
- {
- System.err.println("Exception for URLLink '" + url + "'");
- foo.printStackTrace();
- url = null;
- continue;
- }
+ /* String target = null;
+ String url = null;
+ int i = 0;
+ while (url == null && i < links.size())
+ {
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
+ url = links.elementAt(i++).toString();
+ jalview.util.UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(url);
+ target = urlLink.getTarget();
+ } catch (Exception foo)
+ {
+ System.err.println("Exception for URLLink '" + url + "'");
+ foo.printStackTrace();
+ url = null;
+ continue;
+ }
- if (urlLink.usesDBAccession())
- {
- // this URL requires an accession id, not the name of a sequence
- 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());
- url = null;
- continue;
- }
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ url = null;
+ continue;
+ }
- String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0] == null || urls[0].length() < 1)
- {
- url = null;
- continue;
- }
- // just take first URL made from regex
- url = urls[1];
- }
+ String urls[] = urlLink.makeUrls(id, true);
+ if (urls == null || urls[0] == null || urls[0].length() < 1)
+ {
+ url = null;
+ continue;
+ }
+ // just take first URL made from regex
+ url = urls[1];
+ }*/
try
{
-
alignPanel.alignFrame.showURL(url, target);
} catch (Exception ex)
{
// build a new links menu based on the current links + any non-positional
// features
- Vector nlinks = new Vector();
- for (int l = 0, lSize = links.size(); l < lSize; l++)
- {
- nlinks.addElement(links.elementAt(l));
- }
+ Vector<String> nlinks = urlProvider.getLinksForDisplay();
+
SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
*/
package jalview.gui;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import jalview.api.AlignViewportI;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.UrlProviderI;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
{
// check what the actual links are - if it's just the default don't
// bother with the warning
- Vector<String> links = Preferences.sequenceURLLinks;
+ Vector<String> links = Preferences.sequenceUrlLinks
+ .getLinksForDisplay();
// only need to check links if there is one with a
// SEQUENCE_ID which is not the default EMBL_EBI link
while (li.hasNext())
{
String link = li.next();
- if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING))
+ if (link.contains(SEQUENCE_ID)
+ && !link.equals(UrlProviderI.DEFAULT_STRING))
{
check = true;
int barPos = link.indexOf("|");
import jalview.io.SequenceAnnotationReport;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.util.UrlLink;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
return;
}
- Vector links = Preferences.sequenceURLLinks;
- if (links == null || links.size() < 1)
- {
- return;
- }
-
int seq = alignPanel.getSeqPanel().findSeq(e);
- String url = null;
- int i = 0;
String id = av.getAlignment().getSequenceAt(seq).getName();
- while (url == null && i < links.size())
- {
- // DEFAULT LINK IS FIRST IN THE LINK LIST
- // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
- url = links.elementAt(i++).toString();
- jalview.util.UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(url);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
- foo);
- url = null;
- continue;
- }
+ String url = Preferences.sequenceUrlLinks.getDefaultUrl(id);
- 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());
- url = null;
- continue;
- }
-
- String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0] == null || urls[0].length() < 4)
- {
- url = null;
- continue;
- }
- // just take first URL made from regex
- url = urls[1];
- }
try
{
jalview.util.BrowserLauncher.openURL(url);
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
// build a new links menu based on the current links + any non-positional
// features
- Vector<String> nlinks = new Vector<String>(Preferences.sequenceURLLinks);
+ Vector<String> nlinks = Preferences.sequenceUrlLinks
+ .getLinksForDisplay(); // new
+ // Vector<String>(Preferences.sequenceURLLinks);
SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
if (sfs != null)
{
*/
package jalview.gui;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
-
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- // public static Vector<String> sequenceURLLinks;
public static UrlProviderI sequenceUrlLinks;
/**
public static List<String> groupURLLinks;
static
{
- String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
- sequenceUrlLinks = new UrlProvider(EMBLEBI_STRING.split("\\|")[0],
- string); // TODO sort out the default string
- // sequenceURLLinks = new Vector<String>();
+ String string = Cache.getDefault("SEQUENCE_LINKS",
+ UrlProviderI.DEFAULT_STRING);
+ sequenceUrlLinks = new UrlProvider(UrlProviderI.DEFAULT_LABEL, string);
- /* try
- {
- StringTokenizer st = new StringTokenizer(string, "|");
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- String url = st.nextToken();
- // check for '|' within a regex
- int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
- if (rxstart == -1)
- {
- rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
- }
- while (rxstart == -1 && url.indexOf("/=$") == -1)
- {
- url = url + "|" + st.nextToken();
- }
- sequenceURLLinks.addElement(name + "|" + url);
- }
- } catch (Exception ex)
- {
- System.out.println(ex + "\nError parsing sequence links");
- }
- {
- // upgrade old SRS link
- int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
- if (srsPos > -1)
- {
- sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
- }
- }
- */
/**
* TODO: reformulate groupURL encoding so two or more can be stored in the
* .properties file as '|' separated strings
*/
nameLinks = new Vector<String>();
urlLinks = new Vector<String>();
- sequenceUrlLinks.getLinksForDisplay(nameLinks, urlLinks);
- /* for (HashMap.Entry<String, UrlLink> entry: sequenceUrlLinks.getUrlLinks())
- {
- String link = sequenceURLLinks.elementAt(i).toString();
- nameLinks.addElement(link.substring(0, link.indexOf("|")));
- urlLinks.addElement(link.substring(link.indexOf("|") + 1));
- }
- */
+
+ resetStoredLinks();
updateLinkData();
useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
jalview.util.BrowserLauncher.resetBrowser();
+ // save user-defined and selected links
String links = sequenceUrlLinks.writeUrlsAsString();
if (links.isEmpty())
{
links.toString());
}
- /* if (nameLinks.size() > 0)
- {
- StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector<String>();
- for (int i = 0; i < nameLinks.size(); i++)
- {
- sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
- + urlLinks.elementAt(i));
- links.append(sequenceURLLinks.elementAt(i).toString());
- links.append("|");
- }
- // remove last "|"
- links.setLength(links.length() - 1);
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
- links.toString());
- }
- else
- {
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
- sequenceURLLinks.clear();
- }*/
-
Cache.applicationProperties.setProperty("USE_PROXY",
Boolean.toString(useProxy.isSelected()));
{
nameLinks.addElement(link.getName());
urlLinks.addElement(link.getURL());
- updateLinkData();
- valid = true;
+ if (updateLinkData())
+ {
+ valid = true;
+ }
+ else
+ {
+ break;
+ }
}
}
else
{
nameLinks.setElementAt(link.getName(), index);
urlLinks.setElementAt(link.getURL(), index);
- updateLinkData();
- valid = true;
+ if (updateLinkData())
+ {
+ valid = true;
+ }
+ else
+ {
+ break;
+ }
}
}
updateLinkData();
}
- void updateLinkData()
+ private boolean updateLinkData()
+ {
+ try
+ {
+ sequenceUrlLinks.setUrlLinks(nameLinks, urlLinks);
+ linkNameList.setListData(nameLinks);
+ linkURLList.setListData(urlLinks);
+ } catch (IllegalArgumentException e)
+ {
+
+ // put back the old links
+ resetStoredLinks();
+
+ linkNameList.setListData(nameLinks);
+ linkURLList.setListData(urlLinks);
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ e.getMessage(), MessageManager.getString("label.link_name"),
+ JOptionPane.WARNING_MESSAGE);
+
+ return false;
+ }
+ return true;
+ }
+
+ private void resetStoredLinks()
{
- linkNameList.setListData(nameLinks);
- linkURLList.setListData(urlLinks);
+ Vector<String> nlinks = sequenceUrlLinks.getLinksForDisplay();
+
+ nameLinks.clear();
+ urlLinks.clear();
+ for (String entry : nlinks)
+ {
+ nameLinks.addElement(entry.split("\\|")[0]);
+ urlLinks.addElement(entry.split("\\|")[1]);
+ }
}
@Override
package jalview.util;
import static jalview.util.UrlConstants.DB_ACCESSION;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.DELIM;
+//import static jalview.util.UrlConstants.EMBLEBI_LABEL;
+//import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEP;
import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SRS_STRING;
+//import static jalview.util.UrlConstants.SRS_LABEL;
import java.util.HashMap;
import java.util.Iterator;
* @author $author$
* @version $Revision$
*/
-public class CustomUrlProvider implements UrlProviderI
+public class CustomUrlProvider extends UrlProviderImpl
{
+ // minimum length of substitution in url link string
+ private static final int MIN_SUBST_LENGTH = 4;
+
+ // Default sequence URL link label for SRS
+ private static final String SRS_LABEL = "SRS";
+
+ // map of string ids to urlLinks
private HashMap<String, UrlLink> urls;
+ /**
+ * Construct UrlProvider for custom (user-entered) URLs
+ *
+ * @param cachedUrlList
+ * list of URLs in form stored in Cache. i.e. SEP delimited string
+ */
public CustomUrlProvider(String cachedUrlList)
{
try
{
- StringTokenizer st = new StringTokenizer(cachedUrlList, "|");
+ urls = new HashMap<String, UrlLink>();
+
+ // cachedUrlList is in form <label>|<url>|<label>|<url>...
+ // parse cachedUrlList into labels (used as id) and url links
+ StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
while (st.hasMoreElements())
{
String name = st.nextToken();
String url = st.nextToken();
// check for '|' within a regex
- int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
+ int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
if (rxstart == -1)
{
- rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+ rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
}
- while (rxstart == -1 && url.indexOf("/=$") == -1)
+ while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1)
{
- url = url + "|" + st.nextToken();
+ url = url + SEP + st.nextToken();
}
- urls.put(name, new UrlLink(url));
- // sequenceURLLinks.addElement(name + "|" + url);
+ urls.put(name, new UrlLink(name + SEP + url));
}
} catch (Exception ex)
{
System.out.println(ex + "\nError parsing sequence links");
}
+ upgradeOldLinks();
- // upgrade old SRS link
- String srs_key = SRS_STRING.split("\\|")[0];
- if (urls.containsKey(srs_key))
+ }
+
+ /**
+ * Construct UrlProvider for custom (user-entered) URLs
+ *
+ * @param urlList
+ * list of URLs as (label,url) pairs
+ */
+ public CustomUrlProvider(Map<String, String> urlList)
+ {
+ try
{
- urls.remove(srs_key);
- urls.put(EMBLEBI_STRING.split("//|")[0],
- new UrlLink(EMBLEBI_STRING.split("//|")[1]));
+ urls = new HashMap<String, UrlLink>();
+ Iterator<Map.Entry<String, String>> it = urlList.entrySet()
+ .iterator();
+ while (it.hasNext())
+ {
+ Map.Entry<String, String> pair = it.next();
+ urls.put(pair.getKey(),
+ new UrlLink(pair.getKey() + SEP + pair.getValue()));
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(ex + "\nError parsing sequence links");
}
+ upgradeOldLinks();
}
- @Override
- public HashMap<String, UrlLink> getUrlLinks()
+ private void upgradeOldLinks()
{
- // TODO Auto-generated method stub
- return null;
+ // upgrade old SRS link
+ if (urls.containsKey(SRS_LABEL))
+ {
+ urls.remove(SRS_LABEL);
+ urls.put(DEFAULT_LABEL, new UrlLink(DEFAULT_STRING));
+ }
}
@Override
- public void getLinksForDisplay(Vector<String> nameLinks,
- Vector<String> urlLinks)
+ public Vector<String> getLinksForDisplay()
{
+ Vector<String> links = new Vector<String>();
Iterator<Map.Entry<String, UrlLink>> it = urls.entrySet().iterator();
while (it.hasNext())
{
Map.Entry<String, UrlLink> pair = it.next();
- nameLinks.addElement(pair.getKey());
- urlLinks.addElement(pair.getValue().toString()); // TODO check this is
- // right
+ links.add(pair.getValue().toString());
}
+ return links;
}
@Override
- public String getDefaultUrl()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void setDefaultUrl(String id)
+ public boolean setDefaultUrl(String id)
{
- // TODO Auto-generated method stub
-
+ if (urls.containsKey(id))
+ {
+ defaultUrl = id;
+ }
+ else
+ {
+ defaultUrl = null;
+ }
+ return urls.containsKey(id);
}
@Override
for (UrlLink link : urls.values())
{
links.append(link.toString());
- links.append("|");
+ links.append(SEP);
}
- // remove last "|"
+ // remove last SEP
links.setLength(links.length() - 1);
}
else
}
@Override
- public void setUrlLinks(String cachedUrl)
+ public String getDefaultUrl(String seqid)
{
- // TODO Auto-generated method stub, maybe don't need this? watch out for
- // superclass interactions
+ if (defaultUrl == null)
+ {
+ return null;
+ }
+ String url = null;
+ UrlLink urlLink = urls.get(defaultUrl);
+ String[] defaultUrls = urlLink.makeUrls(seqid, true);
+ if (defaultUrls == null || defaultUrls[0] == null
+ || defaultUrls[0].length() < MIN_SUBST_LENGTH)
+ {
+ url = null;
+ }
+ else
+ {
+ // just take first URL made from regex
+ url = defaultUrls[1];
+ }
+ return url;
}
@Override
- public void setUrlLinks(HashMap<String, UrlLink> links)
+ public String getDefaultTarget(String seqid)
{
- // TODO Auto-generated method stub
+ return urls.get(defaultUrl).getTarget();
+ }
+
+ @Override
+ public void setUrlLinks(Vector<String> names, Vector<String> urlstrings)
+ {
+ HashMap<String, UrlLink> newurls = new HashMap<String, UrlLink>();
+
+ // should check that lists are same length but this function is likely
+ // to change once the Preferences dialog is rebuilt
+
+ for (int i = 0; i < names.size(); ++i)
+ {
+ // don't allow MIRIAM ids as custom url names (as the links will overwrite
+ // each other)
+ // unlikely user would try to do this, but...
+ if (isMiriamId(names.elementAt(i)))
+ {
+ throw new IllegalArgumentException(MessageManager.formatMessage(
+ "exception.url_cannot_have_miriam_id", names.elementAt(i)));
+ }
+ // don't allow duplicate key names as entries will be overwritten
+ if (newurls.containsKey(names.elementAt(i)))
+ {
+ throw new IllegalArgumentException(MessageManager.formatMessage(
+ "exception.url_cannot_have_duplicate_id",
+ names.elementAt(i)));
+ }
+ newurls.put(names.elementAt(i), new UrlLink(names.elementAt(i) + SEP
+ + urlstrings.elementAt(i)));
+ }
+
+ // don't update until we're sure this set is ok
+ urls = newurls;
}
+ @Override
+ public String chooseDefaultUrl()
+ {
+ // unilaterally set the default id to the EMBL_EBI link
+
+ if (!urls.containsKey(DEFAULT_LABEL))
+ {
+ urls.put(DEFAULT_LABEL, new UrlLink(DEFAULT_STRING));
+ }
+ return DEFAULT_LABEL;
+ }
+
}
package jalview.util;
-import java.util.HashMap;
+import java.util.Map;
import java.util.Vector;
/**
* @author $author$
* @version $Revision$
*/
-public class IdentifiersUrlProvider implements UrlProviderI
+public class IdentifiersUrlProvider extends UrlProviderImpl
{
public IdentifiersUrlProvider(String cachedUrlList)
}
- @Override
- public HashMap<String, UrlLink> getUrlLinks()
+ public IdentifiersUrlProvider(Map<String, String> urlList)
{
- // TODO Auto-generated method stub
- return null;
+
}
@Override
}
@Override
- public void setDefaultUrl(String id)
+ public boolean setDefaultUrl(String id)
{
- // TODO Auto-generated method stub
-
+ return false;
}
@Override
public String writeUrlsAsString()
{
+ return "";
+ }
+
+ @Override
+ public Vector<String> getLinksForDisplay()
+ {
// TODO Auto-generated method stub
return null;
}
@Override
- public void setUrlLinks(String cachedUrl)
+ public String getDefaultUrl(String seqid)
{
// TODO Auto-generated method stub
-
+ return null;
}
@Override
- public void setUrlLinks(HashMap<String, UrlLink> links)
+ public String getDefaultTarget(String seqid)
{
// TODO Auto-generated method stub
+ return null;
+ }
+ @Override
+ public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ {
+ // deliberately left empty
+ // TODO throw exception if called
}
@Override
- public void getLinksForDisplay(Vector<String> nameLinks,
- Vector<String> urlLinks)
+ public String chooseDefaultUrl()
{
// TODO Auto-generated method stub
-
+ return null;
}
}
public static final String SEQUENCE_ID = "SEQUENCE_ID";
/*
- * Default sequence URL link string for EMBL-EBI search
+ * Separator character used in Url links
*/
- public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
+ public static final String SEP = "|";
/*
- * Default sequence URL link string for SRS
+ * Delimiter character used in Url links
*/
- public static final String SRS_STRING = "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry";
+ public static final String DELIM = "$";
/*
* not instantiable
package jalview.util;
import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.DELIM;
+import static jalview.util.UrlConstants.SEP;
import static jalview.util.UrlConstants.SEQUENCE_ID;
import jalview.datamodel.DBRefEntry;
* documentation todo.
*/
- // Internal constants
- private static final String SEP = "|";
-
- private static final String DELIM = "$";
-
private String urlSuffix;
private String urlPrefix;
package jalview.util;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
/**
// List of actual URL link providers
private List<UrlProviderI> providers;
- // Record of default URL
- private String defaultUrl;
-
+ // Specific reference to custom URL link provider
+ private UrlProviderI customProvider;
+
/**
* Construct URL provider from string of cached URLs, and set default URL
*
- * @param defaultUrl
+ * @param defaultUrlString
* id of the current default URL
* @param cachedUrlList
* string listing current active URLs, expected to be custom URLs
* separated by |, or ids of URLs
*/
- public UrlProvider(String defaultUrl, String cachedUrlList)
+ public UrlProvider(String defaultUrlString, String cachedUrlList)
{
// create all the UrlProviders we need
providers = new ArrayList<UrlProviderI>();
UrlProviderI idProvider = new IdentifiersUrlProvider(cachedUrlList);
- UrlProviderI customProvider = new CustomUrlProvider(cachedUrlList);
+ customProvider = new CustomUrlProvider(cachedUrlList);
providers.add(idProvider);
providers.add(customProvider);
// check that the defaultUrl still exists
+ if (!setDefaultUrl(defaultUrlString))
+ {
+ chooseDefaultUrl();
+ }
}
/**
- * Get all the URL links
- * @return all URL links
+ * Construct URL provider from a map of (label,url) pairs, and set default URL
+ *
+ * @param defaultUrlString
+ * id of the current default URL
+ * @param urlList
+ * vector of (label, url) pairs
*/
- @Override
- public HashMap<String, UrlLink> getUrlLinks()
+ public UrlProvider(String defaultUrlString, Map<String, String> urlList)
{
- HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
- for (UrlProviderI p : providers)
+ // create all the UrlProviders we need
+ providers = new ArrayList<UrlProviderI>();
+
+ UrlProviderI idProvider = new IdentifiersUrlProvider(urlList);
+ customProvider = new CustomUrlProvider(urlList);
+ providers.add(idProvider);
+ providers.add(customProvider);
+
+ // check that the defaultUrl still exists
+ if (!setDefaultUrl(defaultUrlString))
{
- urls.putAll(p.getUrlLinks());
+ chooseDefaultUrl();
}
- return urls;
}
-
- /**
- * Get the default URL
- * @return id of the default URL
- */
+
@Override
public String getDefaultUrl()
{
+ String defaultUrl = null;
+ for (UrlProviderI p : providers)
+ {
+ defaultUrl = p.getDefaultUrl();
+ if (defaultUrl != null)
+ {
+ return defaultUrl;
+ }
+ }
+
+ // no provider has a default set, just choose one
+ if (defaultUrl == null)
+ {
+ defaultUrl = chooseDefaultUrl();
+ }
return defaultUrl;
}
- /**
- * Set the default URL
- * @param id the id of the URL to set as default
- */
@Override
- public void setDefaultUrl(String id)
+ public boolean setDefaultUrl(String id)
{
- defaultUrl = id;
+ for (UrlProviderI p : providers)
+ {
+ if (p.setDefaultUrl(id))
+ {
+ return true;
+ }
+ }
+ return false;
}
- /**
- * Write out all URLs as a string suitable for serialising
- * @return string representation of available URLs
- */
@Override
public String writeUrlsAsString()
{
}
return result;
}
-
- /**
- * Set URL links from string
- *
- * @param cachedUrl
- * string representation of URL links, i.e. | separated
- */
+
@Override
- public void setUrlLinks(String cachedUrl)
+ public Vector<String> getLinksForDisplay()
{
+ Vector<String> fullLinks = new Vector<String>();
for (UrlProviderI p : providers)
{
- p.setUrlLinks(cachedUrl);
+ List<String> links = p.getLinksForDisplay();
+ if (links != null)
+ {
+ // will obliterate links with same keys from different providers
+ // must have checks in place to prevent user from duplicating ids
+ fullLinks.addAll(links);
+ }
}
+ return fullLinks;
}
-
- /**
- * Set URL links from collection
- *
- * @param links
- * hashmap containing string indexed UrlLinks
- */
+
@Override
- public void setUrlLinks(HashMap<String, UrlLink> links)
+ public String getDefaultUrl(String seqid)
{
+ String link = null;
for (UrlProviderI p : providers)
{
- p.setUrlLinks(links);
+ if (p.getDefaultUrl(seqid) == null)
+ {
+ continue;
+ }
+ else
+ {
+ link = p.getDefaultUrl(seqid);
+ break;
+ }
}
+ return link;
}
@Override
- public void getLinksForDisplay(Vector<String> nameLinks,
- Vector<String> urlLinks)
+ public String getDefaultTarget(String seqid)
{
- Vector<String> names = new Vector<String>();
- Vector<String> links = new Vector<String>();
+ String target = null;
for (UrlProviderI p : providers)
{
- p.getLinksForDisplay(names, links);
- nameLinks.addAll(names);
- urlLinks.addAll(links);
+ if (p.getDefaultTarget(seqid) == null)
+ {
+ continue;
+ }
+ else
+ {
+ target = p.getDefaultTarget(seqid);
+ break;
+ }
}
+ return target;
+ }
+
+ @Override
+ public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ {
+ // only allow custom urls to be updated by user
+ customProvider.setUrlLinks(names, urls);
}
+ @Override
+ public String chooseDefaultUrl()
+ {
+ // choose a custom url default
+ return customProvider.chooseDefaultUrl();
+ }
+
}
*/
package jalview.util;
-import java.util.HashMap;
import java.util.Vector;
/**
*/
public interface UrlProviderI
{
- /**
- * Get all the URL links
- *
- * @return all URL links
+
+ /*
+ * Default sequence URL link label for EMBL-EBI search
*/
- public HashMap<String, UrlLink> getUrlLinks();
+ public static final String DEFAULT_LABEL = "EMBL-EBI Search";
+
+ /*
+ * Default sequence URL link string for EMBL-EBI search
+ */
+ public static final String DEFAULT_STRING = DEFAULT_LABEL
+ + "|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
/**
* Get names and urls in as strings for display
*
- * @param nameLinks
- * @param urlLinks
*/
- public void getLinksForDisplay(Vector<String> nameLinks,
- Vector<String> urlLinks);
+ Vector<String> getLinksForDisplay();
/**
- * Get the default URL
+ * Get the id of the default URL
*
* @return id of the default URL
*/
- public String getDefaultUrl();
+ String getDefaultUrl();
+
+ /**
+ * Get the link for the default URL
+ *
+ * @seqid sequence id for which to build link
+ * @return link for the default URL
+ */
+ String getDefaultUrl(String seqid);
+
+ /**
+ * Get the target of thelink for the default URL
+ *
+ * @seqid sequence id for which to build link
+ * @return target of link for the default URL
+ */
+ String getDefaultTarget(String seqid);
/**
* Set the default URL
*
* @param id
* the id of the URL to set as default
+ * @return true if setting was successful, false otherwise
*/
- public void setDefaultUrl(String id);
+ boolean setDefaultUrl(String id);
/**
* Write out all URLs as a string suitable for serialising
*
* @return string representation of available URLs
*/
- public String writeUrlsAsString();
+ String writeUrlsAsString();
/**
- * Set URL links from string
+ * Set URL links from pair of collections
*
- * @param cachedUrl
- * string representation of URL links, i.e. | separated
+ * @param names
+ * @param urls
*/
- public void setUrlLinks(String cachedUrl);
+ void setUrlLinks(Vector<String> names, Vector<String> urls)
+ throws IllegalArgumentException;
/**
- * Set URL links from collection
+ * Choose the default URL in the event of the selected default being
+ * unavailable
*
- * @param links
- * hashmap containing string indexed UrlLinks
+ * @return id of chosen default url
*/
- public void setUrlLinks(HashMap<String, UrlLink> links);
+ String chooseDefaultUrl();
}
--- /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.util;
+
+import java.util.Vector;
+import java.util.regex.Pattern;
+
+public class UrlProviderImpl implements UrlProviderI
+{
+ private static final Pattern MIRIAM_PATTERN = Pattern
+ .compile("^MIR:\\d{8}$");
+ protected String defaultUrl;
+
+ @Override
+ public Vector<String> getLinksForDisplay()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getDefaultUrl()
+ {
+ return defaultUrl;
+ }
+
+ @Override
+ public String getDefaultUrl(String seqid)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getDefaultTarget(String seqid)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean setDefaultUrl(String id)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public String writeUrlsAsString()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String chooseDefaultUrl()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ protected boolean isMiriamId(String id)
+ {
+ return MIRIAM_PATTERN.matcher(id).matches();
+ }
+
+
+
+}
git://source.jalview.org / jalview.git / commitdiff