--- /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.urls;
+
+//import static jalview.util.UrlConstants.EMBLEBI_LABEL;
+//import static jalview.util.UrlConstants.EMBLEBI_STRING;
+//import static jalview.util.UrlConstants.SRS_LABEL;
+
+
+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.util.MessageManager;
+import jalview.util.UrlLink;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+/**
+ *
+ * Implements the UrlProviderI interface for a UrlProvider object which serves
+ * custom URLs defined by the user
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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
+ {
+ 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(DELIM + DB_ACCESSION + DELIM);
+ if (rxstart == -1)
+ {
+ rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
+ }
+ while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1)
+ {
+ url = url + SEP + st.nextToken();
+ }
+ urls.put(name, new UrlLink(name + SEP + url));
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(ex + "\nError parsing sequence links");
+ }
+ upgradeOldLinks();
+
+ }
+
+ /**
+ * Construct UrlProvider for custom (user-entered) URLs
+ *
+ * @param urlList
+ * list of URLs as (label,url) pairs
+ */
+ public CustomUrlProvider(Map<String, String> urlList)
+ {
+ try
+ {
+ 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();
+ }
+
+ /*
+ * Upgrade any legacy links which may have been left lying around
+ */
+ private void upgradeOldLinks()
+ {
+ // upgrade old SRS link
+ if (urls.containsKey(SRS_LABEL))
+ {
+ urls.remove(SRS_LABEL);
+ urls.put(DEFAULT_LABEL, new UrlLink(DEFAULT_STRING));
+ }
+ }
+
+ @Override
+ 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();
+ links.add(pair.getValue().toString());
+ }
+ return links;
+ }
+
+ @Override
+ public boolean setDefaultUrl(String id)
+ {
+ if (urls.containsKey(id))
+ {
+ defaultUrl = id;
+ }
+ else
+ {
+ defaultUrl = null;
+ }
+ return urls.containsKey(id);
+ }
+
+ @Override
+ public String writeUrlsAsString()
+ {
+ StringBuffer links = new StringBuffer();
+ if (urls.size() > 0)
+ {
+ for (UrlLink link : urls.values())
+ {
+ links.append(link.toString());
+ links.append(SEP);
+ }
+
+ // remove last SEP
+ links.setLength(links.length() - 1);
+ }
+ else
+ {
+ urls.clear();
+ }
+ return links.toString();
+ }
+
+ @Override
+ public String getDefaultUrl(String seqid)
+ {
+ 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 String getDefaultTarget(String seqid)
+ {
+ 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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff