--- /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.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.UrlConstants;
+import jalview.util.UrlLink;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.StringTokenizer;
+
+/**
+ *
+ * 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
+{
+ // Default sequence URL link label for SRS
+ private static final String SRS_LABEL = "SRS";
+
+ // map of string ids to urlLinks (selected)
+ private HashMap<String, UrlLink> selectedUrls;
+
+ // map of string ids to urlLinks (not selected)
+ private HashMap<String, UrlLink> nonselectedUrls;
+
+ /**
+ * Construct UrlProvider for custom (user-entered) URLs
+ *
+ * @param inMenuUrlList
+ * list of URLs set to be displayed in menu, in form stored in Cache.
+ * i.e. SEP delimited string
+ * @param storedUrlList
+ * list of custom URLs entered by user but not currently displayed in
+ * menu, in form stored in Cache
+ */
+ public CustomUrlProvider(String inMenuUrlList, String storedUrlList)
+ {
+ try
+ {
+ selectedUrls = parseUrlStrings(inMenuUrlList);
+ nonselectedUrls = parseUrlStrings(storedUrlList);
+ } catch (Exception ex)
+ {
+ System.out
+ .println(ex.getMessage() + "\nError parsing sequence links");
+ }
+ }
+
+ /**
+ * Construct UrlProvider for custom (user-entered) URLs
+ *
+ * @param urlList
+ * list of URLs to be displayed in menu, as (label,url) pairs
+ * @param storedUrlList
+ * list of custom URLs entered by user but not currently displayed in
+ * menu, as (label,url) pairs
+ */
+ public CustomUrlProvider(Map<String, String> inMenuUrlList,
+ Map<String, String> storedUrlList)
+ {
+ try
+ {
+ selectedUrls = parseUrlList(inMenuUrlList);
+ nonselectedUrls = parseUrlList(storedUrlList);
+ } catch (Exception ex)
+ {
+ System.out
+ .println(ex.getMessage() + "\nError parsing sequence links");
+ }
+ }
+
+ private HashMap<String, UrlLink> parseUrlStrings(String urlStrings)
+ {
+ // cachedUrlList is in form <label>|<url>|<label>|<url>...
+ // parse cachedUrlList into labels (used as id) and url links
+ HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+
+ StringTokenizer st = new StringTokenizer(urlStrings, SEP);
+ while (st.hasMoreElements())
+ {
+ String name = st.nextToken();
+
+ if (!isMiriamId(name))
+ {
+ // this one of our custom urls
+ 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
+ && st.hasMoreTokens())
+ {
+ url = url + SEP + st.nextToken();
+ }
+ urls.put(name, new UrlLink(name, url, name));
+ }
+ }
+ upgradeOldLinks(urls);
+ return urls;
+ }
+
+ private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
+ {
+ HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+ if (urlList == null)
+ {
+ return urls;
+ }
+
+ 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(), pair.getValue(),
+ pair.getKey()));
+ }
+ upgradeOldLinks(urls);
+ return urls;
+ }
+
+ /*
+ * Upgrade any legacy links which may have been left lying around
+ */
+ private void upgradeOldLinks(HashMap<String, UrlLink> urls)
+ {
+ // upgrade old SRS link
+ if (urls.containsKey(SRS_LABEL))
+ {
+ urls.remove(SRS_LABEL);
+ UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
+ link.setLabel(UrlConstants.DEFAULT_LABEL);
+ urls.put(UrlConstants.DEFAULT_LABEL, link);
+ }
+ }
+
+ @Override
+ public List<String> getLinksForMenu()
+ {
+ List<String> links = new ArrayList<String>();
+ Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
+ .iterator();
+ while (it.hasNext())
+ {
+ Map.Entry<String, UrlLink> pair = it.next();
+ links.add(pair.getValue().toString());
+ }
+ return links;
+ }
+
+ @Override
+ public List<UrlLinkDisplay> getLinksForTable()
+ {
+ ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+ displayLinks = getLinksForTable(selectedUrls, true);
+ displayLinks.addAll(getLinksForTable(nonselectedUrls, false));
+ return displayLinks;
+ }
+
+ private ArrayList<UrlLinkDisplay> getLinksForTable(
+ HashMap<String, UrlLink> urlList, boolean selected)
+ {
+ return super.getLinksForTable(urlList, null, selected);
+ }
+
+ @Override
+ public boolean setPrimaryUrl(String id)
+ {
+ if (selectedUrls.containsKey(id))
+ {
+ primaryUrl = id;
+ }
+ else if (nonselectedUrls.containsKey(id))
+ {
+ primaryUrl = id;
+ }
+ else
+ {
+ primaryUrl = null;
+ }
+
+ return (primaryUrl != null);
+ }
+
+ @Override
+ public String writeUrlsAsString(boolean selected)
+ {
+ StringBuffer links = new StringBuffer();
+ HashMap<String, UrlLink> urls;
+ if (selected)
+ {
+ urls = selectedUrls;
+ }
+ else
+ {
+ urls = nonselectedUrls;
+ }
+ if (urls.size() > 0)
+ {
+ for (Entry<String, UrlLink> entry : urls.entrySet())
+ {
+ links.append(entry.getValue().toString());
+ links.append(SEP);
+ }
+
+ // remove last SEP
+ links.setLength(links.length() - 1);
+ }
+ else
+ {
+ urls.clear();
+ }
+ return links.toString();
+ }
+
+ @Override
+ public String getPrimaryUrl(String seqid)
+ {
+ String result = super.getPrimaryUrl(seqid, selectedUrls);
+ if (result == null)
+ {
+ result = super.getPrimaryUrl(seqid, nonselectedUrls);
+ }
+ return result;
+ }
+
+ @Override
+ public String getPrimaryUrlId()
+ {
+ return primaryUrl;
+ }
+
+ @Override
+ public String getPrimaryTarget(String seqid)
+ {
+ return selectedUrls.get(primaryUrl).getTarget();
+ }
+
+ @Override
+ public void setUrlData(List<UrlLinkDisplay> links)
+ {
+ HashMap<String, UrlLink> unselurls = new HashMap<String, UrlLink>();
+ HashMap<String, UrlLink> selurls = new HashMap<String, UrlLink>();
+
+ Iterator<UrlLinkDisplay> it = links.iterator();
+ while (it.hasNext())
+ {
+ UrlLinkDisplay link = it.next();
+
+ // MIRIAM ids will be handled by a different UrlProvider class
+ if (!isMiriamId(link.getId()))
+ {
+ // don't allow duplicate key names as entries will be overwritten
+ if (unselurls.containsKey(link.getId())
+ || selurls.containsKey(link.getId()))
+ {
+ throw new IllegalArgumentException(MessageManager.formatMessage(
+ "exception.url_cannot_have_duplicate_id", link.getId()));
+ }
+ if (link.getIsSelected())
+ {
+ selurls.put(link.getId(),
+ new UrlLink(link.getDescription(), link.getUrl(), link.getDescription()));
+ }
+ else
+ {
+ unselurls
+ .put(link.getId(),
+ new UrlLink(link.getDescription(), link.getUrl(), link
+ .getDescription()));
+ }
+ // sort out primary and selected ids
+ if (link.getIsPrimary())
+ {
+ setPrimaryUrl(link.getId());
+ }
+ }
+
+ }
+ nonselectedUrls = unselurls;
+ selectedUrls = selurls;
+ }
+
+ @Override
+ public String choosePrimaryUrl()
+ {
+ // unilaterally set the primary id to the EMBL_EBI link
+ if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
+ && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
+ {
+ UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
+ link.setLabel(UrlConstants.DEFAULT_LABEL);
+ selectedUrls.put(UrlConstants.DEFAULT_LABEL, link);
+ }
+ primaryUrl = UrlConstants.DEFAULT_LABEL;
+ return UrlConstants.DEFAULT_LABEL;
+ }
+
+ @Override
+ public boolean contains(String id)
+ {
+ return (selectedUrls.containsKey(id) || nonselectedUrls.containsKey(id));
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff