X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FCustomUrlProvider.java;fp=src%2Fjalview%2Furls%2FCustomUrlProvider.java;h=07f406849eddc3810bf906f1d7249c83bbb4ca8a;hb=c437fc72420baf7b045d417fb6cabcebe87987c5;hp=0000000000000000000000000000000000000000;hpb=ede54837349adde8f7265c6d8fa58d14165ee215;p=jalview.git

diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java
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+/*
+ * 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));
+  }
+
+}