X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FCustomUrlProvider.java;h=86d5660b3e1df0b749a1c62f9ef46d8133faa78a;hb=14307f5cfcbc90c419c892434613a500ca550ecc;hp=d88c57166eebead3c601d38e7c1c0f73310fddb8;hpb=7b733c615ca6ef20fd2e330c89aa566de0d4836f;p=jalview.git

diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java
index d88c571..86d5660 100644
--- a/src/jalview/urls/CustomUrlProvider.java
+++ b/src/jalview/urls/CustomUrlProvider.java
@@ -27,13 +27,16 @@ 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;
-import java.util.Vector;
 
 /**
  * 
@@ -45,34 +48,75 @@ import java.util.Vector;
  */
 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;
+  // 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 cachedUrlList
-   *          list of URLs in form stored in Cache. i.e. SEP delimited string
+   * @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(String cachedUrlList)
+  public CustomUrlProvider(Map<String, String> inMenuUrlList,
+          Map<String, String> storedUrlList)
   {
     try
     {
-      urls = new HashMap<String, UrlLink>();
+      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>();
 
-      // 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())
+    StringTokenizer st = new StringTokenizer(urlStrings, SEP);
+    while (st.hasMoreElements())
+    {
+      String name = st.nextToken();
+
+      if (!isMiriamId(name))
       {
-        String name = st.nextToken();
+        // this one of our custom urls
         String url = st.nextToken();
         // check for '|' within a regex
         int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
@@ -85,60 +129,67 @@ public class CustomUrlProvider extends UrlProviderImpl
         {
           url = url + SEP + st.nextToken();
         }
-        urls.put(name, new UrlLink(name + SEP + url));
+        urls.put(name, new UrlLink(name, url, name));
       }
-    } catch (Exception ex)
-    {
-      System.out.println(ex + "\nError parsing sequence links");
     }
-    upgradeOldLinks();
-
+    upgradeOldLinks(urls);
+    return urls;
   }
 
-  /**
-   * Construct UrlProvider for custom (user-entered) URLs
-   * 
-   * @param urlList
-   *          list of URLs as (label,url) pairs
-   */
-  public CustomUrlProvider(Map<String, String> urlList)
+  private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
   {
-    try
+    HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
+    if (urlList == null)
     {
-      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)
+      return urls;
+    }
+
+    Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator();
+    while (it.hasNext())
     {
-      System.out.println(ex + "\nError parsing sequence links");
+      Map.Entry<String, String> pair = it.next();
+      urls.put(pair.getKey(),
+              new UrlLink(pair.getKey(), pair.getValue(), pair.getKey()));
     }
-    upgradeOldLinks();
+    upgradeOldLinks(urls);
+    return urls;
   }
 
   /*
    * Upgrade any legacy links which may have been left lying around
    */
-  private void upgradeOldLinks()
+  private void upgradeOldLinks(HashMap<String, UrlLink> urls)
   {
+    boolean upgrade = false;
     // upgrade old SRS link
     if (urls.containsKey(SRS_LABEL))
     {
       urls.remove(SRS_LABEL);
-      urls.put(DEFAULT_LABEL, new UrlLink(DEFAULT_STRING));
+      upgrade = true;
+    }
+    // upgrade old EBI link - easier just to remove and re-add than faffing
+    // around checking exact url
+    if (urls.containsKey(UrlConstants.DEFAULT_LABEL))
+    {
+      // note because this is called separately for selected and nonselected
+      // urls, the default url will not always be present
+      urls.remove(UrlConstants.DEFAULT_LABEL);
+      upgrade = true;
+    }
+    if (upgrade)
+    {
+      UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
+      link.setLabel(UrlConstants.DEFAULT_LABEL);
+      urls.put(UrlConstants.DEFAULT_LABEL, link);
     }
   }
 
   @Override
-  public Vector<String> getLinksForDisplay()
+  public List<String> getLinksForMenu()
   {
-    Vector<String> links = new Vector<String>();
-    Iterator<Map.Entry<String, UrlLink>> it = urls.entrySet().iterator();
+    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();
@@ -148,28 +199,57 @@ public class CustomUrlProvider extends UrlProviderImpl
   }
 
   @Override
-  public boolean setDefaultUrl(String id)
+  public List<UrlLinkDisplay> getLinksForTable()
   {
-    if (urls.containsKey(id))
+    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))
     {
-      defaultUrl = id;
+      primaryUrl = id;
     }
     else
     {
-      defaultUrl = null;
+      primaryUrl = null;
     }
-    return urls.containsKey(id);
+
+    return (primaryUrl != null);
   }
 
   @Override
-  public String writeUrlsAsString()
+  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 (UrlLink link : urls.values())
+      for (Entry<String, UrlLink> entry : urls.entrySet())
       {
-        links.append(link.toString());
+        links.append(entry.getValue().toString());
         links.append(SEP);
       }
 
@@ -184,80 +264,91 @@ public class CustomUrlProvider extends UrlProviderImpl
   }
 
   @Override
-  public String getDefaultUrl(String seqid)
+  public String getPrimaryUrl(String seqid)
   {
-    if (defaultUrl == null)
+    String result = super.getPrimaryUrl(seqid, selectedUrls);
+    if (result == null)
     {
-      return null;
+      result = super.getPrimaryUrl(seqid, nonselectedUrls);
     }
-
-    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;
+    return result;
   }
 
   @Override
-  public String getDefaultTarget(String seqid)
+  public String getPrimaryUrlId()
   {
-    return urls.get(defaultUrl).getTarget();
+    return primaryUrl;
   }
 
   @Override
-  public void setUrlLinks(Vector<String> names, Vector<String> urlstrings)
+  public String getPrimaryTarget(String seqid)
   {
-    HashMap<String, UrlLink> newurls = new HashMap<String, UrlLink>();
+    return selectedUrls.get(primaryUrl).getTarget();
+  }
 
-    // should check that lists are same length but this function is likely
-    // to change once the Preferences dialog is rebuilt
+  @Override
+  public void setUrlData(List<UrlLinkDisplay> links)
+  {
+    HashMap<String, UrlLink> unselurls = new HashMap<String, UrlLink>();
+    HashMap<String, UrlLink> selurls = new HashMap<String, UrlLink>();
 
-    for (int i = 0; i < names.size(); ++i)
+    Iterator<UrlLinkDisplay> it = links.iterator();
+    while (it.hasNext())
     {
-      // 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)))
+      UrlLinkDisplay link = it.next();
+
+      // MIRIAM ids will be handled by a different UrlProvider class
+      if (!isMiriamId(link.getId()))
       {
-        throw new IllegalArgumentException(MessageManager.formatMessage(
-                "exception.url_cannot_have_duplicate_id",
-                names.elementAt(i)));
+        // 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());
+        }
       }
-      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;
 
+    }
+    nonselectedUrls = unselurls;
+    selectedUrls = selurls;
   }
 
   @Override
-  public String chooseDefaultUrl()
+  public String choosePrimaryUrl()
   {
-    // unilaterally set the default id to the EMBL_EBI link
-    
-    if (!urls.containsKey(DEFAULT_LABEL))
+    // unilaterally set the primary id to the EMBL_EBI link
+    if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
+            && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
     {
-      urls.put(DEFAULT_LABEL, new UrlLink(DEFAULT_STRING));
+      UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
+      link.setLabel(UrlConstants.DEFAULT_LABEL);
+      selectedUrls.put(UrlConstants.DEFAULT_LABEL, link);
     }
-    defaultUrl = DEFAULT_LABEL;
-    return DEFAULT_LABEL;
+    primaryUrl = UrlConstants.DEFAULT_LABEL;
+    return UrlConstants.DEFAULT_LABEL;
+  }
+
+  @Override
+  public boolean contains(String id)
+  {
+    return (selectedUrls.containsKey(id)
+            || nonselectedUrls.containsKey(id));
   }
 
 }