Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / urls / UrlProviderImpl.java

diff --git a/src/jalview/urls/UrlProviderImpl.java b/src/jalview/urls/UrlProviderImpl.java
new file mode 100644 (file)
index 0000000..c1a57ca
--- /dev/null
+++ b/src/jalview/urls/UrlProviderImpl.java
@@ -0,0 +1,123 @@
+/*
+ * 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 jalview.urls.api.UrlProviderI;
+import jalview.util.UrlLink;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map.Entry;
+import java.util.regex.Pattern;
+
+/**
+ * Leaf node of UrlProvider composite
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+
+public abstract class UrlProviderImpl implements UrlProviderI
+{
+  // minimum length of substitution in url link string
+  protected static final int MIN_SUBST_LENGTH = 4;
+
+  private static final Pattern MIRIAM_PATTERN = Pattern
+          .compile("^MIR:\\d{8}$");
+
+  protected String primaryUrl;
+
+  protected String getPrimaryUrl(String seqid, HashMap<String, UrlLink> urls)
+  {
+    if (seqid.length() < MIN_SUBST_LENGTH)
+    {
+      return null;
+    }
+    else if (primaryUrl == null)
+    {
+      return null;
+    }
+    else if (!urls.containsKey(primaryUrl))
+    {
+      return null;
+    }
+    else
+    {
+      String url = null;
+      UrlLink urlLink = urls.get(primaryUrl);
+      String[] primaryUrls = urlLink.makeUrls(seqid, true);
+      if (primaryUrls == null || primaryUrls[0] == null
+              || primaryUrls[0].length() < MIN_SUBST_LENGTH)
+      {
+        url = null;
+      }
+      else
+      {
+        // just take first URL made from regex
+        url = primaryUrls[1];
+      }
+      return url;
+    }
+  }
+
+  @Override
+  public List<UrlLinkDisplay> getLinksForTable()
+  {
+    return null;
+  }
+
+  protected ArrayList<UrlLinkDisplay> getLinksForTable(
+          HashMap<String, UrlLink> urls, ArrayList<String> selectedUrls,
+          boolean selected)
+  {
+    ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+    for (Entry<String, UrlLink> entry : urls.entrySet())
+    {
+      String key = entry.getKey();
+      boolean isPrimary = (key.equals(primaryUrl));
+      boolean isSelected;
+      if (selectedUrls != null)
+      {
+        isSelected = selectedUrls.contains(key);
+      }
+      else
+      {
+        isSelected = selected;
+      }
+      displayLinks.add(new UrlLinkDisplay(key, entry.getValue(),
+              isSelected, isPrimary));
+    }
+    return displayLinks;
+  }
+
+  protected boolean isMiriamId(String id)
+  {
+    return MIRIAM_PATTERN.matcher(id).matches();
+  }
+
+  @Override
+  public boolean isUserEntry(String id)
+  {
+    return !isMiriamId(id);
+  }
+}
+