X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=89f1068e91691599078d0ccf77bf68592d61d3f6;hb=cd06f45d5fedf6fcc87c0d77aa6c2b1fb6ea7a46;hp=8469355a849ce7b56e6401e5110806080eaba833;hpb=5aa038bdff10329d3b895dceb8d6f5161820a55c;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8469355..89f1068 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -23,10 +23,12 @@ package jalview.io;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.util.DBRefUtils;
+import jalview.io.gff.GffConstants;
 import jalview.util.UrlLink;
 
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -140,8 +142,7 @@ public class SequenceAnnotationReport
           }
           else
           {
-            if (tmpString.indexOf("<") > -1
-                    || tmpString.indexOf(">") > -1)
+            if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
             {
               // The description does not specify html is to
               // be used, so we must remove < > symbols
@@ -166,8 +167,7 @@ public class SequenceAnnotationReport
                   .getType());
           if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
           {
-            sb.append(" Score=").append(
-                    String.valueOf(feature.getScore()));
+            sb.append(" Score=").append(String.valueOf(feature.getScore()));
           }
         }
         String status = (String) feature.getValue("status");
@@ -175,7 +175,8 @@ public class SequenceAnnotationReport
         {
           sb.append("; (").append(status).append(")");
         }
-        String clinSig = (String) feature.getValue("clinical_significance");
+        String clinSig = (String) feature
+                .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
         if (clinSig != null)
         {
           sb.append("; ").append(clinSig);
@@ -206,16 +207,17 @@ public class SequenceAnnotationReport
         {
           try
           {
-            for (String[] urllink : createLinksFrom(null, urlstring))
+            for (List<String> urllink : createLinksFrom(null, urlstring))
             {
               sb.append("<br/> <a href=\""
-                      + urllink[3]
+                      + urllink.get(3)
                       + "\" target=\""
-                      + urllink[0]
+                      + urllink.get(0)
                       + "\">"
-                      + (urllink[0].toLowerCase().equals(
-                              urllink[1].toLowerCase()) ? urllink[0]
-                              : (urllink[0] + ":" + urllink[1]))
+                      + (urllink.get(0).toLowerCase()
+                              .equals(urllink.get(1).toLowerCase()) ? urllink
+                              .get(0) : (urllink.get(0) + ":" + urllink
+                              .get(1)))
                       + "</a></br>");
             }
           } catch (Exception x)
@@ -234,127 +236,22 @@ public class SequenceAnnotationReport
    * 
    * @param seq
    * @param link
-   * @return String[][] { String[] { link target, link label, dynamic component
-   *         inserted (if any), url }}
+   * @return Collection< List<String> > { List<String> { link target, link
+   *         label, dynamic component inserted (if any), url }}
    */
-  String[][] createLinksFrom(SequenceI seq, String link)
+  Collection<List<String>> createLinksFrom(SequenceI seq, String link)
   {
-    List<String[]> urlSets = new ArrayList<String[]>();
-    List<String> uniques = new ArrayList<String>();
+    Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
     UrlLink urlLink = new UrlLink(link);
     if (!urlLink.isValid())
     {
       System.err.println(urlLink.getInvalidMessage());
       return null;
     }
-    if (seq != null && urlLink.isDynamic())
-    {
-      urlSets.addAll(createDynamicLinks(seq, urlLink, uniques));
-    }
-    else
-    {
-      String target = urlLink.getTarget();
-      String label = urlLink.getLabel();
-      String unq = label + "|" + urlLink.getUrl_prefix();
-      if (!uniques.contains(unq))
-      {
-        uniques.add(unq);
-        urlSets.add(new String[] { target, label, null,
-            urlLink.getUrl_prefix() });
-      }
-    }
-
-    return urlSets.toArray(new String[][] {});
-  }
 
-  /**
-   * Formats and returns a list of dynamic href links
-   * 
-   * @param seq
-   * @param urlLink
-   * @param uniques
-   */
-  List<String[]> createDynamicLinks(SequenceI seq, UrlLink urlLink,
-          List<String> uniques)
-  {
-    List<String[]> result = new ArrayList<String[]>();
-    final String target = urlLink.getTarget();
-    final String label = urlLink.getLabel();
+    urlLink.createLinksFromSeq(seq, urlSets);
 
-    // collect matching db-refs
-    DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
-            new String[] { target });
-    // collect id string too
-    String id = seq.getName();
-    String descr = seq.getDescription();
-    if (descr != null && descr.length() < 1)
-    {
-      descr = null;
-    }
-    if (dbr != null)
-    {
-      for (int r = 0; r < dbr.length; r++)
-      {
-        if (id != null && dbr[r].getAccessionId().equals(id))
-        {
-          // suppress duplicate link creation for the bare sequence ID
-          // string with this link
-          id = null;
-        }
-        // create Bare ID link for this URL
-        String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
-        if (urls != null)
-        {
-          for (int u = 0; u < urls.length; u += 2)
-          {
-            String unq = urls[u] + "|" + urls[u + 1];
-            if (!uniques.contains(unq))
-            {
-              result.add(new String[] { target, label, urls[u],
-                  urls[u + 1] });
-              uniques.add(unq);
-            }
-          }
-        }
-      }
-    }
-    if (id != null)
-    {
-      // create Bare ID link for this URL
-      String[] urls = urlLink.makeUrls(id, true);
-      if (urls != null)
-      {
-        for (int u = 0; u < urls.length; u += 2)
-        {
-          String unq = urls[u] + "|" + urls[u + 1];
-          if (!uniques.contains(unq))
-          {
-            result.add(new String[] { target, label, urls[u],
-                urls[u + 1] });
-            uniques.add(unq);
-          }
-        }
-      }
-    }
-    if (descr != null && urlLink.getRegexReplace() != null)
-    {
-      // create link for this URL from description only if regex matches
-      String[] urls = urlLink.makeUrls(descr, true);
-      if (urls != null)
-      {
-        for (int u = 0; u < urls.length; u += 2)
-        {
-          String unq = urls[u] + "|" + urls[u + 1];
-          if (!uniques.contains(unq))
-          {
-            result.add(new String[] { target, label, urls[u],
-                urls[u + 1] });
-            uniques.add(unq);
-          }
-        }
-      }
-    }
-    return result;
+    return urlSets.values();
   }
 
   public void createSequenceAnnotationReport(final StringBuffer tip,