X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=c8313664c86b70d07679fb7655dab9dd7d0bc019;hp=676404b941c5c9aadb50697f652f589e7f0450d0;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hpb=2672f9a72ffb8ffaf4b48a08e64de7f3d83ce061

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 676404b..c831366 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,15 +20,28 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.google.common.collect.Lists;
+
+import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 import jalview.util.UrlLink;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 /**
  * generate HTML reports for a sequence
@@ -37,147 +50,346 @@ import java.util.Map;
  */
 public class SequenceAnnotationReport
 {
-  final String linkImageURL;
+  private static final int MAX_DESCRIPTION_LENGTH = 40;
+
+  private static final String COMMA = ",";
+
+  private static final String ELLIPSIS = "...";
+
+  private static final int MAX_REFS_PER_SOURCE = 4;
+
+  private static final int MAX_SOURCES = 40;
+
+  private static String linkImageURL;
 
-  public SequenceAnnotationReport(String linkImageURL)
+  // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
+
+  /*
+   * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
+   * with 'Primary' sources placed before others, and 'chromosome' first of all
+   */
+  private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
   {
-    this.linkImageURL = linkImageURL;
+
+    @Override
+    public int compare(DBRefEntry ref1, DBRefEntry ref2)
+    {
+      if (ref1 instanceof GeneLociI)
+      {
+        return -1;
+      }
+      if (ref2 instanceof GeneLociI)
+      {
+        return 1;
+      }
+      String s1 = ref1.getSource();
+      String s2 = ref2.getSource();
+      boolean s1Primary = DBRefSource.isPrimarySource(s1);
+      boolean s2Primary = DBRefSource.isPrimarySource(s2);
+      if (s1Primary && !s2Primary)
+      {
+        return -1;
+      }
+      if (!s1Primary && s2Primary)
+      {
+        return 1;
+      }
+      int comp = s1 == null ? -1
+              : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
+      if (comp == 0)
+      {
+        String a1 = ref1.getAccessionId();
+        String a2 = ref2.getAccessionId();
+        comp = a1 == null ? -1
+                : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
+      }
+      return comp;
+    }
+
+    // private boolean isPrimarySource(String source)
+    // {
+    // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+    // {
+    // for (String s : primary)
+    // {
+    // if (source.equals(s))
+    // {
+    // return true;
+    // }
+    // }
+    // }
+    // return false;
+    // }
+  };
+
+  private boolean forTooltip;
+
+  /**
+   * Constructor given a flag which affects behaviour
+   * <ul>
+   * <li>if true, generates feature details suitable to show in a tooltip</li>
+   * <li>if false, generates feature details in a form suitable for the sequence
+   * details report</li>
+   * </ul>
+   * 
+   * @param isForTooltip
+   */
+  public SequenceAnnotationReport(boolean isForTooltip)
+  {
+    this.forTooltip = isForTooltip;
+    if (linkImageURL == null)
+    {
+      linkImageURL = getClass().getResource("/images/link.gif").toString();
+    }
   }
 
   /**
-   * Append text for the list of features to the tooltip
+   * Append text for the list of features to the tooltip. Returns the number of
+   * features not added if maxlength limit is (or would have been) reached.
    * 
-   * @param tooltipText2
-   * @param rpos
+   * @param sb
+   * @param residuePos
    * @param features
    * @param minmax
+   * @param maxlength
    */
-  public void appendFeatures(final StringBuffer tooltipText2, int rpos,
-          List<SequenceFeature> features, Map<String, float[][]> minmax)
+  public int appendFeatures(final StringBuilder sb, int residuePos,
+          List<SequenceFeature> features, FeatureRendererModel fr,
+          int maxlength)
   {
-    if (features != null)
+    for (int i = 0; i < features.size(); i++)
     {
-      for (SequenceFeature feature : features)
+      SequenceFeature feature = features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
       {
-        appendFeature(tooltipText2, rpos, minmax, feature);
+        return features.size() - i;
       }
     }
+    return 0;
   }
 
   /**
-   * Appends text for one sequence feature to the string buffer
+   * Appends text for mapped features (e.g. CDS feature for peptide or vice
+   * versa) Returns number of features left if maxlength limit is (or would have
+   * been) reached.
+   * 
+   * @param sb
+   * @param residuePos
+   * @param mf
+   * @param fr
+   * @param maxlength
+   */
+  public int appendFeatures(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr, int maxlength)
+  {
+    for (int i = 0; i < mf.features.size(); i++)
+    {
+      SequenceFeature feature = mf.features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
+      {
+        return mf.features.size() - i;
+      }
+    }
+    return 0;
+  }
+
+  /**
+   * Appends the feature at rpos to the given buffer
    * 
    * @param sb
    * @param rpos
    * @param minmax
-   *          {{min, max}, {min, max}} positional and non-positional feature
-   *          scores for this type
    * @param feature
    */
-  void appendFeature(final StringBuffer sb, int rpos,
-          Map<String, float[][]> minmax, SequenceFeature feature)
+  boolean appendFeature(final StringBuilder sb0, int rpos,
+          FeatureRendererModel fr, SequenceFeature feature,
+          MappedFeatures mf, int maxlength)
   {
-    if ("disulfide bond".equals(feature.getType()))
+    int begin = feature.getBegin();
+    int end = feature.getEnd();
+
+    /*
+     * if this is a virtual features, convert begin/end to the
+     * coordinates of the sequence it is mapped to
+     */
+    int[] beginRange = null; // feature start in local coordinates
+    int[] endRange = null; // feature end in local coordinates
+    if (mf != null)
     {
-      if (feature.getBegin() == rpos || feature.getEnd() == rpos)
+      if (feature.isContactFeature())
       {
-        if (sb.length() > 6)
-        {
-          sb.append("<br>");
-        }
-        sb.append("disulfide bond ").append(feature.getBegin()).append(":")
-                .append(feature.getEnd());
+        /*
+         * map start and end points individually
+         */
+        beginRange = mf.getMappedPositions(begin, begin);
+        endRange = begin == end ? beginRange
+                : mf.getMappedPositions(end, end);
+      }
+      else
+      {
+        /*
+         * map the feature extent
+         */
+        beginRange = mf.getMappedPositions(begin, end);
+        endRange = beginRange;
+      }
+      if (beginRange == null || endRange == null)
+      {
+        // something went wrong
+        return false;
       }
+      begin = beginRange[0];
+      end = endRange[endRange.length - 1];
     }
-    else
+
+    StringBuilder sb = new StringBuilder();
+    if (feature.isContactFeature())
     {
-      if (sb.length() > 6)
+      /*
+       * include if rpos is at start or end position of [mapped] feature
+       */
+      boolean showContact = (mf == null) && (rpos == begin || rpos == end);
+      boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0]
+              && rpos <= beginRange[beginRange.length - 1])
+              || (rpos >= endRange[0]
+                      && rpos <= endRange[endRange.length - 1]));
+      if (showContact || showMappedContact)
       {
-        sb.append("<br>");
+        if (sb0.length() > 6)
+        {
+          sb.append("<br/>");
+        }
+        sb.append(feature.getType()).append(" ").append(begin).append(":")
+                .append(end);
       }
-      // TODO: remove this hack to display link only features
-      boolean linkOnly = feature.getValue("linkonly") != null;
-      if (!linkOnly)
+      return appendText(sb0, sb, maxlength);
+    }
+
+    if (sb0.length() > 6)
+    {
+      sb.append("<br/>");
+    }
+    // TODO: remove this hack to display link only features
+    boolean linkOnly = feature.getValue("linkonly") != null;
+    if (!linkOnly)
+    {
+      sb.append(feature.getType()).append(" ");
+      if (rpos != 0)
       {
-        sb.append(feature.getType()).append(" ");
-        if (rpos != 0)
+        // we are marking a positional feature
+        sb.append(begin);
+        if (begin != end)
         {
-          // we are marking a positional feature
-          sb.append(feature.begin);
+          sb.append(" ").append(end);
         }
-        if (feature.begin != feature.end)
+      }
+
+      String description = feature.getDescription();
+      if (description != null && !description.equals(feature.getType()))
+      {
+        description = StringUtils.stripHtmlTags(description);
+
+        /*
+         * truncate overlong descriptions unless they contain an href
+         * before the truncation point (as truncation could leave corrupted html)
+         */
+        int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
+        boolean hasLink = linkindex > -1
+                && linkindex < MAX_DESCRIPTION_LENGTH;
+        if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
         {
-          sb.append(" " + feature.end);
+          description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+                  + ELLIPSIS;
         }
 
-        if (feature.getDescription() != null
-                && !feature.description.equals(feature.getType()))
-        {
-          String tmpString = feature.getDescription();
-          String tmp2up = tmpString.toUpperCase();
-          final int startTag = tmp2up.indexOf("<HTML>");
-          if (startTag > -1)
-          {
-            tmpString = tmpString.substring(startTag + 6);
-            tmp2up = tmp2up.substring(startTag + 6);
-          }
-          // TODO strips off </body> but not <body> - is that intended?
-          int endTag = tmp2up.indexOf("</BODY>");
-          if (endTag > -1)
-          {
-            tmpString = tmpString.substring(0, endTag);
-            tmp2up = tmp2up.substring(0, endTag);
-          }
-          endTag = tmp2up.indexOf("</HTML>");
-          if (endTag > -1)
-          {
-            tmpString = tmpString.substring(0, endTag);
-          }
+        sb.append("; ").append(description);
+      }
 
-          if (startTag > -1)
-          {
-            sb.append("; ").append(tmpString);
-          }
-          else
-          {
-            if (tmpString.indexOf("<") > -1
-                    || tmpString.indexOf(">") > -1)
-            {
-              // The description does not specify html is to
-              // be used, so we must remove < > symbols
-              tmpString = tmpString.replaceAll("<", "&lt;");
-              tmpString = tmpString.replaceAll(">", "&gt;");
-              sb.append("; ").append(tmpString);
-            }
-            else
-            {
-              sb.append("; ").append(tmpString);
-            }
-          }
-        }
+      if (showScore(feature, fr))
+      {
+        sb.append(" Score=").append(String.valueOf(feature.getScore()));
+      }
+      String status = (String) feature.getValue("status");
+      if (status != null && status.length() > 0)
+      {
+        sb.append("; (").append(status).append(")");
+      }
 
-        /*
-         * score should be shown if there is one, and min != max
-         * for this feature type (e.g. not all 0)
-         */
-        if (!Float.isNaN(feature.getScore()))
+      /*
+       * add attribute value if coloured by attribute
+       */
+      if (fr != null)
+      {
+        FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
+        if (fc != null && fc.isColourByAttribute())
         {
-          float[][] rng = (minmax == null) ? null : minmax.get(feature
-                  .getType());
-          if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
+          String[] attName = fc.getAttributeName();
+          String attVal = feature.getValueAsString(attName);
+          if (attVal != null)
           {
-            sb.append(" Score=").append(
-                    String.valueOf(feature.getScore()));
+            sb.append("; ").append(String.join(":", attName)).append("=")
+                    .append(attVal);
           }
         }
-        String status = (String) feature.getValue("status");
-        if (status != null && status.length() > 0)
+      }
+
+      if (mf != null)
+      {
+        String variants = mf.findProteinVariants(feature);
+        if (!variants.isEmpty())
         {
-          sb.append("; (").append(status).append(")");
+          sb.append(" ").append(variants);
         }
       }
     }
-    appendLinks(sb, feature);
+    return appendText(sb0, sb, maxlength);
+  }
+
+  /**
+   * Appends sb to sb0, and returns false, unless maxlength is not zero and
+   * appending would make the result longer than or equal to maxlength, in which
+   * case the append is not done and returns true
+   * 
+   * @param sb0
+   * @param sb
+   * @param maxlength
+   * @return
+   */
+  private static boolean appendText(StringBuilder sb0, StringBuilder sb,
+          int maxlength)
+  {
+    if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
+    {
+      sb0.append(sb);
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Answers true if score should be shown, else false. Score is shown if it is
+   * not NaN, and the feature type has a non-trivial min-max score range
+   */
+  boolean showScore(SequenceFeature feature, FeatureRendererModel fr)
+  {
+    if (Float.isNaN(feature.getScore()))
+    {
+      return false;
+    }
+    if (fr == null)
+    {
+      return true;
+    }
+    float[][] minMax = fr.getMinMax().get(feature.getType());
+
+    /*
+     * minMax[0] is the [min, max] score range for positional features
+     */
+    if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1])
+    {
+      return false;
+    }
+    return true;
   }
 
   /**
@@ -201,22 +413,21 @@ public class SequenceAnnotationReport
         {
           try
           {
-            for (String[] urllink : createLinksFrom(null, urlstring))
+            for (List<String> urllink : createLinksFrom(null, urlstring))
             {
-              sb.append("<br/> <a href=\""
-                      + urllink[3]
-                      + "\" target=\""
-                      + urllink[0]
-                      + "\">"
-                      + (urllink[0].toLowerCase().equals(
-                              urllink[1].toLowerCase()) ? urllink[0]
-                              : (urllink[0] + ":" + urllink[1]))
-                      + "</a></br>");
+              sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
+                      + urllink.get(0) + "\">"
+                      + (urllink.get(0).toLowerCase(Locale.ROOT).equals(
+                              urllink.get(1).toLowerCase(Locale.ROOT))
+                                      ? urllink.get(0)
+                                      : (urllink.get(0) + ":"
+                                              + urllink.get(1)))
+                      + "</a><br/>");
             }
           } catch (Exception x)
           {
-            System.err.println("problem when creating links from "
-                    + urlstring);
+            System.err.println(
+                    "problem when creating links from " + urlstring);
             x.printStackTrace();
           }
         }
@@ -229,191 +440,204 @@ 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<>();
     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[][] {});
-  }
+    urlLink.createLinksFromSeq(seq, urlSets);
 
-  /**
-   * 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();
-
-    // 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,
+  public void createSequenceAnnotationReport(final StringBuilder tip,
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
-          Map<String, float[][]> minmax)
+          FeatureRendererModel fr)
   {
     createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
-            true, minmax);
+            fr, false);
   }
 
-  public void createSequenceAnnotationReport(final StringBuffer tip,
+  /**
+   * Builds an html formatted report of sequence details and appends it to the
+   * provided buffer.
+   * 
+   * @param sb
+   *          buffer to append report to
+   * @param sequence
+   *          the sequence the report is for
+   * @param showDbRefs
+   *          whether to include database references for the sequence
+   * @param showNpFeats
+   *          whether to include non-positional sequence features
+   * @param fr
+   * @param summary
+   * @return
+   */
+  int createSequenceAnnotationReport(final StringBuilder sb,
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
-          boolean tableWrap, Map<String, float[][]> minmax)
+          FeatureRendererModel fr, boolean summary)
   {
     String tmp;
-    tip.append("<i>");
+    sb.append("<i>");
 
     int maxWidth = 0;
     if (sequence.getDescription() != null)
     {
       tmp = sequence.getDescription();
-      tip.append("<br>" + tmp);
+      sb.append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
+    sb.append("\n");
     SequenceI ds = sequence;
     while (ds.getDatasetSequence() != null)
     {
       ds = ds.getDatasetSequence();
     }
-    DBRefEntry[] dbrefs = ds.getDBRefs();
-    if (showDbRefs && dbrefs != null)
+
+    if (showDbRefs)
+    {
+      maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
+    }
+    sb.append("\n");
+
+    /*
+     * add non-positional features if wanted
+     */
+    if (showNpFeats)
     {
-      for (int i = 0; i < dbrefs.length; i++)
+      for (SequenceFeature sf : sequence.getFeatures()
+              .getNonPositionalFeatures())
       {
-        tip.append("<br>");
-        tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
-        tip.append(tmp);
-        maxWidth = Math.max(maxWidth, tmp.length());
+        int sz = -sb.length();
+        appendFeature(sb, 0, fr, sf, null, 0);
+        sz += sb.length();
+        maxWidth = Math.max(maxWidth, sz);
       }
     }
+    sb.append("</i>");
+    return maxWidth;
+  }
+
+  /**
+   * A helper method that appends any DBRefs, returning the maximum line length
+   * added
+   * 
+   * @param sb
+   * @param ds
+   * @param summary
+   * @return
+   */
+  protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
+          boolean summary)
+  {
+    List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
+
+    if (dbrefset == null)
+    {
+      return 0;
+    }
 
-    // ADD NON POSITIONAL SEQUENCE INFO
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (showNpFeats && features != null)
+    // PATCH for JAL-3980 defensive copy
+
+    dbrefs = new ArrayList<DBRefEntry>();
+
+    dbrefs.addAll(dbrefset);
+
+    // note this sorts the refs held on the sequence!
+    dbrefs.sort(comparator);
+    boolean ellipsis = false;
+    String source = null;
+    String lastSource = null;
+    int countForSource = 0;
+    int sourceCount = 0;
+    boolean moreSources = false;
+    int maxLineLength = 0;
+    int lineLength = 0;
+
+    for (DBRefEntry ref : dbrefs)
     {
-      for (int i = 0; i < features.length; i++)
+      source = ref.getSource();
+      if (source == null)
       {
-        if (features[i].begin == 0 && features[i].end == 0)
+        // shouldn't happen
+        continue;
+      }
+      boolean sourceChanged = !source.equals(lastSource);
+      if (sourceChanged)
+      {
+        lineLength = 0;
+        countForSource = 0;
+        sourceCount++;
+      }
+      if (sourceCount > MAX_SOURCES && summary)
+      {
+        ellipsis = true;
+        moreSources = true;
+        break;
+      }
+      lastSource = source;
+      countForSource++;
+      if (countForSource == 1 || !summary)
+      {
+        sb.append("<br/>\n");
+      }
+      if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
+      {
+        String accessionId = ref.getAccessionId();
+        lineLength += accessionId.length() + 1;
+        if (countForSource > 1 && summary)
+        {
+          sb.append(",\n ").append(accessionId);
+          lineLength++;
+        }
+        else
         {
-          int sz = -tip.length();
-          List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
-          tfeat.add(features[i]);
-          appendFeatures(tip, 0, tfeat, minmax);
-          sz += tip.length();
-          maxWidth = Math.max(maxWidth, sz);
+          sb.append(source).append(" ").append(accessionId);
+          lineLength += source.length();
         }
+        maxLineLength = Math.max(maxLineLength, lineLength);
+      }
+      if (countForSource == MAX_REFS_PER_SOURCE && summary)
+      {
+        sb.append(COMMA).append(ELLIPSIS);
+        ellipsis = true;
       }
     }
-
-    if (tableWrap && maxWidth > 60)
+    if (moreSources)
     {
-      tip.insert(0, "<table width=350 border=0><tr><td><i>");
-      tip.append("</i></td></tr></table>");
+      sb.append("<br/>\n").append(source).append(COMMA).append(ELLIPSIS);
+    }
+    if (ellipsis)
+    {
+      sb.append("<br/>\n(");
+      sb.append(MessageManager.getString("label.output_seq_details"));
+      sb.append(")");
     }
 
+    return maxLineLength;
+  }
+
+  public void createTooltipAnnotationReport(final StringBuilder tip,
+          SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
+          FeatureRendererModel fr)
+  {
+    int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+            showNpFeats, fr, true);
+
+    if (maxWidth > 60)
+    {
+      // ? not sure this serves any useful purpose
+      // tip.insert(0, "<table width=350 border=0><tr><td>");
+      // tip.append("</td></tr></table>");
+    }
   }
 }