X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=369839a8c0fbda24c239edb0dc475f67f022b19f;hp=ffc0be3dddf7fd67353eccce1c65425ab880a1b2;hb=70a6730dba4ab0af6906fd8f874fe853c02efef0;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index ffc0be3..369839a 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,25 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+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.MessageManager;
+import jalview.util.StringUtils;
 import jalview.util.UrlLink;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 /**
  * generate HTML reports for a sequence
@@ -36,351 +47,587 @@ import java.util.List;
  */
 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 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>()
+  {
+
+    @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;
+    // }
+  };
 
-  public SequenceAnnotationReport(String linkImageURL)
+  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.linkImageURL = linkImageURL;
+    this.forTooltip = isForTooltip;
+    if (linkImageURL == null)
+    {
+      linkImageURL = getClass().getResource("/images/link.gif").toString();
+    }
   }
 
   /**
-   * appends the features at rpos to the given stringbuffer ready for display in
-   * a 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 linkImageURL
-   * @param rpos
+   * @param sb
+   * @param residuePos
    * @param features
-   *          TODO refactor to Jalview 'utilities' somehow.
+   * @param minmax
+   * @param maxlength
    */
-  public void appendFeatures(final StringBuffer tooltipText2, int rpos,
-          List<SequenceFeature> features)
+  public int appendFeatures(final StringBuilder sb, int residuePos,
+          List<SequenceFeature> features, FeatureRendererModel fr,
+          int maxlength)
   {
-    appendFeatures(tooltipText2, rpos, features, null);
+    for (int i = 0; i < features.size(); i++)
+    {
+      SequenceFeature feature = features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
+      {
+        return features.size() - i;
+      }
+    }
+    return 0;
   }
 
-  public void appendFeatures(final StringBuffer tooltipText2, int rpos,
-          List<SequenceFeature> features, Hashtable minmax)
+  /**
+   * 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)
   {
-    String tmpString;
-    if (features != null)
+    for (int i = 0; i < mf.features.size(); i++)
     {
-      for (SequenceFeature feature : features)
+      SequenceFeature feature = mf.features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
       {
-        if (feature.getType().equals("disulfide bond"))
+        return mf.features.size() - i;
+      }
+    }
+    return 0;
+  }
+
+  /**
+   * Appends the feature at rpos to the given buffer
+   * 
+   * @param sb
+   * @param rpos
+   * @param minmax
+   * @param feature
+   */
+  boolean appendFeature(final StringBuilder sb0, int rpos,
+          FeatureRendererModel fr, SequenceFeature feature,
+          MappedFeatures mf, int maxlength)
+  {
+    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.isContactFeature())
+      {
+        /*
+         * 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];
+    }
+
+    StringBuilder sb = new StringBuilder();
+    if (feature.isContactFeature())
+    {
+      /*
+       * 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)
+      {
+        if (sb0.length() > 6)
         {
-          if (feature.getBegin() == rpos || feature.getEnd() == rpos)
-          {
-            if (tooltipText2.length() > 6)
-            {
-              tooltipText2.append("<br>");
-            }
-            tooltipText2.append("disulfide bond " + feature.getBegin()
-                    + ":" + feature.getEnd());
-          }
+          sb.append("<br/>");
         }
-        else
+        sb.append(feature.getType()).append(" ").append(begin).append(":")
+                .append(end);
+      }
+      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)
+      {
+        // we are marking a positional feature
+        sb.append(begin);
+        if (begin != end)
         {
-          if (tooltipText2.length() > 6)
-          {
-            tooltipText2.append("<br>");
-          }
-          // TODO: remove this hack to display link only features
-          boolean linkOnly = feature.getValue("linkonly") != null;
-          if (!linkOnly)
-          {
-            tooltipText2.append(feature.getType() + " ");
-            if (rpos != 0)
-            {
-              // we are marking a positional feature
-              tooltipText2.append(feature.begin);
-            }
-            if (feature.begin != feature.end)
-            {
-              tooltipText2.append(" " + feature.end);
-            }
+          sb.append(" ").append(end);
+        }
+      }
 
-            if (feature.getDescription() != null
-                    && !feature.description.equals(feature.getType()))
-            {
-              tmpString = feature.getDescription();
-              String tmp2up = tmpString.toUpperCase();
-              int startTag = tmp2up.indexOf("<HTML>");
-              if (startTag > -1)
-              {
-                tmpString = tmpString.substring(startTag + 6);
-                tmp2up = tmp2up.substring(startTag + 6);
-              }
-              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);
-              }
-
-              if (startTag > -1)
-              {
-                tooltipText2.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;");
-
-                  tooltipText2.append("; ");
-                  tooltipText2.append(tmpString);
-
-                }
-                else
-                {
-                  tooltipText2.append("; " + tmpString);
-                }
-              }
-            }
-            // check score should be shown
-            if (!Float.isNaN(feature.getScore()))
-            {
-              float[][] rng = (minmax == null) ? null : ((float[][]) minmax
-                      .get(feature.getType()));
-              if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
-              {
-                tooltipText2.append(" Score=" + feature.getScore());
-              }
-            }
-            if (feature.getValue("status") != null)
-            {
-              String status = feature.getValue("status").toString();
-              if (status.length() > 0)
-              {
-                tooltipText2.append("; (" + feature.getValue("status")
-                        + ")");
-              }
-            }
-          }
+      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)
+        {
+          description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+                  + ELLIPSIS;
         }
-        if (feature.links != null)
+
+        sb.append("; ").append(description);
+      }
+
+      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(")");
+      }
+
+      /*
+       * add attribute value if coloured by attribute
+       */
+      if (fr != null)
+      {
+        FeatureColourI fc = fr.getFeatureColours().get(feature.getType());
+        if (fc != null && fc.isColourByAttribute())
         {
-          if (linkImageURL != null)
+          String[] attName = fc.getAttributeName();
+          String attVal = feature.getValueAsString(attName);
+          if (attVal != null)
           {
-            tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
-          }
-          else
-          {
-            for (String urlstring : feature.links)
-            {
-              try
-              {
-                for (String[] urllink : createLinksFrom(null, urlstring))
-                {
-                  tooltipText2.append("<br/> <a href=\""
-                          + urllink[3]
-                          + "\" target=\""
-                          + urllink[0]
-                          + "\">"
-                          + (urllink[0].toLowerCase().equals(
-                                  urllink[1].toLowerCase()) ? urllink[0]
-                                  : (urllink[0] + ":" + urllink[1]))
-                          + "</a></br>");
-                }
-              } catch (Exception x)
-              {
-                System.err.println("problem when creating links from "
-                        + urlstring);
-                x.printStackTrace();
-              }
-            }
+            sb.append("; ").append(String.join(":", attName)).append("=")
+                    .append(attVal);
           }
+        }
+      }
 
+      if (mf != null)
+      {
+        String variants = mf.findProteinVariants(feature);
+        if (!variants.isEmpty())
+        {
+          sb.append(" ").append(variants);
         }
       }
     }
+    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 seq
-   * @param link
-   * @return String[][] { String[] { link target, link label, dynamic component
-   *         inserted (if any), url }}
+   * @param sb0
+   * @param sb
+   * @param maxlength
+   * @return
    */
-  public String[][] createLinksFrom(SequenceI seq, String link)
+  private static boolean appendText(StringBuilder sb0, StringBuilder sb,
+          int maxlength)
   {
-    ArrayList<String[]> urlSets = new ArrayList<String[]>();
-    ArrayList<String> uniques = new ArrayList<String>();
-    UrlLink urlLink = new UrlLink(link);
-    if (!urlLink.isValid())
+    if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
     {
-      System.err.println(urlLink.getInvalidMessage());
-      return null;
+      sb0.append(sb);
+      return false;
     }
-    final String target = urlLink.getTarget(); // link.substring(0,
-    // link.indexOf("|"));
-    final String label = urlLink.getLabel();
-    if (seq != null && urlLink.isDynamic())
+    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());
 
-      // collect matching db-refs
-      DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
-              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)
+    /*
+     * 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;
+  }
+
+  /**
+   * Format and appends any hyperlinks for the sequence feature to the string
+   * buffer
+   * 
+   * @param sb
+   * @param feature
+   */
+  void appendLinks(final StringBuffer sb, SequenceFeature feature)
+  {
+    if (feature.links != null)
+    {
+      if (linkImageURL != 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 RUL
-          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))
-              {
-                urlSets.add(new String[] { target, label, urls[u],
-                    urls[u + 1] });
-                uniques.add(unq);
-              }
-            }
-          }
-        }
+        sb.append(" <img src=\"" + linkImageURL + "\">");
       }
-      if (id != null)
+      else
       {
-        // create Bare ID link for this RUL
-        String[] urls = urlLink.makeUrls(id, true);
-        if (urls != null)
+        for (String urlstring : feature.links)
         {
-          for (int u = 0; u < urls.length; u += 2)
+          try
           {
-            String unq = urls[u] + "|" + urls[u + 1];
-            if (!uniques.contains(unq))
+            for (List<String> urllink : createLinksFrom(null, urlstring))
             {
-              urlSets.add(new String[] { target, label, urls[u],
-                  urls[u + 1] });
-              uniques.add(unq);
+              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/>");
             }
-          }
-        }
-      }
-      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)
+          } catch (Exception x)
           {
-            String unq = urls[u] + "|" + urls[u + 1];
-            if (!uniques.contains(unq))
-            {
-              urlSets.add(new String[] { target, label, urls[u],
-                  urls[u + 1] });
-              uniques.add(unq);
-            }
+            System.err.println(
+                    "problem when creating links from " + urlstring);
+            x.printStackTrace();
           }
         }
       }
 
     }
-    else
+  }
+
+  /**
+   * 
+   * @param seq
+   * @param link
+   * @return Collection< List<String> > { List<String> { link target, link
+   *         label, dynamic component inserted (if any), url }}
+   */
+  Collection<List<String>> createLinksFrom(SequenceI seq, String link)
+  {
+    Map<String, List<String>> urlSets = new LinkedHashMap<>();
+    UrlLink urlLink = new UrlLink(link);
+    if (!urlLink.isValid())
     {
-      String unq = label + "|" + urlLink.getUrl_prefix();
-      if (!uniques.contains(unq))
-      {
-        uniques.add(unq);
-        // Add a non-dynamic link
-        urlSets.add(new String[] { target, label, null,
-            urlLink.getUrl_prefix() });
-      }
+      System.err.println(urlLink.getInvalidMessage());
+      return null;
     }
 
-    return urlSets.toArray(new String[][] {});
+    urlLink.createLinksFromSeq(seq, urlSets);
+
+    return urlSets.values();
   }
 
-  public void createSequenceAnnotationReport(final StringBuffer tip,
+  public void createSequenceAnnotationReport(final StringBuilder tip,
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
-          Hashtable 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, Hashtable 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.getDBRef();
-    if (showDbRefs && dbrefs != null)
+
+    if (showDbRefs)
     {
-      for (int i = 0; i < dbrefs.length; i++)
+      maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
+    }
+    sb.append("\n");
+
+    /*
+     * add non-positional features if wanted
+     */
+    if (showNpFeats)
+    {
+      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;
+  }
 
-    // ADD NON POSITIONAL SEQUENCE INFO
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (showNpFeats && features != null)
+  /**
+   * 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 = ds.getDBRefs();
+    if (dbrefs == null)
     {
-      for (int i = 0; i < features.length; i++)
+      return 0;
+    }
+
+    // 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)
+    {
+      source = ref.getSource();
+      if (source == null)
+      {
+        // shouldn't happen
+        continue;
+      }
+      boolean sourceChanged = !source.equals(lastSource);
+      if (sourceChanged)
       {
-        if (features[i].begin == 0 && features[i].end == 0)
+        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(", ").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/>").append(source).append(COMMA).append(ELLIPSIS);
     }
+    if (ellipsis)
+    {
+      sb.append("<br/>(");
+      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>");
+    }
   }
 }