X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=c3b076cb20ffe774079f5e8b24e154d75b88bbea;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=676404b941c5c9aadb50697f652f589e7f0450d0;hpb=2672f9a72ffb8ffaf4b48a08e64de7f3d83ce061;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 676404b..c3b076c 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -21,12 +21,17 @@
 package jalview.io;
 
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.util.DBRefUtils;
+import jalview.io.gff.GffConstants;
+import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-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;
 
@@ -37,8 +42,70 @@ import java.util.Map;
  */
 public class SequenceAnnotationReport
 {
+  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 final String[][] PRIMARY_SOURCES = new String[][] {
+      DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
+      DBRefSource.PROTEINDBS };
+
   final String linkImageURL;
 
+  /*
+   * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
+   * with 'Primary' sources placed before others
+   */
+  private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
+  {
+
+    @Override
+    public int compare(DBRefEntry ref1, DBRefEntry ref2)
+    {
+      String s1 = ref1.getSource();
+      String s2 = ref2.getSource();
+      boolean s1Primary = isPrimarySource(s1);
+      boolean s2Primary = 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 : PRIMARY_SOURCES)
+      {
+        for (String s : primary)
+        {
+          if (source.equals(s))
+          {
+            return true;
+          }
+        }
+      }
+      return false;
+    }
+  };
+
   public SequenceAnnotationReport(String linkImageURL)
   {
     this.linkImageURL = linkImageURL;
@@ -47,37 +114,35 @@ public class SequenceAnnotationReport
   /**
    * Append text for the list of features to the tooltip
    * 
-   * @param tooltipText2
+   * @param sb
    * @param rpos
    * @param features
    * @param minmax
    */
-  public void appendFeatures(final StringBuffer tooltipText2, int rpos,
+  public void appendFeatures(final StringBuilder sb, int rpos,
           List<SequenceFeature> features, Map<String, float[][]> minmax)
   {
     if (features != null)
     {
       for (SequenceFeature feature : features)
       {
-        appendFeature(tooltipText2, rpos, minmax, feature);
+        appendFeature(sb, rpos, minmax, feature);
       }
     }
   }
 
   /**
-   * Appends text for one sequence feature to the string buffer
+   * 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,
+  void appendFeature(final StringBuilder sb, int rpos,
           Map<String, float[][]> minmax, SequenceFeature feature)
   {
-    if ("disulfide bond".equals(feature.getType()))
+    if (feature.isContactFeature())
     {
       if (feature.getBegin() == rpos || feature.getEnd() == rpos)
       {
@@ -85,7 +150,8 @@ public class SequenceAnnotationReport
         {
           sb.append("<br>");
         }
-        sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+        sb.append(feature.getType()).append(" ").append(feature.getBegin())
+                .append(":")
                 .append(feature.getEnd());
       }
     }
@@ -107,7 +173,7 @@ public class SequenceAnnotationReport
         }
         if (feature.begin != feature.end)
         {
-          sb.append(" " + feature.end);
+          sb.append(" ").append(feature.end);
         }
 
         if (feature.getDescription() != null
@@ -115,13 +181,12 @@ public class SequenceAnnotationReport
         {
           String tmpString = feature.getDescription();
           String tmp2up = tmpString.toUpperCase();
-          final int startTag = tmp2up.indexOf("<HTML>");
+          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)
           {
@@ -140,14 +205,15 @@ 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
               tmpString = tmpString.replaceAll("<", "&lt;");
               tmpString = tmpString.replaceAll(">", "&gt;");
-              sb.append("; ").append(tmpString);
+
+              sb.append("; ");
+              sb.append(tmpString);
             }
             else
             {
@@ -155,19 +221,14 @@ public class SequenceAnnotationReport
             }
           }
         }
-
-        /*
-         * score should be shown if there is one, and min != max
-         * for this feature type (e.g. not all 0)
-         */
+        // check score should be shown
         if (!Float.isNaN(feature.getScore()))
         {
           float[][] rng = (minmax == null) ? null : minmax.get(feature
                   .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");
@@ -175,9 +236,14 @@ public class SequenceAnnotationReport
         {
           sb.append("; (").append(status).append(")");
         }
+        String clinSig = (String) feature
+                .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
+        if (clinSig != null)
+        {
+          sb.append("; ").append(clinSig);
+        }
       }
     }
-    appendLinks(sb, feature);
   }
 
   /**
@@ -201,16 +267,17 @@ 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)
@@ -229,149 +296,60 @@ 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[][] {});
-  }
+    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)
   {
     createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
-            true, minmax);
+            minmax, 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 minmax
+   * @param summary
+   * @return
+   */
+  int createSequenceAnnotationReport(final StringBuilder sb,
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
-          boolean tableWrap, Map<String, float[][]> minmax)
+          Map<String, float[][]> minmax, 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("<br>").append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
     SequenceI ds = sequence;
@@ -379,41 +357,135 @@ public class SequenceAnnotationReport
     {
       ds = ds.getDatasetSequence();
     }
-    DBRefEntry[] dbrefs = ds.getDBRefs();
-    if (showDbRefs && dbrefs != null)
+    
+    if (showDbRefs)
     {
-      for (int i = 0; i < dbrefs.length; i++)
+      maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
+    }
+
+    /*
+     * 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, minmax, sf);
+        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)
+  {
+    DBRefEntry[] dbrefs = ds.getDBRefs();
+    if (dbrefs == null)
+    {
+      return 0;
+    }
+
+    // note this sorts the refs held on the sequence!
+    Arrays.sort(dbrefs, 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)
+      {
+        // 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>");
+      }
+      if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
+      {
+        String accessionId = ref.getAccessionId();
+        lineLength += accessionId.length() + 1;
+        if (countForSource > 1 && summary)
         {
-          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(", ").append(accessionId);
+          lineLength++;
         }
+        else
+        {
+          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,
+          Map<String, float[][]> minmax)
+  {
+    int maxWidth = createSequenceAnnotationReport(tip, sequence,
+            showDbRefs, showNpFeats, minmax, 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>");
+    }
   }
 }