X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=59daa8756a7d3f01c8cfcf1d4ddc7ad391bca610;hb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;hp=07b88bff932220fa05b055b7a2a1b3531b0c00c8;hpb=c242d1bd498f606f87c5f3c7854b469dd7120730;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 07b88bf..59daa87 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -21,13 +21,17 @@
 package jalview.io;
 
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.GffConstants;
 import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
 
@@ -38,8 +42,69 @@ 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)
+   */
+  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;
@@ -48,37 +113,36 @@ 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()))
+    String tmpString;
+    if (feature.getType().equals("disulfide bond"))
     {
       if (feature.getBegin() == rpos || feature.getEnd() == rpos)
       {
@@ -108,21 +172,20 @@ public class SequenceAnnotationReport
         }
         if (feature.begin != feature.end)
         {
-          sb.append(" " + feature.end);
+          sb.append(" ").append(feature.end);
         }
 
         if (feature.getDescription() != null
                 && !feature.description.equals(feature.getType()))
         {
-          String tmpString = feature.getDescription();
+          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)
           {
@@ -147,7 +210,9 @@ public class SequenceAnnotationReport
               // 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
             {
@@ -155,18 +220,14 @@ 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());
+          float[][] rng = (minmax == null) ? null : ((float[][]) 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=" + feature.getScore());
           }
         }
         String status = (String) feature.getValue("status");
@@ -182,7 +243,6 @@ public class SequenceAnnotationReport
         }
       }
     }
-    appendLinks(sb, feature);
   }
 
   /**
@@ -247,14 +307,15 @@ public class SequenceAnnotationReport
       System.err.println(urlLink.getInvalidMessage());
       return null;
     }
+    final String target = urlLink.getTarget(); // link.substring(0,
+    // link.indexOf("|"));
+    final String label = urlLink.getLabel();
     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))
       {
@@ -354,26 +415,42 @@ public class SequenceAnnotationReport
     return result;
   }
 
-  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;
@@ -384,16 +461,81 @@ public class SequenceAnnotationReport
     DBRefEntry[] dbrefs = ds.getDBRefs();
     if (showDbRefs && dbrefs != null)
     {
-      for (int i = 0; i < dbrefs.length; i++)
+      // 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 lineLength = 0;
+
+      for (DBRefEntry ref : dbrefs)
+      {
+        source = ref.getSource();
+        if (source == null)
+        {
+          // 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>");
+        }
+        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
+          {
+            sb.append(source).append(" ").append(accessionId);
+            lineLength += source.length();
+          }
+          maxWidth = Math.max(maxWidth, lineLength);
+        }
+        if (countForSource == MAX_REFS_PER_SOURCE && summary)
+        {
+          sb.append(COMMA).append(ELLIPSIS);
+          ellipsis = true;
+        }
+      }
+      if (moreSources)
       {
-        tip.append("<br>");
-        tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
-        tip.append(tmp);
-        maxWidth = Math.max(maxWidth, tmp.length());
+        sb.append("<br>").append(ELLIPSIS).append(COMMA).append(source)
+                .append(COMMA).append(ELLIPSIS);
+      }
+      if (ellipsis)
+      {
+        sb.append("<br>(");
+        sb.append(MessageManager.getString("label.output_seq_details"));
+        sb.append(")");
       }
     }
 
-    // ADD NON POSITIONAL SEQUENCE INFO
+    /*
+     * add non-positional features if wanted
+     */
     SequenceFeature[] features = sequence.getSequenceFeatures();
     if (showNpFeats && features != null)
     {
@@ -401,21 +543,29 @@ public class SequenceAnnotationReport
       {
         if (features[i].begin == 0 && features[i].end == 0)
         {
-          int sz = -tip.length();
-          List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
-          tfeat.add(features[i]);
-          appendFeatures(tip, 0, tfeat, minmax);
-          sz += tip.length();
+          int sz = -sb.length();
+          appendFeature(sb, 0, minmax, features[i]);
+          sz += sb.length();
           maxWidth = Math.max(maxWidth, sz);
         }
       }
     }
+    sb.append("</i>");
+    return maxWidth;
+  }
+
+  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 (tableWrap && maxWidth > 60)
+    if (maxWidth > 60)
     {
-      tip.insert(0, "<table width=350 border=0><tr><td><i>");
-      tip.append("</i></td></tr></table>");
+      // ? not sure this serves any useful purpose
+      // tip.insert(0, "<table width=350 border=0><tr><td>");
+      // tip.append("</td></tr></table>");
     }
-
   }
 }