X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=c3b076cb20ffe774079f5e8b24e154d75b88bbea;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=89f1068e91691599078d0ccf77bf68592d61d3f6;hpb=9fc1c4d049a16cccb933e80b5be07ec36e6bda7f;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 89f1068..c3b076c 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -21,13 +21,16 @@
 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.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;
@@ -39,8 +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;
@@ -49,37 +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)
       {
@@ -87,7 +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());
       }
     }
@@ -109,7 +173,7 @@ public class SequenceAnnotationReport
         }
         if (feature.begin != feature.end)
         {
-          sb.append(" " + feature.end);
+          sb.append(" ").append(feature.end);
         }
 
         if (feature.getDescription() != null
@@ -117,13 +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)
           {
@@ -148,7 +211,9 @@ 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
             {
@@ -156,11 +221,7 @@ 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
@@ -183,7 +244,6 @@ public class SequenceAnnotationReport
         }
       }
     }
-    appendLinks(sb, feature);
   }
 
   /**
@@ -254,26 +314,42 @@ public class SequenceAnnotationReport
     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;
@@ -281,41 +357,135 @@ public class SequenceAnnotationReport
     {
       ds = ds.getDatasetSequence();
     }
-    DBRefEntry[] dbrefs = ds.getDBRefs();
-    if (showDbRefs && dbrefs != null)
+    
+    if (showDbRefs)
+    {
+      maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
+    }
+
+    /*
+     * 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, 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)
     {
-      for (int i = 0; i < features.length; i++)
+      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)
+    {
+      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)
       {
-        if (features[i].begin == 0 && features[i].end == 0)
+        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
         {
-          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)
+    {
+      sb.append("<br>").append(source)
+              .append(COMMA).append(ELLIPSIS);
+    }
+    if (ellipsis)
     {
-      tip.insert(0, "<table width=350 border=0><tr><td><i>");
-      tip.append("</i></td></tr></table>");
+      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>");
+    }
   }
 }