Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / io / SequenceAnnotationReport.java

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 613c01f..f1ebcac 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -57,7 +57,8 @@ public class SequenceAnnotationReport
   final String linkImageURL;
 
   /*
-   * Comparator to order DBRefEntry by Source + accession id (case-insensitive)
+   * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
+   * with 'Primary' sources placed before others
    */
   private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
   {
@@ -353,100 +354,121 @@ public class SequenceAnnotationReport
     {
       ds = ds.getDatasetSequence();
     }
+    
+    if (showDbRefs)
+    {
+      maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
+    }
+
+    /*
+     * add non-positional features if wanted
+     */
+    if (showNpFeats)
+    {
+      for (SequenceFeature sf : sequence.getFeatures()
+              .getNonPositionalFeatures())
+      {
+        int sz = -sb.length();
+        appendFeature(sb, 0, minmax, sf);
+        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)
+  {
     DBRefEntry[] dbrefs = ds.getDBRefs();
-    if (showDbRefs && dbrefs != null)
+    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)
     {
-      // 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)
       {
-        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;
-        }
+        // shouldn't happen
+        continue;
       }
-      if (moreSources)
+      boolean sourceChanged = !source.equals(lastSource);
+      if (sourceChanged)
       {
-        sb.append("<br>").append(ELLIPSIS).append(COMMA).append(source)
-                .append(COMMA).append(ELLIPSIS);
+        lineLength = 0;
+        countForSource = 0;
+        sourceCount++;
       }
-      if (ellipsis)
+      if (sourceCount > MAX_SOURCES && summary)
       {
-        sb.append("<br>(");
-        sb.append(MessageManager.getString("label.output_seq_details"));
-        sb.append(")");
+        ellipsis = true;
+        moreSources = true;
+        break;
       }
-    }
-
-    /*
-     * add non-positional features if wanted
-     */
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (showNpFeats && features != null)
-    {
-      for (int i = 0; i < features.length; i++)
+      lastSource = source;
+      countForSource++;
+      if (countForSource == 1 || !summary)
+      {
+        sb.append("<br>");
+      }
+      if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
-        if (features[i].begin == 0 && features[i].end == 0)
+        String accessionId = ref.getAccessionId();
+        lineLength += accessionId.length() + 1;
+        if (countForSource > 1 && summary)
         {
-          int sz = -sb.length();
-          appendFeature(sb, 0, minmax, features[i]);
-          sz += sb.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;
       }
     }
-    sb.append("</i>");
-    return maxWidth;
+    if (moreSources)
+    {
+      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,