X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=95bd1cc2ca4008a1cfe4248467e7628ff5ab5429;hb=14380adc384f8a1c96f71ef2ea26607cdac22a14;hp=27c1652943c77b81c4bee965bed0d052b04f2cff;hpb=69e8792b5f1ed2c02cff0a1ee328793ab5c0f423;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 27c1652..95bd1cc 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,11 +20,12 @@
  */
 package jalview.io;
 
-import java.util.Arrays;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import jalview.api.FeatureColourI;
@@ -58,9 +59,7 @@ public class SequenceAnnotationReport
 
   private static String linkImageURL;
 
-  private static final String[][] PRIMARY_SOURCES = new String[][] {
-      DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
-      DBRefSource.PROTEINDBS };
+  // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
 
   /*
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
@@ -82,8 +81,8 @@ public class SequenceAnnotationReport
       }
       String s1 = ref1.getSource();
       String s2 = ref2.getSource();
-      boolean s1Primary = isPrimarySource(s1);
-      boolean s2Primary = isPrimarySource(s2);
+      boolean s1Primary = DBRefSource.isPrimarySource(s1);
+      boolean s2Primary = DBRefSource.isPrimarySource(s2);
       if (s1Primary && !s2Primary)
       {
         return -1;
@@ -92,32 +91,32 @@ public class SequenceAnnotationReport
       {
         return 1;
       }
-      int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
-              .compareToIgnoreCase(s2));
+      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));
+        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;
-    }
+    // private boolean isPrimarySource(String source)
+    // {
+    // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+    // {
+    // for (String s : primary)
+    // {
+    // if (source.equals(s))
+    // {
+    // return true;
+    // }
+    // }
+    // }
+    // return false;
+    // }
   };
 
   private boolean forTooltip;
@@ -151,9 +150,9 @@ public class SequenceAnnotationReport
    * @param minmax
    * @param maxlength
    */
-  public int appendFeatures(final StringBuilder sb,
-          int residuePos, List<SequenceFeature> features,
-          FeatureRendererModel fr, int maxlength)
+  public int appendFeatures(final StringBuilder sb, int residuePos,
+          List<SequenceFeature> features, FeatureRendererModel fr,
+          int maxlength)
   {
     for (int i = 0; i < features.size(); i++)
     {
@@ -210,12 +209,27 @@ public class SequenceAnnotationReport
      * if this is a virtual features, convert begin/end to the
      * coordinates of the sequence it is mapped to
      */
-    int[] beginRange = null;
-    int[] endRange = null;
+    int[] beginRange = null; // feature start in local coordinates
+    int[] endRange = null; // feature end in local coordinates
     if (mf != null)
     {
-      beginRange = mf.getMappedPositions(begin, begin);
-      endRange = mf.getMappedPositions(end, end);
+      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
@@ -276,7 +290,7 @@ public class SequenceAnnotationReport
          * truncate overlong descriptions unless they contain an href
          * before the truncation point (as truncation could leave corrupted html)
          */
-        int linkindex = description.toLowerCase().indexOf("<a ");
+        int linkindex = description.toLowerCase(Locale.ROOT).indexOf("<a ");
         boolean hasLink = linkindex > -1
                 && linkindex < MAX_DESCRIPTION_LENGTH;
         if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
@@ -398,21 +412,19 @@ public class SequenceAnnotationReport
           {
             for (List<String> urllink : createLinksFrom(null, urlstring))
             {
-              sb.append("<br/> <a href=\""
-                      + urllink.get(3)
-                      + "\" target=\""
-                      + urllink.get(0)
-                      + "\">"
-                      + (urllink.get(0).toLowerCase()
-                              .equals(urllink.get(1).toLowerCase()) ? urllink
-                              .get(0) : (urllink.get(0) + ":" + urllink
-                                              .get(1)))
+              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/>");
             }
           } catch (Exception x)
           {
-            System.err.println("problem when creating links from "
-                    + urlstring);
+            System.err.println(
+                    "problem when creating links from " + urlstring);
             x.printStackTrace();
           }
         }
@@ -481,6 +493,7 @@ public class SequenceAnnotationReport
       sb.append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
+    sb.append("\n");
     SequenceI ds = sequence;
     while (ds.getDatasetSequence() != null)
     {
@@ -491,6 +504,7 @@ public class SequenceAnnotationReport
     {
       maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
     }
+    sb.append("\n");
 
     /*
      * add non-positional features if wanted
@@ -522,14 +536,21 @@ public class SequenceAnnotationReport
   protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
           boolean summary)
   {
-    DBRefEntry[] dbrefs = ds.getDBRefs();
-    if (dbrefs == null)
+    List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
+
+    if (dbrefset == null)
     {
       return 0;
     }
 
+    // PATCH for JAL-3980 defensive copy
+
+    dbrefs = new ArrayList<DBRefEntry>();
+
+    dbrefs.addAll(dbrefset);
+
     // note this sorts the refs held on the sequence!
-    Arrays.sort(dbrefs, comparator);
+    dbrefs.sort(comparator);
     boolean ellipsis = false;
     String source = null;
     String lastSource = null;
@@ -564,7 +585,7 @@ public class SequenceAnnotationReport
       countForSource++;
       if (countForSource == 1 || !summary)
       {
-        sb.append("<br/>");
+        sb.append("<br/>\n");
       }
       if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
@@ -572,7 +593,7 @@ public class SequenceAnnotationReport
         lineLength += accessionId.length() + 1;
         if (countForSource > 1 && summary)
         {
-          sb.append(", ").append(accessionId);
+          sb.append(",\n ").append(accessionId);
           lineLength++;
         }
         else
@@ -590,11 +611,11 @@ public class SequenceAnnotationReport
     }
     if (moreSources)
     {
-      sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
+      sb.append("<br/>\n").append(source).append(COMMA).append(ELLIPSIS);
     }
     if (ellipsis)
     {
-      sb.append("<br/>(");
+      sb.append("<br/>\n(");
       sb.append(MessageManager.getString("label.output_seq_details"));
       sb.append(")");
     }
@@ -606,8 +627,8 @@ public class SequenceAnnotationReport
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
           FeatureRendererModel fr)
   {
-    int maxWidth = createSequenceAnnotationReport(tip, sequence,
-            showDbRefs, showNpFeats, fr, true);
+    int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+            showNpFeats, fr, true);
 
     if (maxWidth > 60)
     {