X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;fp=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=bf3cd454bd523a1844905a638ad12a28af989fee;hb=3609d4b908fa64cab35f2348401baab3347188fc;hp=66db038818bc4d8c71e4bc197eb74cc9e239f809;hpb=2eea4e73351d902cd88923d863e9780fa57a0ee7;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 66db038..bf3cd45 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,6 +20,13 @@
  */
 package jalview.io;
 
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefEntry;
@@ -33,13 +40,6 @@ import jalview.util.StringUtils;
 import jalview.util.UrlLink;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
 /**
  * generate HTML reports for a sequence
  * 
@@ -47,6 +47,8 @@ import java.util.Map;
  */
 public class SequenceAnnotationReport
 {
+  private static final int MAX_DESCRIPTION_LENGTH = 40;
+
   private static final String COMMA = ",";
 
   private static final String ELLIPSIS = "...";
@@ -55,12 +57,12 @@ public class SequenceAnnotationReport
 
   private static final int MAX_SOURCES = 40;
 
+  private static String linkImageURL;
+
   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, and 'chromosome' first of all
@@ -119,43 +121,75 @@ public class SequenceAnnotationReport
     }
   };
 
-  public SequenceAnnotationReport(String linkURL)
+  private boolean forTooltip;
+
+  /**
+   * Constructor given a flag which affects behaviour
+   * <ul>
+   * <li>if true, generates feature details suitable to show in a tooltip</li>
+   * <li>if false, generates feature details in a form suitable for the sequence
+   * details report</li>
+   * </ul>
+   * 
+   * @param isForTooltip
+   */
+  public SequenceAnnotationReport(boolean isForTooltip)
   {
-    this.linkImageURL = linkURL;
+    this.forTooltip = isForTooltip;
+    if (linkImageURL == null)
+    {
+      linkImageURL = getClass().getResource("/images/link.gif").toString();
+    }
   }
 
   /**
-   * Append text for the list of features to the tooltip
+   * Append text for the list of features to the tooltip. Returns the number of
+   * features not added if maxlength limit is (or would have been) reached.
    * 
    * @param sb
    * @param residuePos
    * @param features
    * @param minmax
+   * @param maxlength
    */
-  public void appendFeatures(final StringBuilder sb, int residuePos,
-          List<SequenceFeature> features, FeatureRendererModel fr)
+  public int appendFeatures(final StringBuilder sb,
+          int residuePos, List<SequenceFeature> features,
+          FeatureRendererModel fr, int maxlength)
   {
-    for (SequenceFeature feature : features)
+    for (int i = 0; i < features.size(); i++)
     {
-      appendFeature(sb, residuePos, fr, feature, null);
+      SequenceFeature feature = features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
+      {
+        return features.size() - i;
+      }
     }
+    return 0;
   }
 
   /**
-   * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
+   * Appends text for mapped features (e.g. CDS feature for peptide or vice
+   * versa) Returns number of features left if maxlength limit is (or would have
+   * been) reached.
    * 
    * @param sb
    * @param residuePos
    * @param mf
    * @param fr
+   * @param maxlength
    */
-  public void appendFeatures(StringBuilder sb, int residuePos,
-          MappedFeatures mf, FeatureRendererModel fr)
+  public int appendFeatures(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr, int maxlength)
   {
-    for (SequenceFeature feature : mf.features)
+    for (int i = 0; i < mf.features.size(); i++)
     {
-      appendFeature(sb, residuePos, fr, feature, mf);
+      SequenceFeature feature = mf.features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
+      {
+        return mf.features.size() - i;
+      }
     }
+    return 0;
   }
 
   /**
@@ -166,27 +200,58 @@ public class SequenceAnnotationReport
    * @param minmax
    * @param feature
    */
-  void appendFeature(final StringBuilder sb, int rpos,
+  boolean appendFeature(final StringBuilder sb0, int rpos,
           FeatureRendererModel fr, SequenceFeature feature,
-          MappedFeatures mf)
+          MappedFeatures mf, int maxlength)
   {
+    int begin = feature.getBegin();
+    int end = feature.getEnd();
+
+    /*
+     * 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;
+    if (mf != null)
+    {
+      beginRange = mf.getMappedPositions(begin, begin);
+      endRange = mf.getMappedPositions(end, end);
+      if (beginRange == null || endRange == null)
+      {
+        // something went wrong
+        return false;
+      }
+      begin = beginRange[0];
+      end = endRange[endRange.length - 1];
+    }
+
+    StringBuilder sb = new StringBuilder();
     if (feature.isContactFeature())
     {
-      if (feature.getBegin() == rpos || feature.getEnd() == rpos)
+      /*
+       * include if rpos is at start or end position of [mapped] feature
+       */
+      boolean showContact = (mf == null) && (rpos == begin || rpos == end);
+      boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0]
+              && rpos <= beginRange[beginRange.length - 1])
+              || (rpos >= endRange[0]
+                      && rpos <= endRange[endRange.length - 1]));
+      if (showContact || showMappedContact)
       {
-        if (sb.length() > 6)
+        if (sb0.length() > 6)
         {
-          sb.append("<br>");
+          sb.append("<br/>");
         }
-        sb.append(feature.getType()).append(" ").append(feature.getBegin())
-                .append(":").append(feature.getEnd());
+        sb.append(feature.getType()).append(" ").append(begin).append(":")
+                .append(end);
       }
-      return;
+      return appendText(sb0, sb, maxlength);
     }
 
-    if (sb.length() > 6)
+    if (sb0.length() > 6)
     {
-      sb.append("<br>");
+      sb.append("<br/>");
     }
     // TODO: remove this hack to display link only features
     boolean linkOnly = feature.getValue("linkonly") != null;
@@ -196,17 +261,31 @@ public class SequenceAnnotationReport
       if (rpos != 0)
       {
         // we are marking a positional feature
-        sb.append(feature.begin);
-      }
-      if (feature.begin != feature.end)
-      {
-        sb.append(" ").append(feature.end);
+        sb.append(begin);
+        if (begin != end)
+        {
+          sb.append(" ").append(end);
+        }
       }
 
       String description = feature.getDescription();
       if (description != null && !description.equals(feature.getType()))
       {
         description = StringUtils.stripHtmlTags(description);
+
+        /*
+         * truncate overlong descriptions unless they contain an href
+         * before the truncation point (as truncation could leave corrupted html)
+         */
+        int linkindex = description.toLowerCase().indexOf("<a ");
+        boolean hasLink = linkindex > -1
+                && linkindex < MAX_DESCRIPTION_LENGTH;
+        if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink)
+        {
+          description = description.substring(0, MAX_DESCRIPTION_LENGTH)
+                  + ELLIPSIS;
+        }
+
         sb.append("; ").append(description);
       }
 
@@ -247,6 +326,28 @@ public class SequenceAnnotationReport
         }
       }
     }
+    return appendText(sb0, sb, maxlength);
+  }
+
+  /**
+   * Appends sb to sb0, and returns false, unless maxlength is not zero and
+   * appending would make the result longer than or equal to maxlength, in which
+   * case the append is not done and returns true
+   * 
+   * @param sb0
+   * @param sb
+   * @param maxlength
+   * @return
+   */
+  private static boolean appendText(StringBuilder sb0, StringBuilder sb,
+          int maxlength)
+  {
+    if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
+    {
+      sb0.append(sb);
+      return false;
+    }
+    return true;
   }
 
   /**
@@ -306,7 +407,8 @@ public class SequenceAnnotationReport
                       + (urllink.get(0).toLowerCase()
                               .equals(urllink.get(1).toLowerCase()) ? urllink
                               .get(0) : (urllink.get(0) + ":" + urllink
-                              .get(1))) + "</a></br>");
+                                              .get(1)))
+                      + "</a><br/>");
             }
           } catch (Exception x)
           {
@@ -377,7 +479,7 @@ public class SequenceAnnotationReport
     if (sequence.getDescription() != null)
     {
       tmp = sequence.getDescription();
-      sb.append("<br>").append(tmp);
+      sb.append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
 
@@ -415,7 +517,7 @@ public class SequenceAnnotationReport
               .getNonPositionalFeatures())
       {
         int sz = -sb.length();
-        appendFeature(sb, 0, fr, sf, null);
+        appendFeature(sb, 0, fr, sf, null, 0);
         sz += sb.length();
         maxWidth = Math.max(maxWidth, sz);
       }
@@ -495,7 +597,7 @@ public class SequenceAnnotationReport
       countForSource++;
       if (countForSource == 1 || !summary)
       {
-        sb.append("<br>");
+        sb.append("<br/>");
       }
       if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
@@ -521,11 +623,11 @@ public class SequenceAnnotationReport
     }
     if (moreSources)
     {
-      sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
+      sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
     }
     if (ellipsis)
     {
-      sb.append("<br>(");
+      sb.append("<br/>(");
       sb.append(MessageManager.getString("label.output_seq_details"));
       sb.append(")");
     }