X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=4933cd6ca9295d404b37cb83ed1e0976b85ac719;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=27e4da212016485e5fbab92d188b796076275840;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 27e4da2..4933cd6 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -23,6 +23,8 @@ package jalview.io;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -44,6 +46,8 @@ 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 = "...";
@@ -66,11 +70,11 @@ public class SequenceAnnotationReport
     @Override
     public int compare(DBRefEntry ref1, DBRefEntry ref2)
     {
-      if (ref1.isChromosome())
+      if (ref1 instanceof GeneLociI)
       {
         return -1;
       }
-      if (ref2.isChromosome())
+      if (ref2 instanceof GeneLociI)
       {
         return 1;
       }
@@ -120,23 +124,65 @@ public class SequenceAnnotationReport
   }
 
   /**
-   * Append text for the list of features to the tooltip
+   * Append text for the list of features to the tooltip Returns number of
+   * features left if maxlength limit is (or would have been) reached
    * 
    * @param sb
-   * @param rpos
+   * @param residuePos
    * @param features
    * @param minmax
+   * @param maxlength
    */
-  public void appendFeatures(final StringBuilder sb, int rpos,
+  public int appendFeaturesLengthLimit(final StringBuilder sb,
+          int residuePos, List<SequenceFeature> features,
+          FeatureRendererModel fr, int maxlength)
+  {
+    for (int i = 0; i < features.size(); i++)
+    {
+      SequenceFeature feature = features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
+      {
+        return features.size() - i;
+      }
+    }
+    return 0;
+  }
+
+  public void appendFeatures(final StringBuilder sb, int residuePos,
           List<SequenceFeature> features, FeatureRendererModel fr)
   {
-    if (features != null)
+    appendFeaturesLengthLimit(sb, residuePos, features, fr, 0);
+  }
+
+  /**
+   * 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 int appendFeaturesLengthLimit(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr, int maxlength)
+  {
+    for (int i = 0; i < mf.features.size(); i++)
     {
-      for (SequenceFeature feature : features)
+      SequenceFeature feature = mf.features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
       {
-        appendFeature(sb, rpos, fr, feature);
+        return mf.features.size() - i;
       }
     }
+    return 0;
+  }
+
+  public void appendFeatures(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr)
+  {
+    appendFeaturesLengthLimit(sb, residuePos, mf, fr, 0);
   }
 
   /**
@@ -147,26 +193,28 @@ public class SequenceAnnotationReport
    * @param minmax
    * @param feature
    */
-  void appendFeature(final StringBuilder sb, int rpos,
-          FeatureRendererModel fr, SequenceFeature feature)
+  boolean appendFeature(final StringBuilder sb0, int rpos,
+          FeatureRendererModel fr, SequenceFeature feature,
+          MappedFeatures mf, int maxlength)
   {
+    StringBuilder sb = new StringBuilder();
     if (feature.isContactFeature())
     {
       if (feature.getBegin() == rpos || feature.getEnd() == rpos)
       {
-        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());
       }
-      return;
+      return appendTextMaxLengthReached(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;
@@ -187,6 +235,20 @@ public class SequenceAnnotationReport
       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);
       }
 
@@ -217,6 +279,36 @@ public class SequenceAnnotationReport
           }
         }
       }
+
+      if (mf != null)
+      {
+        String variants = mf.findProteinVariants(feature);
+        if (!variants.isEmpty())
+        {
+          sb.append(" ").append(variants);
+        }
+      }
+    }
+    return appendTextMaxLengthReached(sb0, sb, maxlength);
+  }
+
+  void appendFeature(final StringBuilder sb, int rpos,
+          FeatureRendererModel fr, SequenceFeature feature,
+          MappedFeatures mf)
+  {
+    appendFeature(sb, rpos, fr, feature, mf, 0);
+  }
+
+  private static boolean appendTextMaxLengthReached(StringBuilder sb0,
+          StringBuilder sb, int maxlength)
+  {
+    boolean ret = false;
+    if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
+    {
+      sb0.append(sb);
+      return false;
+    } else {
+      return true;
     }
   }
 
@@ -277,7 +369,8 @@ 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)
           {
@@ -348,7 +441,7 @@ public class SequenceAnnotationReport
     if (sequence.getDescription() != null)
     {
       tmp = sequence.getDescription();
-      sb.append("<br>").append(tmp);
+      sb.append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
     SequenceI ds = sequence;
@@ -371,7 +464,7 @@ public class SequenceAnnotationReport
               .getNonPositionalFeatures())
       {
         int sz = -sb.length();
-        appendFeature(sb, 0, fr, sf);
+        appendFeature(sb, 0, fr, sf, null);
         sz += sb.length();
         maxWidth = Math.max(maxWidth, sz);
       }
@@ -434,7 +527,7 @@ public class SequenceAnnotationReport
       countForSource++;
       if (countForSource == 1 || !summary)
       {
-        sb.append("<br>");
+        sb.append("<br/>");
       }
       if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
@@ -460,11 +553,11 @@ 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(")");
     }