JAL-1793 spike branch updated to latest

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 4208ce1..8f82a1a 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,7 +20,11 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.FeatureAttributeType;
 import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
+import jalview.util.StringUtils;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -29,10 +33,9 @@ import java.util.TreeMap;
 import java.util.Vector;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A class that models a single contiguous feature on a sequence. If flag
+ * 'contactFeature' is true, the start and end positions are interpreted instead
+ * as two contact points.
  */
 public class SequenceFeature implements FeatureLocationI
 {
@@ -52,6 +55,8 @@ public class SequenceFeature implements FeatureLocationI
   // private key for ENA location designed not to conflict with real GFF data
   private static final String LOCATION = "!Location";
 
+  private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
+
   /*
    * map of otherDetails special keys, and their value fields' delimiter
    */
@@ -60,6 +65,8 @@ public class SequenceFeature implements FeatureLocationI
   static
   {
     INFO_KEYS.put("CSQ", ",");
+    // todo capture second level metadata (CSQ FORMAT)
+    // and delimiter "|" so as to report in a table within a table?
   }
 
   /*
@@ -95,6 +102,12 @@ public class SequenceFeature implements FeatureLocationI
 
   public Vector<String> links;
 
+  /*
+   * the identifier (if known) for the FeatureSource held in FeatureSources,
+   * as a provider of metadata about feature attributes 
+   */
+  private String source;
+
   /**
    * Constructs a duplicate feature. Note: Uses makes a shallow copy of the
    * otherDetails map, so the new and original SequenceFeature may reference the
@@ -166,6 +179,8 @@ public class SequenceFeature implements FeatureLocationI
     this(newType, sf.getDescription(), newBegin, newEnd, newScore,
             newGroup);
 
+    this.source = sf.source;
+
     if (sf.otherDetails != null)
     {
       otherDetails = new HashMap<String, Object>();
@@ -548,30 +563,31 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
-   * Answers a formatted text report of feature details
+   * Answers an html-formatted report of feature details
    * 
    * @return
    */
   public String getDetailsReport()
   {
+    FeatureSourceI metadata = FeatureSources.getInstance()
+            .getSource(source);
+
     StringBuilder sb = new StringBuilder(128);
-    if (begin == end)
-    {
-      sb.append(String.format("%s %d %s", type, begin, description));
-    }
-    else
-    {
-      sb.append(String.format("%s %d-%d %s", type, begin, end, description));
-    }
+    sb.append("<br>");
+    sb.append("<table>");
+    sb.append(String.format(ROW_DATA, "Type", type, ""));
+    sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
+            : begin + (isContactFeature() ? ":" : "-") + end, ""));
+    String desc = StringUtils.stripHtmlTags(description);
+    sb.append(String.format(ROW_DATA, "Description", desc, ""));
     if (!Float.isNaN(score) && score != 0f)
     {
-      sb.append(" score=").append(score);
+      sb.append(String.format(ROW_DATA, "Score", score, ""));
     }
     if (featureGroup != null)
     {
-      sb.append(" (").append(featureGroup).append(")");
+      sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
     }
-    sb.append("\n\n");
 
     if (otherDetails != null)
     {
@@ -591,18 +607,89 @@ public class SequenceFeature implements FeatureLocationI
           /*
            * split selected INFO data by delimiter over multiple lines
            */
-          sb.append(key).append("=\n  ");
           String delimiter = INFO_KEYS.get(key);
-          String value = entry.getValue().toString();
-          sb.append(value.replace(delimiter, "\n  "));
+          String[] values = entry.getValue().toString().split(delimiter);
+          for (String value : values)
+          {
+            sb.append(String.format(ROW_DATA, key, "", value));
+          }
         }
         else
-        {
-          sb.append(key + "=" + entry.getValue().toString() + "\n");
+        { // tried <td title="key"> but it failed to provide a tooltip :-(
+          String attDesc = null;
+          if (metadata != null)
+          {
+            attDesc = metadata.getAttributeName(key);
+          }
+          String value = entry.getValue().toString();
+          if (isValueInteresting(key, value, metadata))
+          {
+            sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+                    : attDesc, value));
+          }
         }
       }
     }
+    sb.append("</table>");
+
     String text = sb.toString();
     return text;
   }
+
+  /**
+   * Answers true if we judge the value is worth displaying, by some heuristic
+   * rules, else false
+   * 
+   * @param key
+   * @param value
+   * @param metadata
+   * @return
+   */
+  boolean isValueInteresting(String key, String value,
+          FeatureSourceI metadata)
+  {
+    /*
+     * currently suppressing zero values as well as null or empty
+     */
+    if (value == null || "".equals(value) || ".".equals(value)
+            || "0".equals(value))
+    {
+      return false;
+    }
+
+    if (metadata == null)
+    {
+      return true;
+    }
+
+    FeatureAttributeType attType = metadata.getAttributeType(key);
+    if (attType != null
+            && (attType == FeatureAttributeType.Float || attType
+                    .equals(FeatureAttributeType.Integer)))
+    {
+      try
+      {
+        float fval = Float.valueOf(value);
+        if (fval == 0f)
+        {
+          return false;
+        }
+      } catch (NumberFormatException e)
+      {
+        // ignore
+      }
+    }
+
+    return true; // default to interesting
+  }
+
+  /**
+   * Sets the feature source identifier
+   * 
+   * @param theSource
+   */
+  public void setSource(String theSource)
+  {
+    source = theSource;
+  }
 }