X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=2110632457bf3f136b600662d1518ad4f3378897;hb=14307f5cfcbc90c419c892434613a500ca550ecc;hp=ba7412c7f132045e9c01c20687d37e58d69c45be;hpb=6ec47c00025dbeb48dba5f5db77754ec50b7a6b5;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index ba7412c..2110632 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,18 +20,23 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureAttributes;
 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;
 import java.util.Map.Entry;
+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
 {
@@ -51,6 +56,20 @@ 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
+   */
+  private static final Map<String, String> INFO_KEYS = new HashMap<>();
+
+  static
+  {
+    INFO_KEYS.put("CSQ", ",");
+    // todo capture second level metadata (CSQ FORMAT)
+    // and delimiter "|" so as to report in a table within a table?
+  }
+
   /*
    * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
    * name1=value1;name2=value2,value3;...etc
@@ -84,6 +103,12 @@ 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
@@ -155,6 +180,8 @@ 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>();
@@ -233,8 +260,8 @@ public class SequenceFeature implements FeatureLocationI
       return false;
     }
 
-    if (!(type + description + featureGroup + getPhase()).equals(sf.type
-            + sf.description + sf.featureGroup + sf.getPhase()))
+    if (!(type + description + featureGroup + getPhase()).equals(
+            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
     {
       return false;
     }
@@ -366,6 +393,23 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
+   * Answers the value of the specified attribute as string, or null if no such
+   * value
+   * 
+   * @param key
+   * @return
+   */
+  public String getValueAsString(String key)
+  {
+    if (otherDetails == null)
+    {
+      return null;
+    }
+    Object value = otherDetails.get(key);
+    return value == null ? null : value.toString();
+  }
+
+  /**
    * Returns a property value for the given key if known, else the specified
    * default value
    * 
@@ -398,9 +442,31 @@ public class SequenceFeature implements FeatureLocationI
       }
 
       otherDetails.put(key, value);
+      recordAttribute(key, value);
     }
   }
 
+  /**
+   * Notifies the addition of a feature attribute. This lets us keep track of
+   * which attributes are present on each feature type, and also the range of
+   * numerical-valued attributes.
+   * 
+   * @param key
+   * @param value
+   */
+  protected void recordAttribute(String key, Object value)
+  {
+    String attDesc = null;
+    if (source != null)
+    {
+      attDesc = FeatureSources.getInstance().getSource(source)
+              .getAttributeName(key);
+    }
+
+    FeatureAttributes.getInstance().addAttribute(this.type, key, attDesc,
+            value.toString());
+  }
+
   /*
    * The following methods are added to maintain the castor Uniprot mapping file
    * for the moment.
@@ -535,4 +601,135 @@ public class SequenceFeature implements FeatureLocationI
   {
     return begin == 0 && end == 0;
   }
+
+  /**
+   * Answers an html-formatted report of feature details
+   * 
+   * @return
+   */
+  public String getDetailsReport()
+  {
+    FeatureSourceI metadata = FeatureSources.getInstance()
+            .getSource(source);
+
+    StringBuilder sb = new StringBuilder(128);
+    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(String.format(ROW_DATA, "Score", score, ""));
+    }
+    if (featureGroup != null)
+    {
+      sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
+    }
+
+    if (otherDetails != null)
+    {
+      TreeMap<String, Object> ordered = new TreeMap<>(
+              String.CASE_INSENSITIVE_ORDER);
+      ordered.putAll(otherDetails);
+
+      for (Entry<String, Object> entry : ordered.entrySet())
+      {
+        String key = entry.getKey();
+        if (ATTRIBUTES.equals(key))
+        {
+          continue; // to avoid double reporting
+        }
+        if (INFO_KEYS.containsKey(key))
+        {
+          /*
+           * split selected INFO data by delimiter over multiple lines
+           */
+          String delimiter = INFO_KEYS.get(key);
+          String[] values = entry.getValue().toString().split(delimiter);
+          for (String value : values)
+          {
+            sb.append(String.format(ROW_DATA, key, "", value));
+          }
+        }
+        else
+        { // 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;
+  }
 }