X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=8a6cb610f5aa912868e80269de8c1a2f291c1d88;hb=8ace2707dd1c5cfbb1688efa265fd0afcec35def;hp=f5a9b42bbe61aa24104b7a14f2313bd02a34fd66;hpb=705d1c84c9a03bb0378593e4d8d8a90c8a11f831;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index f5a9b42..8a6cb61 100755
--- 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.FeatureAttributes;
 import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
 import java.util.HashMap;
@@ -52,17 +56,7 @@ 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></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", ",");
-  }
+  private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
 
   /*
    * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
@@ -97,6 +91,12 @@ 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
@@ -168,9 +168,11 @@ 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>();
+      otherDetails = new HashMap<>();
       for (Entry<String, Object> entry : sf.otherDetails.entrySet())
       {
         otherDetails.put(entry.getKey(), entry.getValue());
@@ -178,7 +180,7 @@ public class SequenceFeature implements FeatureLocationI
     }
     if (sf.links != null && sf.links.size() > 0)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
       for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
       {
         links.addElement(sf.links.elementAt(i));
@@ -345,7 +347,7 @@ public class SequenceFeature implements FeatureLocationI
   {
     if (links == null)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
     }
 
     if (!links.contains(labelLink))
@@ -379,6 +381,30 @@ public class SequenceFeature implements FeatureLocationI
   }
 
   /**
+   * Answers the value of the specified attribute as string, or null if no such
+   * value. If more than one attribute name is provided, tries to resolve as keys
+   * to nested maps. For example, if attribute "CSQ" holds a map of key-value
+   * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
+   * in that map.
+   * 
+   * @param key
+   * @return
+   */
+  public String getValueAsString(String... key)
+  {
+    if (otherDetails == null)
+    {
+      return null;
+    }
+    Object value = otherDetails.get(key[0]);
+    if (key.length > 1 && value instanceof Map<?, ?>)
+    {
+      value = ((Map) value).get(key[1]);
+    }
+    return value == null ? null : value.toString();
+  }
+
+  /**
    * Returns a property value for the given key if known, else the specified
    * default value
    * 
@@ -407,11 +433,33 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<String, Object>();
+        otherDetails = new HashMap<>();
       }
 
       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, attDesc, value,
+            key);
   }
 
   /*
@@ -556,21 +604,24 @@ public class SequenceFeature implements FeatureLocationI
    */
   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, "Type", type, ""));
     sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
-            : begin + (isContactFeature() ? ":" : "-") + end));
+            : begin + (isContactFeature() ? ":" : "-") + end, ""));
     String desc = StringUtils.stripHtmlTags(description);
-    sb.append(String.format(ROW_DATA, "Description", desc));
+    sb.append(String.format(ROW_DATA, "Description", desc, ""));
     if (!Float.isNaN(score) && score != 0f)
     {
-      sb.append(String.format(ROW_DATA, "Score", score));
+      sb.append(String.format(ROW_DATA, "Score", score, ""));
     }
     if (featureGroup != null)
     {
-      sb.append(String.format(ROW_DATA, "Group", featureGroup));
+      sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
     }
 
     if (otherDetails != null)
@@ -586,24 +637,34 @@ public class SequenceFeature implements FeatureLocationI
         {
           continue; // to avoid double reporting
         }
-        sb.append("<tr><td>").append(key).append("</td><td>");
-        if (INFO_KEYS.containsKey(key))
+
+        Object value = entry.getValue();
+        if (value instanceof Map<?, ?>)
         {
           /*
-           * split selected INFO data by delimiter over multiple lines
+           * expand values in a Map attribute across separate lines
            */
-          sb.append("</td></tr>");
-          String delimiter = INFO_KEYS.get(key);
-          String[] values = entry.getValue().toString().split(delimiter);
-          for (String value : values)
+          Map<?, ?> values = (Map<?, ?>) value;
+          for (Entry<?, ?> e : values.entrySet())
           {
-            sb.append("<tr><td>&nbsp</td><td>").append(value)
-                    .append("</td></tr>");
+            sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
+                    .getValue().toString()));
           }
         }
         else
         {
-          sb.append(entry.getValue().toString()).append("</td></tr>");
+          // tried <td title="key"> but it failed to provide a tooltip :-(
+          String attDesc = null;
+          if (metadata != null)
+          {
+            attDesc = metadata.getAttributeName(key);
+          }
+          String s = entry.getValue().toString();
+          if (isValueInteresting(key, s, metadata))
+          {
+            sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+                    : attDesc, s));
+          }
         }
       }
     }
@@ -612,4 +673,61 @@ public class SequenceFeature implements FeatureLocationI
     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;
+  }
 }