X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f498b94abbd5eb688cad365c98a7af9c52eda96;hb=HEAD;hp=25dfc409b232e8bb691f7b63ec9bb642d519614a;hpb=4e77a2d1581819e35ba9e186324c522f1e4b0a25;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 25dfc40..1f498b9 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,18 +20,25 @@
  */
 package jalview.datamodel;
 
-import jalview.datamodel.features.FeatureLocationI;
-
-import java.util.HashMap;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
+import java.util.TreeMap;
 import java.util.Vector;
 
+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;
+
 /**
- * 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
 {
@@ -43,22 +50,18 @@ public class SequenceFeature implements FeatureLocationI
 
   private static final String STATUS = "status";
 
-  private static final String STRAND = "STRAND";
+  public static final String STRAND = "STRAND";
 
-  // private key for Phase designed not to conflict with real GFF data
-  private static final String PHASE = "!Phase";
+  // key for Phase designed not to conflict with real GFF data
+  public static final String PHASE = "!Phase";
 
   // private key for ENA location designed not to conflict with real GFF data
   private static final String LOCATION = "!Location";
 
-  /*
-   * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
-   * name1=value1;name2=value2,value3;...etc
-   */
-  private static final String ATTRIBUTES = "ATTRIBUTES";
+  private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td><td>%s</td></tr>";
 
   /*
-   * type, begin, end, featureGroup and contactFeature are final 
+   * type, begin, end, featureGroup, score and contactFeature are final 
    * to ensure that the integrity of SequenceFeatures data store 
    * can't be broken by direct update of these fields
    */
@@ -84,6 +87,12 @@ 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
@@ -93,8 +102,8 @@ public class SequenceFeature implements FeatureLocationI
    */
   public SequenceFeature(SequenceFeature cpy)
   {
-    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
-            .getScore());
+    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(),
+            cpy.getScore());
   }
 
   /**
@@ -143,36 +152,48 @@ public class SequenceFeature implements FeatureLocationI
    * A copy constructor that allows the value of final fields to be 'modified'
    * 
    * @param sf
+   * @param newType
    * @param newBegin
    * @param newEnd
    * @param newGroup
    * @param newScore
    */
-  public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
-          String newGroup, float newScore)
+  public SequenceFeature(SequenceFeature sf, String newType, int newBegin,
+          int newEnd, String newGroup, float newScore)
   {
-    this(sf.getType(), sf.getDescription(), newBegin, newEnd, newScore,
+    this(newType, sf.getDescription(), newBegin, newEnd, newScore,
             newGroup);
 
+    this.source = sf.source;
+
     if (sf.otherDetails != null)
     {
-      otherDetails = new HashMap<String, Object>();
-      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
-      {
-        otherDetails.put(entry.getKey(), entry.getValue());
-      }
+      otherDetails = new LinkedHashMap<>();
+      otherDetails.putAll(sf.otherDetails);
     }
     if (sf.links != null && sf.links.size() > 0)
     {
-      links = new Vector<String>();
-      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
-      {
-        links.addElement(sf.links.elementAt(i));
-      }
+      links = new Vector<>();
+      links.addAll(sf.links);
     }
   }
 
   /**
+   * A copy constructor that allows the value of final fields to be 'modified'
+   * 
+   * @param sf
+   * @param newBegin
+   * @param newEnd
+   * @param newGroup
+   * @param newScore
+   */
+  public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd,
+          String newGroup, float newScore)
+  {
+    this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore);
+  }
+
+  /**
    * Two features are considered equal if they have the same type, group,
    * description, start, end, phase, strand, and (if present) 'Name', ID' and
    * 'Parent' attributes.
@@ -217,8 +238,8 @@ 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;
     }
@@ -312,11 +333,16 @@ public class SequenceFeature implements FeatureLocationI
     return featureGroup;
   }
 
+  /**
+   * Adds a hyperlink for the feature. This should have the format label|url.
+   * 
+   * @param labelLink
+   */
   public void addLink(String labelLink)
   {
     if (links == null)
     {
-      links = new Vector<String>();
+      links = new Vector<>();
     }
 
     if (!links.contains(labelLink))
@@ -350,6 +376,30 @@ 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
    * 
@@ -378,11 +428,36 @@ public class SequenceFeature implements FeatureLocationI
     {
       if (otherDetails == null)
       {
-        otherDetails = new HashMap<String, Object>();
+        /*
+         * LinkedHashMap preserves insertion order of attributes
+         */
+        otherDetails = new LinkedHashMap<>();
       }
 
       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);
   }
 
   /*
@@ -399,16 +474,6 @@ public class SequenceFeature implements FeatureLocationI
     return (String) getValue(STATUS);
   }
 
-  public void setAttributes(String attr)
-  {
-    setValue(ATTRIBUTES, attr);
-  }
-
-  public String getAttributes()
-  {
-    return (String) getValue(ATTRIBUTES);
-  }
-
   /**
    * Return 1 for forward strand ('+' in GFF), -1 for reverse strand ('-' in
    * GFF), and 0 for unknown or not (validly) specified
@@ -519,4 +584,183 @@ public class SequenceFeature implements FeatureLocationI
   {
     return begin == 0 && end == 0;
   }
+
+  /**
+   * Answers an html-formatted report of feature details. If parameter
+   * {@code mf} is not null, the feature is a virtual linked feature, and
+   * details included both the original location and the mapped location
+   * (CDS/peptide).
+   * 
+   * @param seqName
+   * @param mf
+   * 
+   * @return
+   */
+  public String getDetailsReport(String seqName, MappedFeatures mf)
+  {
+    FeatureSourceI metadata = FeatureSources.getInstance()
+            .getSource(source);
+
+    StringBuilder sb = new StringBuilder(128);
+    sb.append("<br>");
+    sb.append("<table>");
+    String name = mf == null ? seqName : mf.getLinkedSequenceName();
+    sb.append(String.format(ROW_DATA, "Location", name, begin == end ? begin
+            : begin + (isContactFeature() ? ":" : "-") + end));
+
+    String consequence = "";
+    if (mf != null)
+    {
+      int[] localRange = mf.getMappedPositions(begin, end);
+      int from = localRange[0];
+      int to = localRange[localRange.length - 1];
+      String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
+      sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
+              : from + (isContactFeature() ? ":" : "-") + to));
+      if (mf.isFromCds())
+      {
+        consequence = mf.findProteinVariants(this);
+      }
+    }
+    sb.append(String.format(ROW_DATA, "Type", type, ""));
+    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 (!consequence.isEmpty())
+    {
+      sb.append(String.format(ROW_DATA, "Consequence",
+              "<i>Translated by Jalview</i>", consequence));
+    }
+
+    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();
+
+        Object value = entry.getValue();
+        if (value instanceof Map<?, ?>)
+        {
+          /*
+           * expand values in a Map attribute across separate lines
+           * copy to a TreeMap for alphabetical ordering
+           */
+          Map<String, Object> values = (Map<String, Object>) value;
+          SortedMap<String, Object> sm = new TreeMap<>(
+                  String.CASE_INSENSITIVE_ORDER);
+          sm.putAll(values);
+          for (Entry<?, ?> e : sm.entrySet())
+          {
+            sb.append(String.format(ROW_DATA, key, e.getKey().toString(),
+                    e.getValue().toString()));
+          }
+        }
+        else
+        {
+          // 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));
+          }
+        }
+      }
+    }
+    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;
+  }
+}
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getEnd() - b.getEnd();
+  }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getBegin() - b.getBegin();
+  }
 }