JAL-2055 prototype alternate feature colouring based on

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 252f46c..54ff6df 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -39,6 +39,13 @@ public class SequenceFeature
   // private key for Phase designed not to conflict with real GFF data
   private static final String PHASE = "!Phase";
 
+  // private key for feature number designed not to conflict with real GFF data
+  private static final String NUMBER = "!Num";
+
+  /*
+   * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
+   * name1=value1;name2=value2,value3;...etc
+   */
   private static final String ATTRIBUTES = "ATTRIBUTES";
 
   public int begin;
@@ -111,45 +118,146 @@ public class SequenceFeature
     }
   }
 
+  /**
+   * Constructor including a Status value
+   * 
+   * @param type
+   * @param desc
+   * @param status
+   * @param begin
+   * @param end
+   * @param featureGroup
+   */
   public SequenceFeature(String type, String desc, String status,
           int begin, int end, String featureGroup)
   {
+    this(type, desc, begin, end, featureGroup);
+    setStatus(status);
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param type
+   * @param desc
+   * @param begin
+   * @param end
+   * @param featureGroup
+   */
+  SequenceFeature(String type, String desc, int begin, int end,
+          String featureGroup)
+  {
     this.type = type;
     this.description = desc;
-    setValue(STATUS, status);
     this.begin = begin;
     this.end = end;
     this.featureGroup = featureGroup;
   }
 
+  /**
+   * Constructor including a score value
+   * 
+   * @param type
+   * @param desc
+   * @param begin
+   * @param end
+   * @param score
+   * @param featureGroup
+   */
   public SequenceFeature(String type, String desc, int begin, int end,
           float score, String featureGroup)
   {
-    this.type = type;
-    this.description = desc;
-    this.begin = begin;
-    this.end = end;
+    this(type, desc, begin, end, featureGroup);
     this.score = score;
-    this.featureGroup = featureGroup;
   }
 
-  public boolean equals(SequenceFeature sf)
+  /**
+   * 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.
+   * 
+   * Note we need to check Parent to distinguish the same exon occurring in
+   * different transcripts (in Ensembl GFF). This allows assembly of transcript
+   * sequences from their component exon regions.
+   */
+  @Override
+  public boolean equals(Object o)
   {
+    return equals(o, false);
+  }
+
+  /**
+   * Overloaded method allows the equality test to optionally ignore the
+   * 'Parent' attribute of a feature. This supports avoiding adding many
+   * superficially duplicate 'exon' or CDS features to genomic or protein
+   * sequence.
+   * 
+   * @param o
+   * @param ignoreParent
+   * @return
+   */
+  public boolean equals(Object o, boolean ignoreParent)
+  {
+    if (o == null || !(o instanceof SequenceFeature))
+    {
+      return false;
+    }
+
+    SequenceFeature sf = (SequenceFeature) o;
     if (begin != sf.begin || end != sf.end || score != sf.score)
     {
       return false;
     }
 
-    if (!(type + description + featureGroup).equals(sf.type
-            + sf.description + sf.featureGroup))
+    if (getStrand() != sf.getStrand())
     {
       return false;
     }
 
+    if (!(type + description + featureGroup + getPhase()).equals(sf.type
+            + sf.description + sf.featureGroup + sf.getPhase()))
+    {
+      return false;
+    }
+    if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
+    {
+      return false;
+    }
+    if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
+    {
+      return false;
+    }
+    if (!ignoreParent)
+    {
+      if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
+      {
+        return false;
+      }
+    }
     return true;
   }
 
   /**
+   * Returns true if both values are null, are both non-null and equal
+   * 
+   * @param att1
+   * @param att2
+   * @return
+   */
+  protected static boolean equalAttribute(Object att1, Object att2)
+  {
+    if (att1 == null && att2 == null)
+    {
+      return true;
+    }
+    if (att1 != null)
+    {
+      return att1.equals(att2);
+    }
+    return att2.equals(att1);
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
@@ -353,6 +461,12 @@ public class SequenceFeature
     return strand;
   }
 
+  /**
+   * Set the value of strand
+   * 
+   * @param strand
+   *          should be "+" for forward, or "-" for reverse
+   */
   public void setStrand(String strand)
   {
     setValue(STRAND, strand);
@@ -369,6 +483,34 @@ public class SequenceFeature
   }
 
   /**
+   * Set the ordinal number of this feature on the sequence
+   * 
+   * @param num
+   */
+  public void setFeatureNumber(int num)
+  {
+    setValue(NUMBER, String.valueOf(num));
+  }
+
+  /**
+   * Returns the feature number if set, else 0. Intended for use as the ordinal
+   * position of the feature on the sequence for features of the same type.
+   * 
+   * @return
+   */
+  public int getFeatureNumber()
+  {
+    try
+    {
+      return Integer.parseInt((String) getValue(NUMBER));
+    } catch (Exception e)
+    {
+      // property absent or not numeric
+      return 0;
+    }
+  }
+
+  /**
    * Readable representation, for debug only, not guaranteed not to change
    * between versions
    */
@@ -378,4 +520,18 @@ public class SequenceFeature
     return String.format("%d %d %s %s", getBegin(), getEnd(), getType(),
             getDescription());
   }
+
+  /**
+   * Overridden to ensure that whenever two objects are equal, they have the
+   * same hashCode
+   */
+  @Override
+  public int hashCode()
+  {
+    String s = getType() + getDescription() + getFeatureGroup()
+            + getValue("ID") + getValue("Name") + getValue("Parent")
+            + getPhase();
+    return s.hashCode() + getBegin() + getEnd() + (int) getScore()
+            + getStrand();
+  }
 }