X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f17bd3349604541fd923c9da101bf16e77abea80;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=fd240b981420b974982542dbd2060459e47e19e0;hpb=0c355acb1b5ddab95961d703ca6bc383a4464def;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index fd240b9..f17bd33 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,260 +1,557 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
+import jalview.datamodel.features.FeatureLocationI;
+
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Vector;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class SequenceFeature
+public class SequenceFeature implements FeatureLocationI
 {
-    public int begin;
-    public int end;
-    public float score;
-    public String type;
-    public String description;
-    public Hashtable otherDetails;
-    public java.util.Vector links;
-
-    // Feature group can be set from a features file
-    // as a group of features between STARTGROUP and ENDGROUP markers
-    public String featureGroup;
-
-    public SequenceFeature()
-    {}
-    public SequenceFeature(SequenceFeature cpy) {
-        if (cpy!=null) {
-            begin = cpy.begin;
-            end = cpy.end;
-            score = cpy.score;
-            type = new String(cpy.type);
-            description = new String(cpy.description);
-            featureGroup = new String(cpy.featureGroup);
-            if (cpy.otherDetails!=null) {
-                try {
-                    otherDetails = (Hashtable) cpy.otherDetails.clone();
-                } catch (Exception e) {
-                    // Uncloneable objects in the otherDetails - don't complain
-                }
-            }
-            if (cpy.links!=null && cpy.links.size()>0) {
-                links=new Vector();
-                for (int i=0,iSize=cpy.links.size(); i<iSize; i++) {
-                    links.setElementAt(cpy.links.elementAt(i), i);
-                }
-            }
-        }
-    }
-    public SequenceFeature(String type,
-                           String desc,
-                           String status,
-                           int begin, int end,
-                           String featureGroup)
-    {
-      this.type = type;
-      this.description = desc;
-      setValue("status", status);
-      this.begin = begin;
-      this.end = end;
-      this.featureGroup = featureGroup;
-    }
+  /*
+   * score value if none is set; preferably Float.Nan, but see
+   * JAL-2060 and JAL-2554 for a couple of blockers to that
+   */
+  private static final float NO_SCORE = 0f;
+
+  private static final String STATUS = "status";
+
+  private static final String STRAND = "STRAND";
+
+  // private key for Phase designed not to conflict with real GFF data
+  private 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";
+
+  /*
+   * 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
+   */
+  public final String type;
+
+  public final int begin;
+
+  public final int end;
+
+  public final String featureGroup;
+
+  public final float score;
+
+  private final boolean contactFeature;
+
+  public String description;
+
+  /*
+   * a map of key-value pairs; may be populated from GFF 'column 9' data,
+   * other data sources (e.g. GenBank file), or programmatically
+   */
+  public Map<String, Object> otherDetails;
+
+  public Vector<String> links;
+
+  /**
+   * Constructs a duplicate feature. Note: Uses makes a shallow copy of the
+   * otherDetails map, so the new and original SequenceFeature may reference the
+   * same objects in the map.
+   * 
+   * @param cpy
+   */
+  public SequenceFeature(SequenceFeature cpy)
+  {
+    this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
+            .getScore());
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param theType
+   * @param theDesc
+   * @param theBegin
+   * @param theEnd
+   * @param group
+   */
+  public SequenceFeature(String theType, String theDesc, int theBegin,
+          int theEnd, String group)
+  {
+    this(theType, theDesc, theBegin, theEnd, NO_SCORE, group);
+  }
+
+  /**
+   * Constructor including a score value
+   * 
+   * @param theType
+   * @param theDesc
+   * @param theBegin
+   * @param theEnd
+   * @param theScore
+   * @param group
+   */
+  public SequenceFeature(String theType, String theDesc, int theBegin,
+          int theEnd, float theScore, String group)
+  {
+    this.type = theType;
+    this.description = theDesc;
+    this.begin = theBegin;
+    this.end = theEnd;
+    this.featureGroup = group;
+    this.score = theScore;
 
-    public SequenceFeature(String type,
-                           String desc,
-                           int begin, int end,
-                           float score,
-                           String featureGroup)
+    /*
+     * for now, only "Disulfide/disulphide bond" is treated as a contact feature
+     */
+    this.contactFeature = "disulfide bond".equalsIgnoreCase(type)
+            || "disulphide bond".equalsIgnoreCase(type);
+  }
+
+  /**
+   * 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, String newType, int newBegin,
+          int newEnd, String newGroup, float newScore)
+  {
+    this(newType, sf.getDescription(), newBegin, newEnd, newScore,
+            newGroup);
+
+    if (sf.otherDetails != null)
     {
-      this.type = type;
-      this.description = desc;
-      this.begin = begin;
-      this.end = end;
-      this.score = score;
-      this.featureGroup = featureGroup;
+      otherDetails = new HashMap<>();
+      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
+      {
+        otherDetails.put(entry.getKey(), entry.getValue());
+      }
     }
-
-    public boolean equals(SequenceFeature sf)
+    if (sf.links != null && sf.links.size() > 0)
     {
-      if (begin != sf.begin
-          || end != sf.end
-          || score != sf.score)
-        return false;
-
-      if(!(type+description+featureGroup).equals
-         (sf.type+sf.description+sf.featureGroup))
-        return false;
-
-      return true;
+      links = new Vector<>();
+      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
+      {
+        links.addElement(sf.links.elementAt(i));
+      }
     }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getBegin()
+  }
+
+  /**
+   * 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.
+   * 
+   * 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 begin;
+      return false;
     }
 
-    public void setBegin(int start)
+    SequenceFeature sf = (SequenceFeature) o;
+    boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
+            : score == sf.score;
+    if (begin != sf.begin || end != sf.end || !sameScore)
     {
-      this.begin = start;
+      return false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEnd()
+    if (getStrand() != sf.getStrand())
     {
-        return end;
+      return false;
     }
 
-    public void setEnd(int end)
+    if (!(type + description + featureGroup + getPhase()).equals(
+            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
     {
-      this.end = end;
+      return false;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getType()
+    if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
     {
-        return type;
+      return false;
     }
-
-    public void setType(String type)
+    if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
     {
-      this.type = type;
+      return false;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
+    if (!ignoreParent)
     {
-        return description;
+      if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
+      {
+        return false;
+      }
     }
-
-    public void setDescription(String desc)
+    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)
     {
-      description = desc;
-    }
-
-    public String getFeatureGroup()
-    {
-      return featureGroup;
+      return true;
     }
-
-    public void setFeatureGroup(String featureGroup)
+    if (att1 != null)
     {
-      this.featureGroup = featureGroup;
+      return att1.equals(att2);
     }
-
-    public void addLink(String labelLink)
+    return att2.equals(att1);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public int getBegin()
+  {
+    return begin;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  @Override
+  public int getEnd()
+  {
+    return end;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
+
+  public String getFeatureGroup()
+  {
+    return featureGroup;
+  }
+
+  public void addLink(String labelLink)
+  {
+    if (links == null)
     {
-      if(links==null)
-        links = new java.util.Vector();
-
-      links.insertElementAt(labelLink,0);
+      links = new Vector<>();
     }
 
-    public float getScore()
+    if (!links.contains(labelLink))
     {
-      return score;
+      links.insertElementAt(labelLink, 0);
     }
-
-    public void setScore(float value)
+  }
+
+  public float getScore()
+  {
+    return score;
+  }
+
+  /**
+   * Used for getting values which are not in the basic set. eg STRAND, PHASE
+   * for GFF file
+   * 
+   * @param key
+   *          String
+   */
+  public Object getValue(String key)
+  {
+    if (otherDetails == null)
     {
-      score = value;
+      return null;
     }
-
-    /**
-     * Used for getting values which are not in the
-     * basic set. eg STRAND, FRAME for GFF file
-     * @param key String
-     */
-    public Object getValue(String key)
+    else
     {
-      if(otherDetails==null)
-        return null;
-      else
-        return otherDetails.get(key);
+      return otherDetails.get(key);
     }
-
-    /**
-     * Used for setting values which are not in the
-     * basic set. eg STRAND, FRAME for GFF file
-     * @param key   eg STRAND
-     * @param value eg +
-     */
-    public void setValue(String key, Object value)
+  }
+
+  /**
+   * Returns a property value for the given key if known, else the specified
+   * default value
+   * 
+   * @param key
+   * @param defaultValue
+   * @return
+   */
+  public Object getValue(String key, Object defaultValue)
+  {
+    Object value = getValue(key);
+    return value == null ? defaultValue : value;
+  }
+
+  /**
+   * Used for setting values which are not in the basic set. eg STRAND, FRAME
+   * for GFF file
+   * 
+   * @param key
+   *          eg STRAND
+   * @param value
+   *          eg +
+   */
+  public void setValue(String key, Object value)
+  {
+    if (value != null)
     {
-      if(value!=null)
+      if (otherDetails == null)
       {
-        if (otherDetails == null)
-          otherDetails = new Hashtable();
-
-        otherDetails.put(key, value);
+        otherDetails = new HashMap<>();
       }
-    }
-
-
-    /*
-     * The following methods are added to maintain
-     * the castor Uniprot mapping file for the moment.
-     */
-    public void setStatus(String status)
-    {
-      setValue("status", status);
-    }
 
-    public String getStatus()
-    {
-      if (otherDetails != null)
-        return otherDetails.get("status").toString();
-      else
-        return null;
+      otherDetails.put(key, value);
     }
-
-    public void setPosition(int pos)
+  }
+
+  /*
+   * The following methods are added to maintain the castor Uniprot mapping file
+   * for the moment.
+   */
+  public void setStatus(String status)
+  {
+    setValue(STATUS, status);
+  }
+
+  public String getStatus()
+  {
+    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
+   * 
+   * @return
+   */
+  public int getStrand()
+  {
+    int strand = 0;
+    if (otherDetails != null)
     {
-      begin = pos;
-      end = pos;
+      Object str = otherDetails.get(STRAND);
+      if ("-".equals(str))
+      {
+        strand = -1;
+      }
+      else if ("+".equals(str))
+      {
+        strand = 1;
+      }
     }
+    return strand;
+  }
+
+  /**
+   * Set the value of strand
+   * 
+   * @param strand
+   *          should be "+" for forward, or "-" for reverse
+   */
+  public void setStrand(String strand)
+  {
+    setValue(STRAND, strand);
+  }
+
+  public void setPhase(String phase)
+  {
+    setValue(PHASE, phase);
+  }
+
+  public String getPhase()
+  {
+    return (String) getValue(PHASE);
+  }
+
+  /**
+   * Sets the 'raw' ENA format location specifier e.g. join(12..45,89..121)
+   * 
+   * @param loc
+   */
+  public void setEnaLocation(String loc)
+  {
+    setValue(LOCATION, loc);
+  }
+
+  /**
+   * Gets the 'raw' ENA format location specifier e.g. join(12..45,89..121)
+   * 
+   * @param loc
+   */
+  public String getEnaLocation()
+  {
+    return (String) getValue(LOCATION);
+  }
+
+  /**
+   * Readable representation, for debug only, not guaranteed not to change
+   * between versions
+   */
+  @Override
+  public String toString()
+  {
+    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();
+  }
+
+  /**
+   * Answers true if the feature's start/end values represent two related
+   * positions, rather than ends of a range. Such features may be visualised or
+   * reported differently to features on a range.
+   */
+  @Override
+  public boolean isContactFeature()
+  {
+    return contactFeature;
+  }
+
+  /**
+   * Answers true if the sequence has zero start and end position
+   * 
+   * @return
+   */
+  public boolean isNonPositional()
+  {
+    return begin == 0 && end == 0;
+  }
+}
 
-    public int getPosition()
-    {
-      return begin;
-    }
+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();
+  }
 }