X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f17bd3349604541fd923c9da101bf16e77abea80;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=1adff257d1318a19459b6cb4d9a2fbc33feef438;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1adff25..f17bd33 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,137 +1,557 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- * 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.
- *
- * 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
- */
-package jalview.datamodel;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceFeature
-{
-    int position;
-    int begin;
-    int end;
-    String type;
-    String description;
-    String status;
-
-    public SequenceFeature()
-    {}
-
-    public SequenceFeature(String type, String desc, String status, int begin, int end)
-    {
-      this.type = type;
-      this.description = desc;
-      this.status = status;
-      this.position = begin;
-      this.begin = begin;
-      this.end = end;
-    }
-
-    public int getPosition()
-    {
-      return position;
-    }
-
-    public void setPosition(int pos)
-    {
-      position = pos;
-      begin = pos;
-      end = pos;
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getBegin()
-    {
-        return begin;
-    }
-
-    public void setBegin(int start)
-    {
-      this.begin = start;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEnd()
-    {
-        return end;
-    }
-
-    public void setEnd(int end)
-    {
-      this.end = end;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getType()
-    {
-        return type;
-    }
-
-    public void setType(String type)
-    {
-      this.type = type;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
-    {
-        return description;
-    }
-
-    public void setDescription(String desc)
-    {
-      description = desc;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getStatus()
-    {
-        return status;
-    }
-
-    public void setStatus(String status)
-    {
-      this.status = status;
-    }
-
-}
+/*
+ * 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.
+ *  
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+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 implements FeatureLocationI
+{
+  /*
+   * 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;
+
+    /*
+     * 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)
+    {
+      otherDetails = new HashMap<>();
+      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
+      {
+        otherDetails.put(entry.getKey(), entry.getValue());
+      }
+    }
+    if (sf.links != null && sf.links.size() > 0)
+    {
+      links = new Vector<>();
+      for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
+      {
+        links.addElement(sf.links.elementAt(i));
+      }
+    }
+  }
+
+  /**
+   * 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 false;
+    }
+
+    SequenceFeature sf = (SequenceFeature) o;
+    boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
+            : score == sf.score;
+    if (begin != sf.begin || end != sf.end || !sameScore)
+    {
+      return false;
+    }
+
+    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!
+   */
+  @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)
+    {
+      links = new Vector<>();
+    }
+
+    if (!links.contains(labelLink))
+    {
+      links.insertElementAt(labelLink, 0);
+    }
+  }
+
+  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)
+    {
+      return null;
+    }
+    else
+    {
+      return otherDetails.get(key);
+    }
+  }
+
+  /**
+   * 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 (otherDetails == null)
+      {
+        otherDetails = new HashMap<>();
+      }
+
+      otherDetails.put(key, value);
+    }
+  }
+
+  /*
+   * 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)
+    {
+      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;
+  }
+}
+
+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();
+  }
+}