X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f17bd3349604541fd923c9da101bf16e77abea80;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=14ce0ff52437a984de51aefedcba554af7c460ce;hpb=d5e0a42692b58e79e036448772ceebfbfd40ff94;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 14ce0ff..f17bd33 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,270 +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
- * 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;
-
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceFeature
-{
- 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()
- {}
- /**
- * Constructs a duplicate feature.
- * Note: Uses clone on the otherDetails so only shallow copies are made
- * of additional properties and method will silently fail if unclonable
- * objects are found in the hash.
- * @param cpy
- */
- public SequenceFeature(SequenceFeature cpy) {
- if (cpy!=null) {
- begin = cpy.begin;
- end = cpy.end;
- score = cpy.score;
- if (cpy.type != null)
- type = new String(cpy.type);
- if (cpy.description != null)
- description = new String(cpy.description);
- if (cpy.featureGroup != null)
- 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.
+ * 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 otherDetails;
+
+ public Vector 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 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
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getEnd() - b.getEnd();
+ }
+}
+
+class SFSortByBegin implements Comparator
+{
+ @Override
+ public int compare(SequenceFeature a, SequenceFeature b)
+ {
+ return a.getBegin() - b.getBegin();
+ }
+}