X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f17bd3349604541fd923c9da101bf16e77abea80;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=4a7706fa74bd2a59f314ae7aa1d6b96d37cb6354;hpb=908bf85e4afe1e303515797719df5dd8afec06e7;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 4a7706f..f17bd33 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -20,8 +20,12 @@ */ 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; /** @@ -30,8 +34,14 @@ import java.util.Vector; * @author $author$ * @version $Revision$ */ -public class SequenceFeature +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"; @@ -39,30 +49,42 @@ public class SequenceFeature // 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"; - public int begin; + /* + * 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 int end; + public final int end; - public float score; + public final String featureGroup; - public String type; + 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; - // 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 makes a shallow copy of the * otherDetails map, so the new and original SequenceFeature may reference the @@ -72,65 +94,99 @@ public class SequenceFeature */ public SequenceFeature(SequenceFeature cpy) { - if (cpy != null) + 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) { - begin = cpy.begin; - end = cpy.end; - score = cpy.score; - if (cpy.type != null) + otherDetails = new HashMap<>(); + for (Entry entry : sf.otherDetails.entrySet()) { - type = new String(cpy.type); + otherDetails.put(entry.getKey(), entry.getValue()); } - if (cpy.description != null) - { - description = new String(cpy.description); - } - if (cpy.featureGroup != null) - { - featureGroup = new String(cpy.featureGroup); - } - if (cpy.otherDetails != null) - { - try - { - otherDetails = (Map) ((HashMap) cpy.otherDetails) - .clone(); - } catch (Exception e) - { - // ignore - } - } - if (cpy.links != null && cpy.links.size() > 0) + } + if (sf.links != null && sf.links.size() > 0) + { + links = new Vector<>(); + for (int i = 0, iSize = sf.links.size(); i < iSize; i++) { - links = new Vector(); - for (int i = 0, iSize = cpy.links.size(); i < iSize; i++) - { - links.addElement(cpy.links.elementAt(i)); - } + links.addElement(sf.links.elementAt(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; - } - - public SequenceFeature(String type, String desc, int begin, int end, - float score, String featureGroup) + /** + * 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.type = type; - this.description = desc; - this.begin = begin; - this.end = end; - this.score = score; - this.featureGroup = featureGroup; + this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore); } /** @@ -166,7 +222,9 @@ public class SequenceFeature } SequenceFeature sf = (SequenceFeature) o; - if (begin != sf.begin || end != sf.end || score != sf.score) + boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score) + : score == sf.score; + if (begin != sf.begin || end != sf.end || !sameScore) { return false; } @@ -176,8 +234,8 @@ public class SequenceFeature 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; } @@ -224,31 +282,23 @@ public class SequenceFeature * * @return DOCUMENT ME! */ + @Override public int getBegin() { return begin; } - public void setBegin(int start) - { - this.begin = start; - } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ + @Override public int getEnd() { return end; } - public void setEnd(int end) - { - this.end = end; - } - /** * DOCUMENT ME! * @@ -259,11 +309,6 @@ public class SequenceFeature return type; } - public void setType(String type) - { - this.type = type; - } - /** * DOCUMENT ME! * @@ -284,19 +329,17 @@ public class SequenceFeature return featureGroup; } - public void setFeatureGroup(String featureGroup) - { - this.featureGroup = featureGroup; - } - public void addLink(String labelLink) { if (links == null) { - links = new Vector(); + links = new Vector<>(); } - links.insertElementAt(labelLink, 0); + if (!links.contains(labelLink)) + { + links.insertElementAt(labelLink, 0); + } } public float getScore() @@ -304,11 +347,6 @@ public class SequenceFeature return score; } - public void setScore(float value) - { - score = value; - } - /** * Used for getting values which are not in the basic set. eg STRAND, PHASE * for GFF file @@ -357,7 +395,7 @@ public class SequenceFeature { if (otherDetails == null) { - otherDetails = new HashMap(); + otherDetails = new HashMap<>(); } otherDetails.put(key, value); @@ -388,17 +426,6 @@ public class SequenceFeature return (String) getValue(ATTRIBUTES); } - public void setPosition(int pos) - { - begin = pos; - end = pos; - } - - public int getPosition() - { - return begin; - } - /** * Return 1 for forward strand ('+' in GFF), -1 for reverse strand ('-' in * GFF), and 0 for unknown or not (validly) specified @@ -445,6 +472,26 @@ public class SequenceFeature } /** + * 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 */ @@ -468,4 +515,43 @@ public class SequenceFeature 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(); + } }