X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=f17bd3349604541fd923c9da101bf16e77abea80;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=b61dd719e25de5e38b8a8bb07074f9ac97e05c48;hpb=33fb9570b83bbbb5b92ead18043c05f9512a7a2a;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index b61dd71..f17bd33 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -22,8 +22,10 @@ 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; /** @@ -34,6 +36,12 @@ import java.util.Vector; */ 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"; @@ -50,13 +58,22 @@ public class SequenceFeature implements FeatureLocationI */ 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; @@ -68,14 +85,6 @@ public class SequenceFeature implements FeatureLocationI 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 @@ -85,96 +94,99 @@ public class SequenceFeature implements FeatureLocationI */ 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 = (Map) ((HashMap) cpy.otherDetails) - .clone(); - } catch (Exception e) - { - // ignore - } - } - if (cpy.links != null && cpy.links.size() > 0) - { - links = new Vector(); - for (int i = 0, iSize = cpy.links.size(); i < iSize; i++) - { - links.addElement(cpy.links.elementAt(i)); - } - } - } + this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy + .getScore()); } /** - * Constructor including a Status value + * Constructor * - * @param type - * @param desc - * @param status - * @param begin - * @param end - * @param featureGroup + * @param theType + * @param theDesc + * @param theBegin + * @param theEnd + * @param group */ - public SequenceFeature(String type, String desc, String status, - int begin, int end, String featureGroup) + public SequenceFeature(String theType, String theDesc, int theBegin, + int theEnd, String group) { - this(type, desc, begin, end, featureGroup); - setStatus(status); + this(theType, theDesc, theBegin, theEnd, NO_SCORE, group); } /** - * Constructor + * Constructor including a score value * - * @param type - * @param desc - * @param begin - * @param end - * @param featureGroup + * @param theType + * @param theDesc + * @param theBegin + * @param theEnd + * @param theScore + * @param group */ - SequenceFeature(String type, String desc, int begin, int end, - String featureGroup) + public SequenceFeature(String theType, String theDesc, int theBegin, + int theEnd, float theScore, String group) { - this.type = type; - this.description = desc; - this.begin = begin; - this.end = end; - this.featureGroup = featureGroup; + 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); } /** - * Constructor including a score value + * 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 type - * @param desc - * @param begin - * @param end - * @param score - * @param featureGroup + * @param sf + * @param newBegin + * @param newEnd + * @param newGroup + * @param newScore */ - public SequenceFeature(String type, String desc, int begin, int end, - float score, String featureGroup) + public SequenceFeature(SequenceFeature sf, int newBegin, int newEnd, + String newGroup, float newScore) { - this(type, desc, begin, end, featureGroup); - this.score = score; + this(sf, sf.getType(), newBegin, newEnd, newGroup, newScore); } /** @@ -222,8 +234,8 @@ public class SequenceFeature implements FeatureLocationI 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; } @@ -276,11 +288,6 @@ public class SequenceFeature implements FeatureLocationI return begin; } - public void setBegin(int start) - { - this.begin = start; - } - /** * DOCUMENT ME! * @@ -292,11 +299,6 @@ public class SequenceFeature implements FeatureLocationI return end; } - public void setEnd(int end) - { - this.end = end; - } - /** * DOCUMENT ME! * @@ -307,11 +309,6 @@ public class SequenceFeature implements FeatureLocationI return type; } - public void setType(String type) - { - this.type = type; - } - /** * DOCUMENT ME! * @@ -332,19 +329,17 @@ public class SequenceFeature implements FeatureLocationI 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() @@ -352,11 +347,6 @@ public class SequenceFeature implements FeatureLocationI 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 @@ -405,7 +395,7 @@ public class SequenceFeature implements FeatureLocationI { if (otherDetails == null) { - otherDetails = new HashMap(); + otherDetails = new HashMap<>(); } otherDetails.put(key, value); @@ -436,17 +426,6 @@ public class SequenceFeature implements FeatureLocationI 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 @@ -545,13 +524,7 @@ public class SequenceFeature implements FeatureLocationI @Override public boolean isContactFeature() { - // TODO abstract one day to a FeatureType class - if ("disulfide bond".equalsIgnoreCase(type) - || "disulphide bond".equalsIgnoreCase(type)) - { - return true; - } - return false; + return contactFeature; } /** @@ -564,3 +537,21 @@ public class SequenceFeature implements FeatureLocationI 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(); + } +}