From: gmungoc Date: Thu, 25 May 2017 09:35:08 +0000 (+0100) Subject: JAL-2505 simplifying number of SequenceFeature constructors JAL-2060 X-Git-Tag: Release_2_10_3b1~232 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ce4840757da155836d19edb70821fce6d2258d88;p=jalview.git JAL-2505 simplifying number of SequenceFeature constructors JAL-2060 constant for NO_SCORE defined in SequenceFeature --- diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 627e1ae..4df57ef 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -24,6 +24,7 @@ import jalview.datamodel.features.FeatureLocationI; import java.util.HashMap; import java.util.Map; +import java.util.Map.Entry; import java.util.Vector; /** @@ -34,6 +35,12 @@ 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"; @@ -85,81 +92,43 @@ public class SequenceFeature implements FeatureLocationI public SequenceFeature(SequenceFeature cpy) { this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup()); - - score = cpy.score; - description = cpy.description; - 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)); - } - } - } - - /** - * Constructor including a Status value - * - * @param type - * @param desc - * @param status - * @param begin - * @param end - * @param featureGroup - */ - public SequenceFeature(String type, String desc, String status, - int begin, int end, String featureGroup) - { - this(type, desc, begin, end, featureGroup); - setStatus(status); } /** * Constructor * - * @param type - * @param desc - * @param begin - * @param end - * @param featureGroup + * @param theType + * @param theDesc + * @param theBegin + * @param theEnd + * @param group */ - SequenceFeature(String type, String desc, int begin, int end, - String featureGroup) + public SequenceFeature(String theType, String theDesc, int theBegin, + int theEnd, 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 = NO_SCORE; } /** * Constructor including a score value * - * @param type - * @param desc - * @param begin - * @param end - * @param score - * @param featureGroup + * @param theType + * @param theDesc + * @param theBegin + * @param theEnd + * @param theScore + * @param group */ - public SequenceFeature(String type, String desc, int begin, int end, - float score, String featureGroup) + public SequenceFeature(String theType, String theDesc, int theBegin, + int theEnd, float theScore, String group) { - this(type, desc, begin, end, featureGroup); - this.score = score; + this(theType, theDesc, theBegin, theEnd, group); + this.score = theScore; } /** @@ -175,6 +144,24 @@ public class SequenceFeature implements FeatureLocationI String newGroup) { this(sf.getType(), newBegin, newEnd, newGroup); + score = sf.score; + description = sf.description; + 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)); + } + } } /**