X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f34b8b0faf2091daef49bc179419613c291b6f8;hb=a96d51f58325f8429c5792ae554243de5628d62a;hp=094e060662c3f88331227235eab017b45c58c23b;hpb=cfbeda226e2ac27f6d02572b1c9589a3e2f1c747;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 094e060..1f34b8b 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -18,9 +18,7 @@ */ package jalview.datamodel; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Vector; +import java.util.*; /** * DOCUMENT ME! @@ -30,238 +28,270 @@ import java.util.Vector; */ 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; - type = new String(cpy.type); - description = new String(cpy.description); - 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 0) + { + links = new Vector(); + for (int i = 0, iSize = cpy.links.size(); i < iSize; i++) + { + links.addElement(cpy.links.elementAt(i)); + } + } } - - public void setFeatureGroup(String featureGroup) + } + + 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) + { + this.type = type; + this.description = desc; + this.begin = begin; + this.end = end; + this.score = score; + this.featureGroup = featureGroup; + } + + public boolean equals(SequenceFeature sf) + { + if (begin != sf.begin + || end != sf.end + || score != sf.score) { - this.featureGroup = featureGroup; + return false; } - public void addLink(String labelLink) + if (! (type + description + featureGroup).equals + (sf.type + sf.description + sf.featureGroup)) { - if(links==null) - links = new java.util.Vector(); - - links.insertElementAt(labelLink,0); + return false; } - public float getScore() + return true; + } + + /** + * 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; + } + + public String getFeatureGroup() + { + return featureGroup; + } + + public void setFeatureGroup(String featureGroup) + { + this.featureGroup = featureGroup; + } + + public void addLink(String labelLink) + { + if (links == null) { - return score; + links = new java.util.Vector(); } - public void setScore(float value) + links.insertElementAt(labelLink, 0); + } + + public float getScore() + { + return score; + } + + public void setScore(float value) + { + score = value; + } + + /** + * Used for getting values which are not in the + * basic set. eg STRAND, FRAME for GFF file + * @param key String + */ + public Object getValue(String key) + { + if (otherDetails == null) { - score = value; + return null; } - - /** - * Used for getting values which are not in the - * basic set. eg STRAND, FRAME for GFF file - * @param key String - */ - public Object getValue(String key) + else { - if(otherDetails==null) - return null; - else - return otherDetails.get(key); + return otherDetails.get(key); } - - /** - * 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) + } + + /** + * 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(value!=null) + if (otherDetails == null) { - if (otherDetails == null) - otherDetails = new Hashtable(); - - otherDetails.put(key, value); + otherDetails = new Hashtable(); } - } - - /* - * 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() - { - if (otherDetails != null) - return otherDetails.get("status").toString(); - else - return null; + otherDetails.put(key, value); } - - public void setPosition(int pos) - { - begin = pos; - end = pos; - } - - public int getPosition() + } + + /* + * 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() + { + if (otherDetails != null) { - return begin; + String stat = (String) otherDetails.get("status"); + if (stat!=null) + return new String(stat); } + return null; + } + + public void setPosition(int pos) + { + begin = pos; + end = pos; + } + + public int getPosition() + { + return begin; + } }