X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=6fed6ee30eca78d714fccafada01f8a31d99eaed;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=14ce0ff52437a984de51aefedcba554af7c460ce;hpb=d5e0a42692b58e79e036448772ceebfbfd40ff94;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index 14ce0ff..6fed6ee 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -1,270 +1,299 @@ -/* - * 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. + */ +package jalview.datamodel; + +import java.util.*; + +/** + * 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 < iSize; i++) + { + links.addElement(cpy.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) + { + 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) + { + return false; + } + + if (!(type + description + featureGroup).equals(sf.type + + sf.description + sf.featureGroup)) + { + return false; + } + + 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) + { + links = new java.util.Vector(); + } + + 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) + { + return null; + } + else + { + 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) + { + if (value != null) + { + if (otherDetails == null) + { + otherDetails = new Hashtable(); + } + + 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() + { + if (otherDetails != null) + { + 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; + } + +}