X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;fp=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=7d644e8476a27b6de229381d4c3f8053e88dc5eb;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=f8444a09f8c07b4f64fdab05fce14b2c897f3d30;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index f8444a0..7d644e8 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -1,172 +1,236 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class SequenceFeature -{ - public int position; - public int begin; - public int end; - public String type; - public String description; - public String status; - - // Feature group can be set from a features file - // as a group of features between STARTGROUP and ENDGROUP markers - public String featureGroup; - - public SequenceFeature() - {} - - public SequenceFeature(String type, - String desc, - String status, - int begin, int end, - String featureGroup) - { - this.type = type; - this.description = desc; - this.status = status; - this.position = begin; - this.begin = begin; - this.end = end; - this.featureGroup = featureGroup; - } - - public boolean equals(SequenceFeature sf) - { - if(begin != sf.begin - || end != sf.end) - return false; - - - if(!(type+description+status).equals - (sf.type+sf.description+sf.status)) - return false; - - return true; - } - - - public int getPosition() - { - return position; - } - - public void setPosition(int pos) - { - position = pos; - begin = pos; - end = pos; - } - - - /** - * 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; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getStatus() - { - return status; - } - - public void setStatus(String status) - { - this.status = status; - } - - public String getFeatureGroup() - { - return featureGroup; - } - - public void setFeatureGroup(String featureGroup) - { - this.featureGroup = featureGroup; - } - - -} +/* + * 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.Hashtable; + +/** + * 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() + {} + + 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) + return otherDetails.get("status").toString(); + else + return null; + } + + public void setPosition(int pos) + { + begin = pos; + end = pos; + } + + public int getPosition() + { + return begin; + } + +}