From f38bc38ee057bebe07c9b2b5c843d3d7d7d94032 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 23 Mar 2007 15:41:11 +0000 Subject: [PATCH] bugfix for 1.1 conversion. --- src/jalview/datamodel/SequenceFeature.java | 596 ++++++++++++++-------------- 1 file changed, 298 insertions(+), 298 deletions(-) diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java index e8c5a36..8fd713e 100755 --- a/src/jalview/datamodel/SequenceFeature.java +++ b/src/jalview/datamodel/SequenceFeature.java @@ -1,298 +1,298 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * 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 - * 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.*; - -/** - * 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.setElementAt(cpy.links.elementAt(i), 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) - { - return otherDetails.get("status").toString(); - } - else - { - return null; - } - } - - public void setPosition(int pos) - { - begin = pos; - end = pos; - } - - public int getPosition() - { - return begin; - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * 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 + * 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.*; + +/** + * 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) + { + return otherDetails.get("status").toString(); + } + else + { + return null; + } + } + + public void setPosition(int pos) + { + begin = pos; + end = pos; + } + + public int getPosition() + { + return begin; + } + +} -- 1.7.10.2