-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.datamodel;\r
-\r
-public class SequenceFeature {\r
- int begin;\r
- int end;\r
- String type;\r
- String description;\r
- String status;\r
-\r
- public SequenceFeature() {\r
- }\r
-\r
- public SequenceFeature(String type, int start, int end, String description,\r
- String status) {\r
- this.type = type;\r
- this.begin = start;\r
- this.end = end;\r
- this.description = description;\r
- this.status = status;\r
- }\r
-\r
- public int getStart() {\r
- return begin;\r
- }\r
-\r
- public int getEnd() {\r
- return end;\r
- }\r
-\r
- public String getType() {\r
- return type;\r
- }\r
-\r
- public String getDescription() {\r
- return description;\r
- }\r
-\r
- public String getStatus() {\r
- return status;\r
- }\r
-\r
- /*\r
- <xs:enumeration value="active site" />\r
- <xs:enumeration value="binding site" />\r
- <xs:enumeration value="calcium-binding region" />\r
- <xs:enumeration value="chain" />\r
- <xs:enumeration value="cross-link" />\r
- <xs:enumeration value="disulfide bond" />\r
- <xs:enumeration value="DNA-binding region" />\r
- <xs:enumeration value="domain" />\r
- <xs:enumeration value="glycosylation site" />\r
- <xs:enumeration value="helix" />\r
- <xs:enumeration value="initiator methionine" />\r
- <xs:enumeration value="lipid moiety-binding region" />\r
- <xs:enumeration value="metal ion-binding site" />\r
- <xs:enumeration value="modified residue" />\r
- <xs:enumeration value="mutagenesis site" />\r
- <xs:enumeration value="non-consecutive residues" />\r
- <xs:enumeration value="non-terminal residue" />\r
- <xs:enumeration value="nucleotide phosphate-binding region" />\r
- <xs:enumeration value="peptide" />\r
- <xs:enumeration value="propeptide" />\r
- <xs:enumeration value="repeat" />\r
- <xs:enumeration value="selenocysteine" />\r
- <xs:enumeration value="sequence conflict" />\r
- <xs:enumeration value="sequence variant" />\r
- <xs:enumeration value="signal peptide" />\r
- <xs:enumeration value="similar" />\r
- <xs:enumeration value="site" />\r
- <xs:enumeration value="splice variant" />\r
- <xs:enumeration value="strand" />\r
- <xs:enumeration value="thioether bond" />\r
- <xs:enumeration value="thiolester bond" />\r
- <xs:enumeration value="transit peptide" />\r
- <xs:enumeration value="transmembrane region" />\r
- <xs:enumeration value="turn" />\r
- <xs:enumeration value="unsure residue" />\r
- <xs:enumeration value="zinc finger region" />\r
- */\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff