/*
- * 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
+ * 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.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
+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;
- 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<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 int begin;
- 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 int end;
- public boolean equals(SequenceFeature sf)
- {
- if (begin != sf.begin
- || end != sf.end
- || score != sf.score)
- return false;
+ public float score;
- if(!(type+description+featureGroup).equals
- (sf.type+sf.description+sf.featureGroup))
- return false;
+ public String type;
- return true;
- }
+ public String description;
+ public Hashtable otherDetails;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getBegin()
- {
- return begin;
- }
+ 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 void setBegin(int start)
- {
- this.begin = start;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getEnd()
- {
- return end;
- }
+ public SequenceFeature()
+ {
+ }
- public void setEnd(int end)
+ /**
+ * 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)
{
- 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;
+ 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 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff