/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
*/\r
package jalview.datamodel;\r
\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public class SequenceFeature\r
{\r
- public int position;\r
public int begin;\r
public int end;\r
+ public float score;\r
public String type;\r
public String description;\r
- public String status;\r
+ public Hashtable otherDetails;\r
+ public java.util.Vector links;\r
\r
// Feature group can be set from a features file\r
// as a group of features between STARTGROUP and ENDGROUP markers\r
\r
public SequenceFeature()\r
{}\r
-\r
+ /**\r
+ * Constructs a duplicate feature.\r
+ * Note: Uses clone on the otherDetails so only shallow copies are made\r
+ * of additional properties and method will silently fail if unclonable\r
+ * objects are found in the hash.\r
+ * @param cpy\r
+ */\r
+ public SequenceFeature(SequenceFeature cpy) {\r
+ if (cpy!=null) {\r
+ begin = cpy.begin;\r
+ end = cpy.end;\r
+ score = cpy.score;\r
+ if (cpy.type != null)\r
+ type = new String(cpy.type);\r
+ if (cpy.description != null)\r
+ description = new String(cpy.description);\r
+ if (cpy.featureGroup != null)\r
+ featureGroup = new String(cpy.featureGroup);\r
+ if (cpy.otherDetails!=null) {\r
+ try {\r
+ otherDetails = (Hashtable) cpy.otherDetails.clone();\r
+ } catch (Exception e) {\r
+ // Uncloneable objects in the otherDetails - don't complain\r
+ }\r
+ }\r
+ if (cpy.links!=null && cpy.links.size()>0) {\r
+ links=new Vector();\r
+ for (int i=0,iSize=cpy.links.size(); i<iSize; i++) {\r
+ links.setElementAt(cpy.links.elementAt(i), i);\r
+ }\r
+ }\r
+ }\r
+ }\r
public SequenceFeature(String type,\r
String desc,\r
String status,\r
{\r
this.type = type;\r
this.description = desc;\r
- this.status = status;\r
- this.position = begin;\r
+ setValue("status", status);\r
this.begin = begin;\r
this.end = end;\r
this.featureGroup = featureGroup;\r
}\r
\r
- public boolean equals(SequenceFeature sf)\r
+ public SequenceFeature(String type,\r
+ String desc,\r
+ int begin, int end,\r
+ float score,\r
+ String featureGroup)\r
{\r
- if(begin != sf.begin\r
- || end != sf.end)\r
- return false;\r
+ this.type = type;\r
+ this.description = desc;\r
+ this.begin = begin;\r
+ this.end = end;\r
+ this.score = score;\r
+ this.featureGroup = featureGroup;\r
+ }\r
\r
+ public boolean equals(SequenceFeature sf)\r
+ {\r
+ if (begin != sf.begin\r
+ || end != sf.end\r
+ || score != sf.score)\r
+ return false;\r
\r
- if(!(type+description+status).equals\r
- (sf.type+sf.description+sf.status))\r
+ if(!(type+description+featureGroup).equals\r
+ (sf.type+sf.description+sf.featureGroup))\r
return false;\r
\r
return true;\r
}\r
\r
\r
- public int getPosition()\r
- {\r
- return position;\r
- }\r
-\r
- public void setPosition(int pos)\r
- {\r
- position = pos;\r
- begin = pos;\r
- end = pos;\r
- }\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
description = desc;\r
}\r
\r
+ public String getFeatureGroup()\r
+ {\r
+ return featureGroup;\r
+ }\r
+\r
+ public void setFeatureGroup(String featureGroup)\r
+ {\r
+ this.featureGroup = featureGroup;\r
+ }\r
+\r
+ public void addLink(String labelLink)\r
+ {\r
+ if(links==null)\r
+ links = new java.util.Vector();\r
+\r
+ links.insertElementAt(labelLink,0);\r
+ }\r
+\r
+ public float getScore()\r
+ {\r
+ return score;\r
+ }\r
+\r
+ public void setScore(float value)\r
+ {\r
+ score = value;\r
+ }\r
+\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
+ * Used for getting values which are not in the\r
+ * basic set. eg STRAND, FRAME for GFF file\r
+ * @param key String\r
*/\r
- public String getStatus()\r
+ public Object getValue(String key)\r
+ {\r
+ if(otherDetails==null)\r
+ return null;\r
+ else\r
+ return otherDetails.get(key);\r
+ }\r
+\r
+ /**\r
+ * Used for setting values which are not in the\r
+ * basic set. eg STRAND, FRAME for GFF file\r
+ * @param key eg STRAND\r
+ * @param value eg +\r
+ */\r
+ public void setValue(String key, Object value)\r
{\r
- return status;\r
+ if(value!=null)\r
+ {\r
+ if (otherDetails == null)\r
+ otherDetails = new Hashtable();\r
+\r
+ otherDetails.put(key, value);\r
+ }\r
}\r
\r
+\r
+ /*\r
+ * The following methods are added to maintain\r
+ * the castor Uniprot mapping file for the moment.\r
+ */\r
public void setStatus(String status)\r
{\r
- this.status = status;\r
+ setValue("status", status);\r
}\r
\r
- public String getFeatureGroup()\r
+ public String getStatus()\r
{\r
- return featureGroup;\r
+ if (otherDetails != null)\r
+ return otherDetails.get("status").toString();\r
+ else\r
+ return null;\r
}\r
\r
- public void setFeatureGroup(String featureGroup)\r
+ public void setPosition(int pos)\r
{\r
- this.featureGroup = featureGroup;\r
+ begin = pos;\r
+ end = pos;\r
}\r
\r
+ public int getPosition()\r
+ {\r
+ return begin;\r
+ }\r
\r
}\r