/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
+import java.util.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class SequenceFeature\r
{\r
- public int begin;\r
- public int end;\r
- public float score;\r
- public String type;\r
- public String description;\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
- public String featureGroup;\r
-\r
- public SequenceFeature()\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
- int begin, int end,\r
- String featureGroup)\r
- {\r
- this.type = type;\r
- this.description = desc;\r
- setValue("status", status);\r
- this.begin = begin;\r
- this.end = end;\r
- this.featureGroup = featureGroup;\r
- }\r
-\r
- public SequenceFeature(String type,\r
- String desc,\r
- int begin, int end,\r
- float score,\r
- String featureGroup)\r
- {\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+featureGroup).equals\r
- (sf.type+sf.description+sf.featureGroup))\r
- return false;\r
-\r
- return true;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getBegin()\r
- {\r
- return begin;\r
- }\r
-\r
- public void setBegin(int start)\r
- {\r
- this.begin = start;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getEnd()\r
- {\r
- return end;\r
- }\r
-\r
- public void setEnd(int end)\r
- {\r
- this.end = end;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String getType()\r
- {\r
- return type;\r
- }\r
-\r
- public void setType(String type)\r
- {\r
- this.type = type;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String getDescription()\r
+ public int begin;\r
+ public int end;\r
+ public float score;\r
+ public String type;\r
+ public String description;\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
+ public String featureGroup;\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
+ {\r
+ if (cpy != null)\r
{\r
- return description;\r
- }\r
-\r
- public void setDescription(String desc)\r
- {\r
- description = desc;\r
- }\r
-\r
- public String getFeatureGroup()\r
- {\r
- return featureGroup;\r
+ begin = cpy.begin;\r
+ end = cpy.end;\r
+ score = cpy.score;\r
+ if (cpy.type != null)\r
+ {\r
+ type = new String(cpy.type);\r
+ }\r
+ if (cpy.description != null)\r
+ {\r
+ description = new String(cpy.description);\r
+ }\r
+ if (cpy.featureGroup != null)\r
+ {\r
+ featureGroup = new String(cpy.featureGroup);\r
+ }\r
+ if (cpy.otherDetails != null)\r
+ {\r
+ try\r
+ {\r
+ otherDetails = (Hashtable) cpy.otherDetails.clone();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ // Uncloneable objects in the otherDetails - don't complain\r
+ }\r
+ }\r
+ if (cpy.links != null && cpy.links.size() > 0)\r
+ {\r
+ links = new Vector();\r
+ for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)\r
+ {\r
+ links.setElementAt(cpy.links.elementAt(i), i);\r
+ }\r
+ }\r
}\r
-\r
- public void setFeatureGroup(String featureGroup)\r
+ }\r
+\r
+ public SequenceFeature(String type,\r
+ String desc,\r
+ String status,\r
+ int begin, int end,\r
+ String featureGroup)\r
+ {\r
+ this.type = type;\r
+ this.description = desc;\r
+ setValue("status", status);\r
+ this.begin = begin;\r
+ this.end = end;\r
+ this.featureGroup = featureGroup;\r
+ }\r
+\r
+ public SequenceFeature(String type,\r
+ String desc,\r
+ int begin, int end,\r
+ float score,\r
+ String featureGroup)\r
+ {\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
{\r
- this.featureGroup = featureGroup;\r
+ return false;\r
}\r
\r
- public void addLink(String labelLink)\r
+ if (! (type + description + featureGroup).equals\r
+ (sf.type + sf.description + sf.featureGroup))\r
{\r
- if(links==null)\r
- links = new java.util.Vector();\r
-\r
- links.insertElementAt(labelLink,0);\r
+ return false;\r
}\r
\r
- public float getScore()\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getBegin()\r
+ {\r
+ return begin;\r
+ }\r
+\r
+ public void setBegin(int start)\r
+ {\r
+ this.begin = start;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return end;\r
+ }\r
+\r
+ public void setEnd(int end)\r
+ {\r
+ this.end = end;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getType()\r
+ {\r
+ return type;\r
+ }\r
+\r
+ public void setType(String type)\r
+ {\r
+ this.type = type;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDescription()\r
+ {\r
+ return description;\r
+ }\r
+\r
+ public void setDescription(String desc)\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
{\r
- return score;\r
+ links = new java.util.Vector();\r
}\r
\r
- public void setScore(float value)\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
+ * 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 Object getValue(String key)\r
+ {\r
+ if (otherDetails == null)\r
{\r
- score = value;\r
+ return null;\r
}\r
-\r
- /**\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 Object getValue(String key)\r
+ else\r
{\r
- if(otherDetails==null)\r
- return null;\r
- else\r
- return otherDetails.get(key);\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
+\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
+ if (value != null)\r
{\r
- if(value!=null)\r
+ if (otherDetails == null)\r
{\r
- if (otherDetails == null)\r
- otherDetails = new Hashtable();\r
-\r
- otherDetails.put(key, value);\r
+ otherDetails = new Hashtable();\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
- setValue("status", status);\r
- }\r
\r
- public String getStatus()\r
- {\r
- if (otherDetails != null)\r
- return otherDetails.get("status").toString();\r
- else\r
- return null;\r
+ otherDetails.put(key, value);\r
}\r
-\r
- public void setPosition(int pos)\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
+ setValue("status", status);\r
+ }\r
+\r
+ public String getStatus()\r
+ {\r
+ if (otherDetails != null)\r
{\r
- begin = pos;\r
- end = pos;\r
+ return otherDetails.get("status").toString();\r
}\r
-\r
- public int getPosition()\r
+ else\r
{\r
- return begin;\r
+ return null;\r
}\r
+ }\r
+\r
+ public void setPosition(int pos)\r
+ {\r
+ begin = pos;\r
+ end = pos;\r
+ }\r
+\r
+ public int getPosition()\r
+ {\r
+ return begin;\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff