-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\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
- * 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
-import java.util.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\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
- /**\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
- 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
-\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
- return false;\r
- }\r
-\r
- if (! (type + description + featureGroup).equals\r
- (sf.type + sf.description + sf.featureGroup))\r
- {\r
- return false;\r
- }\r
-\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
- links = new java.util.Vector();\r
- }\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
- * 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
- return null;\r
- }\r
- else\r
- {\r
- return otherDetails.get(key);\r
- }\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 (otherDetails == null)\r
- {\r
- otherDetails = new Hashtable();\r
- }\r
-\r
- otherDetails.put(key, value);\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
- {\r
- return otherDetails.get("status").toString();\r
- }\r
- else\r
- {\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
+/*
+ * 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;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff