-/*
- * 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
- */
-package jalview.datamodel;
-
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-/**
- * 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 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;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * 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.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\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
+ * 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
+ {\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
+ 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
+ * 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
+ 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
+ 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
+ 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
+ }\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 / commitdiff