X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=28ab82cda7d0d5c34fb9b88e6a60ee326556a559;hb=7f61a28aad5fe2ef3df8aa4024ea3e7d8fbe1548;hp=8fd713ef473e4e6a91414f7468e87f9d86f304d9;hpb=f38bc38ee057bebe07c9b2b5c843d3d7d7d94032;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 8fd713e..28ab82c 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,53 +1,63 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+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;
+
+ public 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.
+ * 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)
@@ -74,15 +84,14 @@ public class SequenceFeature
try
{
otherDetails = (Hashtable) cpy.otherDetails.clone();
- }
- catch (Exception e)
+ } catch (Exception e)
{
// Uncloneable objects in the otherDetails - don't complain
}
}
if (cpy.links != null && cpy.links.size() > 0)
{
- links = new Vector();
+ links = new Vector();
for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
{
links.addElement(cpy.links.elementAt(i));
@@ -91,11 +100,8 @@ public class SequenceFeature
}
}
- public SequenceFeature(String type,
- String desc,
- String status,
- int begin, int end,
- String featureGroup)
+ public SequenceFeature(String type, String desc, String status,
+ int begin, int end, String featureGroup)
{
this.type = type;
this.description = desc;
@@ -105,11 +111,8 @@ public class SequenceFeature
this.featureGroup = featureGroup;
}
- public SequenceFeature(String type,
- String desc,
- int begin, int end,
- float score,
- String featureGroup)
+ public SequenceFeature(String type, String desc, int begin, int end,
+ float score, String featureGroup)
{
this.type = type;
this.description = desc;
@@ -121,15 +124,13 @@ public class SequenceFeature
public boolean equals(SequenceFeature sf)
{
- if (begin != sf.begin
- || end != sf.end
- || score != sf.score)
+ if (begin != sf.begin || end != sf.end || score != sf.score)
{
return false;
}
- if (! (type + description + featureGroup).equals
- (sf.type + sf.description + sf.featureGroup))
+ if (!(type + description + featureGroup).equals(sf.type
+ + sf.description + sf.featureGroup))
{
return false;
}
@@ -139,7 +140,7 @@ public class SequenceFeature
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getBegin()
@@ -154,7 +155,7 @@ public class SequenceFeature
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getEnd()
@@ -169,7 +170,7 @@ public class SequenceFeature
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getType()
@@ -184,7 +185,7 @@ public class SequenceFeature
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getDescription()
@@ -211,7 +212,7 @@ public class SequenceFeature
{
if (links == null)
{
- links = new java.util.Vector();
+ links = new Vector();
}
links.insertElementAt(labelLink, 0);
@@ -228,9 +229,11 @@ public class SequenceFeature
}
/**
- * Used for getting values which are not in the
- * basic set. eg STRAND, FRAME for GFF file
- * @param key String
+ * 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)
{
@@ -245,10 +248,13 @@ public class SequenceFeature
}
/**
- * Used for setting values which are not in the
- * basic set. eg STRAND, FRAME for GFF file
- * @param key eg STRAND
- * @param value eg +
+ * 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)
{
@@ -264,8 +270,8 @@ public class SequenceFeature
}
/*
- * The following methods are added to maintain
- * the castor Uniprot mapping file for the moment.
+ * The following methods are added to maintain the castor Uniprot mapping file
+ * for the moment.
*/
public void setStatus(String status)
{
@@ -276,12 +282,13 @@ public class SequenceFeature
{
if (otherDetails != null)
{
- return otherDetails.get("status").toString();
- }
- else
- {
- return null;
+ String stat = (String) otherDetails.get("status");
+ if (stat != null)
+ {
+ return new String(stat);
+ }
}
+ return null;
}
public void setPosition(int pos)