X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=14ce0ff52437a984de51aefedcba554af7c460ce;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=a197dfdef19176a02297897ca068349fb7ebc6b1;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index a197dfd..14ce0ff 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,81 +1,270 @@
+/*
+ * 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.awt.*;
-
-public class SequenceFeature {
- int begin;
- int end;
- String type;
- String description;
- String status;
-
- public SequenceFeature()
- {
- }
-
- public SequenceFeature(String type, int start, int end, String description, String status)
- {
- this.type = type;
- this.begin = start;
- this.end = end;
- this.description = description;
- this.status = status;
- }
-
- public int getStart() {
- return begin;
- }
- public int getEnd() {
- return end;
- }
- public String getType() {
- return type;
- }
- public String getDescription() {
- return description;
- }
- public String getStatus()
- {return status;}
+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;
-/*
-
-
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-
-
-
-
-
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-
-
-
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-
-
-*/
+ // 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