X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=674f1e7b543f0b26ad5479153574bbc2f3a480de;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=302f3cd5db433da9909f6588ee926b297c2816c3;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 302f3cd..674f1e7 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,24 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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.
+ *
+ * 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!
@@ -40,7 +43,7 @@ public class SequenceFeature
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
@@ -88,7 +91,7 @@ public class SequenceFeature
}
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));
@@ -209,7 +212,7 @@ public class SequenceFeature
{
if (links == null)
{
- links = new java.util.Vector();
+ links = new Vector();
}
links.insertElementAt(labelLink, 0);
@@ -230,7 +233,7 @@ public class SequenceFeature
* for GFF file
*
* @param key
- * String
+ * String
*/
public Object getValue(String key)
{
@@ -249,9 +252,9 @@ public class SequenceFeature
* for GFF file
*
* @param key
- * eg STRAND
+ * eg STRAND
* @param value
- * eg +
+ * eg +
*/
public void setValue(String key, Object value)
{
@@ -281,7 +284,9 @@ public class SequenceFeature
{
String stat = (String) otherDetails.get("status");
if (stat != null)
+ {
return new String(stat);
+ }
}
return null;
}
@@ -297,4 +302,23 @@ public class SequenceFeature
return begin;
}
+ public int getStrand()
+ {
+ String str;
+ if (otherDetails == null
+ || (str = otherDetails.get("STRAND").toString()) == null)
+ {
+ return 0;
+ }
+ if (str.equals("-"))
+ {
+ return -1;
+ }
+ if (str.equals("+"))
+ {
+ return 1;
+ }
+ return 0;
+ }
+
}