/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
-import java.util.Enumeration;
import java.util.Vector;
+/**
+ * Data model for a <loctaion> child element of a <feature> read
+ * from an EMBL query reply
+ *
+ * @see embl_mapping.xml
+ */
public class EmblFeatureLocations
{
- Vector locElements;
+ Vector<EmblFeatureLocElement> locElements;
String locationType;
/**
* @return the locElements
*/
- public Vector getLocElements()
+ public Vector<EmblFeatureLocElement> getLocElements()
{
return locElements;
}
* @param locElements
* the locElements to set
*/
- public void setLocElements(Vector locElements)
+ public void setLocElements(Vector<EmblFeatureLocElement> locElements)
{
this.locElements = locElements;
}
{
int sepos = 0;
int[] se = new int[locElements.size() * 2];
- if (locationType.equalsIgnoreCase("single"))
+ if (locationType.equalsIgnoreCase("single")) // TODO: or "simple" ?
{
- for (Enumeration le = locElements.elements(); le.hasMoreElements();)
+ for (EmblFeatureLocElement loce : locElements)
{
- EmblFeatureLocElement loce = (EmblFeatureLocElement) le
- .nextElement();
if (accession == null || loce.accession != null
&& accession.equals(loce.accession))
{
}
else if (locationType.equalsIgnoreCase("join"))
{
- for (Enumeration le = locElements.elements(); le.hasMoreElements();)
+ for (EmblFeatureLocElement loce : locElements)
{
- EmblFeatureLocElement loce = (EmblFeatureLocElement) le
- .nextElement();
if (accession == null || loce.accession != null
&& accession.equals(loce.accession))
{
else if (locationType != null)
{
if (jalview.bin.Cache.log != null)
+ {
jalview.bin.Cache.log
.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+ locationType + "'");
+ }
else
+ {
System.err
.println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+ locationType + "'");
+ }
}
// trim range if necessary.
if (se != null && sepos != se.length)