X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFeatureLocations.java;h=94105ae6f5efec4f292e2c13ea7e8e8b0513d35e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2444592253ef54560c0b9a4a975872b7186d0eb6;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index 2444592..94105ae 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,30 +1,36 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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.xdb.embl;
-import java.util.Enumeration;
-import java.util.Iterator;
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 locElements;
String locationType;
@@ -40,7 +46,7 @@ public class EmblFeatureLocations
/**
* @param locationComplement
- * the locationComplement to set
+ * the locationComplement to set
*/
public void setLocationComplement(boolean locationComplement)
{
@@ -57,7 +63,7 @@ public class EmblFeatureLocations
/**
* @param locationType
- * the locationType to set
+ * the locationType to set
*/
public void setLocationType(String locationType)
{
@@ -67,16 +73,16 @@ public class EmblFeatureLocations
/**
* @return the locElements
*/
- public Vector getLocElements()
+ public Vector getLocElements()
{
return locElements;
}
/**
* @param locElements
- * the locElements to set
+ * the locElements to set
*/
- public void setLocElements(Vector locElements)
+ public void setLocElements(Vector locElements)
{
this.locElements = locElements;
}
@@ -100,8 +106,8 @@ public class EmblFeatureLocations
* TODO: deal with multiple accessions
*
* @param accession
- * the accession string for which locations are requested, or
- * null for all locations
+ * the accession string for which locations are requested, or null
+ * for all locations
* @return null or int[] { start1, end1, ... }
*/
@@ -109,12 +115,10 @@ public class EmblFeatureLocations
{
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))
{
@@ -129,10 +133,8 @@ public class EmblFeatureLocations
}
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))
{
@@ -149,13 +151,17 @@ public class EmblFeatureLocations
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)