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JAL-966 SearchResultsI now on viewmodels.AlignmentViewport rather than on SeqCanvas
[jalview.git]
/
src
/
jalview
/
io
/
vamsas
/
Sequencefeature.java
diff --git
a/src/jalview/io/vamsas/Sequencefeature.java
b/src/jalview/io/vamsas/Sequencefeature.java
index
8888c1c
..
61491b2
100644
(file)
--- a/
src/jalview/io/vamsas/Sequencefeature.java
+++ b/
src/jalview/io/vamsas/Sequencefeature.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-27,6
+27,7
@@
import jalview.io.VamsasAppDatastore;
import jalview.util.UrlLink;
import java.util.Enumeration;
import jalview.util.UrlLink;
import java.util.Enumeration;
+import java.util.Iterator;
import java.util.Vector;
import uk.ac.vamsas.objects.core.DataSetAnnotations;
import java.util.Vector;
import uk.ac.vamsas.objects.core.DataSetAnnotations;
@@
-71,6
+72,7
@@
public class Sequencefeature extends Rangetype
doJvUpdate();
}
doJvUpdate();
}
+ @Override
public void addToDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
public void addToDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@
-89,6
+91,7
@@
public class Sequencefeature extends Rangetype
dataset.addDataSetAnnotations(dsa);
}
dataset.addDataSetAnnotations(dsa);
}
+ @Override
public void addFromDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
public void addFromDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@
-106,6
+109,7
@@
public class Sequencefeature extends Rangetype
bindjvvobj(sf, dsa);
}
bindjvvobj(sf, dsa);
}
+ @Override
public void conflict()
{
log.warn("Untested sequencefeature conflict code");
public void conflict()
{
log.warn("Untested sequencefeature conflict code");
@@
-118,6
+122,7
@@
public class Sequencefeature extends Rangetype
addToDocument(); // and create a new feature in the document
}
addToDocument(); // and create a new feature in the document
}
+ @Override
public void updateToDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
public void updateToDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@
-144,6
+149,7
@@
public class Sequencefeature extends Rangetype
}
}
+ @Override
public void updateFromDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
public void updateFromDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@
-229,11
+235,11
@@
public class Sequencefeature extends Rangetype
}
if (feature.otherDetails != null)
{
}
if (feature.otherDetails != null)
{
- Enumeration iter = feature.otherDetails.keys();
+ Iterator<String> iter = feature.otherDetails.keySet().iterator();
Vector props = dsa.getPropertyAsReference();
Vector props = dsa.getPropertyAsReference();
- while (iter.hasMoreElements())
+ while (iter.hasNext())
{
{
- String key = (String) iter.nextElement();
+ String key = iter.next();
if (!key.equalsIgnoreCase("score")
&& !key.equalsIgnoreCase("status"))
{
if (!key.equalsIgnoreCase("score")
&& !key.equalsIgnoreCase("status"))
{