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Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...
[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
5d04c4c
..
61491b2
100644
(file)
--- a/
src/jalview/io/vamsas/Sequencefeature.java
+++ b/
src/jalview/io/vamsas/Sequencefeature.java
@@
-1,24
+1,33
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* 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.
*
*
* 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.io.vamsas;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.UrlLink;
+
import java.util.Enumeration;
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;
@@
-29,11
+38,6
@@
import uk.ac.vamsas.objects.core.RangeAnnotation;
import uk.ac.vamsas.objects.core.Score;
import uk.ac.vamsas.objects.core.Seg;
import uk.ac.vamsas.objects.utils.Properties;
import uk.ac.vamsas.objects.core.Score;
import uk.ac.vamsas.objects.core.Seg;
import uk.ac.vamsas.objects.utils.Properties;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.UrlLink;
/**
* @author JimP
/**
* @author JimP
@@
-68,6
+72,7
@@
public class Sequencefeature extends Rangetype
doJvUpdate();
}
doJvUpdate();
}
+ @Override
public void addToDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
public void addToDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@
-86,6
+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;
@@
-103,6
+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");
@@
-115,6
+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;
@@
-141,6
+149,7
@@
public class Sequencefeature extends Rangetype
}
}
+ @Override
public void updateFromDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
public void updateFromDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@
-197,15
+206,14
@@
public class Sequencefeature extends Rangetype
.debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
.debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
- dsa.setSeg(new Seg[]
- { vSeg });
+ dsa.setSeg(new Seg[] { vSeg });
dsa.setDescription(feature.getDescription());
dsa.setStatus(feature.getStatus());
if (feature.links != null && feature.links.size() > 0)
{
for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
{
dsa.setDescription(feature.getDescription());
dsa.setStatus(feature.getStatus());
if (feature.links != null && feature.links.size() > 0)
{
for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
{
- String link = (String) feature.links.elementAt(i);
+ String link = feature.links.elementAt(i);
UrlLink ulink = new UrlLink(link);
if (ulink.isValid())
{
UrlLink ulink = new UrlLink(link);
if (ulink.isValid())
{
@@
-218,21
+226,20
@@
public class Sequencefeature extends Rangetype
}
}
dsa.setGroup(feature.getFeatureGroup());
}
}
dsa.setGroup(feature.getFeatureGroup());
- if (feature.getScore() != Float.NaN)
+ if (!Float.isNaN(feature.getScore()))
{
Score fscore = new Score();
{
Score fscore = new Score();
- dsa.setScore(new Score[]
- { fscore });
+ dsa.setScore(new Score[] { fscore });
fscore.setContent(feature.getScore());
fscore.setName(feature.getType());
}
if (feature.otherDetails != null)
{
fscore.setContent(feature.getScore());
fscore.setName(feature.getType());
}
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"))
{