git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-722 updated from 2.11.2 develop branch - needs further work before release
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
3202ac9
..
48f65cf
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-22,9
+22,10
@@
package jalview.io;
import java.io.IOException;
import java.util.ArrayList;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Vector;
import jalview.datamodel.AlignmentAnnotation;
import java.util.Vector;
import jalview.datamodel.AlignmentAnnotation;
@@
-66,7
+67,7
@@
public abstract class AlignFile extends FileParse
/**
* Properties to be added to generated alignment object
*/
/**
* Properties to be added to generated alignment object
*/
- private Hashtable properties;
+ private Map<String, String> properties;
long start;
long start;
@@
-288,13
+289,11
@@
public abstract class AlignFile extends FileParse
*/
public void addProperties(AlignmentI al)
{
*/
public void addProperties(AlignmentI al)
{
- if (properties != null && properties.size() > 0)
+ if (properties != null)
{
{
- Enumeration keys = properties.keys();
- Enumeration vals = properties.elements();
- while (keys.hasMoreElements())
+ for (Entry<String, String> prop : properties.entrySet())
{
{
- al.setProperty(keys.nextElement(), vals.nextElement());
+ al.setProperty(prop.getKey(), prop.getValue());
}
}
}
}
}
}
@@
-309,12
+308,12
@@
public abstract class AlignFile extends FileParse
* @param value
* - non-null value
*/
* @param value
* - non-null value
*/
- protected void setAlignmentProperty(Object key, Object value)
+ protected void setAlignmentProperty(String key, String value)
{
if (key == null)
{
{
if (key == null)
{
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(
+ "Implementation error: Cannot have null alignment property key.");
}
if (value == null)
{
}
if (value == null)
{
@@
-322,12
+321,12
@@
public abstract class AlignFile extends FileParse
}
if (properties == null)
{
}
if (properties == null)
{
- properties = new Hashtable();
+ properties = new Hashtable<>();
}
properties.put(key, value);
}
}
properties.put(key, value);
}
- protected Object getAlignmentProperty(Object key)
+ protected String getAlignmentProperty(String key)
{
if (properties != null && key != null)
{
{
if (properties != null && key != null)
{
@@
-341,9
+340,9
@@
public abstract class AlignFile extends FileParse
*/
protected void initData()
{
*/
protected void initData()
{
- seqs = new Vector<SequenceI>();
- annotations = new Vector<AlignmentAnnotation>();
- seqGroups = new ArrayList<SequenceGroup>();
+ seqs = new Vector<>();
+ annotations = new Vector<>();
+ seqGroups = new ArrayList<>();
parseCalled = false;
}
parseCalled = false;
}
@@
-356,7
+355,7
@@
public abstract class AlignFile extends FileParse
@Override
public void setSeqs(SequenceI[] s)
{
@Override
public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
for (int i = 0; i < s.length; i++)
{
@@
-427,7
+426,7
@@
public abstract class AlignFile extends FileParse
{
if (newickStrings == null)
{
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
}
newickStrings.addElement(new String[] { treeName, newickString });
}