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Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop
[jalview.git]
/
src
/
jalview
/
io
/
FeaturesFile.java
diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
11135b7
..
804cefc
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-678,7
+678,7
@@
public class FeaturesFile extends AlignFile
* hash of feature types and colours
* @return features file contents
*/
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+ public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
{
return printJalviewFormat(seqs, visible, true, true);
}
{
return printJalviewFormat(seqs, visible, true, true);
}
@@
-697,7
+697,7
@@
public class FeaturesFile extends AlignFile
* of group or type)
* @return features file contents
*/
* of group or type)
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
+ public String printJalviewFormat(SequenceI[] seqs, Map visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
@@
-714,11
+714,11
@@
public class FeaturesFile extends AlignFile
// write feature colours only if we're given them and we are generating
// viewed features
// TODO: decide if feature links should also be written here ?
// write feature colours only if we're given them and we are generating
// viewed features
// TODO: decide if feature links should also be written here ?
- Enumeration en = visible.keys();
+ Iterator en = visible.keySet().iterator();
String type, color;
String type, color;
- while (en.hasMoreElements())
+ while (en.hasNext())
{
{
- type = en.nextElement().toString();
+ type = en.next().toString();
if (visible.get(type) instanceof GraduatedColor)
{
if (visible.get(type) instanceof GraduatedColor)
{
@@
-926,12
+926,12
@@
public class FeaturesFile extends AlignFile
* @param visible
* @return
*/
* @param visible
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+ public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
{
return printGFFFormat(seqs, visible, true, true);
}
{
return printGFFFormat(seqs, visible, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+ public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();