\r
if (current.getLength() > i)\r
{\r
- /* MC Should move this to a method somewhere */\r
if (!jalview.util.Comparison.isGap(current.getCharAt(i)))\r
{\r
delete = false;\r
\r
\r
/** */\r
- public SequenceGroup findGroup(int i)\r
- {\r
- return findGroup(getSequenceAt(i));\r
- }\r
-\r
- /** */\r
public SequenceGroup findGroup(SequenceI s)\r
{\r
for (int i = 0; i < this.groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
- if (sg.sequences.contains(s))\r
+ if (sg.getSequences(false).contains(s))\r
{\r
return sg;\r
}\r
for (int i = 0; i < gSize; i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(sg==null || sg.sequences==null)\r
+ if(sg==null || sg.getSequences(false)==null)\r
{\r
this.deleteGroup(sg);\r
gSize--;\r
continue;\r
}\r
\r
- if (sg.sequences.contains(s))\r
+ if (sg.getSequences(false).contains(s))\r
{\r
temp.addElement(sg);\r
}\r
for (int i = 0; i < sequences.size(); i++)\r
{\r
Sequence seq = (Sequence) sequences.elementAt(i);\r
- seq.sequence = seq.sequence.replace('.', gc);\r
- seq.sequence = seq.sequence.replace('-', gc);\r
- seq.sequence = seq.sequence.replace(' ', gc);\r
+ seq.setSequence( seq.getSequence().replace('.', gc) );\r
+ seq.setSequence( seq.getSequence().replace('-', gc) );\r
+ seq.setSequence( seq.getSequence().replace(' ', gc) );\r
}\r
}\r
\r