switch(edits[e].command)
{
case INSERT_GAP:
- insertGap(edits[e]);
+ insertGap(edits[e]);
break;
case DELETE_GAP:
- deleteGap(edits[e]);
+ deleteGap(edits[e]);
break;
case CUT:
- cut(edits[e]);
+ cut(edits[e]);
break;
case PASTE:
- paste(edits[e]);
+ paste(edits[e]);
break;
case REPLACE:
replace(edits[e]);
switch (edits[e].command)
{
case INSERT_GAP:
- deleteGap(edits[e]);
+ deleteGap(edits[e]);
break;
case DELETE_GAP:
- insertGap(edits[e]);
+ insertGap(edits[e]);
break;
case CUT:
- paste(edits[e]);
+ paste(edits[e]);
break;
case PASTE:
- cut(edits[e]);
+ cut(edits[e]);
break;
case REPLACE:
replace(edits[e]);
final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
{
+
AlignmentAnnotation[] annotations = null;
if (modifyVisibility && !insert)
for (int aa = 0; aa < temp.length; aa++)
{
temp[aa] = new Annotation(
- command.al.getGapCharacter()+"",
+ command.gapChar+"",
null, ' ', 0);
}
}
this.position = position;
this.number = number;
this.al = al;
+ this.gapChar = al.getGapCharacter();
string = new char[seqs.length][];
for (int i = 0; i < seqs.length; i++)
{
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
}
-
}