import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
+import jalview.util.Comparison;
import java.util.Vector;
+import com.stevesoft.pat.Regex;
+
public class Finder
{
/**
AlignmentI alignment;
- jalview.datamodel.SequenceGroup selection = null;
+ SequenceGroup selection = null;
Vector idMatch = null;
boolean findAll = false;
- com.stevesoft.pat.Regex regex = null;
+ Regex regex = null;
/**
* hold's last-searched position between calles to find(false)
{
searchString = searchString.toUpperCase();
}
- regex = new com.stevesoft.pat.Regex(searchString);
+ regex = new Regex(searchString);
regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
idMatch = new Vector();
for (int j = 0; j < item.length(); j++)
{
- if (!jalview.util.Comparison.isGap(item.charAt(j)))
+ if (!Comparison.isGap(item.charAt(j)))
{
noGapsSB.append(item.charAt(j));
spaces.addElement(new Integer(insertCount));
/**
* @return the selection
*/
- public jalview.datamodel.SequenceGroup getSelection()
+ public SequenceGroup getSelection()
{
return selection;
}
* @param selection
* the selection to set
*/
- public void setSelection(jalview.datamodel.SequenceGroup selection)
+ public void setSelection(SequenceGroup selection)
{
this.selection = selection;
}
/**
* @return the regex
*/
- public com.stevesoft.pat.Regex getRegex()
+ public Regex getRegex()
{
return regex;
}