*/
package jalview.analysis;
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
+
+import com.stevesoft.pat.Regex;
public class ParseProperties
{
public int getScoresFromDescription(String ScoreName,
String ScoreDescriptions, String regex, boolean repeat)
{
- return getScoresFromDescription(new String[]
- { ScoreName }, new String[]
- { ScoreDescriptions }, regex, repeat);
+ return getScoresFromDescription(new String[] { ScoreName },
+ new String[]
+ { ScoreDescriptions }, regex, repeat);
}
public int getScoresFromDescription(String[] ScoreNames,
* description string of each sequence
* @return total number of sequences that matched the regex
*/
- public int getScoresFromDescription(SequenceI[] seqs,
- String[] ScoreNames, String[] ScoreDescriptions, String regex,
- boolean repeat)
+ public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames,
+ String[] ScoreDescriptions, String regex, boolean repeat)
{
int count = 0;
- Regex pattern = new Regex(regex);
+ Regex pattern = Platform.newRegex(regex);
if (pattern.numSubs() > ScoreNames.length)
{
// Check that we have enough labels and descriptions for any parsed
double score = Double.NaN;
try
{
- score = new Double(sstring).doubleValue();
+ score = Double.valueOf(sstring).doubleValue();
} catch (Exception e)
{
// don't try very hard to parse if regex was wrong.
continue;
}
// add score to sequence annotation.
- AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols]
- + ((reps > 0) ? "_" + reps : ""),
+ AlignmentAnnotation an = new AlignmentAnnotation(
+ ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""),
ScoreDescriptions[cols], null);
an.setScore(score);
System.out.println(seqs[i].getName() + " score: '"