*/
package jalview.analysis;
-import com.stevesoft.pat.Regex;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+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);
ScoreNames = tnames;
String descrbase = ScoreDescriptions[onamelen - 1];
if (descrbase == null)
+ {
descrbase = "Score parsed from (" + regex + ")";
+ }
tnames = new String[pattern.numSubs() + 1];
System.arraycopy(ScoreDescriptions, 0, tnames, 0,
ScoreDescriptions.length);
{
String descr = seqs[i].getDescription();
if (descr == null)
+ {
continue;
+ }
int pos = 0;
boolean added = false;
int reps = 0;
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("Score: " + ScoreNames[cols] + "=" + score); // DEBUG
+ System.out.println(seqs[i].getName() + " score: '"
+ + ScoreNames[cols] + "' = " + score); // DEBUG
an.setSequenceRef(seqs[i]);
seqs[i].addAlignmentAnnotation(an);
al.addAnnotation(an);
}
return count;
}
-
- public static void main(String argv[])
- {
- SequenceI[] seqs = new SequenceI[]
- { new Sequence("sq1", "THISISAPLACEHOLDER"),
- new Sequence("sq2", "THISISAPLACEHOLDER"),
- new Sequence("sq3", "THISISAPLACEHOLDER"),
- new Sequence("sq4", "THISISAPLACEHOLDER") };
- seqs[0].setDescription("1 mydescription1");
- seqs[1].setDescription("mydescription2");
- seqs[2].setDescription("2. 0.1 mydescription3");
- seqs[3].setDescription("3 0.01 mydescription4");
- // seqs[4].setDescription("5 mydescription5");
- Alignment al = new Alignment(seqs);
- ParseProperties pp = new ParseProperties(al);
- String regex = ".*([-0-9.+]+)";
- System.out.println("Matched "
- + pp.getScoresFromDescription("my Score",
- "my Score Description", regex, true) + " for " + regex);
- regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
- System.out.println("Matched "
- + pp.getScoresFromDescription("my Score",
- "my Score Description", regex, true) + " for " + regex);
- System.out.println("Finished.");
- }
}