/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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,
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;
+ ((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);