+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import com.stevesoft.pat.Regex;
public class ParseProperties
{
/**
- * Methods for parsing free text properties on alignments and sequences.
- * There are a number of ways we might want to do this:
- * arbitrary regex. and an associated score name for the number that's extracted.
- * Regex that provides both score and name.
+ * Methods for parsing free text properties on alignments and sequences. There
+ * are a number of ways we might want to do this: arbitrary regex. and an
+ * associated score name for the number that's extracted. Regex that provides
+ * both score and name.
*
- * We may also want to :
- * - modify description to remove parsed numbers (this behaviour is dangerous since exporting the alignment would lose the original form then)
- * -
+ * We may also want to : - modify description to remove parsed numbers (this
+ * behaviour is dangerous since exporting the alignment would lose the
+ * original form then) -
*
*/
/**
* The alignment being operated on
*/
- private AlignmentI al=null;
-
+ private AlignmentI al = null;
+
/**
* initialise a new property parser
+ *
* @param al
*/
- public ParseProperties(AlignmentI al) {
+ public ParseProperties(AlignmentI al)
+ {
this.al = al;
}
- public int getScoresFromDescription(String ScoreName, String ScoreDescriptions, String regex, boolean repeat)
+ 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, String[] ScoreDescriptions, String regex, boolean repeat)
+ public int getScoresFromDescription(String[] ScoreNames,
+ String[] ScoreDescriptions, String regex, boolean repeat)
{
- return getScoresFromDescription(al.getSequencesArray(), ScoreNames, ScoreDescriptions, regex, repeat);
+ return getScoresFromDescription(al.getSequencesArray(), ScoreNames,
+ ScoreDescriptions, regex, repeat);
}
+
/**
* Extract scores for sequences by applying regex to description string.
- * @param seqs seuqences to extract annotation from.
- * @param ScoreNames labels for each numeric field in regex match
- * @param ScoreDescriptions description for each numeric field in regex match
- * @param regex Regular Expression string for passing to <code>new com.stevesoft.patt.Regex(regex)</code>
- * @param repeat true means the regex will be applied multiple times along the description string of each sequence
+ *
+ * @param seqs
+ * seuqences to extract annotation from.
+ * @param ScoreNames
+ * labels for each numeric field in regex match
+ * @param ScoreDescriptions
+ * description for each numeric field in regex match
+ * @param regex
+ * Regular Expression string for passing to
+ * <code>new com.stevesoft.patt.Regex(regex)</code>
+ * @param repeat
+ * true means the regex will be applied multiple times along the
+ * 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;
+ int count = 0;
Regex pattern = new Regex(regex);
- if (pattern.numSubs()>ScoreNames.length)
+ if (pattern.numSubs() > ScoreNames.length)
{
- // Check that we have enough labels and descriptions for any parsed scores.
+ // Check that we have enough labels and descriptions for any parsed
+ // scores.
int onamelen = ScoreNames.length;
- String[] tnames = new String[pattern.numSubs()+1];
+ String[] tnames = new String[pattern.numSubs() + 1];
System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
- String base = tnames[ScoreNames.length-1];
+ String base = tnames[ScoreNames.length - 1];
ScoreNames = tnames;
- String descrbase = ScoreDescriptions[onamelen-1];
+ 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);
+ descrbase = "Score parsed from (" + regex + ")";
+ tnames = new String[pattern.numSubs() + 1];
+ System.arraycopy(ScoreDescriptions, 0, tnames, 0,
+ ScoreDescriptions.length);
ScoreDescriptions = tnames;
- for (int i=onamelen; i<ScoreNames.length; i++)
+ for (int i = onamelen; i < ScoreNames.length; i++)
{
- ScoreNames[i] = base+"_"+i;
- ScoreDescriptions[i] = descrbase+" (column "+i+")";
+ ScoreNames[i] = base + "_" + i;
+ ScoreDescriptions[i] = descrbase + " (column " + i + ")";
}
}
- for (int i=0; i<seqs.length; i++)
+ for (int i = 0; i < seqs.length; i++)
{
String descr = seqs[i].getDescription();
- if (descr==null)
+ if (descr == null)
continue;
- int pos=0;
- boolean added=false;
- int reps=0;
- while ((repeat || pos==0) && pattern.searchFrom(descr, pos))
+ int pos = 0;
+ boolean added = false;
+ int reps = 0;
+ while ((repeat || pos == 0) && pattern.searchFrom(descr, pos))
{
pos = pattern.matchedTo();
- for (int cols=0; cols<pattern.numSubs(); cols++)
+ for (int cols = 0; cols < pattern.numSubs(); cols++)
{
- String sstring = pattern.stringMatched(cols+1);
- double score=Double.NaN;
- try {
+ String sstring = pattern.stringMatched(cols + 1);
+ double score = Double.NaN;
+ try
+ {
score = new Double(sstring).doubleValue();
- }
- catch (Exception e)
+ } 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 : ""), ScoreDescriptions[cols], null);
+ 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("Score: " + ScoreNames[cols] + "=" + score); // DEBUG
an.setSequenceRef(seqs[i]);
seqs[i].addAlignmentAnnotation(an);
al.addAnnotation(an);
- added=true;
+ added = true;
}
reps++; // repeated matches
}
count++;
}
}
- return count;
+ 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")};
+
+ 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");
+ // 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);
+ 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("Matched "
+ + pp.getScoresFromDescription("my Score",
+ "my Score Description", regex, true) + " for " + regex);
System.out.println("Finished.");
}
}
git://source.jalview.org / jalview.git / blobdiff