X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FParseProperties.java;h=eb639b63a03108074f74a638f2ff8b71241bb6a9;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=015fcfe760095d9bccecc3ef65628b5b09d64ea4;hpb=1c6e3aa5ffd0d3fbbfe5bffbdeaa9c4f54a61cd3;p=jalview.git
diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 015fcfe..eb639b6 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -1,116 +1,164 @@
-package jalview.analysis;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.*;
-
-public class ParseProperties
-{
- /**
- * Methods for parsing free text properties on alignments and sequences.
- */
- /**
- * The alignment being operated on
- */
- private AlignmentI al=null;
-
- /**
- * initialise a new property parser
- * @param al
- */
- ParseProperties(AlignmentI al) {
- this.al = al;
- }
-
- public int getScoresFromDescription(String ScoreName, String ScoreDescriptions, String regex)
- {
- return getScoresFromDescription(new String[] { ScoreName }, new String[] { ScoreDescriptions}, regex);
- }
-
- public int getScoresFromDescription(String[] ScoreNames, String[] ScoreDescriptions, String regex)
- {
- return getScoresFromDescription(al.getSequencesArray(), ScoreNames, ScoreDescriptions, regex);
- }
- /**
- * 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 new com.stevesoft.patt.Regex(regex)
- * @return total number of sequences that matched the regex
- */
- public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames, String[] ScoreDescriptions, String regex)
- {
- int count=0;
- Regex pattern = new Regex(regex);
- if (pattern.numSubs()>ScoreNames.length)
- {
- // Check that we have enough labels and descriptions for any parsed scores.
- int onamelen = ScoreNames.length;
- String[] tnames = new String[pattern.numSubs()+1];
- System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
- String base = tnames[ScoreNames.length-1];
- ScoreNames = tnames;
- String descrbase = ScoreDescriptions[ScoreNames.length-1];
- if (descrbase == null)
- descrbase = "Score parsed from ("+regex+")";
- tnames = new String[pattern.numSubs()];
- System.arraycopy(ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length);
- ScoreDescriptions = tnames;
- for (int i=onamelen; i.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+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.
+ *
+ * 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;
+
+ /**
+ * initialise a new property parser
+ *
+ * @param al
+ */
+ public ParseProperties(AlignmentI al)
+ {
+ this.al = al;
+ }
+
+ public int getScoresFromDescription(String ScoreName,
+ String ScoreDescriptions, String regex, boolean repeat)
+ {
+ return getScoresFromDescription(new String[] { ScoreName },
+ new String[] { ScoreDescriptions }, regex, repeat);
+ }
+
+ public int getScoresFromDescription(String[] ScoreNames,
+ String[] ScoreDescriptions, String regex, boolean 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
+ * new com.stevesoft.patt.Regex(regex)
+ * @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)
+ {
+ int count = 0;
+ Regex pattern = new Regex(regex);
+ if (pattern.numSubs() > ScoreNames.length)
+ {
+ // Check that we have enough labels and descriptions for any parsed
+ // scores.
+ int onamelen = ScoreNames.length;
+ String[] tnames = new String[pattern.numSubs() + 1];
+ System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
+ String base = tnames[ScoreNames.length - 1];
+ 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);
+ ScoreDescriptions = tnames;
+ for (int i = onamelen; i < ScoreNames.length; i++)
+ {
+ ScoreNames[i] = base + "_" + i;
+ ScoreDescriptions[i] = descrbase + " (column " + i + ")";
+ }
+ }
+ for (int i = 0; i < seqs.length; i++)
+ {
+ String descr = seqs[i].getDescription();
+ if (descr == null)
+ {
+ continue;
+ }
+ 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++)
+ {
+ String sstring = pattern.stringMatched(cols + 1);
+ double score = Double.NaN;
+ try
+ {
+ score = new Double(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 : ""),
+ ScoreDescriptions[cols], null);
+ an.setScore(score);
+ System.out.println(seqs[i].getName() + " score: '"
+ + ScoreNames[cols] + "' = " + score); // DEBUG
+ an.setSequenceRef(seqs[i]);
+ seqs[i].addAlignmentAnnotation(an);
+ al.addAnnotation(an);
+ added = true;
+ }
+ reps++; // repeated matches
+ }
+ if (added)
+ {
+ count++;
+ }
+ }
+ return count;
+ }
+}