-package jalview.analysis;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class ParseProperties\r
-{\r
- /**\r
- * Methods for parsing free text properties on alignments and sequences.\r
- * There are a number of ways we might want to do this:\r
- * arbitrary regex. and an associated score name for the number that's extracted.\r
- * Regex that provides both score and name.\r
- * \r
- * We may also want to :\r
- * - modify description to remove parsed numbers (this behaviour is dangerous since exporting the alignment would lose the original form then)\r
- * - \r
- * \r
- */\r
- /**\r
- * The alignment being operated on\r
- */\r
- private AlignmentI al=null;\r
- \r
- /**\r
- * initialise a new property parser\r
- * @param al\r
- */\r
- public ParseProperties(AlignmentI al) {\r
- this.al = al;\r
- }\r
-\r
- public int getScoresFromDescription(String ScoreName, String ScoreDescriptions, String regex)\r
- {\r
- return getScoresFromDescription(new String[] { ScoreName }, new String[] { ScoreDescriptions}, regex);\r
- }\r
-\r
- public int getScoresFromDescription(String[] ScoreNames, String[] ScoreDescriptions, String regex) \r
- {\r
- return getScoresFromDescription(al.getSequencesArray(), ScoreNames, ScoreDescriptions, regex);\r
- }\r
- /**\r
- * Extract scores for sequences by applying regex to description string.\r
- * @param seqs seuqences to extract annotation from.\r
- * @param ScoreNames labels for each numeric field in regex match\r
- * @param ScoreDescriptions description for each numeric field in regex match\r
- * @param regex Regular Expression string for passing to <code>new com.stevesoft.patt.Regex(regex)</code>\r
- * @return total number of sequences that matched the regex\r
- */\r
- public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames, String[] ScoreDescriptions, String regex) \r
- {\r
- int count=0;\r
- Regex pattern = new Regex(regex);\r
- if (pattern.numSubs()>ScoreNames.length)\r
- {\r
- // Check that we have enough labels and descriptions for any parsed scores.\r
- int onamelen = ScoreNames.length;\r
- String[] tnames = new String[pattern.numSubs()+1];\r
- System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);\r
- String base = tnames[ScoreNames.length-1];\r
- ScoreNames = tnames;\r
- String descrbase = ScoreDescriptions[onamelen-1];\r
- if (descrbase == null)\r
- descrbase = "Score parsed from ("+regex+")";\r
- tnames = new String[pattern.numSubs()+1];\r
- System.arraycopy(ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length);\r
- ScoreDescriptions = tnames;\r
- for (int i=onamelen; i<ScoreNames.length; i++)\r
- {\r
- ScoreNames[i] = base+"_"+i;\r
- ScoreDescriptions[i] = descrbase+" (column "+i+")";\r
- }\r
- }\r
- for (int i=0; i<seqs.length; i++)\r
- {\r
- String descr = seqs[i].getDescription();\r
- if (descr==null)\r
- continue;\r
- if (pattern.search(descr))\r
- {\r
- boolean added=false;\r
- for (int cols=0; cols<pattern.numSubs(); cols++)\r
- {\r
- String sstring = pattern.stringMatched(cols+1);\r
- float score;\r
- try {\r
- score = new Float(sstring).floatValue();\r
- }\r
- catch (Exception e)\r
- {\r
- // don't try very hard to parse if regex was wrong.\r
- continue;\r
- }\r
- // add score to sequence annotation.\r
- AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols], ScoreDescriptions[cols], null);\r
- an.setScore(score);\r
- seqs[i].addAlignmentAnnotation(an);\r
- al.addAnnotation(an);\r
- added=true;\r
- }\r
- if (added)\r
- count++;\r
- }\r
- \r
- }\r
- return count; \r
- }\r
- public static void main(String argv[]) {\r
- SequenceI[] seqs = new SequenceI[] { new Sequence("sq1","THISISAPLACEHOLDER"),\r
- new Sequence("sq2","THISISAPLACEHOLDER"),\r
- new Sequence("sq3","THISISAPLACEHOLDER"),\r
- new Sequence("sq4","THISISAPLACEHOLDER")};\r
- seqs[0].setDescription("1 mydescription1");\r
- seqs[1].setDescription("mydescription2");\r
- seqs[2].setDescription("2. 0.1 mydescription3");\r
- seqs[3].setDescription("3 0.01 mydescription4");\r
- //seqs[4].setDescription("5 mydescription5");\r
- Alignment al = new Alignment(seqs);\r
- ParseProperties pp = new ParseProperties(al);\r
- String regex = ".*([-0-9.+]+)";\r
- System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);\r
- regex = ".*([-0-9.+]+).+([-0-9.+]+).*";\r
- System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);\r
- System.out.println("Finished.");\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.analysis;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.datamodel.*;
+
+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
+ * <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)
+ {
+ 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("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;
+ }
+
+ 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.");
+ }
+}
git://source.jalview.org / jalview.git / blobdiff