From 1c6e3aa5ffd0d3fbbfe5bffbdeaa9c4f54a61cd3 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 25 Apr 2007 11:52:32 +0000
Subject: [PATCH] Functions for parsing free text properties on sequences,
 alignments and annotations.

---
 src/jalview/analysis/ParseProperties.java |  116 +++++++++++++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 src/jalview/analysis/ParseProperties.java

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
new file mode 100644
index 0000000..015fcfe
--- /dev/null
+++ b/src/jalview/analysis/ParseProperties.java
@@ -0,0 +1,116 @@
+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 <code>new com.stevesoft.patt.Regex(regex)</code>
+   * @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<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 (pattern.search(descr))
+      {
+        boolean added=false;
+        for (int cols=0; cols<pattern.numSubs(); cols++)
+        {
+          String sstring = pattern.stringMatched(cols);
+          float score;
+          try {
+            score = new Float(sstring).floatValue();
+          }
+          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], ScoreDescriptions[cols], null);
+          an.setScore(score);
+          seqs[i].addAlignmentAnnotation(an);
+          al.addAnnotation(an);
+          added=true;
+        }
+        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)+" for "+regex);
+    regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
+    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);
+    
+  }
+}
-- 
1.7.10.2