From f683f4d6c8af43be0ffeb96513b52572619efed5 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 26 Aug 2008 08:59:10 +0000
Subject: [PATCH] ensure successive matches to a regex have distinct
 annotation name (indice suffix increases by one each time)

---
 src/jalview/analysis/ParseProperties.java |  266 +++++++++++++++--------------
 1 file changed, 134 insertions(+), 132 deletions(-)

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 587e501..79c1325 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -1,132 +1,134 @@
-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;
-      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], 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;
-        }
-      }
-      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.");
-  }
-}
+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.");
+  }
+}
-- 
1.7.10.2