X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FParseProperties.java;h=d7e2eb50cbe93e355ea5764e069c5f22f592cbb8;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=015fcfe760095d9bccecc3ef65628b5b09d64ea4;hpb=1c6e3aa5ffd0d3fbbfe5bffbdeaa9c4f54a61cd3;p=jalview.git

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 015fcfe..d7e2eb5 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 <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);
-    
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 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
+   *          <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(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;
+  }
+}