[Treebase-guts] SF.net SVN: treebase:[1033] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/matrix/MatrixRow.java

[<rv...@us...>]

Revision: 1033
          http://treebase.svn.sourceforge.net/treebase/?rev=1033&view=rev
Author:   rvos
Date:     2012-02-01 21:29:13 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Now implements getNormalizedSymbolString, which, like getSymbolString returns a string representation of the row's character state sequence. 

- getNormalizedSymbolString (and its helper methods) return a sequence of single character symbols: IUPAC symbols, such as N. 

- getSymbolString returns a sequence with a mini-syntax for indicating ambiguous states, using curled braces, like so: {ACGT}

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java	2012-02-01 21:17:20 UTC (rev 1032)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixRow.java	2012-02-01 21:29:13 UTC (rev 1033)
@@ -5,7 +5,6 @@
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 
 import javax.persistence.AttributeOverride;
@@ -52,6 +51,9 @@
 	private static final int DISPLAY_STRING_LENGTH = 30;
 
 	private String mSymbolString;
+	
+	@Transient
+	private String mNormalizedSymbolString = null;
 
 	private TaxonLabel mTaxonLabel;
 	private CharacterMatrix mMatrix;
@@ -173,16 +175,30 @@
 	 *  
 	 * Note that this method post-processes the output of getSymbolString(), i.e.
 	 * if that method returns an {ACGT} this method replaces that with whatever
-	 * ambiguity mapping was provided. E.g. if the map pMapping holds a slot for 
+	 * ambiguity mapping was provided. E.g. if the mapper holds a slot for 
 	 * "ACGT" => "N" this method will return that N instead.
 	 * 
 	 * @return String 
 	 */	
 	@Transient
-	public String getSymbolString(Map<String,String> pMapping) {
-		String inputString = getSymbolString();
+	public String getNormalizedSymbolString() {
+		if ( null == mNormalizedSymbolString ) {
+			StateSetMapper mapper = StateSetMapper.createMapperForDataType(getMatrix().getDataType().getDescription());
+			String inputString = getSymbolString();
+			if ( null != mapper ) {
+				mNormalizedSymbolString = buildNormalizedSymbolString(mapper,inputString);
+			}
+			else {
+				mNormalizedSymbolString = inputString;
+			}
+		}
+		return mNormalizedSymbolString;
+	}
+	
+	@Transient
+	public static String buildNormalizedSymbolString(StateSetMapper mapper,String inputString) {
 		StringBuffer outputString = new StringBuffer();
-		List<Character> ambiguous = new ArrayList<Character>();
+		HashSet<Character> ambiguous = new HashSet<Character>();
 		boolean isAmbiguous = false;
 		for ( int i = 0; i < inputString.length(); i++ ) {
 			char current = inputString.charAt(i);
@@ -191,15 +207,19 @@
 				ambiguous.clear();
 				continue;
 			}
-			if ( current == '}' ) {
+			else if ( current == '}' ) {
 				isAmbiguous = false;
-				Collections.sort(ambiguous);
-				StringBuffer ambigBuffer = new StringBuffer();
-				ambigBuffer.append(ambiguous.toArray(new Character[ambiguous.size()]));
-				String ambigString = ambigBuffer.toString();
-				if ( pMapping.containsKey(ambigString) ) {
-					outputString.append(pMapping.get(ambigString));
+				if ( null != mapper ) {
+					outputString.append(mapper.getSymbolForAmbiguousSet(ambiguous));
 				}
+				else {
+					Iterator<Character> charIter = ambiguous.iterator();
+					outputString.append('{');
+					while ( charIter.hasNext() ) {
+						outputString.append(charIter.next());
+					}
+					outputString.append('}');
+				}
 				continue;
 			}
 			if ( isAmbiguous ) {
@@ -209,7 +229,7 @@
 				outputString.append(current);
 			}
 		}
-		return outputString.toString();
+		return outputString.toString();		
 	}
 
 	/**

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