split on any whitespace

phylogeography · Mar 11, 2016 · d315849 · d315849
1 parent 69c0d59
commit d315849
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Showing 2 changed files with 15 additions and 16 deletions.
diff --git a/src/parsers/DiscreteLocationsParser.java b/src/parsers/DiscreteLocationsParser.java
@@ -25,8 +25,7 @@ public DiscreteLocationsParser(String locationsFilename, boolean header) {
 
 	}// END: Constructor
 
-	public LinkedList<Location> parseLocations() throws IOException,
-			AnalysisException {
+	public LinkedList<Location> parseLocations() throws IOException, AnalysisException {
 
 		LinkedList<Location> locationsList = new LinkedList<Location>();
 
@@ -40,12 +39,13 @@ public LinkedList<Location> parseLocations() throws IOException,
 		int nrow = lines.length;
 		for (int i = 0; i < nrow; i++) {
 
-			String[] line = lines[i].split("\t");
+			// String[] line = lines[i].split("\t");
+			// TODO:test
+			String[] line = lines[i].split("\\s+");
 
 			if (line.length != 3) {
 				throw new AnalysisException(
-						"Incorrect number of columns in locations file. Expecting 3, found "
-								+ line.length);
+						"Incorrect number of columns in locations file. Expecting 3, found " + line.length);
 			}
 
 			String locationName = line[0];
@@ -55,8 +55,8 @@ public LinkedList<Location> parseLocations() throws IOException,
 			String illegalCharacter = "+";
 			if (locationName.contains(illegalCharacter)) {
 
-				throw new AnalysisException("Location " + locationName
-						+ " contains illegal character " + illegalCharacter);
+				throw new AnalysisException(
+						"Location " + locationName + " contains illegal character " + illegalCharacter);
 
 			}
 

diff --git a/src/parsers/LogParser.java b/src/parsers/LogParser.java
@@ -29,7 +29,9 @@ public LogParser(String log, Double burnin) {
 	public Double[][] parseIndicators() throws IOException, AnalysisException {
 
 		String[] lines = Utils.readLines(logFilename, Utils.HASH_COMMENT);
-		columnNames = lines[HEADER_ROW].split("\t");
+		// columnNames = lines[HEADER_ROW].split("\t");
+		// TODO: test:
+		columnNames = lines[HEADER_ROW].split("\\s+");
 
 		int nrow = lines.length - 1;
 
@@ -49,8 +51,8 @@ public Double[][] parseIndicators() throws IOException, AnalysisException {
 		int ncol = columns.size();
 		// this should be enough when sth silly is parsed
 		if (ncol == 0) {
-			throw new AnalysisException("No " + Utils.INDICATORS
-					+ " columns found. I suspect wrong or malformed log file.");
+			throw new AnalysisException(
+					"No " + Utils.INDICATORS + " columns found. I suspect wrong or malformed log file.");
 		}
 
 		int skip = (int) ((burnin / 100 * nrow));
@@ -67,19 +69,16 @@ public Double[][] parseIndicators() throws IOException, AnalysisException {
 				for (int col = 0; col < ncol; col++) {
 
 					if (columns.get(col) > line.length) {
-						System.out
-								.println("Empty or malformed input at line "
-										+ (row + SKIPPED_LINES)
-										+ " inside log file. Resulting output may not be correct!");
+						System.out.println("Empty or malformed input at line " + (row + SKIPPED_LINES)
+								+ " inside log file. Resulting output may not be correct!");
 
 						// copy array with one less row
 						indicators = cloneArray(indicators, i);
 						break;
 
 					} else {
 
-						indicators[i][col] = Double.valueOf(line[columns
-								.get(col)]);
+						indicators[i][col] = Double.valueOf(line[columns.get(col)]);
 
 					}