refactor(qprofiler qvisualise): adding comments and tweaking logging as per reviewer suggestions

Author: Oliver Holmes

qprofiler/src/org/qcmg/qprofiler/fastq/FastqSummaryReport.java

@@ -292,18 +292,18 @@ void parseFiveElementHeaderWithSpaces(String [] params) {
 		// split by space
 		String [] firstElementParams = params[0].split(" ");
 		if (firstElementParams.length != 2) {
-			throw new UnsupportedOperationException("Incorrect header format encountered in parseFiveElementHeader. Expected '@ERR091788.3104 HSQ955_155:2:1101:13051:2071/2' but received: " + Arrays.deepToString(params));
+			throw new IllegalArgumentException("Incorrect header format encountered in parseFiveElementHeaderWithSpaces. Expected a space (e.g. @ERR091788.3104 HSQ955_155) in the first element in the array, but received: " + Arrays.deepToString(params));
 		}
 		String [] machineAndReadPosition = firstElementParams[0].split("\\.");
 		if (machineAndReadPosition.length != 2) {
-			throw new UnsupportedOperationException("Incorrect header format encountered in parseFiveElementHeader. Expected '@ERR091788.3104 HSQ955_155:2:1101:13051:2071/2' but received: " + Arrays.deepToString(params));
+			throw new IllegalArgumentException("Incorrect header format encountered in parseFiveElementHeaderWithSpaces. Expected a single dot (e.g. @ERR091788.3104 HSQ955_155) in the first part of the first element in the array, but received: " + Arrays.deepToString(params));
 		}
 
 		updateMap(instruments, machineAndReadPosition[0]);
 
 		String [] flowCellAndRunId = firstElementParams[1].split("_");
 		if (flowCellAndRunId.length != 2) {
-			throw new UnsupportedOperationException("Incorrect header format encountered in parseFiveElementHeader. Expected '@ERR091788.3104 HSQ955_155:2:1101:13051:2071/2' but received: " + Arrays.deepToString(params));
+			throw new IllegalArgumentException("Incorrect header format encountered in parseFiveElementHeaderWithSpaces. Expected a single underscore (e.g. @ERR091788.3104 HSQ955_155) in the second part of the first element in the array but received: " + Arrays.deepToString(params));
 		}
 
 		updateMap(flowCellIds, flowCellAndRunId[0]);

qvisualise/src/org/qcmg/qvisualise/QVisualise.java

@@ -45,8 +45,13 @@ public static void examineFileSizeAndXmx(String inputFile) throws IOException {
 		logger.info("supplied Xmx memory: " + xmxSize);
 		double ratio = (double)xmxSize / fileSize;
 		logger.info("memory / file size ratio: " + ratio);
+		/*
+		Warn the user when the xml file size to Xmx setting ratio is below  a certain point
+		(8 in testing performed using java 8 oracle JVM)
+		as this could result in OOM exceptions
+		 */
 		if (ratio < 8) {
-			logger.warn("There may not be enough memory to load the xml input file. Please consider loading a smaller xml file or increasing the Xmx value.");
+			logger.warn("There may not be enough memory to load the xml input file. Please consider visualising a smaller xml file or increasing the Xmx value.");
 		}
 	}
 

qvisualise/src/org/qcmg/qvisualise/util/QProfilerCollectionsUtils.java

@@ -27,6 +27,7 @@
 
 public class QProfilerCollectionsUtils {
 
+	public static final int MAX_TALLY_ITEMS_LENGTH = 100000;
 	public static QLogger log = QLoggerFactory.getLogger(QProfilerCollectionsUtils.class);
 
 	/**
@@ -149,7 +150,7 @@ public static <T> void populateTallyItemMap(Element cycleElement,
 		if (null != cycleElement) {
 
 			final NodeList tallyItemsNL = cycleElement.getElementsByTagName("TallyItem");
-			if (tallyItemsNL.getLength() < 100000) {
+			if (tallyItemsNL.getLength() < MAX_TALLY_ITEMS_LENGTH) {
 				for (int j = 0, size = tallyItemsNL.getLength(); j < size; j++) {
 					if (tallyItemsNL.item(j) instanceof Element) {
 						Element tallyItemElement = (Element) tallyItemsNL.item(j);
@@ -166,7 +167,7 @@ public static <T> void populateTallyItemMap(Element cycleElement,
 					}
 				}
 			} else {
-				log.warn(cycleElement.getTagName() + " has too many elements: " + tallyItemsNL.getLength() + " - will leave out of report");
+				log.warn(cycleElement.getTagName() + " has too many elements: " + tallyItemsNL.getLength() + " - will leave out of report (maximum number of elements set to: " + MAX_TALLY_ITEMS_LENGTH + ")");
 
 			}
 		}