Q-value QC Plot changes

yeastrc · Nov 5, 2015 · 434ff0b · 434ff0b
1 parent a0d3605
commit 434ff0b
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Showing 4 changed files with 137 additions and 28 deletions.
diff --git a/WebRoot/js/qcChartQValueCounts.js b/WebRoot/js/qcChartQValueCounts.js
@@ -673,21 +673,15 @@ QCChartQValueCounts.prototype.createChartResponse = function(requestData, respon
 
 	var lineColors = [];
 
-	var maxPSMCount = 0;
-
-	var updateMaxPSMCountForType = function( chartDataForType ) {
-
-		var bucketsFor_chartDataForType = chartDataForType.chartBuckets;
-
-		var lastBucket = bucketsFor_chartDataForType[ dataArraySize - 1 ];
-
-		var lastBucket_totalCount = lastBucket.totalCount;
-
-		if ( maxPSMCount < lastBucket_totalCount ) {
-
-			maxPSMCount = lastBucket_totalCount;
-		}
-	};
+//	var maxPSMCount = 0;
+//	
+//	var updateMaxPSMCountForType = function( chartDataForType ) {
+//		
+//		if ( maxPSMCount < chartDataForType.totalCountForType ) {
+//			
+//			maxPSMCount = chartDataForType.totalCountForType;
+//		}
+//	};
 
 
 //	red: #A55353
@@ -705,7 +699,7 @@ QCChartQValueCounts.prototype.createChartResponse = function(requestData, respon
 
 		lineColors.push( '#a5a5a5' );	//	combined: #a5a5a5 (gray)
 
-		updateMaxPSMCountForType( alllinkChartData );
+//		updateMaxPSMCountForType( alllinkChartData );
 	}
 
 	if ( crosslinkChartData ) {
@@ -715,7 +709,7 @@ QCChartQValueCounts.prototype.createChartResponse = function(requestData, respon
 
 		lineColors.push( '#A55353' );	//	red: #A55353
 
-		updateMaxPSMCountForType( crosslinkChartData );
+//		updateMaxPSMCountForType( crosslinkChartData );
 	}
 
 	if ( looplinkChartData ) {
@@ -725,7 +719,7 @@ QCChartQValueCounts.prototype.createChartResponse = function(requestData, respon
 
 		lineColors.push( '#53a553' );	//	green: #53a553
 
-		updateMaxPSMCountForType( looplinkChartData );
+//		updateMaxPSMCountForType( looplinkChartData );
 	}
 
 	if ( unlinkedChartData ) {
@@ -735,7 +729,7 @@ QCChartQValueCounts.prototype.createChartResponse = function(requestData, respon
 
 		lineColors.push( '#5353a5' );	//	blue: #5353a5
 
-		updateMaxPSMCountForType( unlinkedChartData );
+//		updateMaxPSMCountForType( unlinkedChartData );
 	}
 
 
@@ -754,23 +748,21 @@ QCChartQValueCounts.prototype.createChartResponse = function(requestData, respon
 		var linkTypeLabel = params.linkTypeLabel;
 
 		if ( dataForType ) {
-
-			var lastBucket = dataForType.chartBuckets[ dataArraySize - 1 ];
-
-			var lastBucket_totalCount = lastBucket.totalCount;
 
 			var bucket = dataForType.chartBuckets[ index ];
 
 			if ( chartDataEntry.length === 0 ) {
 
+				// Add position to chartDataEntry array if chartDataEntry is empty
+
 				chartDataEntry.push( bucket.binEnd );
 			}
 
 			var chartDataValue = bucket.totalCount;
 
 			if ( displayAsPercentage ) {
 
-				chartDataValue = chartDataValue / lastBucket_totalCount * 100;
+				chartDataValue = chartDataValue / dataForType.totalCountForType * 100;
 			}
 
 			chartDataEntry.push( chartDataValue );

diff --git a/...g/yeastrc/xlink/www/qc_plots/psm_count_per_q_value/CreatePsmCountPerQValueQCPlotData.java b/...g/yeastrc/xlink/www/qc_plots/psm_count_per_q_value/CreatePsmCountPerQValueQCPlotData.java
@@ -110,6 +110,13 @@ public PsmCountPerQValueQCPlotDataJSONRoot create( Set<String> selectedLinkTypes
 
 			List<Double> qValuesForPSMsthatMeetCriteriaList = 
 				QValuesFromPsmTblSearcher.getInstance().getQValues( selectedDBLinkTypes, searchId, psmQValueCutoff );
+
+			int totalCountForType = qValuesForPSMsthatMeetCriteriaList.size();
+
+			if ( psmQValueCutoff != null ) {
+
+				totalCountForType = QValuesFromPsmTblSearcher.getInstance().getQValuesCount( selectedDBLinkTypes, searchId );
+			}
 
 			PsmCountPerQValueQCPlotDataJSONPerType linkData = null;
 
@@ -132,10 +139,9 @@ public PsmCountPerQValueQCPlotDataJSONRoot create( Set<String> selectedLinkTypes
 
 				unlinkedData = new PsmCountPerQValueQCPlotDataJSONPerType();
 				linkData = unlinkedData;
-
 			}
-
-
+			
+			
 			int qvalueZeroCount = 0;
 
 			int[] qvalueCounts = new int[ BIN_COUNT ];
@@ -215,6 +221,10 @@ public PsmCountPerQValueQCPlotDataJSONRoot create( Set<String> selectedLinkTypes
 			linkData.setChartBuckets( chartBuckets );
 
 			dataArraySize = chartBuckets.size();
+
+
+			linkData.setTotalCountForType( totalCountForType );
+
 		}
 
 

diff --git a/...strc/xlink/www/qc_plots/psm_count_per_q_value/PsmCountPerQValueQCPlotDataJSONPerType.java b/...strc/xlink/www/qc_plots/psm_count_per_q_value/PsmCountPerQValueQCPlotDataJSONPerType.java
@@ -5,8 +5,15 @@
 public class PsmCountPerQValueQCPlotDataJSONPerType {
 
 	private List<PsmCountPerQValueQCPlotDataJSONChartBucket> chartBuckets;
-//	private int zeroQvalueCount = 0;
 
+	private int totalCountForType;
+
+	public int getTotalCountForType() {
+		return totalCountForType;
+	}
+	public void setTotalCountForType(int totalCountForType) {
+		this.totalCountForType = totalCountForType;
+	}
 	public List<PsmCountPerQValueQCPlotDataJSONChartBucket> getChartBuckets() {
 		return chartBuckets;
 	}

diff --git a/src/org/yeastrc/xlink/www/searcher/QValuesFromPsmTblSearcher.java b/src/org/yeastrc/xlink/www/searcher/QValuesFromPsmTblSearcher.java
@@ -22,6 +22,106 @@ private QValuesFromPsmTblSearcher() { }
 	private static final QValuesFromPsmTblSearcher _INSTANCE = new QValuesFromPsmTblSearcher();
 	public static QValuesFromPsmTblSearcher getInstance() { return _INSTANCE; }
 
+
+
+	/**
+	 * @param selectedDBLinkTypes - NULL for all
+	 * @param searchId
+	 * @return
+	 * @throws Exception
+	 */
+	public int getQValuesCount( 
+			List<String> selectedDBLinkTypes, 
+			int searchId
+			) throws Exception {
+
+
+		int getQValuesCount = 0;
+
+		Connection conn = null;
+		PreparedStatement pstmt = null;
+		ResultSet rs = null;
+
+
+		StringBuilder sqlSB = new StringBuilder( 10000 );
+
+		sqlSB.append( "SELECT COUNT(*) AS count FROM psm WHERE search_id = ? " );
+
+		if ( selectedDBLinkTypes != null && ! selectedDBLinkTypes.isEmpty() ) {
+
+			sqlSB.append( " AND psm.type IN ( " );
+
+			boolean firstWebLinkType = true;
+
+			for ( String selectedDBLinkType : selectedDBLinkTypes ) {
+
+				if ( firstWebLinkType ) {
+
+					firstWebLinkType = false;
+				} else {
+
+					sqlSB.append( " , " );
+				}
+				sqlSB.append( " '" );
+				sqlSB.append( selectedDBLinkType );
+				sqlSB.append( "' " );
+			}
+
+			sqlSB.append( " ) " );
+
+		}
+
+		String sql = sqlSB.toString();
+
+
+		try {
+
+			conn = DBConnectionFactory.getConnection( DBConnectionFactory.CROSSLINKS );
+
+
+			pstmt = conn.prepareStatement( sql );
+
+			int paramCounter = 0;
+
+			paramCounter++;
+			pstmt.setInt( paramCounter, searchId );
+
+			rs = pstmt.executeQuery();
+
+			if( rs.next() ) {
+				getQValuesCount = rs.getInt( "count" );
+			}
+
+		} catch ( Exception e ) {
+
+			String msg = "getQValuesCount(), sql: " + sql;
+
+			log.error( msg, e );
+
+			throw e;
+
+		} finally {
+
+			// be sure database handles are closed
+			if( rs != null ) {
+				try { rs.close(); } catch( Throwable t ) { ; }
+				rs = null;
+			}
+
+			if( pstmt != null ) {
+				try { pstmt.close(); } catch( Throwable t ) { ; }
+				pstmt = null;
+			}
+
+			if( conn != null ) {
+				try { conn.close(); } catch( Throwable t ) { ; }
+				conn = null;
+			}
+		}
+
+		return getQValuesCount;
+	}
+
 
 	/**
 	 * @param selectedDBLinkTypes - NULL for all