Add psm and peptide counts to search_crosslink_lookup and search_loop…

…link_lookup tables. Move getting those counts to proxl_base. Update web app to use those counts when PSM and Peptide cutoffs are defaults.
yeastrc · Oct 31, 2015 · 8dad5ee · 8dad5ee
1 parent 15af2c8
commit 8dad5ee
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Showing 11 changed files with 697 additions and 561 deletions.
diff --git a/WebRoot/WEB-INF/lib/proxl_base.jar b/WebRoot/WEB-INF/lib/proxl_base.jar
diff --git a/src/org/yeastrc/xlink/www/constants/DefaultQValueCutoffConstants.java b/src/org/yeastrc/xlink/www/constants/DefaultQValueCutoffConstants.java
@@ -7,5 +7,10 @@ public class DefaultQValueCutoffConstants {
 	 */
 	public static final double PSM_Q_VALUE_CUTOFF_DEFAULT = 0.01;
 
+	/**
+	 * This value must be kept in sync with the  various fields that end with: _at_pt_01_q_cutoff
+	 */
+	public static final double PEPTIDE_Q_VALUE_CUTOFF_DEFAULT = 0.01;
+
 
 }
diff --git a/src/org/yeastrc/xlink/www/objects/SearchProteinCrosslink.java b/src/org/yeastrc/xlink/www/objects/SearchProteinCrosslink.java
@@ -1,13 +1,14 @@
 package org.yeastrc.xlink.www.objects;
 
 
-import java.util.List;
 
 import org.apache.log4j.Logger;
 import org.yeastrc.xlink.dto.SearchDTO;
-import org.yeastrc.xlink.www.searcher.SearchCrosslinkPeptideSearcher;
-import org.yeastrc.xlink.www.searcher.SearchPeptideCrosslinkSearcher;
-import org.yeastrc.xlink.www.searcher.SearchPsmSearcher;
+import org.yeastrc.xlink.searchers.NumPeptidesForProteinCriteriaSearcher;
+import org.yeastrc.xlink.searchers.NumPsmsForProteinCriteriaSearcher;
+import org.yeastrc.xlink.utils.YRC_NRSEQUtils;
+
+
 
 public class SearchProteinCrosslink implements IProteinCrosslink {	
 
@@ -46,8 +47,23 @@ public void setProtein2Position(int protein2Position) {
 	public int getNumPsms() throws Exception {
 
 		try {
-			if( this.numPsms == null )
-				this.numPsms = SearchPsmSearcher.getInstance().getNumPsms( this );
+			if( this.numPsms == null ) {
+
+				this.numPsms =
+						NumPsmsForProteinCriteriaSearcher.getInstance().getNumPsmsForCrosslink(
+								this.getSearch().getId(),
+								this.getPsmCutoff(),
+								this.getPeptideCutoff(),
+								this.getProtein1().getNrProtein().getNrseqId(),
+								this.getProtein2().getNrProtein().getNrseqId(),
+								this.getProtein1Position(),
+								this.getProtein2Position() );
+
+				//  WAS
+
+				//  this.numPsms = SearchPsmSearcher.getInstance().getNumPsms( this );
+
+			}
 
 			return this.numPsms;
 
@@ -60,24 +76,26 @@ public int getNumPsms() throws Exception {
 			throw e;
 		}
 	}
-
-	public int getNumUniquePsms() {
-		return numUniquePsms;
-	}
-	public void setNumUniquePsms(int numUniquePsms) {
-		this.numUniquePsms = numUniquePsms;
-	}
-	public double getPsmCutoff() {
-		return psmCutoff;
-	}
-	public void setPsmCutoff(double cutoff) {
-		this.psmCutoff = cutoff;
-	}
+
 	public int getNumLinkedPeptides() throws Exception {
 
 		try {
-			if( this.numLinkedPeptides == -1 )
-				this.numLinkedPeptides = SearchCrosslinkPeptideSearcher.getInstance().getNumLinkedPeptides( this );
+			if( this.numLinkedPeptides == -1 ) {
+
+				this.numLinkedPeptides = 
+						NumPeptidesForProteinCriteriaSearcher.getInstance()
+						.getNumLinkedPeptidesForCrosslink( 
+								this.getSearch().getId(),
+								this.getPsmCutoff(),
+								this.getPeptideCutoff(),
+								this.getProtein1().getNrProtein().getNrseqId(),
+								this.getProtein2().getNrProtein().getNrseqId(),
+								this.getProtein1Position(),
+								this.getProtein2Position() );
+
+				// WAS
+				// this.numLinkedPeptides = SearchCrosslinkPeptideSearcher.getInstance().getNumLinkedPeptides( this );
+			}
 
 			return this.numLinkedPeptides;
 
@@ -90,11 +108,27 @@ public int getNumLinkedPeptides() throws Exception {
 			throw e;
 		}
 	}
+
+
 	public int getNumUniqueLinkedPeptides() throws Exception {
 
 		try {
-			if( this.numUniqueLinkedPeptides == -1 )
-				this.numUniqueLinkedPeptides = SearchCrosslinkPeptideSearcher.getInstance().getNumUniqueLinkedPeptides( this );
+			if( this.numUniqueLinkedPeptides == -1 ) {
+
+				this.numUniqueLinkedPeptides = 
+						NumPeptidesForProteinCriteriaSearcher.getInstance()
+						.getNumUniqueLinkedPeptidesForCrosslink(
+								this.getSearch().getId(),
+								this.getPsmCutoff(),
+								this.getPeptideCutoff(),
+								this.getProtein1().getNrProtein().getNrseqId(),
+								this.getProtein2().getNrProtein().getNrseqId(),
+								this.getProtein1Position(),
+								this.getProtein2Position(),
+								YRC_NRSEQUtils.getDatabaseIdFromName( this.getSearch().getFastaFilename() ) );
+				//  WAS
+				// this.numUniqueLinkedPeptides = SearchCrosslinkPeptideSearcher.getInstance().getNumUniqueLinkedPeptides( this );
+			}
 
 			return this.numUniqueLinkedPeptides;
 
@@ -108,6 +142,48 @@ public int getNumUniqueLinkedPeptides() throws Exception {
 		}
 	}
 
+
+
+	/**
+	 * Only set if the PSM and Peptide Cutoffs match
+	 * @param numPsms
+	 */
+	public void setNumPsms(Integer numPsms) {
+		this.numPsms = numPsms;
+	}
+
+	/**
+	 * Only set if the PSM and Peptide Cutoffs match
+	 * @param numLinkedPeptides
+	 */
+	public void setNumLinkedPeptides(int numLinkedPeptides) {
+		this.numLinkedPeptides = numLinkedPeptides;
+	}
+
+	/**
+	 * Only set if the PSM and Peptide Cutoffs match
+	 * @param numUniqueLinkedPeptides
+	 */
+	public void setNumUniqueLinkedPeptides(int numUniqueLinkedPeptides) {
+		this.numUniqueLinkedPeptides = numUniqueLinkedPeptides;
+	}
+
+
+
+
+	public int getNumUniquePsms() {
+		return numUniquePsms;
+	}
+	public void setNumUniquePsms(int numUniquePsms) {
+		this.numUniquePsms = numUniquePsms;
+	}
+	public double getPsmCutoff() {
+		return psmCutoff;
+	}
+	public void setPsmCutoff(double cutoff) {
+		this.psmCutoff = cutoff;
+	}
+
 
 
 	public double getPeptideCutoff() {
@@ -123,24 +199,6 @@ public void setSearch(SearchDTO search) {
 		this.search = search;
 	}
 
-	public List<SearchPeptideCrosslink> getPeptides() throws Exception {
-
-		try {
-			if( this.peptides == null )
-				this.peptides = SearchPeptideCrosslinkSearcher.getInstance().searchOnSearchProteinCrosslink( this );
-
-			return this.peptides;
-
-		} catch ( Exception e ) {
-
-			String msg = "Exception in getPeptides()";
-
-			log.error( msg, e );
-
-			throw e;
-		}
-	}
-
 
 
 	public double getBestPSMQValue() {
@@ -168,9 +226,9 @@ public void setBestPeptideQValue(Double bestPeptideQValue) {
 	private int numUniquePsms;
 
 	private int numLinkedPeptides = -1;
-	List<SearchPeptideCrosslink> peptides;
 
 	private int numUniqueLinkedPeptides = -1;
+
 	private double psmCutoff;
 	private double peptideCutoff;
 	private double bestPSMQValue;