Match object cleaning : function renamed, obsolete functions removed

src/fr/inra/pappso/xtandempipeline/class_msms/Match.java

@@ -32,13 +32,7 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 	@Override
 	public int compareTo(Match p) {
 		int k = 0;
-		try {
-			k = p.get_valid_peptide_number() - this.get_valid_peptide_number();
-		} catch (MSMSException e) {
-			String error = "error in compareTo " + e.getMessage();
-			logger.error(error);
-			return 0;
-		}
+		k = p.getValidSpectraNumber() - this.getValidSpectraNumber();
 		if (k != 0)
 			return (k);
 		int i = p.peptides_match.size() - this.peptides_match.size();
@@ -128,7 +122,7 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 	 * @return
 	 * @throws MSMSException
 	 */
-	private int getSpectraNumberIn(MsRun samp) throws MSMSException {
+	private int getValidSpectraNumberIn(MsRun samp) throws MSMSException {
 		int i = 0;
 		for (Peptide pep : peptides_match.values()) {
 			if (pep.isValidate()) {
@@ -146,7 +140,7 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 	 * @return integer number of spectra
 	 * @throws MSMSException
 	 */
-	private int getSpectraNumber() {
+	public int getValidSpectraNumber() {
 		int i = 0;
 		for (Peptide pep : peptides_match.values()) {
 			if (pep.isValidate()) {
@@ -164,7 +158,7 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 	 */
 	public double getPAI() {
 		// compute PAI
-		double value = (double) this.getSpectraNumber()
+		double value = (double) this.getValidSpectraNumber()
 				/ (double) this.get_protein_match()
 						.getNumberOfTrypticPeptidesForPAI();
 
@@ -178,7 +172,7 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 	 */
 	public double getPAIbyMsRun(MsRun samp) throws MSMSException {
 		// compute PAI
-		double value = (double) this.getSpectraNumberIn(samp)
+		double value = (double) this.getValidSpectraNumberIn(samp)
 				/ (double) this.get_protein_match()
 						.getNumberOfTrypticPeptidesForPAI();
 
@@ -212,15 +206,6 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 		return (sequence.size());
 	}
 
-	public int get_valid_peptide_number() throws MSMSException {
-		int i = 0;
-		for (Peptide pep : peptides_match.values()) {
-			if (pep.isValidate())
-				i++;
-		}
-		return (i);
-	}
-
 	public ArrayList<Peptide> get_peptide_order_inclus_redon() {
 		Collections.sort(peptides_order);
 		return (peptides_order);
@@ -233,16 +218,6 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 		return (peptides);
 	}
 
-	public int get_valid_peptide_number_to(MsRun samp) throws MSMSException {
-		int i = 0;
-		for (Peptide pep : peptides_match.values()) {
-			if (pep.getMsRun().equals(samp) && pep.isValidate()) {
-				i++;
-			}
-		}
-		return (i);
-	}
-
 	public int get_unique_valid_peptide_number() throws MSMSException {
 		HashSet<String> sequence = new HashSet<String>();
 		for (Peptide pep : peptides_match.values()) {
@@ -264,36 +239,6 @@ public class Match implements Comparable<Match>, GrpProtMatch {
 		return (sequence.size());
 	}
 
-	public int get_coverage_to(MsRun samp) throws MSMSException {
-		// Unknown sequence
-		if (this.protein_match.get_sequence().length() == 0) {
-			return 0;
-		}
-
-		HashMap<Integer, Boolean> seq = new HashMap<Integer, Boolean>();
-		for (int i = 0; i < this.protein_match.get_sequence().length(); i++) {
-			int i_po = i + 1;
-			seq.put(i_po, false);
-		}
-		for (Peptide pep : peptides_match.values()) {
-			if (pep.getMsRun().equals(samp)) {
-				for (int j = pep.get_start(); j <= pep.get_stop(); j++) {
-					seq.put(j, true);
-				}
-			}
-		}
-		int k = 0;
-		for (boolean ST : seq.values()) {
-			if (ST)
-				k++;
-		}
-
-		float cov = (float) k
-				/ (this.protein_match.get_sequence().length() + 1) * 100;
-		int cov_temp = (int) cov;
-		return (cov_temp);
-	}
-
 	public int get_coverage() throws MSMSException {
 		// Unknown sequence
 		if (this.protein_match.get_sequence().length() == 0) {

src/fr/inra/pappso/xtandempipeline/filter_print/filter_peptide_evalue.java

@@ -25,7 +25,7 @@ public class filter_peptide_evalue extends filter_base {
 				if (pep.get_evalue() >= this.peptide_evalue)
 					pep.setValidate(false);
 			}
-			if (ms.get_valid_peptide_number() > 0) {
+			if (ms.getValidSpectraNumber() > 0) {
 				numberOfValidMatch++;
 			} else {
 				ms.setIsvalidate(false);