Add toString() to cross linker classes.

yeastrc · Sep 5, 2018 · 9acbbaa · 9acbbaa
1 parent d54775d
commit 9acbbaa
Show file tree

Hide file tree

Showing 12 changed files with 145 additions and 85 deletions.
diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BMOE.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BMOE.java
@@ -13,6 +13,11 @@
  */
 public class BMOE implements ILinker {
 
+	@Override
+	public String toString() {
+		return "BMOE";
+	}
+
 	/**
 	 * Get all theoretically linkable positions (N-terminal residue is position 1)
 	 * in the supplied protein sequence for this crosslinker

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BS2.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BS2.java
@@ -7,6 +7,11 @@
 
 public class BS2 extends AmineLinker {
 
+	@Override
+	public String toString() {
+		return "BS2";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 7.7;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BS3.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BS3.java
@@ -7,6 +7,11 @@
 
 public class BS3 extends AmineLinker {
 
+	@Override
+	public String toString() {
+		return "BS3";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 11.4;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BS3_STY.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/BS3_STY.java
@@ -5,6 +5,11 @@
 
 public class BS3_STY extends AmineLinkerSTY {
 
+	@Override
+	public String toString() {
+		return "BS3 (include STY)";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 11.4;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DFDNB.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DFDNB.java
@@ -7,6 +7,11 @@
 
 public class DFDNB extends AmineLinker {
 
+	@Override
+	public String toString() {
+		return "DFDNB";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 3;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSG.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSG.java
@@ -7,6 +7,11 @@
 
 public class DSG extends AmineLinker {
 
+	@Override
+	public String toString() {
+		return "DSG";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 7.7;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSS.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSS.java
@@ -7,6 +7,11 @@
 
 public class DSS extends AmineLinker {
 
+	@Override
+	public String toString() {
+		return "DSS";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 11.4;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSSO.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSSO.java
@@ -5,6 +5,11 @@
 
 public class DSSO extends AmineLinker {
 
+	@Override
+	public String toString() {
+		return "DSSO";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 10.3;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSS_STY.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/DSS_STY.java
@@ -5,6 +5,11 @@
 
 public class DSS_STY extends AmineLinkerSTY {
 
+	@Override
+	public String toString() {
+		return "DSS (include STY)";
+	}
+
 	@Override
 	public double getLinkerLength() {
 		return 11.4;

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/EDC.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/EDC.java
@@ -7,6 +7,11 @@
 
 public class EDC implements ILinker {
 
+	@Override
+	public String toString() {
+		return "EDC";
+	}
+
 	@Override
 	public Collection<Integer> getLinkablePositions(String proteinSequence) throws Exception {
 

diff --git a/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/SulfoSMCC.java b/proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/SulfoSMCC.java
@@ -1,85 +1,90 @@
-package org.yeastrc.xlink.linkable_positions.linkers;
-
-import java.util.Collection;
-import java.util.HashSet;
-
-import org.yeastrc.xlink.utils.ProteinSequenceUtils;
-
-/*
- * For the Sulfo-SMCC cross-linker
- * From Kai Cai: Sulfo-SMCC;C12H13NO3;K{;C
- * Info at: https://tools.thermofisher.com/content/sfs/manuals/MAN0011295_SMCC_SulfoSMCC_UG.pdf
- */
-public class SulfoSMCC implements ILinker {
-
-	@Override
-	public Collection<Integer> getLinkablePositions(String proteinSequence) throws Exception {
-
-		// add in lysines
-		Collection<Integer> linkablePositions = ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( proteinSequence, "K" );
-
-		// add in cysteines
-		linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( proteinSequence, "C" ) );
-
-		// add in the two n-terminal residues
-		if( !linkablePositions.contains( 1 ) )
-			linkablePositions.add( 1 );
-
-		if( !linkablePositions.contains( 2 ) )
-			linkablePositions.add( 2 );
-
-
-		return linkablePositions;	
-
-	}
-
-	@Override
-	public Collection<Integer> getLinkablePositions(String querySequence, String subjectSequence, int subjectPosition)
-			throws Exception {
-
-		String subjectResidue = subjectSequence.substring( subjectPosition - 1, subjectPosition );
-		Collection<Integer> linkablePositions = new HashSet<Integer>();
-
-		if( subjectResidue.equals( "K" ) ) {
-
-			// lysines interact with C
-			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "C" ) );
-
-		} else if( subjectResidue.equals( "C" ) ) {
-
-			// C interact with K and the two N-terminal residues
-			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "K" ) );
-			linkablePositions.add( 1 );
-			linkablePositions.add( 2 );
-		}
-
-		// if we're at one of the two N-terminal residues, add in all links to C
-		if( subjectPosition == 1 || subjectPosition == 2 ) {
-			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "C" ) );
-		}
-
-		return linkablePositions;
-
-	}
-
-	@Override
-	public double getLinkerLength() {
-		return 8.3;
-	}
-
-	@Override
-	public Collection<String> getCrosslinkFormulas() {
-
-		Collection<String> formulas = new HashSet<>();
-		formulas.add( "C12H13NO3" );
-
-		return formulas;
-
-	}
-
-	@Override
-	public String getCrosslinkFormula(double mass) throws Exception {
-		return "C12H13NO3";			// from 
-	}
-
-}
+package org.yeastrc.xlink.linkable_positions.linkers;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+import org.yeastrc.xlink.utils.ProteinSequenceUtils;
+
+/*
+ * For the Sulfo-SMCC cross-linker
+ * From Kai Cai: Sulfo-SMCC;C12H13NO3;K{;C
+ * Info at: https://tools.thermofisher.com/content/sfs/manuals/MAN0011295_SMCC_SulfoSMCC_UG.pdf
+ */
+public class SulfoSMCC implements ILinker {
+
+	@Override
+	public String toString() {
+		return "Sulfo-SMCC";
+	}
+
+	@Override
+	public Collection<Integer> getLinkablePositions(String proteinSequence) throws Exception {
+
+		// add in lysines
+		Collection<Integer> linkablePositions = ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( proteinSequence, "K" );
+
+		// add in cysteines
+		linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( proteinSequence, "C" ) );
+
+		// add in the two n-terminal residues
+		if( !linkablePositions.contains( 1 ) )
+			linkablePositions.add( 1 );
+
+		if( !linkablePositions.contains( 2 ) )
+			linkablePositions.add( 2 );
+
+
+		return linkablePositions;	
+
+	}
+
+	@Override
+	public Collection<Integer> getLinkablePositions(String querySequence, String subjectSequence, int subjectPosition)
+			throws Exception {
+
+		String subjectResidue = subjectSequence.substring( subjectPosition - 1, subjectPosition );
+		Collection<Integer> linkablePositions = new HashSet<Integer>();
+
+		if( subjectResidue.equals( "K" ) ) {
+
+			// lysines interact with C
+			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "C" ) );
+
+		} else if( subjectResidue.equals( "C" ) ) {
+
+			// C interact with K and the two N-terminal residues
+			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "K" ) );
+			linkablePositions.add( 1 );
+			linkablePositions.add( 2 );
+		}
+
+		// if we're at one of the two N-terminal residues, add in all links to C
+		if( subjectPosition == 1 || subjectPosition == 2 ) {
+			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "C" ) );
+		}
+
+		return linkablePositions;
+
+	}
+
+	@Override
+	public double getLinkerLength() {
+		return 8.3;
+	}
+
+	@Override
+	public Collection<String> getCrosslinkFormulas() {
+
+		Collection<String> formulas = new HashSet<>();
+		formulas.add( "C12H13NO3" );
+
+		return formulas;
+
+	}
+
+	@Override
+	public String getCrosslinkFormula(double mass) throws Exception {
+		return "C12H13NO3";			// from 
+	}
+
+}
diff --git a/...eb_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/Transglutaminase.java b/...eb_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/Transglutaminase.java
@@ -7,6 +7,11 @@
 
 public class Transglutaminase implements ILinker {
 
+	@Override
+	public String toString() {
+		return "tg (transglutaminase)";
+	}
+
 	@Override
 	public Collection<Integer> getLinkablePositions(String proteinSequence) throws Exception {