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remove more invalid fragments
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@juliomarcopineda
juliomarcopineda committed Mar 13, 2018
1 parent 187a646 commit 315aa33
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Showing 2 changed files with 78 additions and 19 deletions.
95 changes: 77 additions & 18 deletions peptideSerumStability/src/com/github/juliomarcopineda/FragmentAnalyzer.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -128,29 +128,42 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
List<List<Integer>> fragmentsWith1 = connectionInFragments.get(connection1);
List<List<Integer>> fragmentsWith2 = connectionInFragments.get(connection2);

// Start building branched fragment using linear fragment with the first connection
for (List<Integer> fragmentWith1 : fragmentsWith1) {
List<Integer> afterConnection1 = fragmentWith1.subList(fragmentWith1.indexOf(connection1), fragmentWith1.size());

StringBuilder sb1 = new StringBuilder();
sb1.append(getPeptideStringRepresentation(fragmentWith1, type));

// Append the linkers to the fragment (DFBP or S or SS) to form branched fragments
switch (type) {
case DFBP:
// Skip if the fragment contains DFBP
if (fragmentWith1.contains(peptideSequence.length())) {
continue;
}

sb1.append("#2");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
// Only append DFBP if the connection is not in the beginning
if (fragmentWith1.get(0) != connection1) {
sb1.append("#2");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
}

break;
case DISULFIDE:
// Skip if the fragment contains S or SS
if (fragmentWith1.contains(peptideSequence.length()) || fragmentWith1.contains(peptideSequence.length() + 1)) {
continue;
}

sb1.append("#S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
sb1.append("S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
// Only append S then SS if the connection is not in the beginning
if (fragmentWith1.get(0) != connection1) {
sb1.append("#S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
sb1.append("S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
}

break;
case AMIDE:
break;
Expand All @@ -160,14 +173,22 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
break;
}

// Start building branched fragments using the linear fragment with the second connection
for (List<Integer> fragmentWith2 : fragmentsWith2) {

// Skip if appending two fragments would form a linear peptide
if (isLinear(fragmentWith1, connection1, fragmentWith2, connection2)) {
continue;
}

List<Integer> beforeConnection2 = fragmentWith2.subList(0, fragmentWith2.indexOf(connection2) + 1);

StringBuilder sb2 = new StringBuilder();
sb2.append(getPeptideStringRepresentation(fragmentWith1, type));
if (isValidBranchedFragment(afterConnection1, beforeConnection2)) {
switch (type) {
case DFBP:
// Skip if the fragment contains DFBP
if (fragmentWith2.contains(peptideSequence.length())) {
continue;
}
Expand All @@ -176,6 +197,7 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
fragmentWeights.put(sb2.toString(), calculateBranchedFragmentWeight(sb2.toString()));
break;
case DISULFIDE:
// Skip if the fragment contains S or SS
if (fragmentWith2.contains(peptideSequence.length()) || fragmentWith2.contains(peptideSequence.length() + 1)) {
continue;
}
Expand All @@ -187,55 +209,70 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
sb2.append("#" + getPeptideStringRepresentation(fragmentWith2, type));
fragmentWeights.put(sb2.toString(), calculateBranchedFragmentWeight(sb2.toString()));
break;
case LINEAR:
break;
default:
break;
}
}
}
}

// Start forming branched fragments starting with fragments with the second connection
for (List<Integer> fragmentWith2 : fragmentsWith2) {
List<Integer> beforeConnection2 = fragmentWith2.subList(0, fragmentWith2.indexOf(connection2) + 1);

StringBuilder sb1 = new StringBuilder();
sb1.append(getPeptideStringRepresentation(fragmentWith2, type));

// Append the linkers (DFBP or S or SS) to form possible branched fragments
switch (type) {
case DFBP:
// Skip if linear fragment contains DFBP
if (fragmentWith2.contains(peptideSequence.length())) {
continue;
}

sb1.append("#2");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
// Only append DFBP if connection is not in the end of the fragment
if (fragmentWith2.get(fragmentWith2.size() - 1) != connection2) {
sb1.append("#2");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
}

break;
case DISULFIDE:
// Skip if linear fragment contains S or SS
if (fragmentWith2.contains(peptideSequence.length()) || fragmentWith2.contains(peptideSequence.length() + 1)) {
continue;
}

sb1.append("#S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
sb1.append("S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
break;
case AMIDE:
break;
case LINEAR:
// Only append S then SS if connection is not in the end of the fragment
if (fragmentWith2.get(fragmentWith2.size() - 1) != connection2) {
sb1.append("#S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
sb1.append("S");
fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
}
break;
default:
break;
}

// Start building branched fragments using linear fragments with the first connection
for (List<Integer> fragmentWith1 : fragmentsWith1) {

// Skip if appending two fragments would form a linear peptide
if (isLinear(fragmentWith1, connection1, fragmentWith2, connection2)) {
continue;
}

List<Integer> afterConnection1 = fragmentWith1.subList(fragmentWith1.indexOf(connection1), fragmentWith1.size());

StringBuilder sb2 = new StringBuilder();
sb2.append(getPeptideStringRepresentation(fragmentWith1, type));
if (isValidBranchedFragment(afterConnection1, beforeConnection2)) {
switch (type) {
case DFBP:
// Skip if fragment contains DFBP
if (fragmentWith1.contains(peptideSequence.length())) {
continue;
}
Expand All @@ -245,6 +282,7 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
fragmentWeights.put(sb2.toString(), calculateBranchedFragmentWeight(sb2.toString()));
break;
case DISULFIDE:
// Skip if fragment contains S or SS
if (fragmentWith1.contains(peptideSequence.length()) || fragmentWith1.contains(peptideSequence.length() + 1)) {
continue;
}
Expand Down Expand Up @@ -277,6 +315,27 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)

}

/**
* Determines if appending fragment1 and fragment2 results in a linear peptide.
*
* @param fragment1
* @param connection1
* @param fragment2
* @param connection2
* @return
*/
private boolean isLinear(List<Integer> fragment1, int connection1, List<Integer> fragment2, int connection2) {
if (fragment1.get(0) == connection1 && fragment2.get(fragment2.size() - 1) == connection2) {
return true;
}
else if (fragment1.get(fragment1.size() - 1) == connection1 && fragment2.get(0) == connection2) {
return true;
}
else {
return false;
}
}

/**
* Given the amino acids after the first connection and the amino acids before a connection, determines if the branched fragments is truly valid.
* A branched fragment is only valid if the two inputs do not share any elements.
Expand Down
2 changes: 1 addition & 1 deletion peptideSerumStability/src/com/github/juliomarcopineda/PeptideSerumStability.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,7 @@ private static void interactiveSession(FragmentAnalyzer analyzer, BufferedReader

System.out.print("Enter data from mass spectrometry: ");
double data = Double.parseDouble(br.readLine());
System.out.print("Enter threshold to comapre theoretical molecular weights: ");
System.out.print("Enter threshold to compare theoretical molecular weights: ");
double threshold = Double.parseDouble(br.readLine());
System.out.println();

Expand Down

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