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Fix a bug when C-term has the link-site. Improve variable names and f…
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…unction names.
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@fcyu
fcyu committed May 23, 2017
1 parent c0d2ea7 commit d9fd9c9
Showing 1 changed file with 19 additions and 20 deletions.
39 changes: 19 additions & 20 deletions src/main/java/proteomics/Index/BuildIndex.java
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ public BuildIndex(Map<String, String> parameter_map) {
boolean proteinCTerm = seq_term_map.get(seq)[1];

// mod free
Set<Short> linkSiteSet = getLinkSiteSet(seq, proteinNTerm);
Set<Short> linkSiteSet = getLinkSiteSet(seq, proteinNTerm, proteinCTerm);
if (!linkSiteSet.isEmpty()) {
float totalMass = (float) (mass_tool_obj.calResidueMass(seq) + MassTool.H2O);
if (totalMass < max_precursor_mass - linker_mass) {
Expand All @@ -140,7 +140,7 @@ public BuildIndex(Map<String, String> parameter_map) {
// mod containing
Set<String> varSeqSet = generateModSeq(seq, linkSiteSet, varModParams, varModMaxNum);
for (String varSeq : varSeqSet) {
linkSiteSet = getLinkSiteSet(varSeq, proteinNTerm);
linkSiteSet = getLinkSiteSet(varSeq, proteinNTerm, proteinCTerm);
if (!linkSiteSet.isEmpty()) {
float totalMass = (float) (mass_tool_obj.calResidueMass(varSeq) + MassTool.H2O);
if (totalMass < max_precursor_mass - linker_mass) {
Expand Down Expand Up @@ -224,10 +224,10 @@ private Map<String, Set<String>> buildSeqProMap(Map<String, String> pro_seq_map,

boolean n_term = false;
boolean c_term = false;
if (pro_seq.startsWith(getNCFreeSeq(target_seq))) {
if (pro_seq.startsWith(target_seq.substring(1, target_seq.length() - 1))) {
n_term = true;
}
if (pro_seq.endsWith(getNCFreeSeq(target_seq))) {
if (pro_seq.endsWith(target_seq.substring(1, target_seq.length() - 1))) {
c_term = true;
}
seq_term_map.put(target_seq, new boolean[]{n_term, c_term});
Expand Down Expand Up @@ -263,10 +263,10 @@ private Map<String, Set<String>> buildSeqProMap(Map<String, String> pro_seq_map,

boolean n_term = false;
boolean c_term = false;
if (decoy_pro_seq.startsWith(getNCFreeSeq(decoy_seq))) {
if (decoy_pro_seq.startsWith(decoy_seq.substring(1, decoy_seq.length() - 1))) {
n_term = true;
}
if (decoy_pro_seq.endsWith(getNCFreeSeq(decoy_seq))) {
if (decoy_pro_seq.endsWith(decoy_seq.substring(1, decoy_seq.length() - 1))) {
c_term = true;
}
seq_term_map.put(decoy_seq, new boolean[]{n_term, c_term});
Expand Down Expand Up @@ -307,11 +307,11 @@ private Set<String> generateModSeq(String seq, Set<Short> modFreeListSites, Set<
Integer[] allIdxArray = idxModMassMap.keySet().toArray(new Integer[idxModMassMap.size()]);
Arrays.sort(allIdxArray);
for (int i = 1; i <= Math.min(varModMaxNum, idxModMassMap.size()); ++i) {
List<int[]> idxArrays = selectIdxes(allIdxArray, i);
List<int[]> idxCombinationList = generateIdxCombinations(allIdxArray, i);
Set<String> varSetSubSet = new HashSet<>();
for (int[] idxArray : idxArrays) {
if (checkIdxArray(idxArray, modFreeListSites)) {
varSetSubSet.addAll(generateModSeqSub(seq, idxArray, idxModMassMap));
for (int[] idxCombination : idxCombinationList) {
if (stillHasLinkSite(idxCombination, modFreeListSites)) {
varSetSubSet.addAll(generateModSeqSub(seq, idxCombination, idxModMassMap));
}
}
if (!varSetSubSet.isEmpty()) {
Expand All @@ -322,7 +322,7 @@ private Set<String> generateModSeq(String seq, Set<Short> modFreeListSites, Set<
return varSeqSet;
}

private List<int[]> selectIdxes(Integer[] allIdxArray, int num) {
private List<int[]> generateIdxCombinations(Integer[] allIdxArray, int num) {
List<int[]> outputList = new LinkedList<>();
Iterator<int[]> tempIterator = CombinatoricsUtils.combinationsIterator(allIdxArray.length, num);
while (tempIterator.hasNext()) {
Expand All @@ -338,17 +338,17 @@ private List<int[]> selectIdxes(Integer[] allIdxArray, int num) {
return outputList;
}

private boolean checkIdxArray(int[] idxArray, Set<Short> modFreeLinkSites) {
private boolean stillHasLinkSite(int[] idxCombination, Set<Short> modFreeLinkSites) {
for (int modFreeLinkSite : modFreeLinkSites) {
if (Arrays.binarySearch(idxArray, modFreeLinkSite) < 0) {
if (Arrays.binarySearch(idxCombination, modFreeLinkSite) < 0) {
return true;
}
}
return false;
}

private Set<String> generateModSeqSub(String seq, int[] idxArray, Map<Integer, List<Float>> idxModMassMap) {
List<Map<Integer, Float>> localIdxModMassMaps = generateLocalIdxModMassMap(idxArray, idxModMassMap);
private Set<String> generateModSeqSub(String seq, int[] idxCombination, Map<Integer, List<Float>> idxModMassMap) {
List<Map<Integer, Float>> localIdxModMassMaps = generateLocalIdxModMassMap(idxCombination, idxModMassMap);

Set<String> outputSet = new HashSet<>();
for (Map<Integer, Float> localIdxModMassMap : localIdxModMassMaps) {
Expand Down Expand Up @@ -470,7 +470,7 @@ private Set<String> checkKCTermMod(Set<String> varSeqSet) { // eliminate those s
}
}

private Set<Short> getLinkSiteSet(String seq, boolean n_term) {
private Set<Short> getLinkSiteSet(String seq, boolean n_term, boolean c_term) {
AA[] aa_list = MassTool.seqToAAList(seq);
Set<Short> output = new HashSet<>();
for (int i = 1; i < aa_list.length - 2; ++i) {
Expand All @@ -481,13 +481,12 @@ private Set<Short> getLinkSiteSet(String seq, boolean n_term) {
if (n_term && !output.contains((short) 1) && (Math.abs(aa_list[0].delta_mass) < varModMassResolution)) {
output.add((short) 0);
}
if (c_term && aa_list[aa_list.length - 2].aa == 'K' && (Math.abs(aa_list[aa_list.length - 2].delta_mass) < varModMassResolution)) {
output.add((short) (aa_list.length - 2));
}
return output;
}

private String getNCFreeSeq(String seq) {
return seq.substring(1, seq.length() - 1);
}

private Set<VarModParam> getVarModParams(String v) {
Set<VarModParam> varModParams = new HashSet<>();

Expand Down

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