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Add initialCapacity and loadFactor to HashMap and HashSet.
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@fcyu
fcyu committed Jun 16, 2017
1 parent c0b0b40 commit 60db667
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Showing 4 changed files with 22 additions and 22 deletions.
2 changes: 1 addition & 1 deletion src/main/java/proteomics/ECL2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@ public static void main(String[] args) {

// check progress every minute, record results,and delete finished tasks.
int lastProgress = 0;
Set<FinalResultEntry> final_search_results = new HashSet<>();
Set<FinalResultEntry> final_search_results = new HashSet<>(scanNumArray.length + 1, 1);
try {
while (!taskList.isEmpty()) {
// record search results and delete finished ones.
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36 changes: 18 additions & 18 deletions src/main/java/proteomics/Index/BuildIndex.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ public class BuildIndex {

private final MassTool mass_tool_obj;
private final Map<String, String> pro_annotate_map;
private Map<Character, Float> fix_mod_map = new HashMap<>();
private Map<Character, Float> fix_mod_map = new HashMap<>(25, 1);
private TreeMap<Integer, Set<String>> bin_seq_map = new TreeMap<>();
private Map<Integer, Long> bin_candidate_num_map = new HashMap<>();
private Map<String, ChainEntry> seq_entry_map = new HashMap<>();
Expand Down Expand Up @@ -92,8 +92,8 @@ public BuildIndex(Map<String, String> parameter_map) {
seqProMap = buildSeqProMap(pro_seq_map, min_chain_length, max_chain_length);

// read var mods
Set<VarModParam> varModParamSet = new HashSet<>();
Set<BinaryModParam> binaryModParamSet = new HashSet<>();
Set<VarModParam> varModParamSet = new HashSet<>(30, 1);
Set<BinaryModParam> binaryModParamSet = new HashSet<>(10, 1);
for (String k : parameter_map.keySet()) {
if (k.contentEquals("var_mod1")) {
getVarModParams(parameter_map.get(k), varModParamSet, binaryModParamSet);
Expand Down Expand Up @@ -145,7 +145,7 @@ public BuildIndex(Map<String, String> parameter_map) {
// mod containing
Set<VarSequence> varSeqSet = generateModSeq(seq, linkSiteSet, varModParamSet, binaryModParamSet, varModMaxNum);
for (VarSequence varSeq : varSeqSet) {
linkSiteSet = new HashSet<>();
linkSiteSet = new HashSet<>(5, 1);
linkSiteSet.add(varSeq.linkSite);
if (!linkSiteSet.isEmpty()) {
float totalMass = (float) (mass_tool_obj.calResidueMass(varSeq.seq) + MassTool.H2O);
Expand Down Expand Up @@ -223,7 +223,7 @@ public Map<Integer, Long> getBinCandidateNumMap() {
}

private Map<String, Set<String>> buildSeqProMap(Map<String, String> pro_seq_map, int min_chain_length, int max_chain_length) {
Map<String, Set<String>> seq_pro_map = new HashMap<>();
Map<String, Set<String>> seq_pro_map = new HashMap<>(pro_seq_map.size() * 150, 1);
for (String pro_id : pro_seq_map.keySet()) {
String pro_seq = pro_seq_map.get(pro_id);
Set<String> seq_set = mass_tool_obj.buildChainSet(pro_seq);
Expand All @@ -248,7 +248,7 @@ private Map<String, Set<String>> buildSeqProMap(Map<String, String> pro_seq_map,
if (seq_pro_map.containsKey(target_seq)) {
seq_pro_map.get(target_seq).add(pro_id);
} else {
Set<String> pro_list = new HashSet<>();
Set<String> pro_list = new HashSet<>(5, 1);
pro_list.add(pro_id);
seq_pro_map.put(target_seq, pro_list);
}
Expand Down Expand Up @@ -287,7 +287,7 @@ private Map<String, Set<String>> buildSeqProMap(Map<String, String> pro_seq_map,
if (seq_pro_map.containsKey(decoy_seq)) {
seq_pro_map.get(decoy_seq).add("DECOY_" + pro_id);
} else {
Set<String> pro_list = new HashSet<>();
Set<String> pro_list = new HashSet<>(5, 1);
pro_list.add("DECOY_" + pro_id);
seq_pro_map.put(decoy_seq, pro_list);
}
Expand All @@ -303,7 +303,7 @@ private Set<VarSequence> generateModSeq(String seq, Set<Short> modFreeListSites,
// has binary mod
for (BinaryModParam binaryModParam : binaryModParamSet) {
// get all locations having binary mod
Map<Integer, List<Float>> idxBinaryModMassMap = new HashMap<>();
Map<Integer, List<Float>> idxBinaryModMassMap = new HashMap<>(seq.length(), 1);
for (int i = 0; i < seq.length(); ++i) {
if (i != linkSite) {
String aa = seq.substring(i, i + 1);
Expand All @@ -328,7 +328,7 @@ private Set<VarSequence> generateModSeq(String seq, Set<Short> modFreeListSites,
if (idxBinaryModMassMap.size() < varModMaxNum) {
// generate sequences containing the binary mod and additional var mod
// get all locations having var mods
Map<Integer, List<Float>> idxVarModMassMap = new HashMap<>();
Map<Integer, List<Float>> idxVarModMassMap = new HashMap<>(seq.length(), 1);
for (int i = 0; i < seq.length(); ++i) {
if (i != linkSite) {
if (!idxBinaryModMassMap.containsKey(i)) {
Expand All @@ -349,14 +349,14 @@ private Set<VarSequence> generateModSeq(String seq, Set<Short> modFreeListSites,
}
if (!idxVarModMassMap.isEmpty()) {
// generate var containing sequences
Map<Integer, List<Float>> idxBinaryVarModMassMap = new HashMap<>();
Map<Integer, List<Float>> idxBinaryVarModMassMap = new HashMap<>(seq.length(), 1);
idxBinaryVarModMassMap.putAll(idxBinaryModMassMap);
idxBinaryVarModMassMap.putAll(idxVarModMassMap);
Integer[] allIdxArray = idxVarModMassMap.keySet().toArray(new Integer[idxVarModMassMap.size()]);
Arrays.sort(allIdxArray);
for (int i = 1; i <= Math.min(varModMaxNum - idxBinaryModMassMap.size(), idxVarModMassMap.size()); ++i) {
List<int[]> idxCombinationList = generateIdxCombinations(allIdxArray, i);
Set<VarSequence> varSetSubSet = new HashSet<>();
Set<VarSequence> varSetSubSet = new HashSet<>(seq.length(), 1);
for (int[] idxCombination : idxCombinationList) {
int[] allIdxCombination = new int[idxCombination.length + idxBinaryModMassMap.size()];
int j = 0;
Expand All @@ -381,7 +381,7 @@ private Set<VarSequence> generateModSeq(String seq, Set<Short> modFreeListSites,

// does not have binary mod
// get all locations' var lists
Map<Integer, List<Float>> idxVarModMassMap = new HashMap<>();
Map<Integer, List<Float>> idxVarModMassMap = new HashMap<>(seq.length(), 1);
for (int i = 0; i < seq.length(); ++i) {
if (i != linkSite) {
char aa = seq.charAt(i);
Expand Down Expand Up @@ -456,7 +456,7 @@ private List<Map<Integer, Float>> generateLocalIdxModMassMap(int[] idxArray, Map
for (int i2 = 0; i2 < idxModMassMap.get(idxArray[2]).size(); ++i2) {
for (int i3 = 0; i3 < idxModMassMap.get(idxArray[3]).size(); ++i3) {
for (int i4 = 0; i4 < idxModMassMap.get(idxArray[4]).size(); ++i4) {
Map<Integer, Float> localIdxModMassMap = new HashMap<>();
Map<Integer, Float> localIdxModMassMap = new HashMap<>(6, 1);
localIdxModMassMap.put(idxArray[0], idxModMassMap.get(idxArray[0]).get(i0));
localIdxModMassMap.put(idxArray[1], idxModMassMap.get(idxArray[1]).get(i1));
localIdxModMassMap.put(idxArray[2], idxModMassMap.get(idxArray[2]).get(i2));
Expand All @@ -473,7 +473,7 @@ private List<Map<Integer, Float>> generateLocalIdxModMassMap(int[] idxArray, Map
for (int i1 = 0; i1 < idxModMassMap.get(idxArray[1]).size(); ++i1) {
for (int i2 = 0; i2 < idxModMassMap.get(idxArray[2]).size(); ++i2) {
for (int i3 = 0; i3 < idxModMassMap.get(idxArray[3]).size(); ++i3) {
Map<Integer, Float> localIdxModMassMap = new HashMap<>();
Map<Integer, Float> localIdxModMassMap = new HashMap<>(5, 1);
localIdxModMassMap.put(idxArray[0], idxModMassMap.get(idxArray[0]).get(i0));
localIdxModMassMap.put(idxArray[1], idxModMassMap.get(idxArray[1]).get(i1));
localIdxModMassMap.put(idxArray[2], idxModMassMap.get(idxArray[2]).get(i2));
Expand All @@ -487,7 +487,7 @@ private List<Map<Integer, Float>> generateLocalIdxModMassMap(int[] idxArray, Map
for (int i0 = 0; i0 < idxModMassMap.get(idxArray[0]).size(); ++i0) {
for (int i1 = 0; i1 < idxModMassMap.get(idxArray[1]).size(); ++i1) {
for (int i2 = 0; i2 < idxModMassMap.get(idxArray[2]).size(); ++i2) {
Map<Integer, Float> localIdxModMassMap = new HashMap<>();
Map<Integer, Float> localIdxModMassMap = new HashMap<>(4, 1);
localIdxModMassMap.put(idxArray[0], idxModMassMap.get(idxArray[0]).get(i0));
localIdxModMassMap.put(idxArray[1], idxModMassMap.get(idxArray[1]).get(i1));
localIdxModMassMap.put(idxArray[2], idxModMassMap.get(idxArray[2]).get(i2));
Expand All @@ -498,15 +498,15 @@ private List<Map<Integer, Float>> generateLocalIdxModMassMap(int[] idxArray, Map
} else if (idxArray.length == 2) {
for (int i0 = 0; i0 < idxModMassMap.get(idxArray[0]).size(); ++i0) {
for (int i1 = 0; i1 < idxModMassMap.get(idxArray[1]).size(); ++i1) {
Map<Integer, Float> localIdxModMassMap = new HashMap<>();
Map<Integer, Float> localIdxModMassMap = new HashMap<>(3, 1);
localIdxModMassMap.put(idxArray[0], idxModMassMap.get(idxArray[0]).get(i0));
localIdxModMassMap.put(idxArray[1], idxModMassMap.get(idxArray[1]).get(i1));
outputList.add(localIdxModMassMap);
}
}
} else if (idxArray.length == 1) {
for (int i0 = 0; i0 < idxModMassMap.get(idxArray[0]).size(); ++i0) {
Map<Integer, Float> localIdxModMassMap = new HashMap<>();
Map<Integer, Float> localIdxModMassMap = new HashMap<>(2, 1);
localIdxModMassMap.put(idxArray[0], idxModMassMap.get(idxArray[0]).get(i0));
outputList.add(localIdxModMassMap);
}
Expand Down Expand Up @@ -555,7 +555,7 @@ private Set<String> checkKCTermMod(Set<String> varSeqSet) { // eliminate those s

private Set<Short> getLinkSiteSet(String seq, boolean n_term, boolean c_term) {
AA[] aa_list = MassTool.seqToAAList(seq);
Set<Short> output = new HashSet<>();
Set<Short> output = new HashSet<>(5, 1);
for (int i = 1; i < aa_list.length - 2; ++i) {
if (aa_list[i].aa == 'K' && (Math.abs(aa_list[i].delta_mass) < varModMassResolution)) {
output.add((short) i);
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/proteomics/Spectrum/PreSpectrum.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ public PreSpectrum(MassTool mass_tool_obj, boolean flankingPeaks) {

public SparseVector preSpectrum (Map<Double, Double> peaks_map, float precursor_mass, int scanNum) {
// sqrt the intensity
Map<Double, Double> sqrt_pl_map = new HashMap<>();
Map<Double, Double> sqrt_pl_map = new HashMap<>(peaks_map.size() + 1, 1);
for (double mz : peaks_map.keySet()) {
if ((peaks_map.get(mz) > 1e-6) && (mz < precursor_mass)) {
sqrt_pl_map.put(mz, Math.sqrt(peaks_map.get(mz)));
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/proteomics/TheoSeq/MassTool.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ public class MassTool {

public static final double H2O = 18.010564684;

private final Map<Character, Float> mass_table = new HashMap<>();
private final Map<Character, Float> mass_table = new HashMap<>(25, 1);
private final int missed_cleavage;
private final String cut_site;
private final String protect_site;
Expand Down Expand Up @@ -237,7 +237,7 @@ Map<Integer, List<int[]>> digestTrypsin(String pro_seq) {
Collections.sort(cut_point_list);

// Deal with missed cleavage
Map<Integer, List<int[]>> digest_range_map = new HashMap<>();
Map<Integer, List<int[]>> digest_range_map = new HashMap<>(5, 1);
for (int time = 0; time <= missed_cleavage; ++time) {
List<int[]> temp = new LinkedList<>();
int left_point;
Expand Down

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