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Change indents to space.
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@fcyu
fcyu committed Jan 4, 2016
1 parent 5f96918 commit d556d45
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Showing 9 changed files with 511 additions and 511 deletions.
394 changes: 197 additions & 197 deletions src/main/java/proteomics/Index/BuildIndex.java
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28 changes: 14 additions & 14 deletions src/main/java/proteomics/Index/ChainEntry.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,18 @@
import java.util.*;

public class ChainEntry {
public float chain_mass = 0;
public String pro_id = null;
public String chain_type = null;
public List<Integer> linksite_list = null;
public float[][] chain_ion_array = null;
public ChainEntry(float chain_mass, String pro_id, String chain_type, List<Integer> linksite_list, float[][] chain_ion_array) {
this.chain_mass = chain_mass;
this.pro_id = pro_id;
this.chain_type = chain_type;
this.linksite_list = linksite_list;
this.chain_ion_array = chain_ion_array;
}

public float chain_mass = 0;
public String pro_id = null;
public String chain_type = null;
public List<Integer> linksite_list = null;
public float[][] chain_ion_array = null;

public ChainEntry(float chain_mass, String pro_id, String chain_type, List<Integer> linksite_list, float[][] chain_ion_array) {
this.chain_mass = chain_mass;
this.pro_id = pro_id;
this.chain_type = chain_type;
this.linksite_list = linksite_list;
this.chain_ion_array = chain_ion_array;
}
}
74 changes: 37 additions & 37 deletions src/main/java/proteomics/Math/CalScore.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,41 +3,41 @@

public class CalScore {

private float[][] alignment_matrix = null;

public CalScore(float[][] exp_matrix, float[] theo_vector, float ms2_tolerance) {
alignment_matrix = new float[2][exp_matrix[0].length + theo_vector.length];

int start = 0;
int idx = 0;
for (float theo_mz : theo_vector) {
if (exp_matrix[0][0] - theo_mz > ms2_tolerance) {
continue;
}
int j = start;
while (j < exp_matrix[0].length) {
float exp_mz = exp_matrix[0][j];
float temp = exp_mz - theo_mz;
if ((temp >= -ms2_tolerance) && (temp <= ms2_tolerance)) {
alignment_matrix[0][idx] = exp_mz;
alignment_matrix[1][idx] = exp_matrix[1][j];
++idx;
} else if (temp > ms2_tolerance) {
start = j - 1;
break;
}
++j;
}
}
}

public float cal_dot_product() {
float dot_value = 0;
for (int i = 0; i < alignment_matrix[0].length; ++i) {
dot_value += alignment_matrix[1][i];
}

return dot_value;
}
private float[][] alignment_matrix = null;

public CalScore(float[][] exp_matrix, float[] theo_vector, float ms2_tolerance) {
alignment_matrix = new float[2][exp_matrix[0].length + theo_vector.length];

int start = 0;
int idx = 0;
for (float theo_mz : theo_vector) {
if (exp_matrix[0][0] - theo_mz > ms2_tolerance) {
continue;
}

int j = start;
while (j < exp_matrix[0].length) {
float exp_mz = exp_matrix[0][j];
float temp = exp_mz - theo_mz;
if ((temp >= -ms2_tolerance) && (temp <= ms2_tolerance)) {
alignment_matrix[0][idx] = exp_mz;
alignment_matrix[1][idx] = exp_matrix[1][j];
++idx;
} else if (temp > ms2_tolerance) {
start = j - 1;
break;
}
++j;
}
}
}

public float cal_dot_product() {
float dot_value = 0;
for (int i = 0; i < alignment_matrix[0].length; ++i) {
dot_value += alignment_matrix[1][i];
}

return dot_value;
}
}
134 changes: 67 additions & 67 deletions src/main/java/proteomics/Parameter/Parameter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,74 +9,74 @@

public class Parameter {

private static final Logger logger = LoggerFactory.getLogger(Parameter.class);
private static final Logger logger = LoggerFactory.getLogger(Parameter.class);

private String parameter_file = "./src/main/resources/parameter.def";
private Map<String, String> parameter_map = new HashMap<>();

public Parameter() throws Exception {
Pattern comment_line_pattern = Pattern.compile("^#.*");
Pattern comment_pattern = Pattern.compile("([^#]+)#?.*");
private String parameter_file = "./src/main/resources/parameter.def";
private Map<String, String> parameter_map = new HashMap<>();

try (BufferedReader parameter_reader = new BufferedReader(new FileReader(parameter_file))) {
String line;
while ((line = parameter_reader.readLine()) != null) {
line = line.trim();
Matcher comment_line_matcher = comment_line_pattern.matcher(line);
if (!comment_line_matcher.matches()) {
// This is not a comment line
Matcher line_matcher = comment_pattern.matcher(line);
String parameter_string;
if (line_matcher.matches()) {
parameter_string = line_matcher.group(1).trim();
String[] parameter_array = parameter_string.split("=");
String parameter_name = parameter_array[0].trim();
String parameter_value = parameter_array[1].trim();
parameter_map.put(parameter_name, parameter_value);
}
}
}
parameter_reader.close();
} catch (IOException | IllegalStateException ex) {
logger.error(ex.getMessage());
System.exit(1);
}
}


public Parameter(String parameter_file) throws Exception {
this.parameter_file = parameter_file;

Pattern comment_line_pattern = Pattern.compile("^#.*");
Pattern comment_pattern = Pattern.compile("([^#]+)#?.*");
public Parameter() throws Exception {
Pattern comment_line_pattern = Pattern.compile("^#.*");
Pattern comment_pattern = Pattern.compile("([^#]+)#?.*");

try (BufferedReader parameter_reader = new BufferedReader(new FileReader(parameter_file))) {
String line;
while ((line = parameter_reader.readLine()) != null) {
line = line.trim();
Matcher comment_line_matcher = comment_line_pattern.matcher(line);
if (!comment_line_matcher.matches()) {
// This is not a comment line
Matcher line_matcher = comment_pattern.matcher(line);
String parameter_string;
if (line_matcher.matches()) {
parameter_string = line_matcher.group(1).trim();
String[] parameter_array = parameter_string.split("=");
String parameter_name = parameter_array[0].trim();
String parameter_value = parameter_array[1].trim();
parameter_map.put(parameter_name, parameter_value);
}
}
}
parameter_reader.close();
} catch (IOException | IllegalStateException ex) {
logger.error(ex.getMessage());
System.exit(1);
}
}


public Map<String, String> returnParameterMap() {
return parameter_map;
}
try (BufferedReader parameter_reader = new BufferedReader(new FileReader(parameter_file))) {
String line;
while ((line = parameter_reader.readLine()) != null) {
line = line.trim();
Matcher comment_line_matcher = comment_line_pattern.matcher(line);
if (!comment_line_matcher.matches()) {
// This is not a comment line
Matcher line_matcher = comment_pattern.matcher(line);
String parameter_string;
if (line_matcher.matches()) {
parameter_string = line_matcher.group(1).trim();
String[] parameter_array = parameter_string.split("=");
String parameter_name = parameter_array[0].trim();
String parameter_value = parameter_array[1].trim();
parameter_map.put(parameter_name, parameter_value);
}
}
}
parameter_reader.close();
} catch (IOException | IllegalStateException ex) {
logger.error(ex.getMessage());
System.exit(1);
}
}


public Parameter(String parameter_file) throws Exception {
this.parameter_file = parameter_file;

Pattern comment_line_pattern = Pattern.compile("^#.*");
Pattern comment_pattern = Pattern.compile("([^#]+)#?.*");

try (BufferedReader parameter_reader = new BufferedReader(new FileReader(parameter_file))) {
String line;
while ((line = parameter_reader.readLine()) != null) {
line = line.trim();
Matcher comment_line_matcher = comment_line_pattern.matcher(line);
if (!comment_line_matcher.matches()) {
// This is not a comment line
Matcher line_matcher = comment_pattern.matcher(line);
String parameter_string;
if (line_matcher.matches()) {
parameter_string = line_matcher.group(1).trim();
String[] parameter_array = parameter_string.split("=");
String parameter_name = parameter_array[0].trim();
String parameter_value = parameter_array[1].trim();
parameter_map.put(parameter_name, parameter_value);
}
}
}
parameter_reader.close();
} catch (IOException | IllegalStateException ex) {
logger.error(ex.getMessage());
System.exit(1);
}
}


public Map<String, String> returnParameterMap() {
return parameter_map;
}
}
78 changes: 39 additions & 39 deletions src/main/java/proteomics/Search/FinalResultEntry.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,47 +2,47 @@

public class FinalResultEntry implements Comparable<FinalResultEntry> {

public int spectrum_id = 0;
public int rank = 0;
public int charge = 0;
public float spectrum_precursor_mz = 0;
public float abs_ppm = 0;
public double score = 0;
public double delta_score = 0;
public String seq_1 = null;
public int link_site_1 = -1;
public String mod_1 = null;
public String pro_id_1 = null;
public String seq_2 = null;
public int link_site_2 = -1;
public String mod_2 = null;
public String pro_id_2 = null;
public String cl_type = null;
public String type = null;
public float qvalue = 0;
public int spectrum_id = 0;
public int rank = 0;
public int charge = 0;
public float spectrum_precursor_mz = 0;
public float abs_ppm = 0;
public double score = 0;
public double delta_score = 0;
public String seq_1 = null;
public int link_site_1 = -1;
public String mod_1 = null;
public String pro_id_1 = null;
public String seq_2 = null;
public int link_site_2 = -1;
public String mod_2 = null;
public String pro_id_2 = null;
public String cl_type = null;
public String type = null;
public float qvalue = 0;

public FinalResultEntry(int spectrum_id, int rank, int charge, float spectrum_precursor_mz, float abs_ppm, double score, double delta_score, String seq_1, int link_site_1, String mod_1, String pro_id_1, String seq_2, int link_site_2, String mod_2, String pro_id_2, String cl_type, String type, float qvalue) {
this.spectrum_id = spectrum_id;
this.rank = rank;
this.charge = charge;
this.spectrum_precursor_mz= spectrum_precursor_mz;
this.abs_ppm = abs_ppm;
this.score = score;
this.delta_score = delta_score;
this.seq_1 = seq_1;
this.link_site_1 = link_site_1;
this.mod_1 = mod_1;
this.pro_id_1 = pro_id_1;
this.seq_2 = seq_2;
this.link_site_2 = link_site_2;
this.mod_2 = mod_2;
this.pro_id_2 = pro_id_2;
this.cl_type = cl_type;
this.type = type;
this.qvalue = qvalue;
}
public FinalResultEntry(int spectrum_id, int rank, int charge, float spectrum_precursor_mz, float abs_ppm, double score, double delta_score, String seq_1, int link_site_1, String mod_1, String pro_id_1, String seq_2, int link_site_2, String mod_2, String pro_id_2, String cl_type, String type, float qvalue) {
this.spectrum_id = spectrum_id;
this.rank = rank;
this.charge = charge;
this.spectrum_precursor_mz= spectrum_precursor_mz;
this.abs_ppm = abs_ppm;
this.score = score;
this.delta_score = delta_score;
this.seq_1 = seq_1;
this.link_site_1 = link_site_1;
this.mod_1 = mod_1;
this.pro_id_1 = pro_id_1;
this.seq_2 = seq_2;
this.link_site_2 = link_site_2;
this.mod_2 = mod_2;
this.pro_id_2 = pro_id_2;
this.cl_type = cl_type;
this.type = type;
this.qvalue = qvalue;
}

public int compareTo(FinalResultEntry other) {
public int compareTo(FinalResultEntry other) {
if (this.score > other.score) {
return 1;
} else if (this.score < other.score) {
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