Improve Exception handling.

fcyu · Feb 11, 2018 · da0345c · da0345c
1 parent 0c60e56
commit da0345c
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Showing 5 changed files with 12 additions and 24 deletions.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -10,10 +10,8 @@
 import proteomics.TheoSeq.MassTool;
 import proteomics.Validation.CalFDR;
 import uk.ac.ebi.pride.tools.jmzreader.JMzReader;
-import uk.ac.ebi.pride.tools.jmzreader.JMzReaderException;
 import uk.ac.ebi.pride.tools.mgf_parser.MgfFile;
 import uk.ac.ebi.pride.tools.mzxml_parser.MzXMLFile;
-import uk.ac.ebi.pride.tools.mzxml_parser.MzXMLParsingException;
 
 import java.io.*;
 import java.net.InetAddress;
@@ -64,18 +62,17 @@ public static void main(String[] args) {
             logger.info("Spectra file: {}.", spectra_path);
 
             new ECL2(parameter_path, spectra_path, dbName);
-        } catch (IOException | MzXMLParsingException | JMzReaderException | ExecutionException | InterruptedException | ClassNotFoundException | IllegalAccessException | InstantiationException | SQLException ex) {
+        } catch (Exception ex) {
             ex.printStackTrace();
             logger.error(ex.toString());
-            System.exit(1);
         } finally {
             if (dbName != null) {
                 (new File(dbName)).delete();
             }
         }
     }
 
-    private ECL2(String parameter_path, String spectra_path, String dbName) throws IOException, MzXMLParsingException, JMzReaderException, ExecutionException, InterruptedException, ClassNotFoundException, IllegalAccessException, InstantiationException, SQLException {
+    private ECL2(String parameter_path, String spectra_path, String dbName) throws Exception{
         // Get the parameter map
         Parameter parameter = new Parameter(parameter_path);
         Map<String, String> parameter_map = parameter.returnParameterMap();
@@ -133,8 +130,7 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws I
         } else if (ext.toLowerCase().contentEquals("mgf")) {
             spectra_parser = new MgfFile(spectra_file);
         } else {
-            logger.error("Unsupported data format {}. ECL2 only support mzXML and MGF.", ext);
-            System.exit(1);
+            throw new Exception(String.format(Locale.US, "Unsupported data format %s. ECL2 only support mzXML and MGF.", ext));
         }
 
         double ms1Tolerance = Double.valueOf(parameter_map.get("ms1_tolerance"));

diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
@@ -7,7 +7,6 @@
 import proteomics.TheoSeq.MassTool;
 import proteomics.Types.*;
 
-import java.io.IOException;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -31,7 +30,7 @@ public class BuildIndex {
     private final double ms1_bin_size;
     private final double inverseMs1BinSize;
 
-    public BuildIndex(Map<String, String> parameter_map) throws IOException {
+    public BuildIndex(Map<String, String> parameter_map) throws Exception {
         // initialize parameters
         int min_chain_length = Integer.valueOf(parameter_map.get("min_chain_length")) + 2; // n and c are counted in the sequence
         int max_chain_length = Integer.valueOf(parameter_map.get("max_chain_length")) + 2; // n and c are counted in the sequence
@@ -75,17 +74,15 @@ public BuildIndex(Map<String, String> parameter_map) throws IOException {
         if (linker_type == 1) {
             if (Math.abs(fix_mod_map.get('K') - fix_mod_map.get('n')) > 1e-6) {
                 linker_mass = 0;
-                logger.error("The link sites have different fix modifications.");
-                System.exit(1);
+                throw new Exception("The link sites have different fix modifications.");
             } else {
                 linker_mass = Double.valueOf(parameter_map.get("cl_mass")) - fix_mod_map.get('K');
             }
         } else if (linker_type == 2) {
             linker_mass = Double.valueOf(parameter_map.get("cl_mass"));
         } else {
             linker_mass = 0;
-            logger.error("The cross-linker type cannot be recognized.");
-            System.exit(1);
+            throw new Exception("The cross-linker type cannot be recognized.");
         }
 
         // read protein database
@@ -576,7 +573,7 @@ private Set<Short> getLinkSiteSet(String seq, boolean n_term, boolean c_term, sh
         return output;
     }
 
-    private void getVarModParams(String v, Set<VarModParam> varModParamSet, Set<BinaryModParam> binaryModParamSet) {
+    private void getVarModParams(String v, Set<VarModParam> varModParamSet, Set<BinaryModParam> binaryModParamSet) throws Exception {
         Matcher varModMatcher = varModParamPattern.matcher(v);
         if (varModMatcher.matches()) {
             double modMass = Double.valueOf(varModMatcher.group(1));
@@ -594,8 +591,7 @@ private void getVarModParams(String v, Set<VarModParam> varModParamSet, Set<Bina
                 }
             }
         } else {
-            logger.error("Cannot parse variable modification parameter from {}.", v);
-            System.exit(1);
+            throw new Exception(String.format(Locale.US, "Cannot parse variable modification parameter from %s.", v));
         }
     }
 }
diff --git a/src/main/java/proteomics/Parameter/Parameter.java b/src/main/java/proteomics/Parameter/Parameter.java
@@ -18,12 +18,11 @@ public class Parameter {
 
     private Map<String, String> parameterMap = new LinkedHashMap<>(); // keep the parameter order as it is in the parameter.def
 
-    public Parameter(String parameterFile) throws IOException {
+    public Parameter(String parameterFile) throws Exception {
         BufferedReader parameterReader = new BufferedReader(new FileReader(parameterFile));
         String line = parameterReader.readLine().trim();
         if (!line.contentEquals("# " + ECL2.version)) {
-            logger.error("The parameter file version ({}) is not compatible with current ECL2 version ({}).", line.substring(2), ECL2.version);
-            System.exit(1);
+            throw new Exception(String.format(Locale.US, "The parameter file version (%s) is not compatible with current ECL2 version (%s).", line.substring(2), ECL2.version));
         }
         while ((line = parameterReader.readLine()) != null) {
             line = line.trim();

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -115,8 +115,7 @@ public PreSpectra(JMzReader spectra_parser, double ms1Tolerance, double leftInve
                     } else if (matcher3.find()) {
                         scan_num = Integer.valueOf(matcher3.group(1));
                     } else {
-                        logger.error("Cannot get scan number from the MGF title {}. Please report your MGF title to the author.", mgfTitle);
-                        System.exit(1);
+                        throw new NullPointerException(String.format(Locale.US, "Cannot get scan number from the MGF title %s. Please report your MGF title to the author.", mgfTitle));
                     }
                 } else {
                     scan_num = Integer.valueOf(spectrum.getId());

diff --git a/src/main/java/proteomics/TheoSeq/DbTool.java b/src/main/java/proteomics/TheoSeq/DbTool.java
@@ -31,9 +31,7 @@ public DbTool(String db_name, String databaseType) throws IOException {
         } else if (databaseType.contentEquals("Others")) {
             header_pattern = Pattern.compile("^>(.+)$");
         } else {
-            header_pattern = null;
-            logger.error("Incorrect database type ({}) in the parameter file.", databaseType);
-            System.exit(1);
+            throw new NullPointerException(String.format(Locale.US, "Incorrect database type (%s) in the parameter file.", databaseType));
         }
 
         BufferedReader db_reader;