Change ex.getMessage() to ex.toString().

fcyu · Nov 10, 2017 · cedd170 · cedd170
1 parent b1b3de9
commit cedd170
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Showing 8 changed files with 14 additions and 14 deletions.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -112,7 +112,7 @@ public static void main(String[] args) {
                 System.exit(1);
             }
         } catch (Exception ex) {
-            logger.error(ex.getMessage());
+            logger.error(ex.toString());
             ex.printStackTrace();
             System.exit(1);
         }
@@ -255,7 +255,7 @@ private static void saveTargetResult(List<FinalResultEntry> result, Map<String,
             }
             writer.close();
         } catch (IOException ex) {
-            logger.error(ex.getMessage());
+            logger.error(ex.toString());
             System.exit(1);
         }
     }
@@ -301,7 +301,7 @@ private static void saveDecoyResult(List<FinalResultEntry> result, Map<String, S
             }
             writer.close();
         } catch (IOException ex) {
-            logger.error(ex.getMessage());
+            logger.error(ex.toString());
             System.exit(1);
         }
     }

diff --git a/src/main/java/proteomics/Parameter/Parameter.java b/src/main/java/proteomics/Parameter/Parameter.java
@@ -53,7 +53,7 @@ public Parameter(String parameterFile) {
             }
         } catch (IOException | IllegalStateException ex) {
             ex.printStackTrace();
-            logger.error(ex.getMessage());
+            logger.error(ex.toString());
             System.exit(1);
         }
     }

diff --git a/src/main/java/proteomics/Search/CalEValue.java b/src/main/java/proteomics/Search/CalEValue.java
@@ -71,7 +71,7 @@ public class CalEValue {
                         writer.write(String.format(Locale.US, "%d\n", score_histogram[i]));
                     }
                 } catch (IOException ex) {
-                    logger.error(ex.getMessage());
+                    logger.error(ex.toString());
                     ex.printStackTrace();
                     System.exit(1);
                 }
@@ -198,7 +198,7 @@ public class CalEValue {
                     }
                 }
             } catch (IOException ex) {
-                logger.error(ex.getMessage());
+                logger.error(ex.toString());
                 ex.printStackTrace();
                 System.exit(1);
             }

diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
@@ -212,7 +212,7 @@ ResultEntry doSearch(SpectrumEntry spectrumEntry, SparseVector xcorrPL, int spec
                     writer.write(String.format(Locale.US, "%s,%d,%f,%f\n", addFixMod(t.chain, t.link_site), t.link_site, t.mass, t.score));
                 }
             } catch (IOException ex) {
-                logger.error(ex.getMessage());
+                logger.error(ex.toString());
                 ex.printStackTrace();
                 System.exit(1);
             }

diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
@@ -53,7 +53,7 @@ public FinalResultEntry call() {
                 }
             } catch (IOException ex) {
                 ex.printStackTrace();
-                logger.error(ex.getMessage());
+                logger.error(ex.toString());
                 System.exit(1);
             }
         }
@@ -73,7 +73,7 @@ public FinalResultEntry call() {
                     }
                 } catch (IOException ex) {
                     ex.printStackTrace();
-                    logger.error(ex.getMessage());
+                    logger.error(ex.toString());
                     System.exit(1);
                 }
             }

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -102,7 +102,7 @@ public void write(int b) throws IOException {}
                         }
                     } catch (IOException ex) {
                         ex.printStackTrace();
-                        logger.error(ex.getMessage());
+                        logger.error(ex.toString());
                         System.exit(1);
                     }
                 }
@@ -133,15 +133,15 @@ public void write(int b) throws IOException {}
                     }
                 } catch (Exception ex) {
                     ex.printStackTrace();
-                    logger.error(ex.getMessage());
+                    logger.error(ex.toString());
                     System.exit(1);
                 }
 
                 SpectrumEntry spectrum_entry = new SpectrumEntry(scan_num, spectrum.getId(), (float) precursor_mz, precursor_mass, precursor_charge, rt, raw_mz_intensity_map, build_index_obj.linker_mass, mgfTitle);
                 num_spectrum_map.put(scan_num, spectrum_entry);
             }
         } catch (Exception ex) {
-            logger.error(ex.getMessage());
+            logger.error(ex.toString());
             ex.printStackTrace();
             System.exit(1);
         }

diff --git a/src/main/java/proteomics/Spectrum/PreSpectrum.java b/src/main/java/proteomics/Spectrum/PreSpectrum.java
@@ -47,7 +47,7 @@ public SparseVector preSpectrum (Map<Double, Double> peaks_map, float precursor_
                 }
             } catch (IOException ex) {
                 ex.printStackTrace();
-                logger.error(ex.getMessage());
+                logger.error(ex.toString());
                 System.exit(1);
             }
         }

diff --git a/src/main/java/proteomics/TheoSeq/DbTool.java b/src/main/java/proteomics/TheoSeq/DbTool.java
@@ -52,7 +52,7 @@ public DbTool(String db_name) {
             // Last protein
             pro_seq_map.put(id, seq.toString());
         } catch (IOException | PatternSyntaxException ex) {
-            logger.error(ex.getMessage());
+            logger.error(ex.toString());
             ex.printStackTrace();
             System.exit(1);
         }