Fix exception handling when messages are null

.gitignore

@@ -38,6 +38,9 @@ antbuild/
 .classpath
 .project
 
+#emacs
+*~
+
 # LaTeX auxiliary files
 *.aux
 *.blg

src/megan/algorithms/AssignmentUsingBestHit.java

@@ -112,7 +112,7 @@ private Map<String, Integer> loadAssignmentFiles(String cName, String fileName)
                     }
                 }
             } catch (IOException ex) {
-                System.err.println(ex.getMessage());
+                System.err.println(ex);
             }
             System.err.println("Count: " + map.size());
             if (map.size() > 0)

src/megan/algorithms/DataProcessor.java

@@ -416,7 +416,7 @@ else if (id > 0)
             return (int) doc.getDataTable().getTotalReads();
         } catch (IOException ex) {
             Basic.caught(ex);
-            NotificationsInSwing.showInternalError("Data Processor failed: " + ex.getMessage());
+            NotificationsInSwing.showInternalError("Data Processor failed: " + ex);
         }
         return 0;
     }

src/megan/alignment/commands/ExportAlignmentCommand.java

@@ -77,7 +77,7 @@ public void apply(NexusStreamParser np) throws Exception {
                 w.close();
             }
         } catch (IOException e) {
-            NotificationsInSwing.showError("Export Alignment failed: " + e.getMessage());
+            NotificationsInSwing.showError("Export Alignment failed: " + e);
         }
     }
 

src/megan/alignment/commands/ExportConsensusCommand.java

@@ -77,7 +77,7 @@ public void apply(NexusStreamParser np) throws Exception {
                 w.close();
             }
         } catch (IOException e) {
-            NotificationsInSwing.showError("Export Consensus failed: " + e.getMessage());
+            NotificationsInSwing.showError("Export Consensus failed: " + e);
         }
     }
 

src/megan/alignment/commands/ExportOverlapGraphCommand.java

@@ -83,7 +83,7 @@ public void apply(NexusStreamParser np) throws Exception {
             if (showGraph)
                 alignmentAssembler.showOverlapGraph(dir, dir.getDocument().getProgressListener());
         } catch (IOException e) {
-            NotificationsInSwing.showError("Export overlap file FAILED: " + e.getMessage());
+            NotificationsInSwing.showError("Export overlap file FAILED: " + e);
         }
     }
 

src/megan/alignment/commands/ExportReferenceCommand.java

@@ -76,7 +76,7 @@ public void apply(NexusStreamParser np) throws Exception {
                 w.close();
             }
         } catch (IOException e) {
-            NotificationsInSwing.showError("Export Reference failed: " + e.getMessage());
+            NotificationsInSwing.showError("Export Reference failed: " + e);
         }
     }
 

src/megan/blastclient/RemoteBlastDialog.java

@@ -229,7 +229,7 @@ public void actionPerformed(ActionEvent e) {
                                         break;
                                 }
                             } catch (IOException ex) {
-                                NotificationsInSwing.showError("Write file failed: " + ex.getMessage());
+                                NotificationsInSwing.showError("Write file failed: " + ex);
                                 return;
                             }
                             System.err.println("Reads written to: " + readsFile);

src/megan/chart/commands/ExportDataCommand.java

@@ -59,7 +59,7 @@ public void apply(NexusStreamParser np) throws Exception {
             chartViewer.getChartDrawer().writeData(w);
             w.close();
         } catch (IOException e) {
-            NotificationsInSwing.showError("Export Data failed: " + e.getMessage());
+            NotificationsInSwing.showError("Export Data failed: " + e);
         }
     }
 

src/megan/chart/drawers/CoOccurrenceToolBar.java

@@ -205,7 +205,7 @@ public void actionPerformed(ActionEvent actionEvent) {
 
                     chartViewer.getDir().execute("show what=all target=classes;", chartViewer.getCommandManager());
                 } catch (Exception ex) {
-                    NotificationsInSwing.showInternalError(chartViewer.getFrame(), "CoOccurrence drawer: " + ex.getMessage());
+                    NotificationsInSwing.showInternalError(chartViewer.getFrame(), "CoOccurrence drawer: " + ex);
                 }
             }
         });

src/megan/classification/Classification.java

@@ -89,7 +89,7 @@ public void load(String treeFile, String mapFile, ProgressListener progress) {
             progress.setProgress(2);
         } catch (Exception e) {
             Basic.caught(e);
-            NotificationsInSwing.showError(MainViewer.getLastActiveFrame(), "Failed to open files: " + treeFile + " and " + mapFile + ": " + e.getMessage());
+            NotificationsInSwing.showError(MainViewer.getLastActiveFrame(), "Failed to open files: " + treeFile + " and " + mapFile + ": " + e);
         } finally {
             progress.setCancelable(true);
         }

src/megan/classification/commandtemplates/LoadMappingFile4ViewerCommand.java

@@ -99,7 +99,7 @@ public void actionPerformed(ActionEvent ev) {
                         ClassificationManager.setMeganMapDBFile(file.toString());
                         ClassificationManager.setUseFastAccessionMappingMode(true);
                     } catch (IOException e) {
-                        NotificationsInSwing.showError("Load MEGAN mapping db failed: " + e.getMessage());
+                        NotificationsInSwing.showError("Load MEGAN mapping db failed: " + e);
                         return;
                     }
                     final Collection<String> supportedClassifications = AccessAccessionMappingDatabase.getContainedClassificationsIfDBExists(file.getPath());

src/megan/commands/MeganizeDAACommand.java

@@ -282,8 +282,8 @@ public void apply(NexusStreamParser np) throws Exception {
             } catch (CanceledException ex) {
                 throw ex;
             } catch (Exception ex) {
-                NotificationsInSwing.showError(ex.getMessage());
-                System.err.println(ex.getMessage());
+                NotificationsInSwing.showError(ex.toString());
+                System.err.println(ex);
                 countFailed++;
             }
         }

src/megan/commands/SetWindowSizeCommand.java

@@ -59,7 +59,7 @@ public void actionPerformed(ActionEvent event) {
                     throw new NumberFormatException("Unexpected characters at end of string");
                 execute("set windowSize=" + width + " x " + height + ";");
             } catch (NumberFormatException e) {
-                NotificationsInSwing.showError("Window Size: Invalid entry: " + e.getMessage());
+                NotificationsInSwing.showError("Window Size: Invalid entry: " + e.toString());
             }
         }
     }

src/megan/commands/additional/RunBlastOnNCBICommand.java

@@ -193,7 +193,7 @@ public void apply(NexusStreamParser np) throws Exception {
                                     }
                                 }
                             } catch (Exception ex) {
-                                NotificationsInSwing.showError("Create RMA file failed: " + ex.getMessage());
+                                NotificationsInSwing.showError("Create RMA file failed: " + ex);
                                 getDir().notifyUnlockInput();
                                 getDir().executeImmediately("close what=current;", ((Director) getDir()).getCommandManager());
                             }

src/megan/commands/export/ExportTaxonParentMappingCommand.java

@@ -101,7 +101,7 @@ public void apply(NexusStreamParser np) throws Exception {
             exception.setIfCurrentValueIsNull(ex);
         }
         if(exception.isNotNull()) {
-            NotificationsInSwing.showError("Write failed: "+exception.get().getMessage());
+            NotificationsInSwing.showError("Write failed: "+exception.get());
         }
     }
 

src/megan/core/Director.java

@@ -286,7 +286,7 @@ public boolean executeImmediately(final String command, CommandManager commandMa
 
             return false;
         } catch (Exception ex) {
-            NotificationsInSwing.showError("Command failed: " + ex.getMessage());
+            NotificationsInSwing.showError("Command failed: " + ex);
             return false;
         }
     }

src/megan/dialogs/attributes/AttributeData.java

@@ -79,7 +79,7 @@ private AttributeData(String filename) {
             System.err.println("done (" + attribute2kind2taxaNames.size() + ")");
         } catch (IOException e) {
             Basic.caught(e);
-            NotificationsInSwing.showError(MainViewer.getLastActiveFrame(), "Init failed: " + e.getMessage());
+            NotificationsInSwing.showError(MainViewer.getLastActiveFrame(), "Init failed: " + e);
         }
         setTaxaAttributes();
         setAttributes2Properties();

src/megan/dialogs/compare/Comparer.java

@@ -267,7 +267,7 @@ else if (useRelative) {
                 service.shutdownNow();
             }
             if(exception.isNotNull())
-                throw new IOException("Comparison computation failed: " + exception.get().getMessage(), exception.get());
+                throw new IOException("Comparison computation failed: " + exception.get(), exception.get());
 
             // if we have a taxonomy classification, then use it to get exact values:
             if (result.getClassification2Class2Counts().containsKey(Classification.Taxonomy)) {

src/megan/dialogs/lrinspector/commands/ExportSelectedCommand.java

@@ -54,7 +54,7 @@ public void apply(NexusStreamParser np) throws Exception {
                 FileUtils.writeStreamToFile(new ByteInputStream(selection, selection.length), new File(fileName));
                 NotificationsInSwing.showInformation("Exported " + StringUtils.countOccurrences(selection, '\n') + " lines to file: " + fileName);
 			} catch (IOException ex) {
-                NotificationsInSwing.showError("Export failed: " + ex.getMessage());
+                NotificationsInSwing.showError("Export failed: " + ex);
             }
         }
     }

src/megan/dialogs/parameters/commands/ListContaminantsCommand.java

@@ -69,7 +69,7 @@ public void actionPerformed(ActionEvent ev) {
                     executeImmediately("show window=message; list taxa=" + contaminantManager.getTaxonIdsString() + " title='Contaminants';");
 
                 } catch (IOException e) {
-                    NotificationsInSwing.showWarning("Read contaminant file failed: " + e.getMessage());
+                    NotificationsInSwing.showWarning("Read contaminant file failed: " + e);
                 }
             }
         }

src/megan/importblast/commands/ChooseReadsFileCommand.java

@@ -83,7 +83,7 @@ public void actionPerformed(ActionEvent event) {
 				importBlastDialog.setReadFileName(StringUtils.toString(files, "\n"));
 				importBlastDialog.getReadFileNameField().setText(StringUtils.toString(files, "\n"));
 			} catch (IOException ex) {
-                NotificationsInSwing.showError(getViewer().getFrame(), "Failed to load file: " + ex.getMessage());
+                NotificationsInSwing.showError(getViewer().getFrame(), "Failed to load file: " + ex);
             }
         }
     }

src/megan/importblast/commands/ListContaminantsCommand.java

@@ -65,7 +65,7 @@ public void actionPerformed(ActionEvent ev) {
                 contaminantManager.read(((ImportBlastDialog) getViewer()).getContaminantsFileName());
             } catch (IOException e) {
                 NotificationsInSwing.showError("Failed to parse file: " + ((ImportBlastDialog) getViewer()).getContaminantsFileName()
-                        + ":\n" + e.getMessage());
+                        + ":\n" + e);
             }
             executeImmediately("show window=message;list taxa=" + contaminantManager.getTaxonIdsString() + " title='Contaminants';");
         }

src/megan/inspector/Loader.java

@@ -78,7 +78,7 @@ private void processQueue() {
                             // System.err.println("USER CANCELED EXECUTE");
                         } catch (Exception ex) {
                             Basic.caught(ex);
-                            NotificationsInSwing.showError(inspectorWindow.getFrame(), "Load data failed: " + ex.getMessage());
+                            NotificationsInSwing.showError(inspectorWindow.getFrame(), "Load data failed: " + ex);
                         }
                     }
                 } finally {

src/megan/io/InputOutputReaderWriter.java

@@ -100,7 +100,7 @@ public String readString() throws IOException {
             try {
                 return compressor.inflateByteArray2String(-size, bytes);
             } catch (DataFormatException e) {
-                throw new IOException(e.getMessage());
+                throw new IOException(e.toString());
             }
         } else {
             return Compressor.convertUncompressedByteArray2String(size, bytes);

src/megan/io/InputReader.java

@@ -155,7 +155,7 @@ public String readString() throws IOException {
             try {
                 return compressor.inflateByteArray2String(-size, bytes);
             } catch (DataFormatException e) {
-                throw new IOException(e.getMessage());
+                throw new IOException(e.toString());
             }
         } else {
             return Compressor.convertUncompressedByteArray2String(size, bytes);
@@ -183,7 +183,7 @@ public int readString(byte[] tmp, byte[] target) throws IOException {
             try {
                 return compressor.inflateByteArray(size, tmp, target);
             } catch (DataFormatException e) {
-                throw new IOException(e.getMessage());
+                throw new IOException(e.toString());
             }
         }
     }

src/megan/main/Megan6.java

@@ -83,7 +83,7 @@ public static void main(String[] args) {
 
         } catch (Throwable th) {
             //catch any exceptions and the like that propagate up to the top level
-            if (!th.getMessage().equals("Help")) {
+            if (!"Help".equals(th.getMessage())) {
                 System.err.println("MEGAN fatal error:" + "\n" + th);
                 Basic.caught(th);
                 System.exit(1);

src/megan/ms/server/RequestHandler.java

@@ -69,7 +69,7 @@ static RequestHandler getHelp(String url) {
                 }
                 throw new IOException("Resource not found: ms/help.html");
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -80,7 +80,7 @@ static RequestHandler getVersion() {
                 checkKnownParameters(p);
                 return MeganServer.Version.getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -108,7 +108,7 @@ static RequestHandler getListDataset(Database database) {
                 }
 				return StringUtils.toString(list, "\n").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -125,7 +125,7 @@ static RequestHandler getNumberOfReads(Database database) {
                 }
 				return StringUtils.toString(list, " ").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -142,7 +142,7 @@ static RequestHandler getNumberOfMatches(Database database) {
                 }
 				return StringUtils.toString(list, " ").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -159,7 +159,7 @@ static RequestHandler getClassifications(Database database) {
                 }
 				return StringUtils.toString(list, "\n").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -186,7 +186,7 @@ static RequestHandler getAuxiliaryData(Database database) {
                 }
 				return StringUtils.toString(list, "\n").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -214,7 +214,7 @@ static RequestHandler getFileUid(Database database) {
                 }
 				return StringUtils.toString(list, "\n").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -243,7 +243,7 @@ static RequestHandler getClassificationBlock(Database database) {
 					return StringUtils.toString(list, "\n").getBytes();
                 }
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -274,7 +274,7 @@ static RequestHandler getClassSize(Database database) {
                 }
 				return StringUtils.toString(list, "\n").getBytes();
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -304,7 +304,7 @@ static RequestHandler getRead(Database database) {
                     return ReadBlockMS.writeToString(database.getRead(fileName, readId, format.isMatches()), format.isReadIds(), format.isHeaders(), format.isSequences(), format.isMatches()).getBytes();
                 }
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -337,7 +337,7 @@ static RequestHandler getReads(Database database,int defaultReadsPerPage) {
 				final ReadIteratorPagination.Page page = database.getReads(fileName, format, pageSize);
                 return getReads(c, binary, page);
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -364,7 +364,7 @@ static RequestHandler getReadsForMultipleClassIdsIterator(Database database,int
                 final ReadIteratorPagination.Page page = database.getReadsForMultipleClassIds(fileName, classification, classIds, format, pageSize);
                 return getReads(c, binary, page);
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }
@@ -382,7 +382,7 @@ static RequestHandler getNextPage(Database database) {
                 final ReadIteratorPagination.Page page = database.getNextPage(pageId, pageSize);
                 return getReads(c, binary, page);
             } catch (IOException ex) {
-                return reportError(c, p, ex.getMessage());
+                return reportError(c, p, ex.toString());
             }
         };
     }

src/megan/ms/server/RequestHandlerAdditional.java

@@ -44,7 +44,7 @@ static RequestHandler getDownloadPage(Database database) {
                 final var file = database.getRecord(name).getFile();
                 return (DOWNLOAD_FILE_PREFIX + file).getBytes();
             } catch (IOException ex) {
-                return RequestHandler.reportError(c, p, ex.getMessage());
+                return RequestHandler.reportError(c, p, ex.toString());
             }
         };
     }