Merge branch '19-bedgraph-loads-too-long' into 'main'

Resolve "Bedgraph loads too long"

Closes #19

See merge request !18

src/main/java/cz/mendelu/dnaAnalyser/exporter/ExporterService.java

@@ -181,13 +181,12 @@ public class ExporterService {
                 analysisColumnMapper = new ArrayList<String>();;
                 break;
         }
-
         try {
-            // add analysis specific header
-            result = String.format(result, name, description);
+            // Add analysis specific header
+            StringBuilder resultBuilder = new StringBuilder();
+            resultBuilder.append(String.format(result, name, description));
 
             while (rs.next()) {
-
                 try {
                     chromStart = rs.getInt("POSITION");
                     if (sequenceStart == null) {
@@ -196,47 +195,48 @@ public class ExporterService {
                     chromEnd = rs.getInt("POSITION") + rs.getInt("LENGTH");
 
                     String strand = null;
-                    Integer score = 0;
-                    
+                    int score = 0;
+
                     if (analysis == Analysis.RLOOP) {
                         strand = rs.getString("STRAND");
 
-                        Integer g3 = rs.getInt("G3");
-                        Integer g4 = rs.getInt("G4");
-                        Integer gn = rs.getInt("GN");
+                        int g3 = rs.getInt("G3");
+                        int g4 = rs.getInt("G4");
+                        int gn = rs.getInt("GN");
 
-                        Double rizG = rs.getDouble("RIZGRICHNESS");
-                        Double rloopG = rs.getDouble("RLOOPGRICHNESS");
+                        double rizG = rs.getDouble("RIZGRICHNESS");
+                        double rloopG = rs.getDouble("RLOOPGRICHNESS");
 
-                        Integer scoreCalc = (int) Math.ceil(- (g3 + g4*2 + gn*3) * rizG * rloopG);
+                        int scoreCalc = (int) Math.ceil(-(g3 + g4 * 2 + gn * 3) * rizG * rloopG);
                         score = strand.equals("+") ? Math.abs(scoreCalc) : scoreCalc;
-                    }
-                    else if (analysis == Analysis.QUADRUPLEX || analysis == Analysis.AGGREGATE) {
+                    } else if (analysis == Analysis.QUADRUPLEX || analysis == Analysis.AGGREGATE) {
                         // G4 Hunter score calculation
                         score = (int) Math.ceil(rs.getDouble("SCORE") * 100);
-                    }
-                    else if (analysis == Analysis.ZDNA) {
+                    } else if (analysis == Analysis.ZDNA) {
                         score = (int) Math.ceil(rs.getDouble("SCORE"));
                     }
 
                     dataValue = String.format(" %d", score);
 
-                } catch (SQLException e) { // score is for g4hunter, r
+                } catch (SQLException e) {
                     log.error("Error fetching analysis data: {}", e);
-                }    
+                    continue; // Skip the rest of this loop iteration and continue with the next
+                }
 
-                result += String.format(format, 
+                resultBuilder.append(String.format(format,
                     chrom,
-                    posInGenomeStart+chromStart,
-                    posInGenomeStart+chromEnd,
+                    posInGenomeStart + chromStart,
+                    posInGenomeStart + chromEnd,
                     dataValue
-                );
+                )); // This is now using StringBuilder
 
                 dataValue = "";
             }
-        }
-        catch (NullPointerException | NotFoundException e) {
-            log.error("Error finding analysis by id: {}\n {}", id, e);
+            // Convert the StringBuilder to a String
+            result = resultBuilder.toString();
+
+        } catch (SQLException e) {
+            log.error("Error processing result set: {}", e);
         }
 
         // update browser header