This commit contains the same fixes as previous, but for the GUI runt…

…ime. Fix the summary file generation to include headers. (Closes #15) Fix the hdm value assignment. (Closes #16)
FrancisCrickInstitute · Jul 16, 2024 · 8c0adf0 · 8c0adf0
1 parent cd8dc89
commit 8c0adf0
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Showing 2 changed files with 18 additions and 5 deletions.
diff --git a/src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIBatchRunner.java b/src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIBatchRunner.java
@@ -158,7 +158,7 @@ private void generateSummaries() {
                 if (doHeader) {
                     String headerItems = anamorfEntries.get(0);
                     String[] hdmHeaderItems = hdmEntries.get(0).split(",");
-                    String header = headerItems + hdmHeaderItems[hdmHeaderItems.length - 1] + ",Alignment (Coherency [%]),Size";
+                    String header = headerItems + "," + hdmHeaderItems[hdmHeaderItems.length - 1] + ",Alignment (Coherency [%]),Size";
                     lines.add(header);
                     doHeader = false;
                 }

diff --git a/src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIWindow.java b/src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIWindow.java
@@ -701,6 +701,7 @@ private void generateSummaries() {
         // Loop through our results and generate a summary
         Path gapsOutputPath = Paths.get(this.outputDirectory, "gaps_summary.csv");
         Path twombliOutputPath = Paths.get(this.outputDirectory, "twombli_summary.csv");
+        boolean doHeader = true;
         for (CommandModule output : this.finishedFutures) {
             // Gather our basic info
             String filePrefix = (String) output.getInput("filePrefix");
@@ -712,14 +713,26 @@ private void generateSummaries() {
 
             // Write to our twombli summary
             try {
+                List<String> lines = new ArrayList<>();
                 List<String> anamorfEntries = Files.readAllLines(anamorfSummaryPath);
-                String anamorfData = anamorfEntries.get(anamorfEntries.size() - 1);
-
                 List<String> hdmEntries = Files.readAllLines(hdmSummaryPath);
+
+                // Conditionally write out our header
+                if (doHeader) {
+                    String headerItems = anamorfEntries.get(0);
+                    String[] hdmHeaderItems = hdmEntries.get(0).split(",");
+                    String header = headerItems + "," + hdmHeaderItems[hdmHeaderItems.length - 1] + ",Alignment (Coherency [%]),Size";
+                    lines.add(header);
+                    doHeader = false;
+                }
+
+                // Get the data
+                String anamorfData = anamorfEntries.get(anamorfEntries.size() - 1);
                 String[] hdmData = hdmEntries.get(hdmEntries.size() - 1).split(",");
+                double hdmValue = 1 - Double.parseDouble(hdmData[hdmData.length - 1]);
+                lines.add(anamorfData + "," + hdmValue + "," + alignment + "," + dimension);
 
-                List<String> lines = new ArrayList<>();
-                lines.add(anamorfData + "," + hdmData[hdmData.length - 1] + "," + alignment + "," + dimension);
+                // Write
                 Files.write(twombliOutputPath, lines, StandardOpenOption.CREATE, StandardOpenOption.APPEND);
             }