removed unused code

JaneliaSciComp · Jun 4, 2024 · 856227a · 856227a
1 parent 1b0e136
commit 856227a
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Showing 3 changed files with 8 additions and 25 deletions.
diff --git a/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/CreateCDSDataInputCmd.java b/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/CreateCDSDataInputCmd.java
@@ -380,14 +380,14 @@ private <N extends AbstractNeuronEntity> void populateOtherComputeFilesFromInput
                                                                                      Set<ComputeFileType> computeFileTypes,
                                                                                      List<LibraryVariantArg> libraryVariants) {
         String searchableMIPFile = new File(neuronEntity.getComputeFileName(ComputeFileType.InputColorDepthImage)).getName();
-        String searchableMIPBaseName = RegExUtils.replacePattern(searchableMIPFile, "(_CDM)?\\..*$", "");
+        String searchableMIPBaseName = RegExUtils.replacePattern(searchableMIPFile, "(?:_CDM)?\\..*$", "");
         String[] searchableMIPNameComps = StringUtils.split(searchableMIPBaseName, "-_");
         StringBuilder patternBuilder = new StringBuilder(".*")
                 .append(neuronEntity.getNeuronId()).append(".*");
         if (searchableMIPNameComps.length > 1) {
             if (!MIPsHandlingUtils.isEmLibrary(neuronEntity.getLibraryName())) {
                 LMNeuronEntity lmNeuronEntity = (LMNeuronEntity) neuronEntity;
-                patternBuilder.append(lmNeuronEntity.getObjective())
+                patternBuilder.append("(?:").append(lmNeuronEntity.getObjective()).append(")?") // make the objective optional
                         .append(".*");
                 patternBuilder
                         .append(searchableMIPNameComps[searchableMIPNameComps.length-2])
@@ -399,8 +399,8 @@ private <N extends AbstractNeuronEntity> void populateOtherComputeFilesFromInput
         }
         patternBuilder.append(searchableMIPNameComps[searchableMIPNameComps.length-1]);
         // add searchable MIP name to the pattern
-        patternBuilder.insert(0, "(")
-                .append(")|(.*")
+        patternBuilder.insert(0, "(?:")
+                .append(")|(?:.*")
                 .append(searchableMIPBaseName)
                 .append(".*)");
         Pattern variantPattern = Pattern.compile(patternBuilder.toString());

diff --git a/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/LibraryVariantArg.java b/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/LibraryVariantArg.java
@@ -76,7 +76,11 @@ public LibraryVariantArg convert(String value) {
     }
 
     String libraryName;
+    // variant type: CDM, grad, zgap, 3d-vol
     String variantType;
+    // there can be more than one location for a specific variant
+    // very often there is a location with significant variants and one with "junk" variants
+    // and we may still want to keep these separate
     Collection<String> variantPaths;
     String variantIgnoredPattern;
     String variantTypeSuffix; // this is typically the suffix appended to a foldername such as _gradient or _RGB20x

diff --git a/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/MIPsHandlingUtils.java b/colormipsearch-tools/src/main/java/org/janelia/colormipsearch/cmd/MIPsHandlingUtils.java
@@ -113,27 +113,6 @@ static String extractEMBodyIdFromName(String name) {
         }
     }
 
-    static String extractObjectiveFromMIPName(String mipName) {
-        Pattern regExPattern = Pattern.compile("[_-]([0-9]+x)[_-]", Pattern.CASE_INSENSITIVE);
-        Matcher objectiveMatcher = regExPattern.matcher(mipName);
-        if (objectiveMatcher.find()) {
-            return objectiveMatcher.group(1);
-        } else {
-            return null;
-        }
-    }
-
-    static String extractGenderFromMIPName(String mipName) {
-        // this assumes the gender is right before the objective
-        Pattern regExPattern = Pattern.compile("(m|f)[_-]([0-9]+x)[_-]", Pattern.CASE_INSENSITIVE);
-        Matcher objectiveMatcher = regExPattern.matcher(mipName);
-        if (objectiveMatcher.find()) {
-            return objectiveMatcher.group(1);
-        } else {
-            return null;
-        }
-    }
-
     static boolean isEmLibrary(String lname) {
         return lname != null && (
                 StringUtils.startsWithIgnoreCase(lname, "flyem") ||