fixed ignore formulas setting

fixed adduct filter, improved filter code
sirius-ms · Nov 7, 2023 · 4a8d778 · 4a8d778
1 parent ac488a8
commit 4a8d778
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Showing 5 changed files with 33 additions and 18 deletions.
diff --git a/sirius_cli/src/main/resources/sirius.properties b/sirius_cli/src/main/resources/sirius.properties
@@ -25,6 +25,7 @@ de.unijena.bioinf.sirius.ui.cite = false
 de.unijena.bioinf.sirius.ui.cite.classyfire = false
 
 de.unijena.bioinf.sirius.ui.allowMs1Only=true
+de.unijena.bioinf.sirius.ui.ignoreFormulas=false
 
 # S3 CustomDB config
 #de.unijena.bioinf.stores.customdb.s3.host=

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/settings/GerneralSettingsPanel.java b/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/settings/GerneralSettingsPanel.java
@@ -112,6 +112,7 @@ public boolean restartRequired() {
     public void saveProperties() {
         props.setProperty("de.unijena.bioinf.sirius.treebuilder.solvers", (String) solver.getSelectedItem());
         props.setProperty("de.unijena.bioinf.sirius.ui.allowMs1Only", String.valueOf(allowMS1Only.isSelected()));
+        props.setProperty("de.unijena.bioinf.sirius.ui.ignoreFormulas", String.valueOf(ignoreFormulas.isSelected()));
 //        props.setProperty("de.unijena.bioinf.sirius.treebuilder.timeout", treeTimeout.getNumber().toString());
         final Path dir = Paths.get(db.getFilePath());
         if (Files.isDirectory(dir)) {

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/utils/CompoundFilterMatcher.java b/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/utils/CompoundFilterMatcher.java
@@ -57,28 +57,32 @@ public boolean matches(InstanceBean item) {
         double mz = item.getIonMass();
         double rt = item.getID().getRt().map(RetentionTime::getRetentionTimeInSeconds).orElse(Double.NaN);
         //todo hotfix, since the confidence score is a FormulaScore which sets all NaN to -Infinity (after computation, and thus also in project space)
-        double confidence = item.getID().getConfidenceScore().map(conf -> Double.isInfinite(conf) ? Double.NaN : conf).orElse(Double.NaN);
-        if ((mz < filterModel.getCurrentMinMz()) ||
-                (filterModel.isMaxMzFilterActive() && mz > filterModel.getCurrentMaxMz())) {
-            return false;
+        double confidence = item.getID().getConfidenceScore().filter(conf -> !Double.isInfinite(conf)).orElse(Double.NaN);
+
+        {
+            if (mz < filterModel.getCurrentMinMz())
+                return false;
+            if (filterModel.isMaxMzFilterActive() && mz > filterModel.getCurrentMaxMz())
+                return false;
         }
-        if (!Double.isNaN(rt)) {
-            if ((rt < filterModel.getCurrentMinRt()) ||
-                    (filterModel.isMaxRtFilterActive() && rt > filterModel.getCurrentMaxRt())) {
+
+        if (!Double.isNaN(rt)) { //never filter NaN because RT is just not available
+            if (rt < filterModel.getCurrentMinRt())
+                return false;
+            if (filterModel.isMaxRtFilterActive() && rt > filterModel.getCurrentMaxRt())
                 return false;
-            }
         }
+
         if (!Double.isNaN(confidence)) {
-            if ((confidence < filterModel.getCurrentMinConfidence()) ||
-                    (filterModel.isMaxConfidenceFilterActive() && confidence > filterModel.getCurrentMaxConfidence())) {
+            if (filterModel.isMinConfidenceFilterActive() && confidence < filterModel.getCurrentMinConfidence())
+                return false;
+            if (filterModel.isMaxConfidenceFilterActive() && confidence > filterModel.getCurrentMaxConfidence())
+                return false;
+        } else if (filterModel.isMinConfidenceFilterActive()) { // filter NaN if min filter is set
                 return false;
-            }
-        } else {
-            return Double.compare(filterModel.getMinConfidence(), filterModel.getCurrentMinConfidence()) == 0;
         }
 
-        final Set<PrecursorIonType> adducts = filterModel.getAdducts();
-        if (!adducts.isEmpty() && !adducts.contains(item.getIonization()))
+        if (filterModel.isAdductFilterActive() && !filterModel.getAdducts().contains(item.getIonization()))
             return false;
 
         return anyIOIntenseFilterMatches(item, filterModel);
@@ -166,8 +170,8 @@ private boolean matchesElementFilter(InstanceBean item, CompoundFilterModel filt
         boolean r1 = item.loadTopFormulaResult(List.of(TopCSIScore.class)).map(FormulaResult::getId)
                 .map(id ->
                         (filter.matchFormula && constraints.isSatisfied(id.getMolecularFormula(), id.getIonType().getIonization()))
-                        ||
-                        (filter.matchPrecursorFormula && constraints.isSatisfied(id.getPrecursorFormula(), id.getIonType().getIonization()))
+                                ||
+                                (filter.matchPrecursorFormula && constraints.isSatisfied(id.getPrecursorFormula(), id.getIonType().getIonization()))
                 ).orElse(false);
 
         boolean r2 = item.loadTopFormulaResult(List.of(ZodiacScore.class, SiriusScore.class)).map(FormulaResult::getId)

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/utils/CompoundFilterModel.java b/sirius_gui/src/main/java/de/unijena/bioinf/ms/gui/utils/CompoundFilterModel.java
@@ -302,6 +302,10 @@ public boolean isMaxConfidenceFilterActive() {
         return currentMaxConfidence != maxConfidence;
     }
 
+    public boolean isMinConfidenceFilterActive() {
+        return currentMinConfidence != minConfidence;
+    }
+
 
     public void setAdducts(Set<PrecursorIonType> adducts) {
         this.adducts = adducts;
@@ -310,6 +314,11 @@ public void setAdducts(Set<PrecursorIonType> adducts) {
     public Set<PrecursorIonType> getAdducts() {
         return Collections.unmodifiableSet(adducts);
     }
+    public boolean isAdductFilterActive() {
+        return adducts != null && !adducts.isEmpty();
+    }
+
+
 
     @Override
     public HiddenChangeSupport pcs() {

diff --git a/sirius_gui/src/main/java/de/unijena/bioinf/projectspace/GuiProjectSpaceManager.java b/sirius_gui/src/main/java/de/unijena/bioinf/projectspace/GuiProjectSpaceManager.java
@@ -155,7 +155,7 @@ public synchronized void importOneExperimentPerLocation(@NotNull final List<File
     //ATTENTION Synchronizing around background tasks that block gui thread is dangerous
     public synchronized void importOneExperimentPerLocation(@NotNull final InputFilesOptions input) {
         input.msInput.setAllowMS1Only(PropertyManager.getBoolean("de.unijena.bioinf.sirius.ui.allowMs1Only", true));
-        input.msInput.setIgnoreFormula(PropertyManager.getBoolean("de.unijena.bioinf.sirius.ui.ignoreFormulas", true));
+        input.msInput.setIgnoreFormula(PropertyManager.getBoolean("de.unijena.bioinf.sirius.ui.ignoreFormulas", false));
         boolean align = Jobs.runInBackgroundAndLoad(MF, "Checking for alignable input...", () ->
                         (input.msInput.msParserfiles.size() > 1 && input.msInput.projects.size() == 0 && input.msInput.msParserfiles.keySet().stream().map(p -> p.getFileName().toString().toLowerCase()).allMatch(n -> n.endsWith(".mzml") || n.endsWith(".mzxml"))))
                 .getResult();