review #1

omokshyna · Aug 29, 2023 · b90d879 · b90d879
1 parent d556a9e
commit b90d879
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Showing 6 changed files with 20 additions and 107 deletions.
diff --git a/src/main/java/io/github/mzmine/datamodel/features/ModularFeatureList.java b/src/main/java/io/github/mzmine/datamodel/features/ModularFeatureList.java
@@ -40,7 +40,6 @@
 import io.github.mzmine.datamodel.features.types.modifiers.GraphicalColumType;
 import io.github.mzmine.datamodel.features.types.numbers.IDType;
 import io.github.mzmine.datamodel.features.types.tasks.NodeGenerationThread;
-import io.github.mzmine.datamodel.features.types.tasks.NodeRequest;
 import io.github.mzmine.main.MZmineCore;
 import io.github.mzmine.modules.io.projectload.CachedIMSFrame;
 import io.github.mzmine.modules.io.projectload.CachedIMSRawDataFile;
@@ -65,7 +64,6 @@
 import java.util.Objects;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
-import java.util.concurrent.locks.ReentrantLock;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
@@ -76,7 +74,6 @@
 import javafx.collections.ObservableMap;
 import javafx.scene.Node;
 import javafx.scene.control.Label;
-import javafx.scene.layout.Pane;
 import javafx.scene.layout.StackPane;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -122,6 +119,15 @@ public class ModularFeatureList implements FeatureList {
   // grouping
   private List<RowGroup> groups;
 
+  /**
+   * Used to buffer charts of rows and features to display in the
+   * {@link io.github.mzmine.modules.visualization.featurelisttable_modular.FeatureTableFX}. The key
+   * is of the following format: "<row id>-<DataType.getUniqueID()>-<raw file name or empty
+   * string>:
+   * <p>
+   * final String key = "%d-%s-%s".formatted(row.getID(), type.getUniqueID(), (file != null ?
+   * file.getName() : ""));
+   */
   private final Map<String, Node> bufferedCharts = new HashMap<>();
 
   public ModularFeatureList(String name, @Nullable MemoryMapStorage storage,
@@ -881,9 +887,9 @@ public <S, T extends DataType<S>> Node getChartForRow(FeatureListRow row, T type
     }
 
     final StackPane parentPane = new StackPane(new Label("Preparing content..."));
-    parentPane.setPrefHeight(((GraphicalColumType)type).getCellHeight());
-    parentPane.setMinHeight(((GraphicalColumType)type).getCellHeight());
-    parentPane.setMaxHeight(((GraphicalColumType)type).getCellHeight());
+    parentPane.setPrefHeight(((GraphicalColumType) type).getCellHeight());
+    parentPane.setMinHeight(((GraphicalColumType) type).getCellHeight());
+    parentPane.setMaxHeight(((GraphicalColumType) type).getCellHeight());
     bufferedCharts.putIfAbsent(key, parentPane);
 
     ensureNodeThreadRunnning();

diff --git a/...thub/mzmine/datamodel/features/types/FeatureShapeIonMobilityRetentionTimeHeatMapType.java b/...thub/mzmine/datamodel/features/types/FeatureShapeIonMobilityRetentionTimeHeatMapType.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2004-2023 The MZmine Development Team
+ * Copyright (c) 2004-2022 The MZmine Development Team
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -75,12 +75,6 @@ public String getHeaderString() {
       return null;
     }
 
-    /*StackPane node = (StackPane) row.getBufferedColChart(getHeaderString());
-    if (node == null) {
-      logger.info("Cannot create mobilogram chart, no buffered chart available for row.");
-      return null;
-    }*/
-
     if (!(feature.getFeatureData() instanceof IonMobilogramTimeSeries)) {
       Label label = new Label("Processed with\nLC-MS workflow");
       label.setTextAlignment(TextAlignment.CENTER);

diff --git a/src/main/java/io/github/mzmine/datamodel/features/types/FeatureShapeType.java b/src/main/java/io/github/mzmine/datamodel/features/types/FeatureShapeType.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2004-2023 The MZmine Development Team
+ * Copyright (c) 2004-2022 The MZmine Development Team
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -68,11 +68,6 @@ public String getHeaderString() {
     if (row == null || cellData == null || !cellData) {
       return null;
     }
-    /*StackPane node = (StackPane) row.getBufferedColChart(getHeaderString());
-    if (node == null) {
-      logger.info("Cannot create shape chart, no buffered chart available for row.");
-      return null;
-    }*/
 
     var chart = new FeatureShapeChart(row, progress);
     return chart;

diff --git a/src/main/java/io/github/mzmine/datamodel/features/types/ImageType.java b/src/main/java/io/github/mzmine/datamodel/features/types/ImageType.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2004-2023 The MZmine Development Team
+ * Copyright (c) 2004-2022 The MZmine Development Team
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -70,12 +70,6 @@ public String getHeaderString() {
       return null;
     }
 
-//    StackPane node = (StackPane) row.getBufferedColChart(getHeaderString());
-//    if (node == null) {
-//      logger.info("Cannot create mobilogram chart, no buffered chart available for row.");
-//      return null;
-//    }
-
     var chart = new ImageChart(feature, progress);
     return chart;
   }

diff --git a/src/main/java/io/github/mzmine/datamodel/features/types/tasks/NodeGenerationThread.java b/src/main/java/io/github/mzmine/datamodel/features/types/tasks/NodeGenerationThread.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2004-2023 The MZmine Development Team
+ * Copyright (c) 2004-2022 The MZmine Development Team
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -76,8 +76,6 @@ public double getFinishedPercentage() {
   public void run() {
     setStatus(TaskStatus.PROCESSING);
 
-    // generateAllCharts();
-
     // if there was no chart request for this time, stop the thread
     final PauseTransition waitTimer = new PauseTransition(new Duration(500));
     waitTimer.setOnFinished(e -> setStatus(TaskStatus.CANCELED));
@@ -89,7 +87,9 @@ public void run() {
         try {
           TimeUnit.MILLISECONDS.sleep(10);
         } catch (InterruptedException e) {
-          throw new RuntimeException(e);
+          logger.log(Level.WARNING, e.getMessage(), e);
+          setStatus(TaskStatus.CANCELED);
+          return;
         }
         continue;
       }
@@ -135,76 +135,6 @@ public void run() {
     setStatus(TaskStatus.FINISHED);
   }
 
-/*  private boolean generateAllCharts() {
-    final List<LinkedGraphicalType> rowTypes = flist.getRowTypes().values().stream()
-        .filter(type -> type instanceof LinkedGraphicalType).map(t -> (LinkedGraphicalType) t)
-        .toList();
-    final List<LinkedGraphicalType> featureTypes = flist.getFeatureTypes().values().stream()
-        .filter(type -> type instanceof LinkedGraphicalType).map(t -> (LinkedGraphicalType) t)
-        .toList();
-
-    for (FeatureListRow row : flist.getRows()) {
-      for (LinkedGraphicalType rowType : rowTypes) {
-        final String header = rowType.getHeaderString();
-        Node base = ((ModularFeatureListRow) row).getBufferedColChart(header);
-        if (base == null) {
-          base = new StackPane(new Label("Preparing content..."));
-          ((ModularFeatureListRow) row).addBufferedColChart(header, base);
-        }
-        try {
-          var chart = rowType.createCellContent((ModularFeatureListRow) row, row.get(rowType), null,
-              new AtomicDouble());
-          nodeChartMap.put(base, chart);
-        } catch (Exception ex) {
-          logger.log(Level.WARNING, "Cannot create chart " + ex.getMessage(), ex);
-          nodeChartMap.put(base, new Label("Failed to create chart"));
-        }
-      }
-
-      for (LinkedGraphicalType featureType : featureTypes) {
-        for (ModularFeature feature : row.getFeatures()) {
-          if (feature != null && feature.getFeatureStatus() != FeatureStatus.UNKNOWN) {
-            final String header = featureType.getHeaderString();
-            Node base = ((ModularFeature) feature).getBufferedColChart(header);
-            if (base == null) {
-              base = new StackPane(new Label("Preparing content..."));
-              ((ModularFeature) feature).addBufferedColChart(header, base);
-            }
-            try {
-              var chart = featureType.createCellContent((ModularFeatureListRow) row,
-                  row.get(featureType), feature.getRawDataFile(), new AtomicDouble());
-              nodeChartMap.put(base, chart);
-            } catch (Exception ex) {
-              logger.log(Level.WARNING, "Cannot create chart " + ex.getMessage(), ex);
-              nodeChartMap.put(base, new Label("Failed to create chart"));
-            }
-          }
-        }
-      }
-      if (isCanceled()) {
-        return true;
-      }
-      rows++;
-    }
-
-    Platform.runLater(() -> {
-      logger.info("Updating all charts.");
-      nodeChartMap.forEach((node, chart) -> {
-        if (chart == null) {
-          return;
-        }
-        try {
-          ((StackPane) node).getChildren().clear();
-          ((StackPane) node).getChildren().add(chart);
-        } catch (ClassCastException e) {
-          logger.log(Level.INFO, e.getMessage(), e);
-        }
-      });
-      logger.info("All charts updated.");
-    });
-    return false;
-  }*/
-
   public <T> void requestNode(@NotNull ModularFeatureListRow row, DataType<T> type, T value,
       RawDataFile raw, Pane parentNode) {
     nodeRequestQueue.add(new NodeRequest<>(row, type, value, raw, parentNode));

diff --git a/...java/io/github/mzmine/modules/visualization/featurelisttable_modular/FeatureTableTab.java b/...java/io/github/mzmine/modules/visualization/featurelisttable_modular/FeatureTableTab.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2004-2023 The MZmine Development Team
+ * Copyright (c) 2004-2022 The MZmine Development Team
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -27,12 +27,9 @@
 
 import io.github.mzmine.datamodel.RawDataFile;
 import io.github.mzmine.datamodel.features.FeatureList;
-import io.github.mzmine.datamodel.features.types.tasks.NodeGenerationThread;
 import io.github.mzmine.gui.mainwindow.MZmineTab;
-import io.github.mzmine.main.MZmineCore;
 import io.github.mzmine.util.javafx.FxIconUtil;
 import java.io.IOException;
-import java.time.Instant;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.logging.Level;
@@ -76,9 +73,6 @@ public FeatureTableTab(FeatureList flist) {
     controller = loader.getController();
 
     controller.setFeatureList(flist);
-    //final NodeGenerationThread nodeGenerationThread = new NodeGenerationThread(null, Instant.now(),
-    //    flist);
-    //MZmineCore.getTaskController().addTask(nodeGenerationThread);
 
     // TODO: if there would be only selectColumnsButton in the toolbar, then remove toolbar and
     //  improve "+" button behaviour of the feature table header