items = property.checkComboBox.getCheckModel().getCheckedItems();
+ if (items.size() > 0 && !items.stream().anyMatch(s -> s.equals(valueOfRow))) {
+ return false;
+ }
}
- if (searchString == null || searchString.isEmpty()) {
+ String lowerCaseFilter = filterField.getText().toLowerCase();
+ if (lowerCaseFilter.isEmpty()) {
return true;
}
- String lowerCaseFilter = searchString.toLowerCase();
+ for (CategoricalProperty property : map.values()) {
+ String valueOfRow = getValueForColumnName(property.name, annotation);
+ if (valueOfRow.toLowerCase().contains(lowerCaseFilter)) {
+ return true;
+ }
+ }
+
return annotation.specimenId.toLowerCase().contains(lowerCaseFilter)
- || annotation.specimenType.toLowerCase().contains(lowerCaseFilter)
- || annotation.genotypicDSTPattern.toLowerCase().contains(lowerCaseFilter)
- || annotation.phenotypicDSTPattern.toLowerCase().contains(lowerCaseFilter);
+ || annotation.specimenType.toLowerCase().contains(lowerCaseFilter);
});
}
/**
- * @return true when ComboBox has NOT selected checkAgainst.
+ * This is a list of column names that are known to be categorical.
+ *
+ *
+ * In an ideal situation the Metadata class would also support this and
+ * the reader would be able to read any sheet.
+ *
+ */
+ private static final String[] knownCategoricalColumns = {
+ "genotypicDST",
+ "phenotypicDST",
+ "Lineage",
+ "hivStatus",
+ "cohort",
+ "studyGeographicDistrict",
+ "specimenType",
+ "microscopySmearStatus",
+ "dnaIsolation",
+ "capreomycin",
+ "ethambutol",
+ "ethionamide",
+ "isoniazid",
+ "kanamycin",
+ "pyrazinamide",
+ "ofloxacin",
+ "rifampin",
+ "streptomycin",
+ "digitalSpoligotype",
+ "sex",
+ };
+
+ /**
+ * This method take the correct field from the metaData class for a given name.
+ *
+ *
+ * See {@link #knownCategoricalColumns}, when the metadata+its reader would understand
+ * dynamic columns, this method would be unnecessary.
+ *
+ * @param columnName the name of the column.
+ * @param metaData the metaData instanec you'd like the value of.
+ * @return the value corresponding to the column.
*/
- private boolean isNotSelected(ComboBox comboBox, String checkAgainst) {
- String selectedItem = comboBox.getSelectionModel().getSelectedItem();
- return selectedItem != null && !checkAgainst.equals(selectedItem);
+ @SuppressWarnings("checkstyle:MethodLength")
+ private static String getValueForColumnName(String columnName, MetaData metaData) {
+ switch (columnName) {
+ case "genotypicDST":
+ return metaData.genotypicDSTPattern;
+ case "phenotypicDST":
+ return metaData.phenotypicDSTPattern;
+ case "Lineage":
+ return metaData.lineage;
+ case "hivStatus":
+ return metaData.hivStatus.name();
+ case "cohort":
+ return metaData.cohort;
+ case "studyGeographicDistrict":
+ return metaData.studyGeographicDistrict;
+ case "specimenType":
+ return metaData.specimenType;
+ case "microscopySmearStatus":
+ return metaData.microscopySmearStatus.name();
+ case "dnaIsolation":
+ return metaData.dnaIsolation.name();
+ case "capreomycin":
+ return metaData.capreomycin;
+ case "ethambutol":
+ return metaData.ethambutol;
+ case "ethionamide":
+ return metaData.ethionamide;
+ case "isoniazid":
+ return metaData.isoniazid;
+ case "kanamycin":
+ return metaData.kanamycin;
+ case "pyrazinamide":
+ return metaData.pyrazinamide;
+ case "ofloxacin":
+ return metaData.ofloxacin;
+ case "rifampin":
+ return metaData.rifampin;
+ case "streptomycin":
+ return metaData.streptomycin;
+ case "digitalSpoligotype":
+ return metaData.digitalSpoligotype;
+ case "sex":
+ return metaData.sex.name();
+ default:
+ throw new RuntimeException("Undefined column in temp method");
+ }
}
private void initializeGoTo() {
@@ -221,42 +348,64 @@ private void initializeGoTo() {
});
}
+ /**
+ * initializes the categorical comboboxes.
+ */
@SuppressWarnings("checkstyle:MethodLength")
private void initializeExtendedSearchPane() {
masterData.addListener((ListChangeListener) c -> {
- Stream.of(setGenotypicDSTpattern, setPhenotypicDSTPattern).forEach(Set::clear);
- c.getList().forEach(annotation -> {
- setGenotypicDSTpattern.add(annotation.genotypicDSTPattern);
- setPhenotypicDSTPattern.add(annotation.phenotypicDSTPattern);
+
+ categoricalGridPane.getChildren().clear();
+
+ map.clear();
+ masterData.forEach(metaData -> {
+ Arrays.stream(knownCategoricalColumns).forEach(columnName -> {
+ final CategoricalProperty property;
+ if (map.containsKey(columnName)) {
+ property = map.get(columnName);
+ } else {
+ property = new CategoricalProperty(columnName);
+ property.checkComboBox.getCheckModel().getCheckedItems()
+ .addListener((ListChangeListener) change -> updateTable());
+ map.put(property.name, property);
+ }
+ property.addValue(getValueForColumnName(columnName, metaData));
+ });
});
- });
- // add set listeners
- setGenotypicDSTpattern.addListener(setChangeListener(genotypicDSTPatternComboBox));
- setPhenotypicDSTPattern.addListener(setChangeListener(phenotypicDSTPatternComboBox));
- // add comboBox listeners
- genotypicDSTPatternComboBox.valueProperty().addListener((observable, oldValue, newValue) -> {
- updateTable();
- });
- phenotypicDSTPatternComboBox.valueProperty().addListener((observable, oldValue, newValue) -> {
- updateTable();
- });
+ int rowIndex = 1;
+ for (CategoricalProperty property : map.values()) {
- // set button actions
- genotypicDSTPatternButton.setOnAction(getButtonAction(genotypicDSTPatternComboBox));
- phenotypicDSTPatternButton.setOnAction(getButtonAction(phenotypicDSTPatternComboBox));
- }
+ Label label = new Label(property.name);
+ Button button = new Button("clear");
- private SetChangeListener setChangeListener(ComboBox comboBox) {
- return change -> comboBox.setItems(FXCollections.observableArrayList(change.getSet()));
- }
+ button.setOnAction(actionEvent -> {
+ property.checkComboBox.getCheckModel().clearChecks();
+ });
+
+ GridPane.setColumnIndex(label, 1);
+ GridPane.setColumnIndex(property.checkComboBox, 2);
+ GridPane.setColumnIndex(button, 3);
+
+ GridPane.setRowIndex(label, rowIndex);
+ GridPane.setRowIndex(property.checkComboBox, rowIndex);
+ GridPane.setRowIndex(button, rowIndex);
+ rowIndex++;
- private EventHandler getButtonAction(ComboBox genotypicDSTPatternComboBox) {
- return event -> genotypicDSTPatternComboBox.getSelectionModel().clearSelection();
+ categoricalGridPane.getChildren().add(label);
+ categoricalGridPane.getChildren().add(property.checkComboBox);
+ categoricalGridPane.getChildren().add(button);
+ }
+
+ });
}
- public void setData(Collection metaDatas) {
+ /**
+ * Sets the data for this controller. When not called, no genomes are shown.
+ * @param metaData the metadata object.
+ */
+ public void setData(Collection metaData) {
masterData.clear();
- masterData.addAll(metaDatas);
+ masterData.addAll(metaData);
}
}
diff --git a/PL2/PL2-gui/src/main/resources/pages/SearchPane.fxml b/PL2/PL2-gui/src/main/resources/pages/SearchPane.fxml
index 9aae4fa2..97625869 100644
--- a/PL2/PL2-gui/src/main/resources/pages/SearchPane.fxml
+++ b/PL2/PL2-gui/src/main/resources/pages/SearchPane.fxml
@@ -1,7 +1,5 @@
-
-
@@ -12,14 +10,14 @@
+
+
-
+
-
-
@@ -31,17 +29,15 @@
+
-
-
-
-
-
-
+
+
+