List of usage examples for org.apache.commons.collections15.set ListOrderedSet ListOrderedSet
public ListOrderedSet()
ListOrderedSet using a HashSet and an ArrayList internally. From source file:org.isatools.isacreator.api.utils.SpreadsheetUtils.java
public static Set<String> getDataInColumn(Spreadsheet targetSheet, int tableViewIndex) { int rowCount = targetSheet.getTable().getRowCount(); Set<String> columnContents = new ListOrderedSet<String>(); if (tableViewIndex < targetSheet.getTable().getColumnCount()) { for (int rowNo = 0; rowNo < rowCount; rowNo++) { columnContents.add(targetSheet.getTable().getValueAt(rowNo, tableViewIndex).toString()); }/*from w ww . j av a2 s .co m*/ } return columnContents; }
From source file:org.isatools.isacreator.common.filterableTree.TreeFilterModel.java
/** * Add an element to the Map of items, and then refilter the list in case the new item is being shown when it * shouldn't be./*w w w .j ava2 s .c om*/ * * @param key - where the item should be added * @param item - the item to be added */ public void addElement(T key, V item) { if (!items.containsKey(key)) { items.put(key, new ListOrderedSet<V>()); } items.get(key).add(item); refilter(); }
From source file:org.isatools.isacreator.common.filterableTree.TreeFilterModel.java
/** * Refilter method clears the previously filtered items and then using the value typed into * the FilterField JTextField, items which contain the value typed into the field are added to * the filterItems list of terms./*from w w w .java2 s. com*/ */ public void refilter() { filterItems.clear(); String term = targetJTree.getFilterField().getText().toLowerCase(); for (T key : items.keySet()) { for (V value : items.get(key)) { if (value.toString().toLowerCase().contains(term)) { if (!filterItems.containsKey(key)) { filterItems.put(key, new ListOrderedSet<V>()); } filterItems.get(key).add(value); } } targetJTree.clearSelection(); } rebuildTree(); }
From source file:org.isatools.isacreator.model.ISASection.java
public void addToReferenceObject(OrderedMap<InvestigationFileSection, Set<String>> sectionFields) { for (InvestigationFileSection section : sectionFields.keySet()) { if (!referenceObject.getSectionDefinition().containsKey(section)) { referenceObject.getSectionDefinition().put(section, new ListOrderedSet<String>()); }/*w w w. j a va 2 s . c om*/ referenceObject.getSectionDefinition().get(section).addAll(sectionFields.get(section)); } }
From source file:org.isatools.isacreator.spreadsheet.SpreadsheetFunctions.java
public Set<String> getValuesInSelectedRowsForColumn(String columnName) { int[] selectedRows = spreadsheet.getTable().getSelectedRows(); Set<String> values = new ListOrderedSet<String>(); for (int columnIndex = 0; columnIndex < spreadsheet.getColumnCount(); columnIndex++) { String colName = spreadsheet.spreadsheetModel.getColumnName(columnIndex); if (colName.equals(columnName)) { // add all values for this column. for (int row : selectedRows) { values.add(spreadsheet.spreadsheetModel.getValueAt(row, columnIndex).toString()); }/*from www. j av a 2 s .com*/ break; } } return values; }
From source file:org.isatools.isacreator.wizard.CreationAlgorithm.java
protected void runAlgorithm() { // Retrieve a list of string values dictating where elements are supposed to occur in a table. System.out.println("Running algorithm"); tableStructure = buildingModel.getTableStructure(); headers = new ArrayList<String>(); colsToUse = new ListOrderedSet<Integer>(); int count = tableStructure.size() + 1; for (int i = 0; i < tableStructure.size(); i++) { // modify this to only add those factors which appear in temp factors. if (tableStructure.get(i)[0].toLowerCase().equals("factors")) { for (PropertyType factor : factorsToAdd) { String newFactor = "Factor Value[" + factor.getPropertyName().trim() + "]"; addFactor(count, newFactor, factor, i); }// ww w . j ava2s . c om } else if (tableStructure.get(i)[0].toLowerCase().contains("factor value[")) { // doing nothing with this factor } else if (tableStructure.get(i)[0].toLowerCase().contains("characteristics[")) { String newChar = tableStructure.get(i)[0]; headers.add(newChar); colsToUse.add(i); } else { headers.add(tableStructure.get(i)[0]); colsToUse.add(i); } } performAssayCentricTask(); }
From source file:org.isatools.isacreator.wizard.StudySampleCreationAlgorithm.java
public void runAlgorithm() { // need to create table reference object for study sample file first. tableStructure = buildingModel.getTableStructure(); headers = new ArrayList<String>(); FieldObject newFo;//w ww . ja v a 2 s . c o m int count = tableStructure.size() + 1; rowFormat = ""; for (int columnIndex = 0; columnIndex < tableStructure.size(); columnIndex++) { String fieldName = tableStructure.get(columnIndex)[0]; if (fieldName != null) { if (colsToUse == null) { colsToUse = new ListOrderedSet<Integer>(); } if (fieldName.toLowerCase().equals("characteristics")) { // SHOULD CHECK IF ONE is available newFo = buildingModel.getFieldByName("Characteristics[Organism]"); headers.add("Characteristics[Organism]"); if (newFo == null) { newFo = new FieldObject(count, "Characteristics[Organism]", "The organism being studied", DataTypes.ONTOLOGY_TERM, "", false, false, false); buildingModel.addField(newFo); } count++; rowFormat += (organism + "\t"); newFo = buildingModel.getFieldByName("Characteristics[Organism Part]"); headers.add("Characteristics[Organism Part]"); if (newFo == null) { newFo = new FieldObject(count, "Characteristics[Organism Part]", "Part of the organism being studied", DataTypes.ONTOLOGY_TERM, "", false, false, false); buildingModel.addField(newFo); } count++; rowFormat += "[ORGANISM_PART]\t"; } else if (fieldName.toLowerCase().contains("characteristics[")) { // then a check needs to be done to ensure the characteristic isn't added if it is already there! String value = fieldName.toLowerCase(); if (!value.contains("organism") && !value.contains("organism part")) { headers.add(fieldName); colsToUse.add(columnIndex); rowFormat += " \t"; } } else if (fieldName.toLowerCase().equals("factors")) { for (PropertyType tf : factorsToAdd) { headers.add("Factor Value[" + tf.getPropertyName().trim() + "]"); boolean unitAdded = false; for (PropertyValue tup : tf.getValuesAndUnits()) { if (!tup.getUnit().trim().equals("")) { headers.add("Unit"); unitAdded = true; break; } } if (unitAdded) { // add factor column field first newFo = new FieldObject(count, "Factor Value[" + tf.getPropertyName().trim() + "]", "Factor", DataTypes.STRING, "", false, false, false); buildingModel.addField(newFo); count++; newFo = new FieldObject(count, "Unit", "Unit to give meaning to its associated value", DataTypes.ONTOLOGY_TERM, "", false, false, false); buildingModel.addField(newFo); count++; } else { newFo = new FieldObject(count, "Factor Value[" + tf.getPropertyName().trim() + "]", "Factor", DataTypes.ONTOLOGY_TERM, "", false, false, false); buildingModel.addField(newFo); count++; } } rowFormat += "[FACTORS]"; } else if (fieldName.toLowerCase().contains("factor value[")) { if (!checkForFactorExistence(fieldName)) { headers.add(fieldName); colsToUse.add(columnIndex); rowFormat += " \t"; } } else if (fieldName.equals(GeneralFieldTypes.PROTOCOL_REF.name)) { // we have a protocol. Do two things: set value to its default value and add it to the study protocols headers.add(fieldName); colsToUse.add(columnIndex); rowFormat += buildingModel.getDefaultValue(columnIndex + 1) + "\t"; } else { headers.add(fieldName); if (fieldName.equalsIgnoreCase("source name")) { rowFormat += (SOURCE_NAME_PLACE_HOLDER + "\t"); } else if (fieldName.equalsIgnoreCase("sample name")) { rowFormat += SAMPLE_NAMES_PLACE_HOLDER + "\t"; } else { rowFormat += " \t"; } } } } Vector<String> headersForReferenceObject = new Vector<String>(); String[] headersAsArray = new String[headers.size()]; headersForReferenceObject.add(TableReferenceObject.ROW_NO_TEXT); for (int i = 0; i < headers.size(); i++) { headersForReferenceObject.add(headers.get(i)); headersAsArray[i] = headers.get(i); } buildingModel.setPreDefinedHeaders(headersForReferenceObject); addRowsToModel(headersAsArray); TableReferenceObjectWrapper troAdapter = new TableReferenceObjectWrapper(buildingModel); troAdapter.setConstructProtocolsWithDefaultValues(true); List<Protocol> protocols = troAdapter.findProtocols(); study.getProtocols().addAll(protocols); studySample.setTableReferenceObject(buildingModel); }