Changeset 5521

Timestamp:

06/23/08 17:04:21 (5 months ago)

Author:

will

Message:

ITreeManager is interface between Model and Tree.
NodeManagerMethods? is the new location of static node-manipulation methods.

Location:

branches/OmeroEditor/src

Files:

• main/ProtocolEditor.java (modified) (2 diffs)
• ols/ObservationCreator.java (deleted)
• tree/ITreeManager.java (added)
• tree/NodeManagerMethods.java (added)
• tree/Tree.java (modified) (28 diffs)
• tree/edit/EditAddField.java (modified) (2 diffs)
• tree/edit/EditDeleteField.java (modified) (2 diffs)
• tree/edit/EditDemoteFields.java (modified) (2 diffs)
• tree/edit/EditDuplicateFields.java (modified) (2 diffs)
• tree/edit/EditImportFields.java (modified) (2 diffs)
• tree/edit/EditMoveFieldsDown.java (modified) (2 diffs)
• tree/edit/EditMoveFieldsUp.java (modified) (2 diffs)
• tree/edit/EditPasteFields.java (modified) (2 diffs)
• tree/edit/EditPromoteFields.java (modified) (3 diffs)
• ui/XMLView.java (modified) (1 diff)
• xmlMVC/XMLModel.java (modified) (11 diffs)

branches/OmeroEditor/src/main/ProtocolEditor.java

@@ -30 +30 @@
 
 import ols.Observation;
-import ols.ObservationCreator;
 
 import ui.XMLView;
@@ -125 +124 @@
         }
         
-        /**
-         * Returns a list of <code>Observation</code> objects 
-         * These are fields that the user chooses, to correspond to observations they intend to make from their results.
-         * An external application, such as Phenote, will use these to create a results table, for collection of data.
-         * 
-         * @return      a list of Observation objects
-         */
-        public List<Observation> getObservations() {
-                return ObservationCreator.getObservations(model);
-        }
+        
 }

branches/OmeroEditor/src/tree/Tree.java

@@ -74 +74 @@
 
 public class Tree 
-        implements ITreeModel {
+        implements  
+        ITreeManager {
         
         // this enum specifies a constructor that takes a String name, returned by toString();
@@ -320 +321 @@
                 
                 // if fields are highlighted, lock them.
-                if (highlightedFields.size() > 0) {
-                        UndoableEdit edit = new EditLockFields(highlightedFields, lockingAttributes);
+                if (getHighlightedFields().size() > 0) {
+                        UndoableEdit edit = new EditLockFields(getHighlightedFields(),
+                                        lockingAttributes);
                         undoSupport.postEdit(edit);
                         setTreeEdited(true);
-                        
-                // or if the root node is highlighted, lock it.
-                } else if (rootNode.isHighlighted()) {
-                        UndoableEdit edit = new EditLockFields(rootNode, lockingAttributes);
-                        undoSupport.postEdit(edit);
-                        setTreeEdited(true);
                 }
                 
@@ -338 +334 @@
         private void setRequiredFields() {
                 // if fields are highlighted, set required for them.
-                if (highlightedFields.size() > 0) {
-                        UndoableEdit edit = new EditRequiredField(highlightedFields);
-                        undoSupport.postEdit(edit);
-                        setTreeEdited(true);
-                        
-                        // or if the root node is highlighted, make required!
-                } else if (rootNode.isHighlighted()) {
-                        UndoableEdit edit = new EditRequiredField(rootNode);
+                
+                if (getHighlightedFields().size() > 0) {
+                        UndoableEdit edit = new EditRequiredField(getHighlightedFields());
                         undoSupport.postEdit(edit);
                         setTreeEdited(true);
@@ -373 +364 @@
         }
 
+        /**
+         * For all highlighted fields that are Number Fields, the numerical value
+         * they contain is multiplied by the factor argument. 
+         * Fields of other types are ignored. 
+         * 
+         * @param factor        The value to multiply numerical field values by. 
+         */
         public void multiplyValueOfSelectedFields(float factor) {
                 
@@ -458 +456 @@
         }
 
-        // duplicates all branches below oldNode, adding them to newNode
-        private static void duplicateDataFieldTree(DataFieldNode oldNode, DataFieldNode newNode) {
-                
-                ArrayList<DataFieldNode> children = oldNode.getChildren();
-                if (children.size() == 0) return;
-                        
-                        for (DataFieldNode copyThisChild: children){
-                         
-                                DataFieldNode newChild = new DataFieldNode(copyThisChild);
-                                
-                                newNode.addChild(newChild);
-                                
-                                duplicateDataFieldTree(copyThisChild, newChild);
-                        }
-        }
-        
         // add a blank dataField
         private void addDataField() {
@@ -481 +463 @@
                 
                 DataFieldNode newNode = new DataFieldNode(this);// make a new default-type field
-                addDataField(newNode);  // adds after last highlighted field, or last child of root
-                
-                UndoableEdit edit = new EditAddField(newNode);
-                undoSupport.postEdit(edit);
-        }
-
-        /**
-         *  add the newNode as a child of parentNode at the specified index
-         */
-        public static void addDataField(DataFieldNode newNode, DataFieldNode parentNode, int indexToInsert) {
-                newNode.setParent(parentNode);
-                parentNode.addChild(indexToInsert, newNode);
-        }
-        
-        /* add a blank dataField, by name
-         * This is used for adding new OME-XML fields, therefore "inputType"=custom
-         */
-        public void addDataField(String fieldName) {
-                // add the undo action (include rootNode reference, in case no highlighted fields)
-                // undoActions.push(new TreeAction(Actions.ADD_NEW_FIELD, highlightedFields, rootNode));
-                setTreeEdited(true);
-                
-                DataFieldNode newNode = new DataFieldNode(this);// make a new default-type field
-                newNode.getDataField().setAttribute(DataFieldConstants.ELEMENT_NAME, fieldName, false);
-                newNode.getDataField().setAttribute(DataFieldConstants.INPUT_TYPE, DataFieldConstants.CUSTOM, false);
-                addDataField(newNode);  // adds after last highlighted field, or last child of root
-                
-                UndoableEdit edit = new EditAddField(newNode);
-                undoSupport.postEdit(edit);
-        }
-        
-        /*
-         * Add a dataField of a defined inputType
-         */
-        public void addDataFieldByType(String inputType) {
-                setTreeEdited(true);
-                
-                DataFieldNode newNode = new DataFieldNode(this);// make a new default-type field
-                newNode.getDataField().setAttribute(DataFieldConstants.INPUT_TYPE, inputType, false);
                 addDataField(newNode);  // adds after last highlighted field, or last child of root
                 
@@ -543 +486 @@
                 }
                 
-                addDataField(newNode, parentNode, indexToInsert);
+                NodeManagerMethods.addDataField(newNode, parentNode, indexToInsert);
                 
                 nodeSelected(newNode, true); // select the new node
         }
 
+        /**
+         * Used to take a list of Nodes, eg from clip-board, or another tree,
+         * to duplicate them, then insert them after the last highlighted
+         * field (or after last child of root if none highlighted)
+         * 
+         * @param dataFieldNodes
+         */
         public void copyAndInsertDataFields(ArrayList<DataFieldNode> dataFieldNodes) {
                 copyAndInsertDataFields(dataFieldNodes, highlightedFields);
@@ -557 +507 @@
         }
         
-        public void copyAndInsertDataFields(ArrayList<DataFieldNode> dataFieldNodes, ArrayList<DataFieldNode> selectedFields) {
+        /**
+         * Duplicates the dataFieldNodes, and inserts them as siblings to 
+         * selectedFields (after the last selected field)
+         * 
+         * @param dataFieldNodes        The nodes to duplicate
+         * @param selectedFields        Add as siblings to these nodes, after last one.
+         */
+        private void copyAndInsertDataFields(ArrayList<DataFieldNode> dataFieldNodes, 
+                        ArrayList<DataFieldNode> selectedFields) {
                 
                 int indexToInsert = 0;
@@ -570 +528 @@
                         indexToInsert = lastHighlightedField.getMyIndexWithinSiblings() + 1;
                 }
-                copyAndInsertDataFields(dataFieldNodes, parentNode, indexToInsert);
-                
-        }
-        
-        // copy and add new dataFields
-        // used by import, paste, and duplicate functions
-        public static void copyAndInsertDataFields(ArrayList<DataFieldNode> dataFieldNodes,DataFieldNode parentNode, int indexToInsert) {
-                
-                if (dataFieldNodes.isEmpty()) return;
-                
-                
-                //remember the first node added, so all new nodes can be selected when done
-                DataFieldNode firstNewNode = null;
-                DataFieldNode newNode = null;
-                
-                for (int i=0; i< dataFieldNodes.size(); i++){
-                        
-                        newNode = new DataFieldNode(dataFieldNodes.get(i));
-                        duplicateDataFieldTree(dataFieldNodes.get(i), newNode);
-                        
-                        addDataField(newNode, parentNode, indexToInsert);       
-                        indexToInsert++;
-                        
-                        if (i == 0) firstNewNode = newNode;
-                }
-                
-                newNode.nodeClicked(true);
-                firstNewNode.nodeClicked(false);   // will select the range 
-        }
-        
-        // don't copy DataFields, just insert the same ones
-        public static void insertTheseDataFields(ArrayList<DataFieldNode> dataFieldNodes,DataFieldNode parentNode, int indexToInsert) {
-                
-                if (dataFieldNodes.isEmpty()) return;
-                
-                //remember the first node added, so all new nodes can be selected when done
-                DataFieldNode firstNewNode = null;
-                DataFieldNode newNode = null;
-                
-                for (int i=0; i< dataFieldNodes.size(); i++){
-                        
-                        newNode = dataFieldNodes.get(i);
-                        
-                        addDataField(newNode, parentNode, indexToInsert);       
-                        indexToInsert++;
-                        
-                        if (i == 0) firstNewNode = newNode;
-                }
-                
-                newNode.nodeClicked(true);
-                firstNewNode.nodeClicked(false);   // will select the range 
+                NodeManagerMethods.copyAndInsertDataFields(dataFieldNodes, parentNode, indexToInsert);
+                
         }
         
@@ -627 +536 @@
                 
                 try {
-                        demoteDataFields(highlightedFields);
+                        NodeManagerMethods.demoteDataFields(highlightedFields);
                         
                         // add the undo action 
@@ -639 +548 @@
         }
         
-        public static void demoteDataFields(ArrayList<DataFieldNode> fields) {
-                
-                if (fields.isEmpty()) return;
-                
-                // fields need to become children of their preceding sibling (if they have one)
-                DataFieldNode firstNode = fields.get(0);
-                int indexOfFirstSibling = firstNode.getMyIndexWithinSiblings();
-                
-                // if no preceding sibling, can't demote
-                if (indexOfFirstSibling == 0) {
-                        throw (new NullPointerException("Can't demote because no preceding sibling"));
-                }
-                
-                DataFieldNode parentNode = firstNode.getParentNode();
-                DataFieldNode preceedingSiblingNode = parentNode.getChild(indexOfFirstSibling-1);
-                
-                // move nodes
-                for (DataFieldNode highlightedField: fields) {
-                        preceedingSiblingNode.addChild(highlightedField);
-                }
-//               delete them from the end (reverse order)
-                for (int i=fields.size()-1; i>=0; i--) {
-                        parentNode.removeChild(fields.get(i));
-                }
-        }
-        
-        
         private void promoteDataFields() {
                 if (highlightedFields.isEmpty()) return;
@@ -673 +555 @@
                         UndoableEdit edit = new EditPromoteFields(highlightedFields);
                         
-                        promoteDataFields(highlightedFields);
+                        NodeManagerMethods.promoteDataFields(highlightedFields);
                         
                         // if promoting went OK, add the undo action 
@@ -685 +567 @@
         }
         
-        public static void promoteDataFields(ArrayList<DataFieldNode> fields) {
-                
-                if (fields.isEmpty()) return;
-                
-                DataFieldNode node = fields.get(0);
-                DataFieldNode parentNode = node.getParentNode();
-                DataFieldNode grandParentNode = parentNode.getParentNode();
-                // if parent is root (grandparent null) then can't promote
-                if (grandParentNode == null) {
-                        throw (new NullPointerException("Can't promote because grandparent is null"));
-                }
-                
-                // any fields that are children of the last to be promoted, 
-                // must first become children of that node. 
-                DataFieldNode lastNode = fields.get(fields.size()-1);
-                DataFieldNode lastNodeParent = lastNode.getParentNode();
-                
-                int indexOfLast = lastNodeParent.indexOfChild(lastNode);
-                int numChildren = lastNodeParent.getChildren().size();
-                
-                // copy children in correct order
-                for (int i=indexOfLast+1; i< numChildren; i++) {
-                        DataFieldNode nodeToCopy = lastNodeParent.getChild(i);
-                        lastNode.addChild(nodeToCopy);
-                }
-                // delete them from the end (reverse order)
-                for (int i=numChildren-1; i>indexOfLast; i--) {
-                        lastNodeParent.removeChild(lastNodeParent.getChild(i));
-                }
-                
-                // loop backwards so that the top field is last added, next to parent
-                for (int i=fields.size()-1; i >=0; i--) {
-                        promoteDataField(fields.get(i));
-                }
-                
-        }
-        
-        // promotes a dataField to become a sibling of it's parent
-        public static void promoteDataField(DataFieldNode node) {
-                
-                DataFieldNode parentNode = node.getParentNode();
-                DataFieldNode grandParentNode = parentNode.getParentNode();
-                
-                // if parent is root (grandparent null) then can't promote
-                // if (grandParentNode == null) return;         catch any null pointer exception later
-                
-                int indexOfParent = grandParentNode.indexOfChild(parentNode);
-                
-                grandParentNode.addChild(indexOfParent + 1, node);      // adds after parent
-                node.setParent(grandParentNode);
-                parentNode.removeChild(node);
-        }
-        
-//       if the highlighted fields have a preceding sister, move it below the highlighted fields
+        //       if the highlighted fields have a preceding sister, move it below the highlighted fields
         private void moveFieldsUp() {
                 
@@ -746 +575 @@
                         UndoableEdit edit = new EditMoveFieldsUp(highlightedFields);
                         
-                        moveFieldsUp(highlightedFields);
+                        NodeManagerMethods.moveFieldsUp(highlightedFields);
                         
                         undoSupport.postEdit(edit);
@@ -755 +584 @@
         }
         
-        public static void moveFieldsUp(ArrayList<DataFieldNode> fields) throws IndexOutOfBoundsException {
-                int numFields = fields.size();
-
-                DataFieldNode firstNode = fields.get(0);
-                int firstNodeIndex = firstNode.getMyIndexWithinSiblings();
-                
-                DataFieldNode parentNode = firstNode.getParentNode();
-                DataFieldNode preceedingNode = parentNode.getChild(firstNodeIndex - 1);
-                // add the preceding node after the last node
-                parentNode.addChild(firstNodeIndex + numFields, preceedingNode);
-                parentNode.removeChild(preceedingNode);
-        }
-        
-//       if the highlighted fields have a preceding sister, move it below the highlighted fields
+        //       if the highlighted fields have a preceding sister, move it below the highlighted fields
         private void moveFieldsDown() {
                 
@@ -776 +592 @@
                         UndoableEdit edit = new EditMoveFieldsDown(highlightedFields);
                         
-                        moveFieldsDown(highlightedFields);
+                        NodeManagerMethods.moveFieldsDown(highlightedFields);
                         
                         undoSupport.postEdit(edit);
@@ -783 +599 @@
                         // ignore
                 }
-        }
-        
-        public static void moveFieldsDown(ArrayList<DataFieldNode> fields) throws IndexOutOfBoundsException {
-                
-                int numFields = fields.size();
-
-                DataFieldNode lastNode = fields.get(numFields-1);
-                DataFieldNode parentNode = lastNode.getParentNode();
-                
-                int lastNodeIndex = lastNode.getMyIndexWithinSiblings();
-
-                DataFieldNode succeedingNode = parentNode.getChild(lastNodeIndex + 1);
-                // add the succeeding node before the first node
-                int indexToMoveTo = lastNodeIndex - numFields + 1;
-                parentNode.addChild(indexToMoveTo, succeedingNode);
-                // remove the succeeding node (now 1 more position down the list - after inserting above)
-                parentNode.removeChild(lastNodeIndex + 2);
-                
         }
         
@@ -935 +733 @@
                 setTreeEdited(true);
                 
-                deleteDataFields(highlightedFields);
+                NodeManagerMethods.deleteDataFields(highlightedFields);
                 highlightedFields.clear();
                 
         }
-//       delete the highlighted dataFields 
-        public static void deleteDataFields(ArrayList<DataFieldNode> fields) {
-                for (DataFieldNode node: fields) {
-                        deleteDataField(node);
-                }
-        }
-        public static void deleteDataField(DataFieldNode node) {
-                DataFieldNode parentNode = node.getParentNode();
-                parentNode.removeChild(node);
-        }
-        
-        
+
         // called (via dataField) by clicking on FormField to highlight it
         public void nodeSelected(DataFieldNode selectedNode, boolean clearOthers) {
@@ -1042 +829 @@
         }
         
-        /*
+        /**
          *  getSearchResults(searchWord)
          *  returns an ArrayList of DataField objects that contain the seachWord
@@ -1062 +849 @@
         }
         
-        /*
-         * Goes through the Tree, adding the observation fields to a list
-         */
-        public ArrayList<IAttributeSaver> getObservationFields() {
-                ArrayList<IAttributeSaver> observationFields = new ArrayList<IAttributeSaver>();
-                
-                Iterator <DataFieldNode>iterator = rootNode.iterator();
-
-                while (iterator.hasNext()) {
-                        DataFieldNode node = iterator.next();
-                        IAttributeSaver field = node.getDataField();
-                        if (field.getAttribute(DataFieldConstants.INPUT_TYPE).equals(DataFieldConstants.OBSERVATION_DEFINITION)) {
-                                observationFields.add(field);
-                        }
-                }
-                return observationFields;
-        }
-        
-        // called when the UI needs to display the FieldEditor
-        // if only one field is currently selected, return it. Else return blank
+        
+        /**
+         * called when the UI needs to display the FieldEditor.
+         * If only one field is currently selected, return it. Else return
+         * a blank panel
+         */ 
         public JPanel getFieldEditorToDisplay() {
                 
@@ -1096 +869 @@
                 
                 return currentFieldEditor;
-        }
-        
-        /* getNameOfCurrnentField()
-         * returns name of current field if one is highlighted
-         * otherwise, returns the name of the parent field
-         */
-        public String getNameOfCurrentFieldsParent() {
-                if (highlightedFields.isEmpty()) {
-                        return rootNode.getName();
-                } else {
-                        return (highlightedFields.get(0).getParentNode().getName());
-                }
         }
         
@@ -1126 +887 @@
         }
         
-        public void selectionChanged() {
+        private void selectionChanged() {
                 if (selectionObserver != null) {
                         // System.out.println("Tree.selectionChanged");
@@ -1133 +894 @@
         }
         
+        /**
+         * Gets a list of the currently highlighted nodes. 
+         * Used by other classes for copy and paste, or within this 
+         * class for applying tree edits. 
+         * 
+         * @return              The highlighted nodes. 
+         */
         public ArrayList<DataFieldNode> getHighlightedFields() {
                 if (rootNode.isHighlighted()) {
@@ -1402 +1170 @@
         }
         
-        // keep a note of the file that corresponds to this tree
+        /**
+         * keep a note of the file that corresponds to this tree
+         */ 
         public void setFile (File file) {
                 this.file = file;
         }
+        
+        /**
+         * Get the file that corresponds to this tree.
+         * @return              The file that this tree is read from/saved to.
+         */
         public File getFile () {
                 return file;
@@ -1431 +1206 @@
         }
         
-        // turn on/off xmlValidation
-        public void setXmlValidation(boolean validationOn) {
-                this.xmlValidationOn = validationOn;
-        }
-        public boolean getXmlValidation() {
-                return xmlValidationOn;
-        }
-        
-        // when the data structure changes, edited = true. When saved, edited = false
+        /** 
+         * when the data structure changes, edited = true. 
+         * When saved, edited = false
+         */
         public void setTreeEdited(boolean edited) {
                 System.out.println("Tree Edited = " + edited);
@@ -1445 +1215 @@
         }
         
+        /**
+         * Used (for example) for seeing whether you need to save before closing. 
+         */
         public boolean isTreeEdited() {
                 return treeEdited;
         }
         
+        /**
+         * For UI - Undo button
+&n