Examples with StringFilter org.cytoscape.filter.internal.filters.model.StringFilter used on opensource projects

Example 1 with StringFilter

use of org.cytoscape.filter.internal.filters.model.StringFilter in project cytoscape-impl by cytoscape.

the class ApplyFilterThread method passAtomicFilter.

private boolean passAtomicFilter(CyNetwork network, Object pObject, AtomicFilter pAtomicFilter) {
    CyRow data = null;
    if (pObject instanceof CyNode) {
        CyNode node = (CyNode) pObject;
        data = network.getRow(node);
    } else {
        CyEdge edge = (CyEdge) pObject;
        data = network.getRow(edge);
    }
    if (pAtomicFilter instanceof StringFilter) {
        StringFilter theStringFilter = (StringFilter) pAtomicFilter;
        String value = data.get(theStringFilter.getControllingAttribute().substring(5), String.class);
        if (value == null) {
            return false;
        }
        if (theStringFilter == null) {
            return false;
        }
        if (theStringFilter.getSearchStr() == null) {
            return false;
        }
        String[] pattern = theStringFilter.getSearchStr().split("\\s");
        for (int p = 0; p < pattern.length; ++p) {
            if (!Strings.isLike(value, pattern[p], 0, true)) {
                // this is an OR function
                return false;
            }
        }
    } else if (pAtomicFilter instanceof NumericFilter) {
        NumericFilter theNumericFilter = (NumericFilter) pAtomicFilter;
        Number value;
        if (data.getTable().getColumn(theNumericFilter.getControllingAttribute().substring(5)).getType() == Double.class)
            value = data.get(theNumericFilter.getControllingAttribute().substring(5), Double.class);
        else
            value = data.get(theNumericFilter.getControllingAttribute().substring(5), Integer.class);
        if (value == null) {
            return false;
        }
        Double lowValue = (Double) theNumericFilter.getLowBound();
        Double highValue = (Double) theNumericFilter.getHighBound();
        // To correct the boundary values for lowValue and highValue
        if (lowValue.doubleValue() > 0.0) {
            lowValue = lowValue * 0.99999;
        } else {
            lowValue = lowValue * 1.00001;
        }
        if (highValue.doubleValue() > 0.0) {
            highValue = highValue * 1.00001;
        } else {
            highValue = highValue * 0.99999;
        }
        // if (!(value.doubleValue() >= lowValue.doubleValue() && value.doubleValue()<= highValue.doubleValue())) {
        if (!((Double.compare(value.doubleValue(), lowValue.doubleValue()) >= 0) && (Double.compare(value.doubleValue(), highValue.doubleValue())) <= 0)) {
            return false;
        }
    }
    return true;
}

Example 2 with StringFilter

use of org.cytoscape.filter.internal.filters.model.StringFilter in project cytoscape-impl by cytoscape.

the class FilterSettingPanel method refreshIndicesForWidgets.

// Refresh indices for widget after network switch or Cytoscape.ATTRIBUTES_CHANGED event is received
// The method may be triggered by event of NETWORK_VIEW_FOCUSED
public void refreshIndicesForWidgets() {
    // Check if each widget has associatd index, if not, try to create one
    // System.out.println("FilterSettingpanel:refreshIndicesForWidgets()...\n");
    List<CyFilter> children = theFilter.getChildren();
    if ((children == null) || (children.size() == 0)) {
        return;
    }
    CyNetwork network = applicationManager.getCurrentNetwork();
    for (int i = 0; i < children.size(); i++) {
        CyFilter child = children.get(i);
        if (child instanceof StringFilter) {
            if (pnlCustomSettings.getComponent(i * 5 + 3) instanceof TextIndexComboBox) {
                TextIndexComboBox theBox = (TextIndexComboBox) pnlCustomSettings.getComponent(i * 5 + 3);
                if (network != null) {
                    CyNetworkView networkView = applicationManager.getCurrentNetworkView();
                    if (networkView != null) {
                        TextIndex textIndex = createTextIndex((StringFilter) child);
                        ;
                        if (textIndex != null) {
                            theBox.setTextIndex(textIndex);
                            StringFilter aFilter = (StringFilter) child;
                            aFilter.setIndex(textIndex);
                        }
                    }
                }
            }
        }
        if (child instanceof NumericFilter) {
            if (pnlCustomSettings.getComponent(i * 5 + 3) instanceof JRangeSliderExtended) {
                JRangeSliderExtended theSlider = (JRangeSliderExtended) pnlCustomSettings.getComponent(i * 5 + 3);
                if (network != null) {
                    CyNetworkView networkView = applicationManager.getCurrentNetworkView();
                    if (networkView != null) {
                        NumberIndex numIndex = createNumberIndex((NumericFilter) child);
                        ;
                        if (numIndex != null) {
                            NumberRangeModel rangeModel = (NumberRangeModel) theSlider.getModel();
                            rangeModel.setMinValue(numIndex.getMinimumValue());
                            rangeModel.setMaxValue(numIndex.getMaximumValue());
                            NumericFilter aFilter = (NumericFilter) child;
                            aFilter.setIndex(numIndex);
                        }
                    }
                }
            }
        }
    }
}

Example 3 with StringFilter

use of org.cytoscape.filter.internal.filters.model.StringFilter in project cytoscape-impl by cytoscape.

the class FilterSettingPanel method getAtomicFilterFromStr.

private AtomicFilter getAtomicFilterFromStr(String pCtrlAttribute, int pIndexType) {
    AtomicFilter retFilter = null;
    // quickFind.addNetwork(cyNetwork, new TaskMonitorBase());
    // index_by_UniqueIdentification = (TextIndex) quickFind.getIndex(cyNetwork);
    CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
    quickFind.reindexNetwork(cyNetwork, pIndexType, pCtrlAttribute, new TaskMonitorBase());
    Class<?> attributeType = null;
    if (pIndexType == QuickFind.INDEX_NODES) {
        if (cyNetwork.getNodeCount() > 0) {
            attributeType = cyNetwork.getDefaultNodeTable().getColumn(pCtrlAttribute).getType();
        }
    } else if (pIndexType == QuickFind.INDEX_EDGES) {
        if (cyNetwork.getEdgeCount() > 0) {
            attributeType = cyNetwork.getDefaultEdgeTable().getColumn(pCtrlAttribute).getType();
        }
    }
    if ((attributeType == Integer.class) || (attributeType == Double.class)) {
        retFilter = new NumericFilter(quickFind);
        retFilter.setControllingAttribute(pCtrlAttribute);
        retFilter.setIndexType(pIndexType);
        // NumberIndex index_by_thisAttr = (NumberIndex) quickFind.getIndex(Cytoscape.getCurrentNetwork());
        retFilter.setIndex(quickFind.getIndex(cyNetwork));
    } else if ((attributeType == String.class || (attributeType == List.class || (attributeType == Boolean.class)))) {
        retFilter = new StringFilter(quickFind);
        retFilter.setControllingAttribute(pCtrlAttribute);
        retFilter.setIndexType(pIndexType);
        // TextIndex index_by_thisAttr = (TextIndex) quickFind.getIndex(Cytoscape.getCurrentNetwork());
        retFilter.setIndex(quickFind.getIndex(cyNetwork));
    } else {
        logger.error("AttributeType is not numeric/string/list/boolean.");
    }
    if (retFilter != null) {
        retFilter.setNetwork(cyNetwork);
    }
    return retFilter;
}

Example 4 with StringFilter

use of org.cytoscape.filter.internal.filters.model.StringFilter in project cytoscape-impl by cytoscape.

the class FilterSettingPanel method addWidgetRow.

private void addWidgetRow(CyFilter pFilter, int pGridY) {
    GridBagConstraints gridBagConstraints = new GridBagConstraints();
    if (pGridY > 0) {
        // add a row to indicate the relationship between the widgets
        String relationStr = "AND";
        if (theFilter.getAdvancedSetting().getRelation() == Relation.OR) {
            relationStr = "OR";
        }
        // Col 2 ---> Label to indicate relationship between widgets
        gridBagConstraints = new java.awt.GridBagConstraints();
        gridBagConstraints.gridx = 2;
        gridBagConstraints.gridy = pGridY - 1;
        JLabel lbRelation = new JLabel(relationStr);
        lbRelation.setName("RelationLabel");
        pnlCustomSettings.add(lbRelation, gridBagConstraints);
    }
    // Col 0 -- label with attributeName/Filter
    JLabel theLabel_col0 = new JLabel();
    if (pFilter instanceof AtomicFilter) {
        AtomicFilter atomicFilter = (AtomicFilter) pFilter;
        theLabel_col0.setText(atomicFilter.getControllingAttribute());
    } else {
        theLabel_col0.setText("Filter");
    }
    gridBagConstraints = new java.awt.GridBagConstraints();
    gridBagConstraints.gridy = pGridY;
    gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
    // gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
    pnlCustomSettings.add(theLabel_col0, gridBagConstraints);
    // Col 1 ---> chk box -- NOT
    final JCheckBox chkNot = new JCheckBox("Not");
    chkNot.setName(Integer.toString(pGridY));
    chkNot.setSelected(pFilter.getNegation());
    chkNot.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            updateNegationStatus(chkNot);
        }
    });
    gridBagConstraints = new java.awt.GridBagConstraints();
    gridBagConstraints.gridy = pGridY;
    // gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 0);
    pnlCustomSettings.add(chkNot, gridBagConstraints);
    gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
    gridBagConstraints.weightx = 1.0;
    // Col 2 ---> Widget if atomicFilter
    if (pFilter instanceof StringFilter) {
        JComboBox aBox = getTextIndexComboBox((StringFilter) pFilter);
        pnlCustomSettings.add(aBox, gridBagConstraints);
    } else if (pFilter instanceof NumericFilter) {
        JRangeSliderExtended theSlider = getRangerSlider((NumericFilter) pFilter);
        pnlCustomSettings.add(theSlider, gridBagConstraints);
    } else {
        // CompositeFilter
        gridBagConstraints.fill = java.awt.GridBagConstraints.NONE;
        // gridBagConstraints.weightx = 0.0;
        // gridBagConstraints.anchor = java.awt.GridBagConstraints.
        pnlCustomSettings.add(new JLabel(pFilter.getName()), gridBagConstraints);
    }
    gridBagConstraints.weightx = 0.0;
    // Col 3 ---> label (a trash can) for delete of the row
    JLabel theDelLabel = new JLabel();
    theDelLabel.setIcon(delIcon);
    gridBagConstraints = new java.awt.GridBagConstraints();
    gridBagConstraints.gridy = pGridY;
    // gridBagConstraints.insets = new java.awt.Insets(0, 5, 0, 0);
    pnlCustomSettings.add(theDelLabel, gridBagConstraints);
    theDelLabel.setName(Integer.toString(pGridY));
    theDelLabel.addMouseListener(new MouseAdapter() {

        public void mouseClicked(MouseEvent e) {
            removeFilterWidget(e);
        }
    });
    this.validate();
}

Example 5 with StringFilter

use of org.cytoscape.filter.internal.filters.model.StringFilter in project cytoscape-impl by cytoscape.

the class FilterReader method getFilterFromStrList.

private CompositeFilter getFilterFromStrList(List<String> strList, Collection<CompositeFilter> filters) {
    boolean isTopologyFilter = false;
    boolean isInteractionFilter = false;
    if (strList.get(0).startsWith("<TopologyFilter>")) {
        isTopologyFilter = true;
    }
    if (strList.get(0).startsWith("<InteractionFilter>")) {
        isInteractionFilter = true;
    }
    List<String> advSettingStrVect = new ArrayList<String>();
    List<String> filterStrVect = new ArrayList<String>();
    // Seperate AdvancedSetting from the rest
    int startIndex = -1, endIndex = -1;
    String line = null;
    for (int i = 0; i < strList.size(); i++) {
        line = strList.get(i);
        if (line.startsWith("<AdvancedSetting>")) {
            startIndex = i;
        }
        if (line.startsWith("</AdvancedSetting>")) {
            endIndex = i;
            break;
        }
    }
    advSettingStrVect.addAll(strList.subList(startIndex + 1, endIndex));
    filterStrVect.addAll(strList.subList(1, startIndex));
    filterStrVect.addAll(strList.subList(endIndex + 1, strList.size()));
    CompositeFilter retFilter = new CompositeFilter(ServicesUtil.cyApplicationManagerServiceRef);
    retFilter.setAdvancedSetting(getAdvancedSettingFromStr(advSettingStrVect));
    if (isTopologyFilter) {
        retFilter = new TopologyFilter(ServicesUtil.cyApplicationManagerServiceRef);
        retFilter.setAdvancedSetting(getAdvancedSettingFromStr(advSettingStrVect));
        getTopologyFilterFromStr((TopologyFilter) retFilter, filterStrVect, filters);
        return retFilter;
    }
    if (isInteractionFilter) {
        AdvancedSetting advSetting = getAdvancedSettingFromStr(advSettingStrVect);
        if (advSetting.isNodeChecked()) {
            retFilter = new NodeInteractionFilter(ServicesUtil.cyApplicationManagerServiceRef);
        } else {
            // advSetting.isEdgeChecked() == true
            retFilter = new EdgeInteractionFilter(ServicesUtil.cyApplicationManagerServiceRef);
        }
        retFilter.setAdvancedSetting(advSetting);
        getInteractionFilterFromStr((InteractionFilter) retFilter, filterStrVect, filters);
        return retFilter;
    }
    Collection<CompositeFilter> allFilters = new LinkedHashSet<CompositeFilter>();
    for (int i = 0; i < filterStrVect.size(); i++) {
        line = filterStrVect.get(i);
        if (line.startsWith("name=")) {
            String name = line.substring(5);
            retFilter.setName(name);
        }
        if (line.startsWith("Negation=true")) {
            retFilter.setNegation(true);
        }
        if (line.startsWith("Negation=false")) {
            retFilter.setNegation(false);
        }
        if (line.startsWith("StringFilter=")) {
            String _stringFilterValue = line.substring(13);
            String[] _values = _stringFilterValue.split(":");
            // controllingAttribute+":" + negation+ ":"+searchStr+":"+index_type;
            StringFilter _strFilter = new StringFilter(quickFind);
            _strFilter.setParent(retFilter);
            _strFilter.setControllingAttribute(_values[0]);
            _strFilter.setNegation((new Boolean(_values[1])).booleanValue());
            // handle the case where ':' is part of the search string
            String _searchStr = _stringFilterValue.substring(_values[0].length() + _values[1].length() + 2, _stringFilterValue.length() - _values[_values.length - 1].length() - 1);
            _strFilter.setSearchStr(_searchStr);
            _strFilter.setIndexType((new Integer(_values[_values.length - 1])).intValue());
            retFilter.addChild(_strFilter);
        }
        if (line.startsWith("NumericFilter=")) {
            String[] _values = line.substring(14).split(":");
            // controllingAttribute + ":" + negation+ ":"+lowBound+":" +
            // highBound+ ":"+index_type;
            // Determine data type of the attribute
            String dataType = "int";
            if (_values[2].indexOf(".") >= 0 || _values[2].indexOf("E") >= 0 || _values[3].indexOf(".") >= 0 || _values[3].indexOf("E") >= 0) {
                dataType = "double";
            }
            if (dataType.equalsIgnoreCase("double")) {
                NumericFilter<Double> _numFilter = new NumericFilter<Double>(quickFind);
                _numFilter.setParent(retFilter);
                _numFilter.setControllingAttribute(_values[0]);
                _numFilter.setNegation((new Boolean(_values[1])).booleanValue());
                _numFilter.setLowBound(Double.valueOf(_values[2]));
                _numFilter.setHighBound(Double.valueOf(_values[3]));
                _numFilter.setIndexType((new Integer(_values[4])).intValue());
                retFilter.addChild(_numFilter);
            } else {
                // dataType = "int"
                NumericFilter<Integer> _numFilter = new NumericFilter<Integer>(quickFind);
                _numFilter.setParent(retFilter);
                _numFilter.setControllingAttribute(_values[0]);
                _numFilter.setNegation((new Boolean(_values[1])).booleanValue());
                _numFilter.setLowBound(Integer.valueOf(_values[2]));
                _numFilter.setHighBound(Integer.valueOf(_values[3]));
                _numFilter.setIndexType((new Integer(_values[4])).intValue());
                retFilter.addChild(_numFilter);
            }
        }
        if (line.startsWith("CompositeFilter=")) {
            // e.g. CompositeFilter=AAA:true
            String[] _values = line.substring(16).split(":");
            String name = _values[0].trim();
            String notValue = _values[1].trim();
            // get the reference CompositeFilter
            CompositeFilter cmpFilter = null;
            for (CompositeFilter cf : allFilters) {
                if (cf.getName().equalsIgnoreCase(name)) {
                    cmpFilter = cf;
                    break;
                }
            }
            if (cmpFilter != null) {
                retFilter.addChild(cmpFilter, (new Boolean(notValue)).booleanValue());
            }
        }
        if (line.startsWith("TopologyFilter=")) {
            // e.g. TopologyFilter=AAA:true
            String[] _values = line.substring(15).split(":");
            String name = _values[0].trim();
            String notValue = _values[1].trim();
            // get the reference TopologyFilter
            TopologyFilter topoFilter = null;
            for (CompositeFilter cf : allFilters) {
                if (cf.getName().equalsIgnoreCase(name)) {
                    topoFilter = (TopologyFilter) cf;
                    break;
                }
            }
            if (topoFilter != null) {
                retFilter.addChild(topoFilter, (new Boolean(notValue)).booleanValue());
            }
        }
        if (line.startsWith("InteractionFilter=")) {
            // e.g. InteractionFilter=AAA:true
            String[] _values = line.substring(15).split(":");
            String name = _values[0].trim();
            String notValue = _values[1].trim();
            // get the reference InteractionFilter
            InteractionFilter interactionFilter = null;
            for (CompositeFilter cf : allFilters) {
                if (cf.getName().equalsIgnoreCase(name)) {
                    interactionFilter = (InteractionFilter) cf;
                    break;
                }
            }
            if (interactionFilter != null) {
                retFilter.addChild(interactionFilter, (new Boolean(notValue)).booleanValue());
            }
        }
    }
    return retFilter;
}