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package jalview.gui; |
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import java.awt.event.MouseAdapter; |
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import java.awt.event.MouseEvent; |
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import java.beans.PropertyVetoException; |
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import java.util.List; |
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import javax.swing.JInternalFrame; |
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import javax.swing.JLayeredPane; |
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import javax.swing.event.ChangeEvent; |
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import javax.swing.event.ChangeListener; |
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import javax.swing.event.InternalFrameAdapter; |
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import javax.swing.event.InternalFrameEvent; |
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import jalview.analysis.Conservation; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.jbgui.GSliderPanel; |
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import jalview.renderer.ResidueShaderI; |
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import jalview.util.MessageManager; |
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@author |
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@version |
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| 63.6% |
Uncovered Elements: 94 (258) |
Complexity: 72 |
Complexity Density: 0.44 |
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public class SliderPanel extends GSliderPanel |
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{ |
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private static final String BACKGROUND = "Background"; |
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static JInternalFrame conservationSlider; |
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static JInternalFrame consensusSecondaryStructureSlider; |
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static JInternalFrame PIDSlider; |
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AlignmentPanel ap; |
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boolean forConservation = true; |
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boolean forConsensusSecondaryStructure = false; |
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ResidueShaderI cs; |
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|
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@return |
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| 53.8% |
Uncovered Elements: 6 (13) |
Complexity: 7 |
Complexity Density: 1 |
|
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public static SliderPanel getSliderPanel()... |
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{ |
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if (conservationSlider != null && conservationSlider.isVisible()) |
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{ |
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return (SliderPanel) conservationSlider.getContentPane(); |
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} |
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if (PIDSlider != null && PIDSlider.isVisible()) |
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{ |
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return (SliderPanel) PIDSlider.getContentPane(); |
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} |
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if (consensusSecondaryStructureSlider != null |
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&& consensusSecondaryStructureSlider.isVisible()) |
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{ |
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return (SliderPanel) consensusSecondaryStructureSlider |
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.getContentPane(); |
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} |
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return null; |
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} |
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@param |
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@param |
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@param |
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@param |
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| 84% |
Uncovered Elements: 4 (25) |
Complexity: 3 |
Complexity Density: 0.14 |
|
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public SliderPanel(final AlignmentPanel ap, int value,... |
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boolean forConserve, boolean forConsensusSS, |
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ResidueShaderI scheme) |
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{ |
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this.ap = ap; |
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this.cs = scheme; |
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forConservation = forConserve; |
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forConsensusSecondaryStructure = forConsensusSS; |
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undoButton.setVisible(false); |
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applyButton.setVisible(false); |
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if (forConservation) |
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{ |
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label.setText(MessageManager.getString( |
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"label.enter_value_increase_conservation_visibility")); |
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slider.setMinimum(0); |
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slider.setMaximum(100); |
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} |
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if (forConsensusSS) |
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{ |
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label.setText(MessageManager.getString( |
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"label.enter_value_increase_conservation_visibility")); |
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slider.setMinimum(0); |
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slider.setMaximum(100); |
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} |
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else |
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{ |
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label.setText(MessageManager.getString( |
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"label.enter_percentage_identity_above_which_colour_residues")); |
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slider.setMinimum(0); |
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slider.setMaximum(100); |
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} |
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|
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slider.addChangeListener(new ChangeListener() |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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@Override... |
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public void stateChanged(ChangeEvent evt) |
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{ |
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valueField.setText(String.valueOf(slider.getValue())); |
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valueChanged(slider.getValue()); |
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} |
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}); |
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slider.addMouseListener(new MouseAdapter() |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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public void mouseReleased(MouseEvent evt) |
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{ |
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ap.paintAlignment(true, true); |
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} |
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}); |
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slider.setValue(value); |
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valueField.setText(String.valueOf(value)); |
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} |
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@param |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (25) |
Complexity: 5 |
Complexity Density: 0.26 |
|
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public static int setConservationSlider(AlignmentPanel ap,... |
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ResidueShaderI rs, String source) |
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{ |
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SliderPanel sliderPanel = null; |
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|
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if (conservationSlider == null) |
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{ |
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sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, |
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false, rs); |
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conservationSlider = new JInternalFrame(); |
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conservationSlider.setFrameIcon(null); |
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conservationSlider.setContentPane(sliderPanel); |
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conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); |
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} |
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else |
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{ |
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sliderPanel = (SliderPanel) conservationSlider.getContentPane(); |
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4 |
sliderPanel.valueField |
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.setText(String.valueOf(rs.getConservationInc())); |
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sliderPanel.cs = rs; |
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sliderPanel.ap = ap; |
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sliderPanel.slider.setValue(rs.getConservationInc()); |
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} |
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conservationSlider.setTitle(MessageManager.formatMessage( |
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"label.conservation_colour_increment", new String[] |
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{ source == null ? BACKGROUND : source })); |
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|
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List<SequenceGroup> groups = ap.av.getAlignment().getGroups(); |
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if (groups != null && !groups.isEmpty()) |
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{ |
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sliderPanel.setAllGroupsCheckEnabled(true); |
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sliderPanel.allGroupsCheck |
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.setSelected(ap.av.getColourAppliesToAllGroups()); |
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} |
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else |
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{ |
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sliderPanel.setAllGroupsCheckEnabled(false); |
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} |
209 |
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return sliderPanel.getValue(); |
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} |
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213 |
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214 |
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215 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
216 |
158 |
public static void hidePIDSlider()... |
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{ |
218 |
158 |
if (PIDSlider != null) |
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{ |
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8 |
try |
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{ |
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PIDSlider.setClosed(true); |
223 |
8 |
PIDSlider = null; |
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} catch (PropertyVetoException ex) |
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{ |
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} |
227 |
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} |
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} |
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230 |
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231 |
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|
232 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
233 |
157 |
public static void hideConservationSlider()... |
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{ |
235 |
157 |
if (conservationSlider != null) |
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{ |
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6 |
try |
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{ |
239 |
6 |
conservationSlider.setClosed(true); |
240 |
6 |
conservationSlider = null; |
241 |
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} catch (PropertyVetoException ex) |
242 |
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{ |
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} |
244 |
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} |
245 |
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} |
246 |
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247 |
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248 |
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|
249 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
250 |
9 |
public static void showConservationSlider()... |
251 |
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{ |
252 |
9 |
hidePIDSlider(); |
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|
254 |
9 |
if (!conservationSlider.isVisible()) |
255 |
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{ |
256 |
7 |
Desktop.addInternalFrame(conservationSlider, |
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conservationSlider.getTitle(), true, FRAME_WIDTH, |
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FRAME_HEIGHT, false, true); |
259 |
7 |
conservationSlider.addInternalFrameListener(new InternalFrameAdapter() |
260 |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
261 |
7 |
@Override... |
262 |
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public void internalFrameClosed(InternalFrameEvent e) |
263 |
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{ |
264 |
7 |
conservationSlider = null; |
265 |
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} |
266 |
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}); |
267 |
7 |
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); |
268 |
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} |
269 |
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} |
270 |
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 5 |
Complexity Density: 0.26 |
|
271 |
0 |
public static int setConsensusSecondaryStructureSlider(AlignmentPanel ap,... |
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ResidueShaderI rs, String source) |
273 |
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{ |
274 |
0 |
SliderPanel sliderPanel = null; |
275 |
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|
276 |
0 |
if (consensusSecondaryStructureSlider == null) |
277 |
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{ |
278 |
0 |
sliderPanel = new SliderPanel(ap, |
279 |
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rs.getConsensusSecondaryStructureThreshold(), false, true, |
280 |
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rs); |
281 |
0 |
consensusSecondaryStructureSlider = new JInternalFrame(); |
282 |
0 |
consensusSecondaryStructureSlider.setFrameIcon(null); |
283 |
0 |
consensusSecondaryStructureSlider.setContentPane(sliderPanel); |
284 |
0 |
consensusSecondaryStructureSlider |
285 |
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.setLayer(JLayeredPane.PALETTE_LAYER); |
286 |
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} |
287 |
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else |
288 |
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{ |
289 |
0 |
sliderPanel = (SliderPanel) consensusSecondaryStructureSlider |
290 |
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.getContentPane(); |
291 |
0 |
sliderPanel.valueField.setText( |
292 |
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String.valueOf(rs.getConsensusSecondaryStructureThreshold())); |
293 |
0 |
sliderPanel.cs = rs; |
294 |
0 |
sliderPanel.ap = ap; |
295 |
0 |
sliderPanel.slider |
296 |
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.setValue(rs.getConsensusSecondaryStructureThreshold()); |
297 |
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} |
298 |
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|
299 |
0 |
consensusSecondaryStructureSlider.setTitle(MessageManager.formatMessage( |
300 |
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"label.secondary_structure_conservation_threshold", new String[] |
301 |
0 |
{ source == null ? BACKGROUND : source })); |
302 |
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|
303 |
0 |
List<SequenceGroup> groups = ap.av.getAlignment().getGroups(); |
304 |
0 |
if (groups != null && !groups.isEmpty()) |
305 |
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{ |
306 |
0 |
sliderPanel.setAllGroupsCheckEnabled(true); |
307 |
0 |
sliderPanel.allGroupsCheck |
308 |
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.setSelected(ap.av.getColourAppliesToAllGroups()); |
309 |
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} |
310 |
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else |
311 |
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{ |
312 |
0 |
sliderPanel.setAllGroupsCheckEnabled(false); |
313 |
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} |
314 |
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|
315 |
0 |
return sliderPanel.getValue(); |
316 |
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} |
317 |
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|
|
|
| 33.3% |
Uncovered Elements: 4 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
318 |
148 |
public static void hideConsensusSecondaryStructureSlider()... |
319 |
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{ |
320 |
148 |
if (consensusSecondaryStructureSlider != null) |
321 |
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{ |
322 |
0 |
try |
323 |
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{ |
324 |
0 |
consensusSecondaryStructureSlider.setClosed(true); |
325 |
0 |
consensusSecondaryStructureSlider = null; |
326 |
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} catch (PropertyVetoException ex) |
327 |
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{ |
328 |
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} |
329 |
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} |
330 |
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} |
331 |
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|
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|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
332 |
0 |
public static void showConsensusSecondaryStructureSlider()... |
333 |
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{ |
334 |
0 |
hidePIDSlider(); |
335 |
0 |
hideConservationSlider(); |
336 |
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|
337 |
0 |
if (!consensusSecondaryStructureSlider.isVisible()) |
338 |
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{ |
339 |
0 |
Desktop.addInternalFrame(consensusSecondaryStructureSlider, |
340 |
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consensusSecondaryStructureSlider.getTitle(), true, |
341 |
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FRAME_WIDTH, FRAME_HEIGHT, false, true); |
342 |
0 |
consensusSecondaryStructureSlider |
343 |
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.addInternalFrameListener(new InternalFrameAdapter() |
344 |
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{ |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
345 |
0 |
@Override... |
346 |
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public void internalFrameClosed(InternalFrameEvent e) |
347 |
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{ |
348 |
0 |
consensusSecondaryStructureSlider = null; |
349 |
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} |
350 |
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}); |
351 |
0 |
consensusSecondaryStructureSlider |
352 |
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.setLayer(JLayeredPane.PALETTE_LAYER); |
353 |
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} |
354 |
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} |
355 |
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356 |
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357 |
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358 |
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|
359 |
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@param |
360 |
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|
361 |
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@param |
362 |
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|
363 |
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@param |
364 |
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|
365 |
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|
366 |
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@return |
367 |
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| 91.7% |
Uncovered Elements: 2 (24) |
Complexity: 4 |
Complexity Density: 0.22 |
|
368 |
11 |
public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,... |
369 |
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String source) |
370 |
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{ |
371 |
11 |
int threshold = rs.getThreshold(); |
372 |
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|
373 |
11 |
SliderPanel sliderPanel = null; |
374 |
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|
375 |
11 |
if (PIDSlider == null) |
376 |
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{ |
377 |
10 |
sliderPanel = new SliderPanel(ap, threshold, false, false, rs); |
378 |
10 |
PIDSlider = new JInternalFrame(); |
379 |
10 |
PIDSlider.setFrameIcon(null); |
380 |
10 |
PIDSlider.setContentPane(sliderPanel); |
381 |
10 |
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); |
382 |
|
} |
383 |
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else |
384 |
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{ |
385 |
1 |
sliderPanel = (SliderPanel) PIDSlider.getContentPane(); |
386 |
1 |
sliderPanel.cs = rs; |
387 |
1 |
sliderPanel.ap = ap; |
388 |
1 |
sliderPanel.valueField.setText(String.valueOf(rs.getThreshold())); |
389 |
1 |
sliderPanel.slider.setValue(rs.getThreshold()); |
390 |
|
} |
391 |
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|
392 |
11 |
PIDSlider.setTitle(MessageManager.formatMessage( |
393 |
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"label.percentage_identity_threshold", new String[] |
394 |
11 |
{ source == null ? BACKGROUND : source })); |
395 |
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|
396 |
11 |
if (ap.av.getAlignment().getGroups() != null) |
397 |
|
{ |
398 |
11 |
sliderPanel.setAllGroupsCheckEnabled(true); |
399 |
|
} |
400 |
|
else |
401 |
|
{ |
402 |
0 |
sliderPanel.setAllGroupsCheckEnabled(false); |
403 |
|
} |
404 |
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|
405 |
11 |
return sliderPanel.getValue(); |
406 |
|
} |
407 |
|
|
408 |
|
|
409 |
|
|
410 |
|
|
411 |
|
@return |
412 |
|
|
|
|
| 88.9% |
Uncovered Elements: 1 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
413 |
9 |
public static JInternalFrame showPIDSlider()... |
414 |
|
{ |
415 |
9 |
hideConservationSlider(); |
416 |
|
|
417 |
9 |
if (!PIDSlider.isVisible()) |
418 |
|
{ |
419 |
9 |
Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), true, |
420 |
|
FRAME_WIDTH, FRAME_HEIGHT, false, true); |
421 |
9 |
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); |
422 |
9 |
PIDSlider.addInternalFrameListener(new InternalFrameAdapter() |
423 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
424 |
9 |
@Override... |
425 |
|
public void internalFrameClosed(InternalFrameEvent e) |
426 |
|
{ |
427 |
9 |
PIDSlider = null; |
428 |
|
} |
429 |
|
}); |
430 |
9 |
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); |
431 |
|
} |
432 |
9 |
return PIDSlider; |
433 |
|
} |
434 |
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|
435 |
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|
436 |
|
|
437 |
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|
438 |
|
|
439 |
|
|
440 |
|
@param |
441 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
|
442 |
37 |
public void valueChanged(int percent)... |
443 |
|
{ |
444 |
37 |
if (!forConservation && !forConsensusSecondaryStructure) |
445 |
|
{ |
446 |
21 |
ap.av.setThreshold(percent); |
447 |
|
} |
448 |
37 |
updateColourScheme(percent, cs, null); |
449 |
|
|
450 |
37 |
if (allGroupsCheck.isSelected()) |
451 |
|
{ |
452 |
2 |
List<SequenceGroup> groups = ap.av.getAlignment().getGroups(); |
453 |
2 |
for (SequenceGroup sg : groups) |
454 |
|
{ |
455 |
2 |
updateColourScheme(percent, sg.getGroupColourScheme(), sg); |
456 |
|
} |
457 |
|
} |
458 |
|
|
459 |
37 |
ap.getSeqPanel().seqCanvas.repaint(); |
460 |
|
} |
461 |
|
|
462 |
|
|
463 |
|
|
464 |
|
|
465 |
|
|
466 |
|
@param |
467 |
|
@param |
468 |
|
@param |
469 |
|
|
|
|
| 54.5% |
Uncovered Elements: 10 (22) |
Complexity: 6 |
Complexity Density: 0.43 |
|
470 |
39 |
protected void updateColourScheme(int percent, ResidueShaderI scheme,... |
471 |
|
SequenceGroup sg) |
472 |
|
{ |
473 |
39 |
if (scheme == null) |
474 |
|
{ |
475 |
0 |
return; |
476 |
|
} |
477 |
39 |
if (forConservation) |
478 |
|
{ |
479 |
18 |
if (!scheme.conservationApplied() && sg != null) |
480 |
|
{ |
481 |
|
|
482 |
|
|
483 |
|
|
484 |
|
|
485 |
0 |
Conservation c = new Conservation("Group", sg.getSequences(null), |
486 |
|
sg.getStartRes(), sg.getEndRes()); |
487 |
0 |
c.calculate(); |
488 |
0 |
c.verdict(false, ap.av.getConsPercGaps()); |
489 |
0 |
sg.cs.setConservation(c); |
490 |
|
|
491 |
|
} |
492 |
18 |
scheme.setConservationApplied(true); |
493 |
18 |
scheme.setConservationInc(percent); |
494 |
|
} |
495 |
21 |
else if(forConsensusSecondaryStructure) |
496 |
|
{ |
497 |
0 |
scheme.setConsensusSecondaryStructureColouring(true); |
498 |
0 |
scheme.setConsensusSecondaryStructureThreshold(percent); |
499 |
|
} |
500 |
|
else |
501 |
|
{ |
502 |
21 |
scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus()); |
503 |
|
|
504 |
|
} |
505 |
|
} |
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
@param |
511 |
|
|
512 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
513 |
22 |
public void setAllGroupsCheckEnabled(boolean b)... |
514 |
|
{ |
515 |
22 |
allGroupsCheck.setEnabled(b); |
516 |
|
} |
517 |
|
|
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
@param |
522 |
|
|
523 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
524 |
0 |
@Override... |
525 |
|
public void valueField_actionPerformed() |
526 |
|
{ |
527 |
0 |
try |
528 |
|
{ |
529 |
0 |
int i = Integer.parseInt(valueField.getText()); |
530 |
0 |
slider.setValue(i); |
531 |
|
} catch (NumberFormatException ex) |
532 |
|
{ |
533 |
0 |
valueField.setText(slider.getValue() + ""); |
534 |
|
} |
535 |
|
} |
536 |
|
|
537 |
|
|
538 |
|
|
539 |
|
|
540 |
|
@param |
541 |
|
|
542 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
543 |
0 |
public void setValue(int value)... |
544 |
|
{ |
545 |
0 |
slider.setValue(value); |
546 |
|
} |
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
|
551 |
|
@return |
552 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
553 |
24 |
public int getValue()... |
554 |
|
{ |
555 |
24 |
return Integer.parseInt(valueField.getText()); |
556 |
|
} |
557 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
558 |
0 |
@Override... |
559 |
|
public void slider_mouseReleased(MouseEvent e) |
560 |
|
{ |
561 |
0 |
if (ap.overviewPanel != null) |
562 |
|
{ |
563 |
0 |
ap.overviewPanel.updateOverviewImage(); |
564 |
|
} |
565 |
|
} |
566 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
567 |
0 |
public static int getConservationValue()... |
568 |
|
{ |
569 |
0 |
return getValue(conservationSlider); |
570 |
|
} |
571 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
572 |
0 |
static int getValue(JInternalFrame slider)... |
573 |
|
{ |
574 |
0 |
return slider == null ? 0 |
575 |
|
: ((SliderPanel) slider.getContentPane()).getValue(); |
576 |
|
} |
577 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
578 |
0 |
public static int getPIDValue()... |
579 |
|
{ |
580 |
0 |
return getValue(PIDSlider); |
581 |
|
} |
582 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
583 |
0 |
public static int getConsensusSecondaryStructureSliderValue()... |
584 |
|
{ |
585 |
0 |
return getValue(consensusSecondaryStructureSlider); |
586 |
|
} |
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
|
@return |
593 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
594 |
24 |
public boolean isForConservation()... |
595 |
|
{ |
596 |
24 |
return forConservation; |
597 |
|
} |
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
|
603 |
|
@return |
604 |
|
|
|
|
| 64.7% |
Uncovered Elements: 6 (17) |
Complexity: 5 |
Complexity Density: 0.56 |
|
605 |
6 |
public String getTitle()... |
606 |
|
{ |
607 |
6 |
String title = null; |
608 |
6 |
if (isForConservation()) |
609 |
|
{ |
610 |
4 |
if (conservationSlider != null) |
611 |
|
{ |
612 |
4 |
title = conservationSlider.getTitle(); |
613 |
|
} |
614 |
|
} |
615 |
2 |
else if (PIDSlider != null) |
616 |
|
{ |
617 |
2 |
title = PIDSlider.getTitle(); |
618 |
|
} |
619 |
0 |
else if (consensusSecondaryStructureSlider != null) |
620 |
|
{ |
621 |
0 |
title = consensusSecondaryStructureSlider.getTitle(); |
622 |
|
} |
623 |
6 |
return title; |
624 |
|
} |
625 |
|
} |