+++ /dev/null
-package jalview.gui;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.GraphLine;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JPanel;
-import javax.swing.JSlider;
-import javax.swing.JTextField;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
-import net.miginfocom.swing.MigLayout;
-
-public class AnnotationColumnSelection extends JPanel
-{
- JInternalFrame frame;
-
- AlignViewport av;
-
- AlignmentPanel ap;
-
- ColourSchemeI oldcs;
-
- Hashtable oldgroupColours;
-
- private JComboBox annotations;
-
- int[] annmap;
-
- JPanel minColour = new JPanel();
-
- JPanel maxColour = new JPanel();
-
- JButton defColours = new JButton();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- private JComboBox threshold = new JComboBox();
-
- JSlider slider = new JSlider();
-
- JTextField thresholdValue = new JTextField(20);
-
- JCheckBox currentColours = new JCheckBox();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- JCheckBox seqAssociated = new JCheckBox();
-
- private jalview.datamodel.AlignmentAnnotation currentAnnotation;
-
- boolean adjusting = false;
-
- /**
- * enabled if the user is dragging the slider - try to keep updates to a
- * minimun
- */
- boolean sliderDragging = false;
-
- public AnnotationColumnSelection(AlignViewport av, final AlignmentPanel ap)
- {
-
- this.av = av;
- this.ap = ap;
- frame = new JInternalFrame();
- frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
-
- slider.addChangeListener(new ChangeListener()
- {
- @Override
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText((slider.getValue() / 1000f) + "");
- valueChanged(!sliderDragging);
- }
- }
- });
- slider.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent e)
- {
- sliderDragging = true;
- super.mousePressed(e);
- }
-
- @Override
- public void mouseDragged(MouseEvent e)
- {
- sliderDragging = true;
- super.mouseDragged(e);
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (sliderDragging)
- {
- sliderDragging = false;
- valueChanged(true);
- }
- ap.paintAlignment(true);
- }
- });
-
- if (av.getAlignment().getAlignmentAnnotation() == null)
- {
- return;
- }
-
- // Always get default shading from preferences.
- setDefaultMinMax();
-
- adjusting = true;
-
- setAnnotations(new JComboBox(
- getAnnotationItems(seqAssociated.isSelected())));
-
- threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
- threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
- threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
-
- if (av.getCurrentAnnotationColumnSelectionState() != null)
- {
- annotations.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getAnnotations()
- .getSelectedIndex());
- threshold.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getThreshold()
- .getSelectedIndex());
- System.out.println("selected annotation : "
- + av.getCurrentAnnotationColumnSelectionState()
- .getAnnotations().getSelectedIndex());
- System.out.println("selected threshold : "
- + av.getCurrentAnnotationColumnSelectionState()
- .getThreshold().getSelectedIndex());
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- }
-
- adjusting = false;
-
- changeColumnSelection();
- frame.invalidate();
- frame.pack();
-
- }
-
- private Vector<String> getAnnotationItems(boolean isSeqAssociated)
- {
- Vector<String> list = new Vector<String>();
- int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss = false;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
- {
- if (isSeqAssociated)
- {
- continue;
- }
- }
- else
- {
- enableSeqAss = true;
- }
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- {
- anmap[list.size()] = i;
- list.add(label);
-
- }
- else
- {
- if (!isSeqAssociated)
- {
- anmap[list.size()] = i;
- list.add(label + "_" + (index++));
- }
- }
- }
- seqAssociated.setEnabled(enableSeqAss);
- this.annmap = new int[list.size()];
- System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
- return list;
- }
-
- private void setDefaultMinMax()
- {
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
- }
-
- public AnnotationColumnSelection()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
-
- getAnnotations().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- getThreshold().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed(e);
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
- thresholdIsMin.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- thresholdIsMin_actionPerformed(actionEvent);
- }
- });
- seqAssociated.setBackground(Color.white);
- seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
- seqAssociated.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- seqAssociated_actionPerformed(arg0);
- }
- });
-
- this.setLayout(borderLayout1);
- jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
- jPanel1.setBackground(Color.white);
- jPanel2.setBackground(Color.white);
-
- jPanel1.add(ok);
- jPanel1.add(cancel);
- jPanel2.add(getAnnotations(), "grow, wrap");
- jPanel2.add(seqAssociated, "wrap");
- jPanel2.add(getThreshold(), "grow, wrap");
- jPanel2.add(thresholdIsMin, "wrap");
- jPanel2.add(slider, "grow");
- jPanel2.add(thresholdValue, "grow");
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.CENTER);
- this.validate();
- }
-
- protected void seqAssociated_actionPerformed(ActionEvent arg0)
- {
- adjusting = true;
- String cursel = (String) getAnnotations().getSelectedItem();
- boolean isvalid = false, isseqs = seqAssociated.isSelected();
- this.getAnnotations().removeAllItems();
- for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
- {
- if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
- {
- isvalid = true;
- cursel = anitem;
- }
- this.getAnnotations().addItem(anitem);
- }
- adjusting = false;
- if (isvalid)
- {
- this.getAnnotations().setSelectedItem(cursel);
- }
- else
- {
- if (getAnnotations().getItemCount() > 0)
- {
- getAnnotations().setSelectedIndex(0);
- }
- }
- }
-
-
- void changeColumnSelection()
- {
- // Check if combobox is still adjusting
- if (adjusting)
- {
- return;
- }
-
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]]);
-
- int aboveThreshold = -1;
- if (getThreshold().getSelectedIndex() == 1)
- {
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
- }
- else if (getThreshold().getSelectedIndex() == 2)
- {
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
- }
-
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
-
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
- {
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
- }
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && getCurrentAnnotation().threshold == null)
- {
- getCurrentAnnotation()
- .setThreshold(new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
- }
-
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
- {
- adjusting = true;
- float range = getCurrentAnnotation().graphMax * 1000
- - getCurrentAnnotation().graphMin * 1000;
-
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
- slider.setMajorTickSpacing((int) (range / 10f));
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- adjusting = false;
- }
-
- markColumnsContaining(getCurrentAnnotation(), aboveThreshold);
- av.setCurrentAnnotationColumnSelectionState(this);
- ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of
- // updated colours.
- ap.paintAlignment(true);
- }
-
- public boolean markColumnsContaining(
- AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
- {
- try
- {
- if (currentAnnotation != null)
- {
- Annotation[] annotations = currentAnnotation.annotations;
- ColumnSelection cs = av.getColumnSelection();
- cs.clear();
- if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (currentAnnotation.label.equals("Secondary Structure")
- && annotations[count].secondaryStructure != ' ')
- {
- cs.addElement(count);
- }
- else if (currentAnnotation.label
- .equals("Iron Sulphur Contacts"))
- {
- cs.addElement(count);
- }
- else if (annotations[count].value != 0.0)
- {
- cs.addElement(count);
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- else
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- if (annotations[count].value > currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
- else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- if (annotations[count].value < currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- }
-
- return true;
- } catch (Exception e)
- {
- e.printStackTrace();
- return false;
- }
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
-
- public void cancel_actionPerformed(ActionEvent e)
- {
- reset();
- // ensure all original colouring is propagated to listeners.
- ap.paintAlignment(true);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
-
- void reset()
- {
- av.getColumnSelection().clear();
- }
-
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
- {
- changeColumnSelection();
- }
-
- public void thresholdValue_actionPerformed(ActionEvent e)
- {
- try
- {
- float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
- changeColumnSelection();
- } catch (NumberFormatException ex)
- {
- }
- }
-
- public void valueChanged(boolean updateAllAnnotation)
- {
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
- changeColumnSelection();
- // propagateSeqAssociatedThreshold(updateAllAnnotation);
- ap.paintAlignment(false);
- }
-
- private void propagateSeqAssociatedThreshold(boolean allAnnotation)
- {
- if (getCurrentAnnotation().sequenceRef == null
- || getCurrentAnnotation().threshold == null)
- {
- return;
- }
-
-
- float thr = getCurrentAnnotation().threshold.value;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
- {
- AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
- if (aa.label.equals(getCurrentAnnotation().label)
- && (getCurrentAnnotation().getCalcId() == null ? aa
- .getCalcId() == null : getCurrentAnnotation()
- .getCalcId()
- .equals(aa.getCalcId())))
- {
- if (aa.threshold == null)
- {
- aa.threshold = new GraphLine(getCurrentAnnotation().threshold);
- }
- else
- {
- aa.threshold.value = thr;
- }
- }
- }
- }
-
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
- {
- reset();
- }
-
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
-
- changeColumnSelection();
- }
-
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
- {
- changeColumnSelection();
- }
-
- public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
- {
- return currentAnnotation;
- }
-
- public void setCurrentAnnotation(
- jalview.datamodel.AlignmentAnnotation currentAnnotation)
- {
- this.currentAnnotation = currentAnnotation;
- }
-
- public JComboBox getThreshold()
- {
- return threshold;
- }
-
- public void setThreshold(JComboBox threshold)
- {
- this.threshold = threshold;
- }
-
- public JComboBox getAnnotations()
- {
- return annotations;
- }
-
- public void setAnnotations(JComboBox annotations)
- {
- this.annotations = annotations;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff