--- /dev/null
+package jalview.gui;
+
+import jalview.api.AnnotationRowFilterI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Vector;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+@SuppressWarnings("serial")
+public abstract class AnnotationRowFilter extends JPanel implements
+ AnnotationRowFilterI
+{
+ protected AlignViewport av;
+
+ protected AlignmentPanel ap;
+
+ protected int[] annmap;
+
+ protected boolean enableSeqAss = false;
+
+ private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
+ protected boolean adjusting = false;
+
+ protected JCheckBox currentColours = new JCheckBox();
+
+ protected JPanel minColour = new JPanel();
+
+ protected JPanel maxColour = new JPanel();
+
+ protected JCheckBox seqAssociated = new JCheckBox();
+
+ protected JCheckBox thresholdIsMin = new JCheckBox();
+
+ protected JSlider slider = new JSlider();
+
+ protected JTextField thresholdValue = new JTextField(20);
+
+ protected JInternalFrame frame;
+ /**
+ * enabled if the user is dragging the slider - try to keep updates to a
+ * minimun
+ */
+ protected boolean sliderDragging = false;
+
+ protected void addSliderChangeListener()
+ {
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ valueChanged(!sliderDragging);
+ }
+ }
+ });
+ }
+
+ protected void addSliderMouseListeners()
+ {
+
+ 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);
+ }
+ });
+ }
+
+
+ public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
+ {
+ this.av = av;
+ this.ap = ap;
+ }
+
+ public AnnotationRowFilter()
+ {
+
+ }
+
+ @Override
+ public Vector<String> getAnnotationItems(boolean isSeqAssociated)
+ {
+ Vector<String> list = new Vector<String>();
+ int index = 1;
+ int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+ 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;
+ }
+
+ protected int getSelectedThresholdItem(int indexValue)
+ {
+ int selectedThresholdItem = -1;
+ if (indexValue == 1)
+ {
+ selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
+ }
+ else if (indexValue == 2)
+ {
+ selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
+ }
+ return selectedThresholdItem;
+ }
+
+ public void modelChanged()
+ {
+ seqAssociated.setEnabled(enableSeqAss);
+ }
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ reset();
+ ap.paintAlignment(true);
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void thresholdCheck_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ }
+
+ public void annotations_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ }
+
+ public void threshold_actionPerformed(ActionEvent e)
+ {
+ updateView();
+ }
+
+ public void thresholdValue_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ float f = Float.parseFloat(thresholdValue.getText());
+ slider.setValue((int) (f * 1000));
+ updateView();
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+
+ public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ {
+ updateView();
+ }
+
+ protected void populateThresholdComboBox(JComboBox<String> threshold)
+ {
+ 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"));
+ }
+
+ protected void seqAssociated_actionPerformed(ActionEvent arg0,
+ JComboBox<String> annotations, JCheckBox seqAssociated)
+ {
+ adjusting = true;
+ String cursel = (String) annotations.getSelectedItem();
+ boolean isvalid = false, isseqs = seqAssociated.isSelected();
+ annotations.removeAllItems();
+ for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
+ {
+ if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
+ {
+ isvalid = true;
+ cursel = anitem;
+ }
+ annotations.addItem(anitem);
+ }
+ adjusting = false;
+ if (isvalid)
+ {
+ annotations.setSelectedItem(cursel);
+ }
+ else
+ {
+ if (annotations.getItemCount() > 0)
+ {
+ annotations.setSelectedIndex(0);
+ }
+ }
+ }
+
+ protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
+ AlignmentAnnotation annotation)
+ {
+ if (annotation.sequenceRef == null || annotation.threshold == null)
+ {
+ return;
+ }
+
+ float thr = annotation.threshold.value;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+ if (aa.label.equals(annotation.label)
+ && (annotation.getCalcId() == null ? aa.getCalcId() == null
+ : annotation.getCalcId().equals(aa.getCalcId())))
+ {
+ if (aa.threshold == null)
+ {
+ aa.threshold = new GraphLine(annotation.threshold);
+ }
+ else
+ {
+ aa.threshold.value = thr;
+ }
+ }
+ }
+ }
+
+ protected boolean colorAlignmContaining(
+ AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+ {
+
+ AnnotationColourGradient acg = null;
+ if (currentColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnnotation,
+ av.getGlobalColourScheme(), selectedThresholdItem);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdItem);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnnotation.graphMin == 0f
+ && currentAnnotation.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+ av.setGlobalColourScheme(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ if (currentColours.isSelected())
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+ selectedThresholdItem);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+
+ }
+ else
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdItem);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+
+ }
+ }
+ return false;
+ }
+
+ protected 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 jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+ {
+ return currentAnnotation;
+ }
+
+ public void setCurrentAnnotation(
+ jalview.datamodel.AlignmentAnnotation currentAnnotation)
+ {
+ this.currentAnnotation = currentAnnotation;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff