X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=f13cb10579c79b4690885d4000b059e23723ca7c;hb=1a7569b26f3f24011b33f0551ecbf5377b1fb85b;hp=ea531f289511704c4de866d1fbeff39af3cd310a;hpb=4be2c7d1bcf79664267750cb1187079305794363;p=jalview.git diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java index ea531f2..f13cb10 100644 --- a/src/jalview/gui/AnnotationRowFilter.java +++ b/src/jalview/gui/AnnotationRowFilter.java @@ -20,18 +20,25 @@ */ package jalview.gui; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.GraphLine; +import jalview.schemes.AnnotationColourGradient; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.HashMap; import java.util.Map; import java.util.Vector; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceGroup; -import jalview.schemes.AnnotationColourGradient; -import jalview.util.MessageManager; - import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; @@ -51,27 +58,11 @@ public abstract class AnnotationRowFilter extends JPanel protected int[] annmap; - /* - * map from annotation to its menu item display label - * - so we know which item to pre-select on restore - */ - private Map annotationLabels; - - protected boolean enableSeqAss = false; - - private 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 JCheckBox percentThreshold = new JCheckBox(); protected JSlider slider = new JSlider(); @@ -89,6 +80,39 @@ public abstract class AnnotationRowFilter extends JPanel */ protected boolean sliderDragging = false; + protected JComboBox threshold = new JComboBox<>(); + + protected JComboBox annotations; + + /* + * map from annotation to its menu item display label + * - so we know which item to pre-select on restore + */ + private Map annotationLabels; + + private AlignmentAnnotation currentAnnotation; + + /** + * Constructor + * + * @param viewport + * @param alignPanel + */ + public AnnotationRowFilter(AlignViewport viewport, + final AlignmentPanel alignPanel) + { + this.av = viewport; + this.ap = alignPanel; + thresholdValue.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + thresholdValue_actionPerformed(); + } + }); + } + protected void addSliderChangeListener() { @@ -99,13 +123,33 @@ public abstract class AnnotationRowFilter extends JPanel { if (!adjusting) { - thresholdValue.setText((slider.getValue() / 1000f) + ""); + setThresholdValueText(); valueChanged(!sliderDragging); } } }); } + /** + * update the text field from the threshold slider. preserves state of + * 'adjusting' so safe to call in init. + */ + protected void setThresholdValueText() + { + boolean oldadj = adjusting; + adjusting = true; + if (percentThreshold.isSelected()) + { + thresholdValue.setText("" + (slider.getValue() - slider.getMinimum()) + * 100f / (slider.getMaximum() - slider.getMinimum())); + } + else + { + thresholdValue.setText((slider.getValue() / 1000f) + ""); + } + adjusting = oldadj; + } + protected void addSliderMouseListeners() { @@ -128,27 +172,11 @@ public abstract class AnnotationRowFilter extends JPanel @Override public void mouseReleased(MouseEvent evt) { - if (sliderDragging) - { - sliderDragging = false; - valueChanged(true); - } - ap.paintAlignment(true); + sliderDragReleased(); } }); } - public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap) - { - this.av = av; - this.ap = ap; - } - - public AnnotationRowFilter() - { - - } - /** * Builds and returns a list of menu items (display text) for choice of * annotation. Also builds maps between annotations, their positions in the @@ -159,12 +187,15 @@ public abstract class AnnotationRowFilter extends JPanel */ public Vector getAnnotationItems(boolean isSeqAssociated) { - annotationLabels = new HashMap(); + annotationLabels = new HashMap<>(); - Vector list = new Vector(); + Vector list = new Vector<>(); int index = 1; - int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + int[] anmap = new int[av.getAlignment() + .getAlignmentAnnotation().length]; + seqAssociated.setEnabled(false); + for (int i = 0; i < av.getAlignment() + .getAlignmentAnnotation().length; i++) { AlignmentAnnotation annotation = av.getAlignment() .getAlignmentAnnotation()[i]; @@ -177,7 +208,7 @@ public abstract class AnnotationRowFilter extends JPanel } else { - enableSeqAss = true; + seqAssociated.setEnabled(true); } String label = annotation.label; // add associated sequence ID if available @@ -222,11 +253,6 @@ public abstract class AnnotationRowFilter extends JPanel return selectedThresholdItem; } - public void modelChanged() - { - seqAssociated.setEnabled(enableSeqAss); - } - public void ok_actionPerformed() { try @@ -240,7 +266,7 @@ public abstract class AnnotationRowFilter extends JPanel public void cancel_actionPerformed() { reset(); - ap.paintAlignment(true); + ap.paintAlignment(true, true); try { frame.setClosed(true); @@ -249,45 +275,58 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void thresholdCheck_actionPerformed() + protected void thresholdCheck_actionPerformed() { updateView(); } - public void annotations_actionPerformed() + protected void selectedAnnotationChanged() { updateView(); } - public void threshold_actionPerformed() + protected void threshold_actionPerformed() { updateView(); } - public void thresholdValue_actionPerformed() + protected void thresholdValue_actionPerformed() { try { float f = Float.parseFloat(thresholdValue.getText()); - slider.setValue((int) (f * 1000)); + if (percentThreshold.isSelected()) + { + slider.setValue(slider.getMinimum() + ((int) ((f / 100f) + * (slider.getMaximum() - slider.getMinimum())))); + } + else + { + slider.setValue((int) (f * 1000)); + } updateView(); } catch (NumberFormatException ex) { } } - public void thresholdIsMin_actionPerformed() + protected void percentageValue_actionPerformed() + { + setThresholdValueText(); + } + + protected void thresholdIsMin_actionPerformed() { updateView(); } - protected void populateThresholdComboBox(JComboBox threshold) + protected void populateThresholdComboBox(JComboBox thresh) { - threshold.addItem(MessageManager + thresh.addItem(MessageManager .getString("label.threshold_feature_no_threshold")); - threshold.addItem(MessageManager + thresh.addItem(MessageManager .getString("label.threshold_feature_above_threshold")); - threshold.addItem(MessageManager + thresh.addItem(MessageManager .getString("label.threshold_feature_below_threshold")); } @@ -295,14 +334,15 @@ public abstract class AnnotationRowFilter extends JPanel * Rebuilds the drop-down list of annotations to choose from when the 'per * sequence only' checkbox is checked or unchecked. * - * @param annotations + * @param anns */ - protected void seqAssociated_actionPerformed(JComboBox annotations) + protected void seqAssociated_actionPerformed(JComboBox anns) { adjusting = true; - String cursel = (String) annotations.getSelectedItem(); - boolean isvalid = false, isseqs = seqAssociated.isSelected(); - annotations.removeAllItems(); + String cursel = (String) anns.getSelectedItem(); + boolean isvalid = false; + boolean isseqs = seqAssociated.isSelected(); + anns.removeAllItems(); for (String anitem : getAnnotationItems(seqAssociated.isSelected())) { if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem))) @@ -310,20 +350,22 @@ public abstract class AnnotationRowFilter extends JPanel isvalid = true; cursel = anitem; } - annotations.addItem(anitem); + anns.addItem(anitem); } - adjusting = false; if (isvalid) { - annotations.setSelectedItem(cursel); + anns.setSelectedItem(cursel); } else { - if (annotations.getItemCount() > 0) + if (anns.getItemCount() > 0) { - annotations.setSelectedIndex(0); + anns.setSelectedIndex(0); } } + adjusting = false; + + updateView(); } protected void propagateSeqAssociatedThreshold(boolean allAnnotation, @@ -335,9 +377,11 @@ public abstract class AnnotationRowFilter extends JPanel } float thr = annotation.threshold.value; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + for (int i = 0; i < av.getAlignment() + .getAlignmentAnnotation().length; i++) { - AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i]; + AlignmentAnnotation aa = av.getAlignment() + .getAlignmentAnnotation()[i]; if (aa.label.equals(annotation.label) && (annotation.getCalcId() == null ? aa.getCalcId() == null : annotation.getCalcId().equals(aa.getCalcId()))) @@ -354,81 +398,134 @@ public abstract class AnnotationRowFilter extends JPanel } } - protected boolean colorAlignmentContaining( - AlignmentAnnotation currentAnn, int selectedThresholdOption) + public AlignmentAnnotation getCurrentAnnotation() { + return currentAnnotation; + } - AnnotationColourGradient acg = null; - if (currentColours.isSelected()) - { - acg = new AnnotationColourGradient(currentAnn, - av.getGlobalColourScheme(), selectedThresholdOption); - } - else - { - acg = new AnnotationColourGradient(currentAnn, - minColour.getBackground(), maxColour.getBackground(), - selectedThresholdOption); - } - acg.setSeqAssociated(seqAssociated.isSelected()); + protected void setCurrentAnnotation(AlignmentAnnotation annotation) + { + this.currentAnnotation = annotation; + } + + /** + * update associated view model and trigger any necessary repaints. + * + * @param updateAllAnnotation + */ + protected abstract void valueChanged(boolean updateAllAnnotation); - if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f) + protected abstract void updateView(); + + protected abstract void reset(); + + protected String getAnnotationMenuLabel(AlignmentAnnotation ann) + { + return annotationLabels.get(ann); + } + + protected void jbInit() + { + ok.setOpaque(false); + ok.setText(MessageManager.getString("action.ok")); + ok.addActionListener(new ActionListener() { - acg.setPredefinedColours(true); - } + @Override + public void actionPerformed(ActionEvent e) + { + ok_actionPerformed(); + } + }); - acg.setThresholdIsMinMax(thresholdIsMin.isSelected()); + cancel.setOpaque(false); + cancel.setText(MessageManager.getString("action.cancel")); + cancel.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + cancel_actionPerformed(); + } + }); - av.setGlobalColourScheme(acg); + annotations.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + selectedAnnotationChanged(); + } + }); + annotations.setToolTipText( + MessageManager.getString("info.select_annotation_row")); - if (av.getAlignment().getGroups() != null) + threshold.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) + { + threshold_actionPerformed(); + } + }); - for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + thresholdValue.setEnabled(false); + thresholdValue.setColumns(7); + thresholdValue.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - if (sg.cs == null) - { - continue; - } + thresholdValue_actionPerformed(); + } + }); - if (currentColours.isSelected()) - { - sg.cs = new AnnotationColourGradient(currentAnn, sg.cs, - selectedThresholdOption); - ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated - .isSelected()); - } - else + percentThreshold + .setText(MessageManager.getString("label.as_percentage")); + percentThreshold.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (!adjusting) { - sg.cs = new AnnotationColourGradient(currentAnn, - minColour.getBackground(), maxColour.getBackground(), - selectedThresholdOption); - ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated - .isSelected()); + percentageValue_actionPerformed(); } } - } - return false; + }); + slider.setPaintLabels(false); + slider.setPaintTicks(true); + slider.setBackground(Color.white); + slider.setEnabled(false); + slider.setOpaque(false); + slider.setPreferredSize(new Dimension(100, 32)); } - public AlignmentAnnotation getCurrentAnnotation() + public JComboBox getThreshold() { - return currentAnnotation; + return threshold; } - public void setCurrentAnnotation(AlignmentAnnotation currentAnnotation) + public void setThreshold(JComboBox thresh) { - this.currentAnnotation = currentAnnotation; + this.threshold = thresh; } - public abstract void valueChanged(boolean updateAllAnnotation); - - public abstract void updateView(); + public JComboBox getAnnotations() + { + return annotations; + } - public abstract void reset(); + public void setAnnotations(JComboBox anns) + { + this.annotations = anns; + } - protected String getAnnotationMenuLabel(AlignmentAnnotation ann) + protected void sliderDragReleased() { - return annotationLabels.get(ann); + if (sliderDragging) + { + sliderDragging = false; + valueChanged(true); + } } }