X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;fp=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=c2bf41bc479187990e12fe51f4b930cc59a21399;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=c8bd69c8389cd2f3a97f41205b16379de47990a6;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java index c8bd69c..c2bf41b 100644 --- a/src/jalview/gui/AnnotationRowFilter.java +++ b/src/jalview/gui/AnnotationRowFilter.java @@ -22,12 +22,21 @@ package jalview.gui; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceGroup; 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 javax.swing.JButton; @@ -49,22 +58,10 @@ public abstract class AnnotationRowFilter extends JPanel protected int[] annmap; - 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 JSlider slider = new JSlider(); protected JTextField thresholdValue = new JTextField(20); @@ -81,6 +78,38 @@ 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() { @@ -130,25 +159,27 @@ public abstract class AnnotationRowFilter extends JPanel }); } - 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 + * list, and their display labels in the list. + * + * @param isSeqAssociated + * @return + */ public Vector getAnnotationItems(boolean isSeqAssociated) { + annotationLabels = new HashMap(); + Vector list = new Vector(); int index = 1; int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; + seqAssociated.setEnabled(false); for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) { - if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null) + AlignmentAnnotation annotation = av.getAlignment() + .getAlignmentAnnotation()[i]; + if (annotation.sequenceRef == null) { if (isSeqAssociated) { @@ -157,30 +188,29 @@ public abstract class AnnotationRowFilter extends JPanel } else { - enableSeqAss = true; + seqAssociated.setEnabled(true); } - String label = av.getAlignment().getAlignmentAnnotation()[i].label; + String label = annotation.label; // add associated sequence ID if available - if (!isSeqAssociated - && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null) + if (!isSeqAssociated && annotation.sequenceRef != null) { - label = label - + "_" - + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef - .getName(); + label = label + "_" + annotation.sequenceRef.getName(); } // make label unique if (!list.contains(label)) { anmap[list.size()] = i; list.add(label); + annotationLabels.put(annotation, label); } else { if (!isSeqAssociated) { anmap[list.size()] = i; - list.add(label + "_" + (index++)); + label = label + "_" + (index++); + list.add(label); + annotationLabels.put(annotation, label); } } } @@ -203,11 +233,6 @@ public abstract class AnnotationRowFilter extends JPanel return selectedThresholdItem; } - public void modelChanged() - { - seqAssociated.setEnabled(enableSeqAss); - } - public void ok_actionPerformed() { try @@ -230,22 +255,22 @@ 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 { @@ -257,27 +282,34 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void thresholdIsMin_actionPerformed() + 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")); } - protected void seqAssociated_actionPerformed(JComboBox annotations) + /** + * Rebuilds the drop-down list of annotations to choose from when the 'per + * sequence only' checkbox is checked or unchecked. + * + * @param anns + */ + 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))) @@ -285,20 +317,22 @@ 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, @@ -329,79 +363,107 @@ public abstract class AnnotationRowFilter extends JPanel } } - protected boolean colorAlignmContaining(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; + } - if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f) - { - acg.setPredefinedColours(true); - } + protected abstract void valueChanged(boolean updateAllAnnotation); + + protected abstract void updateView(); - acg.thresholdIsMinMax = thresholdIsMin.isSelected(); + protected abstract void reset(); - av.setGlobalColourScheme(acg); + protected String getAnnotationMenuLabel(AlignmentAnnotation ann) + { + return annotationLabels.get(ann); + } - if (av.getAlignment().getGroups() != null) + protected void jbInit() + { + ok.setOpaque(false); + ok.setText(MessageManager.getString("action.ok")); + ok.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) + { + ok_actionPerformed(); + } + }); - for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + cancel.setOpaque(false); + cancel.setText(MessageManager.getString("action.cancel")); + cancel.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - if (sg.cs == null) - { - continue; - } + cancel_actionPerformed(); + } + }); - if (currentColours.isSelected()) - { - sg.cs = new AnnotationColourGradient(currentAnn, sg.cs, - selectedThresholdOption); - ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated - .isSelected()); + annotations.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + selectedAnnotationChanged(); + } + }); + annotations.setToolTipText(MessageManager + .getString("info.select_annotation_row")); - } - else - { - sg.cs = new AnnotationColourGradient(currentAnn, - minColour.getBackground(), maxColour.getBackground(), - selectedThresholdOption); - ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated - .isSelected()); - } + threshold.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + threshold_actionPerformed(); + } + }); + thresholdValue.setEnabled(false); + thresholdValue.setColumns(7); + thresholdValue.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + thresholdValue_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 jalview.datamodel.AlignmentAnnotation getCurrentAnnotation() + public JComboBox getThreshold() { - return currentAnnotation; + return threshold; } - public void setCurrentAnnotation( - jalview.datamodel.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; + } }