X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=253a7ec91e03f95ded558a175cee5378f8d91227;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=c8dd889c94d51df951d87fb573c2386edd46ce04;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index c8dd889..253a7ec 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -21,6 +21,8 @@ package jalview.gui; import jalview.bin.Cache; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.GraphLine; import jalview.datamodel.SequenceGroup; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; @@ -35,9 +37,11 @@ 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.BorderFactory; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JInternalFrame; @@ -49,28 +53,25 @@ import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") public class AnnotationColourChooser extends AnnotationRowFilter { + private static final int ONETHOUSAND = 1000; - ColourSchemeI oldcs; + private ColourSchemeI oldcs; - Hashtable oldgroupColours; + private JButton defColours; - /** - * enabled if the user is dragging the slider - try to keep updates to a - * minimun - */ + private Hashtable oldgroupColours; - JComboBox annotations; + private JCheckBox useOriginalColours = new JCheckBox(); - JButton defColours = new JButton(); + private JPanel minColour = new JPanel(); + private JPanel maxColour = new JPanel(); - JPanel jPanel1 = new JPanel(); + private JCheckBox thresholdIsMin = new JCheckBox(); - JPanel jPanel2 = new JPanel(); + protected static final int MIN_WIDTH = 500; - BorderLayout borderLayout1 = new BorderLayout(); - - private JComboBox threshold = new JComboBox(); + protected static final int MIN_HEIGHT = 240; public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { @@ -81,9 +82,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter oldgroupColours = new Hashtable(); for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - if (sg.cs != null) + if (sg.getColourScheme() != null) { - oldgroupColours.put(sg, sg.cs); + oldgroupColours.put(sg, sg.getColourScheme()); } } } @@ -93,7 +94,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215); - + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); addSliderChangeListener(); addSliderMouseListeners(); @@ -109,7 +110,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - currentColours.setSelected(acg.isPredefinedColours() + useOriginalColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour() != null); if (!acg.isPredefinedColours() && acg.getBaseColour() == null) { @@ -119,15 +120,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter seqAssociated.setSelected(acg.isSeqAssociated()); } - annotations = new JComboBox( - getAnnotationItems(seqAssociated.isSelected())); + Vector annotItems = getAnnotationItems(seqAssociated + .isSelected()); + annotations = new JComboBox(annotItems); populateThresholdComboBox(threshold); if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; - annotations.setSelectedItem(acg.getAnnotation()); + String label = getAnnotationMenuLabel(acg.getAnnotation()); + annotations.setSelectedItem(label); switch (acg.getAboveThreshold()) { case AnnotationColourGradient.NO_THRESHOLD: @@ -140,18 +143,15 @@ public class AnnotationColourChooser extends AnnotationRowFilter getThreshold().setSelectedIndex(2); break; default: - throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting")); + throw new Error( + MessageManager + .getString("error.implementation_error_dont_know_about_threshold_setting")); } - thresholdIsMin.setSelected(acg.thresholdIsMinMax); + thresholdIsMin.setSelected(acg.isThresholdIsMinMax()); thresholdValue.setText("" + acg.getAnnotationThreshold()); } - try - { - jbInit(); - } catch (Exception ex) - { - } + jbInit(); adjusting = false; updateView(); @@ -159,19 +159,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter frame.pack(); } - public AnnotationColourChooser() + @Override + protected void jbInit() { - try - { - jbInit(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } + super.jbInit(); - private void jbInit() throws Exception - { minColour.setFont(JvSwingUtils.getLabelFont()); minColour.setBorder(BorderFactory.createEtchedBorder()); minColour.setPreferredSize(new Dimension(40, 20)); @@ -202,26 +194,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } }); - 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); - } - }); + + defColours = new JButton(); defColours.setOpaque(false); defColours.setText(MessageManager.getString("action.set_defaults")); defColours.setToolTipText(MessageManager @@ -232,52 +206,20 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent arg0) { - resetColours_actionPerformed(arg0); + resetColours_actionPerformed(); } }); - annotations.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); - currentColours.setFont(JvSwingUtils.getLabelFont()); - currentColours.setOpaque(false); - currentColours.setText(MessageManager + useOriginalColours.setFont(JvSwingUtils.getLabelFont()); + useOriginalColours.setOpaque(false); + useOriginalColours.setText(MessageManager .getString("label.use_original_colours")); - currentColours.addActionListener(new ActionListener() + useOriginalColours.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - currentColours_actionPerformed(e); + originalColours_actionPerformed(); } }); thresholdIsMin.setBackground(Color.white); @@ -289,7 +231,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent actionEvent) { - thresholdIsMin_actionPerformed(actionEvent); + thresholdIsMin_actionPerformed(); } }); seqAssociated.setBackground(Color.white); @@ -302,11 +244,13 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent arg0) { - seqAssociated_actionPerformed(arg0, annotations, seqAssociated); + seqAssociated_actionPerformed(annotations); } }); - this.setLayout(borderLayout1); + this.setLayout(new BorderLayout()); + JPanel jPanel1 = new JPanel(); + JPanel jPanel2 = new JPanel(); jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]")); jPanel1.setBackground(Color.white); jPanel2.setBackground(Color.white); @@ -315,7 +259,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter jPanel1.add(cancel); jPanel2.add(annotations, "grow, wrap"); jPanel2.add(seqAssociated); - jPanel2.add(currentColours); + jPanel2.add(useOriginalColours); JPanel colpanel = new JPanel(new FlowLayout()); colpanel.setBackground(Color.white); colpanel.add(minColour); @@ -331,7 +275,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter this.validate(); } - protected void resetColours_actionPerformed(ActionEvent arg0) + protected void resetColours_actionPerformed() { setDefaultMinMax(); updateView(); @@ -348,7 +292,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter public void minColour_actionPerformed() { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground()); + MessageManager.getString("label.select_colour_minimum_value"), + minColour.getBackground()); if (col != null) { minColour.setBackground(col); @@ -360,7 +305,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter public void maxColour_actionPerformed() { Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground()); + MessageManager.getString("label.select_colour_maximum_value"), + maxColour.getBackground()); if (col != null) { maxColour.setBackground(col); @@ -369,6 +315,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter updateView(); } + @Override public void reset() { av.setGlobalColourScheme(oldcs); @@ -377,16 +324,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - sg.cs = oldgroupColours.get(sg); + sg.setColourScheme(oldgroupColours.get(sg)); } } } + @Override public void valueChanged(boolean updateAllAnnotation) { if (slider.isEnabled()) { - if (currentColours.isSelected() + if (useOriginalColours.isSelected() && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) { updateView(); @@ -398,24 +346,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } - public JComboBox getThreshold() - { - return threshold; - } - - public void setThreshold(JComboBox threshold) - { - this.threshold = threshold; - } - - public void currentColours_actionPerformed(ActionEvent e) + public void originalColours_actionPerformed() { - if (currentColours.isSelected()) + boolean selected = useOriginalColours.isSelected(); + if (selected) { reset(); } - maxColour.setEnabled(!currentColours.isSelected()); - minColour.setEnabled(!currentColours.isSelected()); + maxColour.setEnabled(!selected); + minColour.setEnabled(!selected); + thresholdIsMin.setEnabled(!selected); updateView(); } @@ -436,7 +376,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter slider.setEnabled(true); thresholdValue.setEnabled(true); - thresholdIsMin.setEnabled(true); + thresholdIsMin.setEnabled(!useOriginalColours.isSelected()); if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) { @@ -449,27 +389,28 @@ public class AnnotationColourChooser extends AnnotationRowFilter && getCurrentAnnotation().threshold == null) { getCurrentAnnotation() - .setThreshold(new jalview.datamodel.GraphLine( - (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f, - "Threshold", Color.black)); + .setThreshold( + new GraphLine( + (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f, + "Threshold", Color.black)); } if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) { adjusting = true; - float range = getCurrentAnnotation().graphMax * 1000 - - getCurrentAnnotation().graphMin * 1000; + float range = getCurrentAnnotation().graphMax * ONETHOUSAND + - getCurrentAnnotation().graphMin * ONETHOUSAND; - slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000)); - slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000)); - slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000)); + slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND)); + slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND)); + slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND)); thresholdValue.setText(getCurrentAnnotation().threshold.value + ""); slider.setMajorTickSpacing((int) (range / 10f)); slider.setEnabled(true); thresholdValue.setEnabled(true); adjusting = false; } - colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem); + colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem); ap.alignmentChanged(); // ensure all associated views (overviews, structures, etc) are notified of @@ -477,4 +418,60 @@ public class AnnotationColourChooser extends AnnotationRowFilter ap.paintAlignment(true); } + protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption) + { + + AnnotationColourGradient acg = null; + if (useOriginalColours.isSelected()) + { + acg = new AnnotationColourGradient(currentAnn, + av.getGlobalColourScheme(), selectedThresholdOption); + } + else + { + acg = new AnnotationColourGradient(currentAnn, + minColour.getBackground(), maxColour.getBackground(), + selectedThresholdOption); + } + acg.setSeqAssociated(seqAssociated.isSelected()); + + if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f) + { + acg.setPredefinedColours(true); + } + + acg.setThresholdIsMinMax(thresholdIsMin.isSelected()); + + av.setGlobalColourScheme(acg); + + if (av.getAlignment().getGroups() != null) + { + + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + { + if (sg.cs == null) + { + continue; + } + + if (useOriginalColours.isSelected()) + { + sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg + .getColourScheme(), selectedThresholdOption)); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); + } + else + { + sg.setColourScheme(new AnnotationColourGradient(currentAnn, + minColour.getBackground(), maxColour.getBackground(), + selectedThresholdOption)); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); + } + } + } + return false; + } + }