X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=850088844206e586aa4b34ef118f909ad37a908b;hb=9eabd6dffd6d19b2826b887a5def80351b9bceed;hp=b2c4255979419f1f01687aca85dbe11d952596da;hpb=2963965a346b42b6b9a2d0878ee076220be7077b;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index b2c4255..8500888 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -20,6 +20,14 @@ */ 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; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -31,15 +39,9 @@ import java.awt.event.MouseEvent; import java.util.Hashtable; import java.util.Vector; -import jalview.bin.Cache; -import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceGroup; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.ColourSchemeI; -import jalview.util.MessageManager; - import javax.swing.BorderFactory; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JInternalFrame; @@ -51,27 +53,21 @@ import net.miginfocom.swing.MigLayout; @SuppressWarnings("serial") public class AnnotationColourChooser extends AnnotationRowFilter { + private static final int ONETHOUSAND = 1000; - ColourSchemeI oldcs; - - Hashtable oldgroupColours; - - /** - * enabled if the user is dragging the slider - try to keep updates to a - * minimun - */ + private ColourSchemeI oldcs; - JComboBox annotations; + private JButton defColours; - JButton defColours = new JButton(); + private Hashtable oldgroupColours; - JPanel jPanel1 = new JPanel(); + private JCheckBox useOriginalColours = new JCheckBox(); - JPanel jPanel2 = new JPanel(); + private JPanel minColour = new JPanel(); - BorderLayout borderLayout1 = new BorderLayout(); + private JPanel maxColour = new JPanel(); - private JComboBox threshold = new JComboBox(); + private JCheckBox thresholdIsMin = new JCheckBox(); public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { @@ -82,9 +78,9 @@ 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()); } } } @@ -110,7 +106,7 @@ 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) { @@ -151,12 +147,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter thresholdValue.setText("" + acg.getAnnotationThreshold()); } - try - { - jbInit(); - } catch (Exception ex) - { - } + jbInit(); adjusting = false; updateView(); @@ -164,19 +155,11 @@ 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)); @@ -207,26 +190,8 @@ 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(); - } - }); - cancel.setOpaque(false); - cancel.setText(MessageManager.getString("action.cancel")); - cancel.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - cancel_actionPerformed(); - } - }); + + defColours = new JButton(); defColours.setOpaque(false); defColours.setText(MessageManager.getString("action.set_defaults")); defColours.setToolTipText(MessageManager @@ -241,48 +206,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter } }); - annotations.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - annotations_actionPerformed(); - } - }); - getThreshold().addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - threshold_actionPerformed(); - } - }); - thresholdValue.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - thresholdValue_actionPerformed(); - } - }); - 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(); + originalColours_actionPerformed(); } }); thresholdIsMin.setBackground(Color.white); @@ -311,7 +244,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter } }); - 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); @@ -320,7 +255,7 @@ 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); @@ -385,7 +320,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter for (SequenceGroup sg : ap.av.getAlignment().getGroups()) { - sg.cs = oldgroupColours.get(sg); + sg.setColourScheme(oldgroupColours.get(sg)); } } } @@ -395,7 +330,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter { if (slider.isEnabled()) { - if (currentColours.isSelected() + if (useOriginalColours.isSelected() && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) { updateView(); @@ -407,24 +342,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } - public JComboBox getThreshold() - { - return threshold; - } - - public void setThreshold(JComboBox threshold) + public void originalColours_actionPerformed() { - this.threshold = threshold; - } - - public void currentColours_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(); } @@ -445,7 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter slider.setEnabled(true); thresholdValue.setEnabled(true); - thresholdIsMin.setEnabled(true); + thresholdIsMin.setEnabled(!useOriginalColours.isSelected()); if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) { @@ -467,12 +394,12 @@ public class AnnotationColourChooser extends AnnotationRowFilter 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); @@ -487,4 +414,60 @@ 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; + } + }