if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- for (SequenceGroup sg:ap.av.getAlignment().getGroups())
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs != null)
{
// Always get default shading from preferences.
setDefaultMinMax();
-
+
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
currentColours.setSelected(acg.predefinedColours);
if (!acg.predefinedColours)
{
- minColour.setBackground(acg.getMinColour());
+ minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
seqAssociated.setSelected(acg.isSeqAssociated());
}
adjusting = true;
- annotations = new JComboBox(getAnnotationItems(seqAssociated.isSelected()));
+ annotations = new JComboBox(
+ getAnnotationItems(seqAssociated.isSelected()));
threshold.addItem("No Threshold");
threshold.addItem("Above Threshold");
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
annotations.setSelectedItem(acg.getAnnotation());
- switch (acg.getAboveThreshold()) {
+ switch (acg.getAboveThreshold())
+ {
case AnnotationColourGradient.NO_THRESHOLD:
- threshold.setSelectedItem("No Threshold");
+ threshold.setSelectedItem("No Threshold");
break;
case AnnotationColourGradient.ABOVE_THRESHOLD:
- threshold.setSelectedItem("Above Threshold");
+ threshold.setSelectedItem("Above Threshold");
break;
case AnnotationColourGradient.BELOW_THRESHOLD:
threshold.setSelectedItem("Below Threshold");
break;
- default:
- throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ default:
+ throw new Error(
+ "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
}
thresholdIsMin.setSelected(acg.thresholdIsMinMax);
- thresholdValue.setText(""+acg.getAnnotationThreshold());
+ thresholdValue.setText("" + acg.getAnnotationThreshold());
}
try
}
- private Vector<String> getAnnotationItems(boolean isSeqAssociated) {
+ private Vector<String> getAnnotationItems(boolean isSeqAssociated)
+ {
Vector<String> list = new Vector<String>();
int index = 1;
int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
- boolean enableSeqAss=false;
+ boolean enableSeqAss = false;
for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
{
- if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef==null)
+ if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
{
if (isSeqAssociated)
- {
+ {
continue;
- }
- } else {
- enableSeqAss=true;
+ }
+ }
+ else
+ {
+ enableSeqAss = true;
}
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
- {anmap[list.size()] = i;
+ {
+ anmap[list.size()] = i;
list.addElement(label);
-
- }else {
- if (!isSeqAssociated) {
+
+ }
+ else
+ {
+ if (!isSeqAssociated)
+ {
anmap[list.size()] = i;
list.addElement(label + "_" + (index++));
}
}
seqAssociated.setEnabled(enableSeqAss);
annmap = new int[list.size()];
- System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+ System.arraycopy(anmap, 0, annmap, 0, annmap.length);
return list;
}
+
private void setDefaultMinMax()
{
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
}
public AnnotationColourChooser()
});
defColours.setOpaque(false);
defColours.setText("Defaults");
- defColours.setToolTipText("Reset min and max colours to defaults from user preferences.");
+ defColours
+ .setToolTipText("Reset min and max colours to defaults from user preferences.");
defColours.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
resetColours_actionPerformed(arg0);
}
});
-
+
annotations.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
seqAssociated.setText("Per-sequence only");
seqAssociated.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent arg0)
{
seqAssociated_actionPerformed(arg0);
}
});
-
+
this.setLayout(borderLayout1);
- jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]"));
+ jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
colpanel.add(maxColour);
jPanel2.add(colpanel, "wrap");
jPanel2.add(threshold);
- jPanel2.add(defColours,"skip 1, wrap");
+ jPanel2.add(defColours, "skip 1, wrap");
jPanel2.add(thresholdIsMin);
jPanel2.add(slider, "grow");
jPanel2.add(thresholdValue, "grow");
protected void seqAssociated_actionPerformed(ActionEvent arg0)
{
- adjusting=true;
+ adjusting = true;
String cursel = (String) annotations.getSelectedItem();
- boolean isvalid=false,isseqs=seqAssociated.isSelected();
+ boolean isvalid = false, isseqs = seqAssociated.isSelected();
this.annotations.removeAllItems();
- for (String anitem:getAnnotationItems(seqAssociated.isSelected()))
+ for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
{
- if (anitem.equals( cursel) || (isseqs && cursel.startsWith(anitem)))
+ if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
{
- isvalid=true;
- cursel=anitem;
+ isvalid = true;
+ cursel = anitem;
}
this.annotations.addItem(anitem);
}
- adjusting=false;
- if (isvalid) { this.annotations.setSelectedItem(cursel); } else {
- if (annotations.getItemCount()>0) {
+ adjusting = false;
+ if (isvalid)
+ {
+ this.annotations.setSelectedItem(cursel);
+ }
+ else
+ {
+ if (annotations.getItemCount() > 0)
+ {
annotations.setSelectedIndex(0);
}
}
}
JComboBox annotations;
+
int[] annmap;
+
JPanel minColour = new JPanel();
JPanel maxColour = new JPanel();
+
JButton defColours = new JButton();
+
JButton ok = new JButton();
JButton cancel = new JButton();
JPanel jPanel1 = new JPanel();
+
JPanel jPanel2 = new JPanel();
-
+
BorderLayout borderLayout1 = new BorderLayout();
JComboBox threshold = new JComboBox();
-
JSlider slider = new JSlider();
JTextField thresholdValue = new JTextField(20);
JCheckBox currentColours = new JCheckBox();
JCheckBox thresholdIsMin = new JCheckBox();
-
+
JCheckBox seqAssociated = new JCheckBox();
public void minColour_actionPerformed()
if (av.getAlignment().getGroups() != null)
{
-
- for (SequenceGroup sg:ap.av.getAlignment().getGroups())
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs == null)
{
{
sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
aboveThreshold);
- ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
}
else
sg.cs = new AnnotationColourGradient(currentAnnotation,
minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
- ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
}
}
}
ap.alignmentChanged();
- // ensure all associated views (overviews, structures, etc) are notified of updated colours.
+ // ensure all associated views (overviews, structures, etc) are notified of
+ // updated colours.
ap.paintAlignment(true);
}
public void cancel_actionPerformed(ActionEvent e)
{
reset();
- // ensure all original colouring is propagated to listeners.
+ // ensure all original colouring is propagated to listeners.
ap.paintAlignment(true);
try
{
av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
-
- for (SequenceGroup sg:ap.av.getAlignment().getGroups())
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
git://source.jalview.org / jalview.git / blobdiff