public class FeatureColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
- Frame frame;
+ JVDialog frame;
FeatureRenderer fr;
- FeatureSettings fs;
- AlignmentPanel ap;
+ FeatureSettings fs = null;
+ // AlignmentPanel ap;
GraduatedColor cs;
Object oldcs;
boolean adjusting = false;
private float min,max;
String type=null;
-
+
+ private AlignFrame af=null;
+ public FeatureColourChooser(AlignFrame af, String type)
+ {
+ this.af = af;
+ init(af.getSeqcanvas().getFeatureRenderer(), type);
+ }
public FeatureColourChooser(FeatureSettings fsettings, String type)
{
this.fs = fsettings;
+ init(fsettings.fr, type);
+ // this.ap = fsettings.ap;
+ }
+ private void init(FeatureRenderer frenderer,String type) {
this.type = type;
- fr = fsettings.fr;
- ap = fsettings.ap;
+ fr = frenderer;
float mm[] = ((float[][]) fr.minmax.get(type))[0];
min = mm[0];
max = mm[1];
}
minColour.setBackground(cs.getMinColor());
maxColour.setBackground(cs.getMaxColor());
+ colourFromLabel.setState(cs.isColourByLabel());
adjusting = true;
try
} catch (Exception ex)
{
}
- // To HERE!
+ threshold.select(cs.getThreshType()==AnnotationColourGradient.NO_THRESHOLD ? 0 : cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1 : 2);
+
adjusting = false;
changeColour();
+ colourFromLabel.addItemListener(this);
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- frame = new Frame();
- frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Graduated Feature Colour for "+type, 480,
- 145);
+ Frame owner = (af!=null) ? af : fs.frame;
+ frame = new JVDialog(owner,"Graduated Feature Colour for "+type,true,480,248);
+ frame.setMainPanel(this);
validate();
+ frame.setVisible(true);
+ if (frame.accept) {
+ changeColour();
+ } else {
+ // cancel
+ reset();
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ frame.setVisible(false);
+ }
}
public FeatureColourChooser()
maxColour.addActionListener(this);
thresholdIsMin.addItemListener(this);
- ok.setLabel("OK");
- ok.addActionListener(this);
-
- cancel.setLabel("Cancel");
- cancel.addActionListener(this);
-
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ this.setLayout(new GridLayout(4,1));
+ jPanel1.setLayout(new FlowLayout());
+ jPanel2.setLayout(new FlowLayout());
+ jPanel3.setLayout(new GridLayout(1,1));
+ jPanel4.setLayout(new FlowLayout());
jPanel1.setBackground(Color.white);
jPanel2.setBackground(Color.white);
+ jPanel4.setBackground(Color.white);
threshold.addItemListener(this);
threshold.addItem("No Threshold");
threshold.addItem("Above Threshold");
threshold.addItem("Below Threshold");
- jPanel3.setLayout(null);
thresholdValue.addActionListener(this);
-
slider.setBackground(Color.white);
slider.setEnabled(false);
- slider.setBounds(new Rectangle(153, 3, 93, 21));
+ slider.setSize(new Dimension(93, 21));
thresholdValue.setEnabled(false);
- thresholdValue.setBounds(new Rectangle(248, 2, 79, 22));
+ thresholdValue.setSize(new Dimension(79,22)); //setBounds(new Rectangle(248, 2, 79, 22));
thresholdValue.setColumns(5);
jPanel3.setBackground(Color.white);
- //currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- //currentColours.setLabel("Use Original Colours");
- //currentColours.addItemListener(this);
-
- threshold.setBounds(new Rectangle(11, 3, 139, 22));
+
+ colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ colourFromLabel.setLabel("Colour by Label");
+ colourFromLabel.setSize(new Dimension(139,22));
+ //threshold.setBounds(new Rectangle(11, 3, 139, 22));
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setLabel("Threshold is min/max");
- thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
- jPanel1.add(ok);
- jPanel1.add(cancel);
- //jPanel2.add(currentColours);
- jPanel2.add(minColour);
- jPanel2.add(maxColour);
- jPanel3.add(threshold);
+ thresholdIsMin.setSize(new Dimension(135,23));
+ //thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
+ jPanel1.add(minColour);
+ jPanel1.add(maxColour);
+ jPanel1.add(colourFromLabel);
+ jPanel2.add(threshold);
jPanel3.add(slider);
- jPanel3.add(thresholdValue);
- jPanel3.add(thresholdIsMin);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ jPanel4.add(thresholdValue);
+ jPanel4.add(thresholdIsMin);
+ this.add(jPanel1);//, java.awt.BorderLayout.NORTH);
+ this.add(jPanel2);//, java.awt.BorderLayout.NORTH);
+ this.add(jPanel3);//, java.awt.BorderLayout.CENTER);
+ this.add(jPanel4);//, java.awt.BorderLayout.CENTER);
}
Button minColour = new Button();
Button maxColour = new Button();
- Button ok = new Button();
-
- Button cancel = new Button();
-
+
Panel jPanel1 = new Panel();
Panel jPanel2 = new Panel();
Choice threshold = new Choice();
- FlowLayout flowLayout1 = new FlowLayout();
-
Panel jPanel3 = new Panel();
+ Panel jPanel4 = new Panel();
Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
TextField thresholdValue = new TextField(20);
- BorderLayout borderLayout1 = new BorderLayout();
+// BorderLayout borderLayout1 = new BorderLayout();
Checkbox thresholdIsMin = new Checkbox();
+ Checkbox colourFromLabel = new Checkbox();
private GraphLine threshline;
{
maxColour_actionPerformed(null);
}
-
- else if (evt.getSource() == ok)
- {
- changeColour();
- frame.setVisible(false);
- }
- else if (evt.getSource() == cancel)
- {
- reset();
- ap.paintAlignment(true);
- frame.setVisible(false);
- }
-
else
{
changeColour();
public void itemStateChanged(ItemEvent evt)
{
-
+ maxColour.setEnabled(!colourFromLabel.getState());
+ minColour.setEnabled(!colourFromLabel.getState());
changeColour();
}
}
}
protected void valueChanged() {
- changeColour();
threshline.value = (float) slider.getValue() / 1000f;
- ap.paintAlignment(false);
+ cs.setThresh(threshline.value);
+ changeColour();
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(false);
}
public void minColour_actionPerformed(Color newCol)
{
- if (newCol != null)
+ if (newCol == null)
{
+ UserDefinedColours udc = new UserDefinedColours(this,minColour.getBackground(), frame, "Select Colour for Minimum Value");
+ } else {
minColour.setBackground(newCol);
minColour.repaint();
changeColour();
}
- else
- {
- new UserDefinedColours(this, "Select Colour for Minimum Value", minColour.getBackground());
- }
-
+
}
public void maxColour_actionPerformed(Color newCol)
{
- if (newCol != null)
+ if (newCol == null)
{
+ UserDefinedColours udc = new UserDefinedColours(this,maxColour.getBackground(), frame, "Select Colour for Maximum Value");// this, "Select Colour for Maximum Value", maxColour.getBackground());
+ } else {
maxColour.setBackground(newCol);
maxColour.repaint();
changeColour();
}
- else
- {
- new UserDefinedColours(this, "Select Colour for Maximum Value", maxColour.getBackground());
- }
}
void changeColour()
thresholdValue.setEnabled(true);
GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max);
+ acg.setColourByLabel(colourFromLabel.getState());
+ maxColour.setEnabled(!colourFromLabel.getState());
+ minColour.setEnabled(!colourFromLabel.getState());
if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
fr.featureColours.put(type,acg);
cs = acg;
- ap.paintAlignment(false);
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(false);
}
void reset()
{
fr.featureColours.put(type, oldcs);
- ap.paintAlignment(true);
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(true);
}
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ PaintRefresher.Refresh(this, fr.av.getSequenceSetId());
+ // ap.paintAlignment(true);
}
public void mouseEntered(MouseEvent evt)
import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
/**
* Creates a new FeatureRenderer object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public FeatureRenderer(AlignViewport av)
{
boolean deleteFeature = false;
- Panel colourPanel;
+ FeatureColourPanel colourPanel;
+ class FeatureColourPanel extends Panel {
+ String label="";
+
+ private Color maxCol;
+ private boolean isColourByLabel,isGcol;
+ /**
+ * render a feature style in the amend feature dialog box
+ */
+ public void updateColor(Object newcol)
+ {
+
+ Color bg,col=null;
+ GraduatedColor gcol=null;
+ String vlabel = "";
+ if (newcol instanceof Color)
+ {
+ isGcol=false;
+ col = (Color) newcol;
+ gcol = null;
+ }
+ else if (newcol instanceof GraduatedColor)
+ {
+ isGcol=true;
+ gcol = (GraduatedColor) newcol;
+ col = null;
+ }
+ else
+ {
+ throw new Error("Invalid color for MyCheckBox");
+ }
+ if (col != null)
+ {
+ setBackground(bg=col);
+ }
+ else
+ {
+ if (gcol.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "+((gcol.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" : "(<)");
+ }
+ if (isColourByLabel=gcol.isColourByLabel()) {
+ setBackground(bg=Color.white);
+ vlabel += " (by Label)";
+ } else {
+ setBackground(bg=gcol.getMinColor());
+ maxCol = gcol.getMaxColor();
+ }
+ }
+ label=vlabel;
+ setBackground(bg);
+ repaint();
+ }
+ FeatureColourPanel() {
+ super(null);
+ }
+ public void paint(Graphics g)
+ {
+ int width=getWidth(),height=getHeight();
+ if (isGcol) {
+ if (isColourByLabel)
+ {
+ g.setColor(Color.white);
+ g.fillRect(width/2, 0,width/2, height);
+ g.setColor(Color.black);
+ Font f=new Font("Verdana", Font.PLAIN,
+ 10);
+ g.setFont(f);
+ g.drawString("Label", 0, 0);
+ }
+ else
+ {
+ g.setColor(maxCol);
+ g.fillRect(width/2, 0,width/2, height);
+
+ }
+ }
+ }
+
+ }
boolean amendFeatures(final SequenceI[] sequences,
final SequenceFeature[] features, boolean newFeatures,
Button deleteButton = new Button("Delete");
deleteFeature = false;
- colourPanel = new Panel(null);
+ colourPanel = new FeatureColourPanel();
colourPanel.setSize(110, 15);
final FeatureRenderer fr = this;
Panel panel = new Panel(new GridLayout(3, 1));
-
+
+ featureIndex = 0; // feature to be amended.
Panel tmp;
// /////////////////////////////////////
.createColourFromName(name.getText());
}
- colourPanel.setBackground(col);
+ colourPanel.updateColor(col);
}
});
start.setText(features[0].getBegin() + "");
end.setText(features[0].getEnd() + "");
description.setText(features[0].getDescription());
-
Color col = getColour(name.getText());
if (col == null)
{
col = new jalview.schemes.UserColourScheme()
.createColourFromName(name.getText());
}
-
- colourPanel.setBackground(col);
-
+ Object fcol = getFeatureStyle(name.getText());
+ // simply display the feature color in a box
+ colourPanel.updateColor(fcol);
dialog.setResizable(true);
-
- colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ // TODO: render the graduated color in the box.
+ if (fcol instanceof Color)
{
- public void mousePressed(java.awt.event.MouseEvent evt)
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
{
- new UserDefinedColours(fr, ap.alignFrame);
- }
- });
+ public void mousePressed(java.awt.event.MouseEvent evt)
+ {
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ });
+ }
+ else
+ {
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ {
+ public void mousePressed(java.awt.event.MouseEvent evt)
+ {
+ FeatureColourChooser fcc = new FeatureColourChooser(ap.alignFrame, name.getText());
+ fcc.setFocusable(true);
+ dialog.transferFocus();
+ }
+ });
+ }
dialog.setVisible(true);
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
if (!newFeatures)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features[featureIndex];
if (dialog.accept)
{
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
- setColour(sf.type, colourPanel.getBackground());
+ if (fcol instanceof Color) {
+ // update colour - otherwise its already done.
+ setColour(sf.type, colourPanel.getBackground());
+ }
try
{
sf.begin = Integer.parseInt(start.getText());
}
col = colourPanel.getBackground();
- setColour(lastFeatureAdded, col);
+ //setColour(lastFeatureAdded, fcol);
if (lastFeatureGroupAdded != null)
{
featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
- av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col
- .getRGB()));
}
+ if (fcol instanceof Color) {
+ setColour(lastFeatureAdded, fcol);
+ }
+ av.featuresDisplayed.put(lastFeatureAdded,
+ getFeatureStyle(lastFeatureAdded));
+
findAllFeatures();
String[] tro = new String[renderOrder.length];
}
}
- findAllFeatures();
+ // findAllFeatures();
ap.paintAlignment(true);
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param sg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param x1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
// String type;
// SequenceFeature sf;
if (sequenceFeatures[sfindex].begin <= start
&& sequenceFeatures[sfindex].end >= start)
{
- currentColour = new Integer(getColour(sequenceFeatures[sfindex]).getRGB());//av.featuresDisplayed
- //.get(sequenceFeatures[sfindex].type);
+ currentColour = new Integer(
+ getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type);
}
}
else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
{
- renderFeature(
- g,
- seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- new Color(((Integer) av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
- renderFeature(
- g,
- seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- new Color(((Integer) av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ renderFeature(g, seq, seq
+ .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
+ .findIndex(sequenceFeatures[sfindex].begin) - 1,
+ getColour(sequenceFeatures[sfindex])
+ // new Color(((Integer) av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type)).intValue())
+ , start, end, y1);
+ renderFeature(g, seq, seq
+ .findIndex(sequenceFeatures[sfindex].end) - 1, seq
+ .findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex])
+ // new Color(((Integer) av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type)).intValue())
+ , start, end, y1);
}
else
{
- renderFeature(g, seq, seq
+ if (showFeature(sequenceFeatures[sfindex]))
+ { renderFeature(g, seq, seq
.findIndex(sequenceFeatures[sfindex].begin) - 1, seq
.findIndex(sequenceFeatures[sfindex].end) - 1,
getColour(sequenceFeatures[sfindex]), start, end, y1);
+ }
}
}
}
}
}
- Hashtable minmax=null;
+
+ Hashtable minmax = null;
+
void findAllFeatures()
{
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
minmax = new Hashtable();
-
+
for (int i = 0; i < av.alignment.getHeight(); i++)
{
SequenceFeature[] features = av.alignment.getSequenceAt(i)
int index = 0;
while (index < features.length)
{
- if (features[index].begin==0 && features[index].end==0) {
+ if (features[index].begin == 0 && features[index].end == 0)
+ {
index++;
continue;
}
getColour(features[index].getType()).getRGB()));
allfeatures.addElement(features[index].getType());
}
- if (features[index].score != Float.NaN)
+ if (features[index].score != Float.NaN)
{
- int nonpos= features[index].getBegin()>=1 ? 0 : 1;
+ int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
float[][] mm = (float[][]) minmax.get(features[index].getType());
if (mm == null)
{
- mm = new float[][] {null, null };
+ mm = new float[][]
+ { null, null };
minmax.put(features[index].getType(), mm);
}
- if (mm[nonpos]==null)
- {
- mm[nonpos] = new float[] { features[index].score, features[index].score };
-
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
}
else
{
}
}
}
-
+
index++;
}
}
}
}
- public Color getColour(String featureType)
+ /**
+ * get a feature style object for the given type string. Creates a
+ * java.awt.Color for a featureType with no existing colourscheme. TODO:
+ * replace return type with object implementing standard abstract colour/style
+ * interface
+ *
+ * @param featureType
+ * @return java.awt.Color or GraduatedColor
+ */
+ public Object getFeatureStyle(String featureType)
{
Object fc = featureColours.get(featureType);
if (fc == null)
{
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, col);
- return col;
+ featureColours.put(featureType, fc = col);
}
- else if (fc instanceof Color)
+ return fc;
+ }
+
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
{
return (Color) fc;
}
{
return ((GraduatedColor) fc).getMaxColor();
}
- // TODO: raise an implementation error here.
- return null; // Color.white;
}
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + featureType);
+ }
+ /**
+ *
+ * @param sequenceFeature
+ * @return true if feature is visible.
+ */
+ private boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
+ } else { return true; }
}
+
/**
* implement graduated colouring for features with scores
*
*/
public Color getColour(SequenceFeature feature)
{
- Object fc = featureColours.get(feature.type);
- if (fc == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(feature.type);
- featureColours.put(feature.type, col);
- return col;
- }
- else if (fc instanceof Color)
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
{
return (Color) fc;
}
{
return ((GraduatedColor) fc).findColor(feature);
}
- // TODO: raise an implementation error here.
- return null; // Color.white;
}
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + feature.getType());
}
- public void setColour(String featureType, Color col)
+ public void setColour(String featureType, Object col)
{
- featureColours.put(featureType, col);
+ // overwrite
+ // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
+ // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
+ // Object c = featureColours.get(featureType);
+ // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
+ // !((GraduatedColor)c).getMaxColor().equals(_col)))
+ {
+ featureColours.put(featureType, col);
+ }
}
public void setFeaturePriority(Object[][] data)
for (int i = 0; i < data.length; i++)
{
String type = data[i][0].toString();
- setColour(type, (Color) data[i][1]);
+ setColour(type, data[i][1]);
if (((Boolean) data[i][2]).booleanValue())
{
av.featuresDisplayed.put(type, new Integer(getColour(type)
* get visible or invisible groups
*
* @param visible
- * true to return visible groups, false to return hidden ones.
+ * true to return visible groups, false to return hidden ones.
* @return list of groups
*/
public String[] getGroups(boolean visible)
* set all feature groups in toset to be visible or invisible
*
* @param toset
- * group names
+ * group names
* @param visible
- * the state of the named groups to set
+ * the state of the named groups to set
*/
public void setGroupState(String[] toset, boolean visible)
{
return alignmentHasFeatures;
}
+
/**
*
* @return the displayed feature type as an array of strings
if (av.featuresDisplayed.get(typ[i]) == null)
{
typ[i] = null;
- }
- }
+ }
}
+ }
return typ;
}
}
import jalview.analysis.AlignmentSorter;
import jalview.commands.OrderCommand;
import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
public class FeatureSettings extends Panel implements ItemListener,
MouseListener, MouseMotionListener, ActionListener,
g.drawString("(Features can be added from searches or", 10, 40);
g.drawString("from Jalview / GFF features files)", 10, 60);
}
- protected void popupSort(final String type, final Hashtable minmax,
+
+ protected void popupSort(final MyCheckbox check, final Hashtable minmax,
int x, int y)
{
+ final String type = check.type;
java.awt.PopupMenu men = new PopupMenu("Settings for " + type);
java.awt.MenuItem scr = new MenuItem("Sort by Score");
men.add(scr);
if (minmax != null)
{
final Object typeMinMax = minmax.get(type);
- final java.awt.CheckboxMenuItem chb = new java.awt.CheckboxMenuItem("Vary Height");
- // this is broken at the moment
- chb.setState(minmax.get(type) != null);
- chb.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- chb.setState(chb.getState());
- if (chb.getState())
- {
- minmax.put(type, null);
- }
- else
- {
- minmax.put(type, typeMinMax);
- }
- }
-
- });
- men.add(chb);
+ /*
+ * final java.awt.CheckboxMenuItem chb = new
+ * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
+ * moment chb.setState(minmax.get(type) != null);
+ * chb.addActionListener(new ActionListener() {
+ *
+ * public void actionPerformed(ActionEvent e) {
+ * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
+ * null); } else { minmax.put(type, typeMinMax); } }
+ *
+ * }); men.add(chb);
+ */
if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
{
- // graduated colourschemes for those where minmax exists for the positional features
- MenuItem mxcol = new MenuItem("Min Max Colour");
+ // graduated colourschemes for those where minmax exists for the
+ // positional features
+ MenuItem mxcol = new MenuItem("Graduated Colour");
men.add(mxcol);
mxcol.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
new FeatureColourChooser(me, type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(type));
}
});
Component[] comps;
int cSize = featurePanel.getComponentCount();
- Checkbox check;
+ MyCheckbox check;
// This will remove any checkboxes which shouldn't be
// visible
for (int i = 0; i < cSize; i++)
{
comps = featurePanel.getComponents();
- check = (Checkbox) comps[i];
- if (!visibleChecks.contains(check.getLabel()))
+ check = (MyCheckbox) comps[i];
+ if (!visibleChecks.contains(check.type))
{
featurePanel.remove(i);
cSize--;
* update the checklist of feature types with the given type
*
* @param groupsChanged
- * true means if the type is not in the display list then it
- * will be added and displayed
+ * true means if the type is not in the display list then it will be
+ * added and displayed
* @param type
- * feature type to be checked for in the list.
+ * feature type to be checked for in the list.
*/
void addCheck(boolean groupsChanged, String type)
{
boolean addCheck;
Component[] comps = featurePanel.getComponents();
- Checkbox check;
+ MyCheckbox check;
addCheck = true;
for (int i = 0; i < featurePanel.getComponentCount(); i++)
{
- check = (Checkbox) comps[i];
- if (check.getLabel().equals(type))
+ check = (MyCheckbox) comps[i];
+ if (check.type.equals(type))
{
addCheck = false;
break;
check = new MyCheckbox(
type,
selected,
- (fr.featureLinks != null && fr.featureLinks.containsKey(type)));
+ (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+ fr.getFeatureStyle(type));
check.addMouseListener(this);
check.addMouseMotionListener(this);
- check.setBackground(fr.getColour(type));
check.addItemListener(this);
if (groupsChanged)
{
int tmpSize = 0;
for (int i = 0; i < cSize; i++)
{
- Checkbox check = (Checkbox) comps[i];
- tmp[tmpSize][0] = check.getLabel();
- tmp[tmpSize][1] = fr.getColour(check.getLabel());
+ MyCheckbox check = (MyCheckbox) comps[i];
+ tmp[tmpSize][0] = check.type;
+ tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
tmp[tmpSize][2] = new Boolean(check.getState());
tmpSize++;
}
selectedCheck = (MyCheckbox) evt.getSource();
if (fr.featureLinks != null
- && fr.featureLinks.containsKey(selectedCheck.getLabel()))
+ && fr.featureLinks.containsKey(selectedCheck.type))
{
if (evt.getX() > selectedCheck.stringWidth + 20)
{
public void mouseClicked(MouseEvent evt)
{
MyCheckbox check = (MyCheckbox) evt.getSource();
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK)!=0)
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
{
- this.popupSort(check.getLabel(), fr.minmax, evt.getX(), evt.getY());
+ this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
}
if (fr.featureLinks != null
- && fr.featureLinks.containsKey(check.getLabel()))
+ && fr.featureLinks.containsKey(check.type))
{
if (evt.getX() > check.stringWidth + 20)
{
evt.consume();
- String link = fr.featureLinks.get(check.getLabel()).toString();
+ String link = fr.featureLinks.get(check.type).toString();
ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), link
.substring(0, link.indexOf("|")));
}
if (evt.getClickCount() > 1)
{
- new UserDefinedColours(this, check.getLabel(), fr.getColour(check
- .getLabel()));
+ Object fcol = fr.getFeatureStyle(check.type);
+ if (fcol instanceof Color)
+ {
+ new UserDefinedColours(this, check.type, (Color) fcol);
+ } else {
+ new FeatureColourChooser(this, check.type);
+ // write back the current colour object to update the table
+ check.updateColor(fr.getFeatureStyle(check.type));
+ }
}
}
class MyCheckbox extends Checkbox
{
+ public String type;
public int stringWidth;
boolean hasLink;
+ GraduatedColor gcol;
+
+ Color col;
+
+ public void updateColor(Object newcol)
+ {
+ if (newcol instanceof Color)
+ {
+ col = (Color) newcol;
+ gcol = null;
+ }
+ else if (newcol instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) newcol;
+ col = null;
+ }
+ else
+ {
+ throw new Error("Invalid color for MyCheckBox");
+ }
+ if (col != null)
+ {
+ setBackground(col);
+ }
+ else
+ {
+ String vlabel = type;
+ if (gcol.getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "+((gcol.getThreshType()==AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" : "(<)");
+ }
+ if (gcol.isColourByLabel()) {
+ setBackground(Color.white);
+ vlabel += " (by Label)";
+ } else {
+ setBackground(gcol.getMinColor());
+ }
+ this.setLabel(vlabel);
+ }
+ repaint();
+ }
+
public MyCheckbox(String label, boolean checked, boolean haslink)
{
super(label, checked);
-
+ type = label;
FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
stringWidth = fm.stringWidth(label);
this.hasLink = haslink;
}
+ public MyCheckbox(String type, boolean selected, boolean b,
+ Object featureStyle)
+ {
+ this(type,selected,b);
+ updateColor(featureStyle);
+ }
+
public void paint(Graphics g)
{
+ int width = getWidth(), height = getHeight();
+ if (gcol != null)
+ {
+ if (gcol.isColourByLabel())
+ {
+ g.setColor(Color.white);
+ g.fillRect(width/2, 0,width/2, height);
+ /*g.setColor(Color.black);
+ Font f=g.getFont().deriveFont(9);
+ g.setFont(f);
+
+ // g.setFont(g.getFont().deriveFont(
+ // AffineTransform.getScaleInstance(
+ // width/g.getFontMetrics().stringWidth("Label"),
+ // height/g.getFontMetrics().getHeight())));
+ g.drawString("Label", width/2, 0); */
+
+ }
+ else
+ {
+ Color maxCol = gcol.getMaxColor();
+ g.setColor(maxCol);
+ g.fillRect(width/2, 0,width/2, height);
+
+ }
+ }
+
if (hasLink)
{
g.drawImage(linkImage, stringWidth + 25,
}
}
}
+
protected void sortByDens(String[] typ)
{
sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
}
+
private String[] getDisplayedFeatureTypes()
{
String[] typ = null;
return typ;
}
-
protected void sortBy(String[] typ, String methodText, final String method)
{
if (typ == null)
}
SequenceI[] oldOrder = al.getSequencesArray();
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av
- .getAlignment()));
+ this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText,
+ oldOrder, alignPanel.av.getAlignment()));
alignPanel.paintAlignment(true);
}
setTargetColour(fr.colourPanel.getBackground());
dialog.setVisible(true);
}
-
public UserDefinedColours(Component caller, Color col1, Frame alignframe)
{
+ this(caller, col1, alignframe, "Select Colour");
+ }
+ public UserDefinedColours(Component caller, Color col1, Container alignframe, String title)
+ {
this.caller = caller;
originalColour = col1;
- originalLabel = "Select Colour";
- setForDialog("Select Colour", alignframe);
+ originalLabel = title;
+ setForDialog(title, alignframe);
setTargetColour(col1);
dialog.setVisible(true);
}
frame.setSize(420, 200);
}
- void setForDialog(String title, Frame alignframe)
+ void setForDialog(String title, Container alignframe)
{
init();
frame.setVisible(false);
remove(buttonPanel);
- dialog = new Dialog(alignframe, title, true);
+ if (alignframe instanceof Frame)
+ {
+ dialog = new Dialog((Frame)alignframe, title, true);
+ }
+ else
+ if (alignframe instanceof JVDialog){
+ dialog = new Dialog(((JVDialog)alignframe), title, true);
+ } else {
+ throw new Error("Unsupported owner for User Colour scheme dialog.");
+ }
dialog.add(this);
this.setSize(400, 123);
{
final Button button = new Button();
Color col = Color.white;
-
+ if (oldColourScheme!=null)
+ {
try
{
col = oldColourScheme.findColour(aa.charAt(0), -1);
} catch (Exception ex)
{
}
-
+ }
button.setBackground(col);
oldColours.addElement(col);
button.setLabel(label);
}
else if (caller instanceof FeatureRenderer)
{
- ((FeatureRenderer) caller).colourPanel.setBackground(getColor());
+ ((FeatureRenderer) caller).colourPanel.updateColor(getColor());
}
else if (caller instanceof FeatureColourChooser)
{
}
else if (caller instanceof FeatureRenderer)
{
- ((FeatureRenderer) caller).colourPanel
- .setBackground(originalColour);
+ ((FeatureRenderer) caller).colourPanel.updateColor(originalColour);
}
+ else if (caller instanceof FeatureColourChooser)
+ {
+ if (originalLabel.indexOf("inimum")>-1)
+ {
+ ((FeatureColourChooser) caller).minColour_actionPerformed(originalColour);
+ } else {
+ ((FeatureColourChooser) caller).maxColour_actionPerformed(originalColour);
+ }
+ }
if (dialog != null)
dialog.setVisible(false);
git://source.jalview.org / jalview.git / commitdiff