/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
import javax.swing.*;
import jalview.datamodel.*;
+import jalview.schemes.GraduatedColor;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
AlignmentPanel ap;
AlignViewport av;
Color resBoxColour;
+
/**
* global transparency for feature
*/
* Creates a new FeatureRenderer object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public FeatureRenderer(AlignmentPanel ap)
{
this.featureOrder = featureOrder;
}
+ /**
+ * create an independent instance of the feature renderer settings
+ *
+ * @param fr
+ */
public FeatureRendererSettings(FeatureRenderer fr)
{
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
+ renderOrder = null;
+ featureGroups = new Hashtable();
+ featureColours = new Hashtable();
+ featureOrder = new Hashtable();
+ if (fr.renderOrder != null)
+ {
+ this.renderOrder = new String[fr.renderOrder.length];
+ System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
+ renderOrder.length);
+ }
+ if (fr.featureGroups != null)
+ {
+ this.featureGroups = new Hashtable(fr.featureGroups);
+ }
+ if (fr.featureColours != null)
+ {
+ this.featureColours = new Hashtable(fr.featureColours);
+ }
+ Enumeration en = fr.featureColours.keys();
+ while (en.hasMoreElements())
+ {
+ Object next = en.nextElement();
+ Object val = featureColours.get(next);
+ if (val instanceof GraduatedColor)
+ {
+ featureColours
+ .put(next, new GraduatedColor((GraduatedColor) val));
+ }
+ }
this.transparency = fr.transparency;
- this.featureOrder = fr.featureOrder;
+ if (fr.featureOrder != null)
+ {
+ this.featureOrder = new Hashtable(fr.featureOrder);
+ }
}
}
public void transferSettings(FeatureRenderer fr)
{
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
- this.transparency = fr.transparency;
- this.featureOrder = fr.featureOrder;
+ FeatureRendererSettings frs = new FeatureRendererSettings(fr);
+ this.renderOrder = frs.renderOrder;
+ this.featureGroups = frs.featureGroups;
+ this.featureColours = frs.featureColours;
+ this.transparency = frs.transparency;
+ this.featureOrder = frs.featureOrder;
+ if (av != null && av!=fr.av)
+ {
+ // copy over the displayed feature settings
+ if (fr.av != null)
+ {
+ if (fr.av.featuresDisplayed != null)
+ {
+ // update display settings
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
+ }
+ else
+ {
+ av.featuresDisplayed.clear();
+ Enumeration en = fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+
+ }
+ }
+ }
+ }
}
BufferedImage offscreenImage;
* This is used by the Molecule Viewer and Overview to get the accurate
* colourof the rendered sequence
*/
- public int findFeatureColour(int initialCol, SequenceI seq, int column)
+ public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column)
{
if (!av.showSequenceFeatures)
{
}
currentColour = null;
-
+ // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized.
offscreenRender = true;
if (offscreenImage != null)
* 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;
/**
* show scores as heights
*/
- protected boolean varyHeight=false;
+ protected boolean varyHeight = false;
synchronized public void drawSequence(Graphics g, SequenceI seq,
int start, int end, int y1)
if (sequenceFeatures[sfindex].begin <= start
&& sequenceFeatures[sfindex].end >= start)
{
- currentColour = av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type);
+ // this is passed out to the overview and other sequence renderers
+ // (e.g. molecule viewer) to get displayed colour for rendered
+ // sequence
+ currentColour = new Integer(
+ getColour(sequenceFeatures[sfindex]).getRGB());
+ // used to be retreived from av.featuresDisplayed
+ // currentColour = av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type);
+
}
}
else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
{
- renderFeature(
- g,
- seq,
+ 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,
+ 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,
- new Color(((Integer) av.featuresDisplayed
- .get(sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ getColour(sequenceFeatures[sfindex])
+ // new Color(((Integer) av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type)).intValue())
+ , start, end, y1);
}
- else
- if (av.showSeqFeaturesHeight && sequenceFeatures[sfindex].score!=Float.NaN)
- {
- renderScoreFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type), start, end, y1, normaliseScore(sequenceFeatures[sfindex]));
- } else
+ else if (showFeature(sequenceFeatures[sfindex]))
{
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type), start, end, y1);
+ if (av.showSeqFeaturesHeight
+ && sequenceFeatures[sfindex].score != Float.NaN)
+ {
+ renderScoreFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1,
+ normaliseScore(sequenceFeatures[sfindex]));
+ }
+ else
+ {
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1);
+ }
}
}
1.0f));
}
}
+
Hashtable minmax = new Hashtable();
+
/**
* normalise a score against the max/min bounds for the feature type.
+ *
* @param sequenceFeature
- * @return byte[] { signed, normalised signed (-127 to 127) or unsigned (0-255) value.
+ * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
+ * (0-255) value.
*/
private final byte[] normaliseScore(SequenceFeature sequenceFeature)
{
- float[] mm = (float[]) minmax.get(sequenceFeature.type);
- final byte[] r=new byte[] { 0, (byte) 255};
- if (mm!=null)
+ float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
+ final byte[] r = new byte[]
+ { 0, (byte) 255 };
+ if (mm != null)
{
- if (r[0]!=0 || mm[0]<0.0)
+ if (r[0] != 0 || mm[0] < 0.0)
+ {
+ r[0] = 1;
+ r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+ }
+ else
{
- r[0]=1;
- r[1]=(byte) ((int) 128.0+127.0*(sequenceFeature.score/mm[1]));
- } else {
- r[1]=(byte) ((int) 255.0*(sequenceFeature.score/mm[1]));
+ r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
}
}
return r;
}
}
}
+
void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
Color featureColour, int start, int end, int y1, byte[] bs)
{
fend = end;
}
int pady = (y1 + av.charHeight) - av.charHeight / 5;
- int ystrt = 0,yend=av.charHeight;
- if (bs[0]!=0)
+ int ystrt = 0, yend = av.charHeight;
+ if (bs[0] != 0)
{
// signed - zero is always middle of residue line.
- if (bs[1]<128)
+ if (bs[1] < 128)
{
- yend = av.charHeight*(128-bs[1])/512;
- ystrt = av.charHeight-yend/2;
- } else {
- ystrt = av.charHeight/2;
- yend = av.charHeight*(bs[1]-128)/512;
+ yend = av.charHeight * (128 - bs[1]) / 512;
+ ystrt = av.charHeight - yend / 2;
}
- } else {
- yend = av.charHeight*bs[1]/255;
- ystrt = av.charHeight-yend;
+ else
+ {
+ ystrt = av.charHeight / 2;
+ yend = av.charHeight * (bs[1] - 128) / 512;
+ }
+ }
+ else
+ {
+ yend = av.charHeight * bs[1] / 255;
+ ystrt = av.charHeight - yend;
}
for (i = fstart; i <= fend; i++)
}
g.setColor(featureColour);
- int x=(i-start)*av.charWidth;
+ int x = (i - start) * av.charWidth;
g.drawRect(x, y1, av.charWidth, av.charHeight);
- g.fillRect(x, y1+ystrt, av.charWidth,
- yend);
+ g.fillRect(x, y1 + ystrt, av.charWidth, yend);
if (offscreenRender || !av.validCharWidth)
{
* Searches alignment for all features and updates colours
*
* @param newMadeVisible
- * if true newly added feature types will be rendered
- * immediatly
+ * if true newly added feature types will be rendered immediatly
*/
synchronized void findAllFeatures(boolean newMadeVisible)
{
}
}
}
- if (minmax==null)
+ if (minmax == null)
{
minmax = new Hashtable();
}
{
allfeatures.addElement(features[index].getType());
}
- if (features[index].score!=Float.NaN)
- {
- float[] mm = (float[]) minmax.get(features[index].getType());
- if (mm==null)
+ if (features[index].score != Float.NaN)
+ {
+ int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
+ float[][] mm = (float[][]) minmax.get(features[index].getType());
+ if (mm == null)
{
- mm = new float[] { features[index].score,features[index].score};
+ mm = new float[][]
+ { null, null };
minmax.put(features[index].getType(), mm);
- } else {
- if (mm[0]>features[index].score)
+ }
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
+ }
+ else
+ {
+ if (mm[nonpos][0] > features[index].score)
{
- mm[0] = features[index].score;
+ mm[nonpos][0] = features[index].score;
}
- if (mm[1]<features[index].score)
+ if (mm[nonpos][1] < features[index].score)
{
- mm[1] = features[index].score;
+ mm[nonpos][1] = features[index].score;
}
}
}
* types, in the order given by getOrder or the order given in allFeatures.
* Note. this operates directly on the featureOrder hash for efficiency. TODO:
* eliminate the float storage for computing/recalling the persistent ordering
+ * New Cability: updates min/max for colourscheme range if its dynamic
*
* @param allFeatures
*/
Vector allfeatures = new Vector(allFeatures);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
+ Object mmrange, fc = null;
boolean initOrders = (featureOrder == null);
int opos = 0;
if (oldRender != null && oldRender.length > 0)
renderOrder[opos++] = oldRender[j]; // existing features always
// appear below new features
allfeatures.removeElement(oldRender[j]);
+ if (minmax != null)
+ {
+ mmrange = minmax.get(oldRender[j]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(oldRender[j]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(
+ ((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
}
}
}
while (en.hasMoreElements())
{
newf[i] = en.nextElement().toString();
+ if (minmax != null)
+ {
+ // update from new features minmax if necessary
+ mmrange = minmax.get(newf[i]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(newf[i]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
if (initOrders || !featureOrder.containsKey(newf[i]))
{
int denom = initOrders ? allfeatures.size() : featureOrder.size();
i--;
}
if (iSize > 1 && sort)
+ {
jalview.util.QuickSort.sort(sortOrder, newf);
+ }
sortOrder = null;
System.arraycopy(newf, 0, renderOrder, opos, newf.length);
}
- 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)
{
- if (!featureColours.containsKey(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);
+ }
+ return fc;
+ }
+
+ /**
+ * return a nominal colour for this feature
+ *
+ * @param featureType
+ * @return standard color, or maximum colour for graduated colourscheme
+ */
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
}
else
- return (Color) featureColours.get(featureType);
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + featureType);
}
+ /**
+ * calculate the render colour for a specific feature using current feature
+ * settings.
+ *
+ * @param feature
+ * @return render colour for the given feature
+ */
+ public Color getColour(SequenceFeature feature)
+ {
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).findColor(feature);
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + feature.getType());
+ }
+
+ private boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ // // /////////////
+ // // Feature Editing Dialog
+ // // Will be refactored in next release.
+
static String lastFeatureAdded;
static String lastFeatureGroupAdded;
static String lastDescriptionAdded;
+ Object oldcol, fcol;
+
int featureIndex = 0;
boolean amendFeatures(final SequenceI[] sequences,
featureIndex = 0;
- JPanel bigPanel = new JPanel(new BorderLayout());
+ final JPanel bigPanel = new JPanel(new BorderLayout());
final JComboBox overlaps;
final JTextField name = new JTextField(25);
final JTextField source = new JTextField(25);
final JSpinner end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
-
- final JPanel colour = new JPanel();
- colour.setBorder(BorderFactory.createEtchedBorder());
- colour.setMaximumSize(new Dimension(40, 10));
+ final FeatureRenderer me = this;
+ final JLabel colour = new JLabel();
+ colour.setOpaque(true);
+ // colour.setBorder(BorderFactory.createEtchedBorder());
+ colour.setMaximumSize(new Dimension(30, 16));
colour.addMouseListener(new MouseAdapter()
{
+ FeatureColourChooser fcc = null;
+
public void mousePressed(MouseEvent evt)
{
- Color col = JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour", colour.getBackground());
- if (col != null)
- colour.setBackground(col);
+ if (fcol instanceof Color)
+ {
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ "Select Feature Colour", ((Color) fcol));
+ if (col != null)
+ {
+ fcol = col;
+ updateColourButton(bigPanel, colour, col);
+ }
+ }
+ else
+ {
+ if (fcc == null)
+ {
+ final String type = features[featureIndex].getType();
+ fcc = new FeatureColourChooser(me, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+
+ fcc.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ fcol = fcc.getLastColour();
+ fcc = null;
+ setColour(type, fcol);
+ updateColourButton(bigPanel, colour, fcol);
+ }
+ });
+
+ }
+ }
}
});
-
JPanel tmp = new JPanel();
JPanel panel = new JPanel(new GridLayout(3, 1));
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
}
- Color col = getColour(name.getText());
+ Object col = getFeatureStyle(name.getText());
if (col == null)
{
col = new jalview.schemes.UserColourScheme()
.createColourFromName(name.getText());
}
-
- colour.setBackground(col);
+ oldcol = fcol = col;
+ updateColourButton(bigPanel, colour, col);
}
});
tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
tmp.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
-
+ colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
+ colour.setForeground(Color.black);
+ colour.setHorizontalAlignment(SwingConstants.CENTER);
+ colour.setVerticalAlignment(SwingConstants.CENTER);
+ colour.setHorizontalTextPosition(SwingConstants.CENTER);
+ colour.setVerticalTextPosition(SwingConstants.CENTER);
bigPanel.add(panel, BorderLayout.NORTH);
panel = new JPanel();
panel.add(new JLabel("Description: ", JLabel.RIGHT));
- description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
panel.add(new JScrollPane(description));
start.setValue(new Integer(features[0].getBegin()));
end.setValue(new Integer(features[0].getEnd()));
description.setText(features[0].getDescription());
- colour.setBackground(getColour(name.getText()));
-
+ updateColourButton(bigPanel, colour,
+ (oldcol = fcol = getFeatureStyle(name.getText())));
Object[] options;
if (!newFeatures)
{
lastFeatureAdded = name.getText().trim();
lastFeatureGroupAdded = source.getText().trim();
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
-
+ // TODO: determine if the null feature group is valid
if (lastFeatureGroupAdded.length() < 1)
lastFeatureGroupAdded = null;
}
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
- setColour(sf.type, colour.getBackground());
- av.featuresDisplayed.put(sf.type, new Integer(colour
- .getBackground().getRGB()));
+ setColour(sf.type, fcol);
+ av.featuresDisplayed.put(sf.type, getColour(sf.type));
try
{
featureGroups = new Hashtable();
featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
}
-
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
+ setColour(lastFeatureAdded, fcol);
av.featuresDisplayed.put(lastFeatureAdded,
- new Integer(col.getRGB()));
+ getColour(lastFeatureAdded));
findAllFeatures(false);
return true;
}
- public void setColour(String featureType, Color col)
+ /**
+ * update the amend feature button dependent on the given style
+ *
+ * @param bigPanel
+ * @param col
+ * @param col2
+ */
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ Object col2)
+ {
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
+
+ if (col2 instanceof Color)
+ {
+ colour.setBackground((Color) col2);
+ }
+ else
+ {
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
+ // colour.setForeground(colour.getBackground());
+ }
+ }
+
+ 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 setTransparency(float value)
/**
* Replace current ordering with new ordering
*
- * @param data {
- * String(Type), Colour(Type), Boolean(Displayed) }
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
*/
public void setFeaturePriority(Object[][] data)
{
/**
*
- * @param data {
- * String(Type), Colour(Type), Boolean(Displayed) }
+ * @param data
+ * { String(Type), Colour(Type), Boolean(Displayed) }
* @param visibleNew
- * when true current featureDisplay list will be cleared
+ * when true current featureDisplay list will be cleared
*/
public void setFeaturePriority(Object[][] data, boolean visibleNew)
{
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]); // todo : typesafety - feature color
+ // interface object
if (((Boolean) data[i][2]).booleanValue())
{
av.featuresDisplayed.put(type, new Integer(getColour(type)
* this rendering context.
*
* @param type
- * Feature type string
+ * Feature type string
* @param position
- * normalized priority - 0 means always appears on top, 1 means
- * always last.
+ * normalized priority - 0 means always appears on top, 1 means
+ * always last.
*/
public float setOrder(String type, float position)
{
git://source.jalview.org / jalview.git / blobdiff