/*
- * 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, J Engelhardt, LM Lui, 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.appletgui;
import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
/**
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
AlignViewport av;
* Creates a new FeatureRenderer object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public FeatureRenderer(AlignViewport av)
{
featureGroups = fr.featureGroups;
featureColours = fr.featureColours;
transparency = fr.transparency;
+ if (av!=null && fr.av!=null && fr.av!=av)
+ {
+ if (fr.av.featuresDisplayed!=null)
+ {
+ if (av.featuresDisplayed==null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ } else {
+ av.featuresDisplayed.clear();
+ }
+ Enumeration en=fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+ }
+ }
}
static String lastFeatureAdded;
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)
+ {
+ Dimension d = getSize();
+ if (isGcol)
+ {
+ if (isColourByLabel)
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.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(d.width / 2, 0, d.width / 2, d.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;
// /////////////////////////////////////
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());
}
- 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);
-
+ // TODO: render the graduated color in the box.
colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
{
public void mousePressed(java.awt.event.MouseEvent evt)
{
- new UserDefinedColours(fr, ap.alignFrame);
+ if (!colourPanel.isGcol)
+ {
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ else
+ {
+ FeatureColourChooser fcc = new FeatureColourChooser(
+ ap.alignFrame, name.getText());
+ 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 (!colourPanel.isGcol)
+ {
+ // 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];
tro[0] = renderOrder[renderOrder.length - 1];
System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1);
renderOrder = tro;
-
- ap.paintAlignment(true);
-
- return true;
}
else
{
+ // no update to the alignment
return false;
}
}
-
- findAllFeatures();
+ // refresh the alignment and the feature settings dialog
+ if (av.featureSettings != null)
+ {
+ av.featureSettings.refreshTable();
+ }
+ // 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,
+ 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
{
- renderFeature(g, seq, seq
- .findIndex(sequenceFeatures[sfindex].begin) - 1, seq
- .findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
+ 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;
+
+ /**
+ * Called when alignment in associated view has new/modified features to
+ * discover and display.
+ *
+ */
+ public void featuresAdded()
+ {
+ lastSeq = null;
+ findAllFeatures();
+ }
+
+ /**
+ * find all features on the alignment
+ */
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;
}
{
if (getColour(features[index].getType()) == null)
{
- featureColours.put(features[index].getType(), ucs
- .createColourFromName(features[index].getType()));
+ featureColours.put(features[index].getType(),
+ ucs.createColourFromName(features[index].getType()));
}
av.featuresDisplayed.put(features[index].getType(), new Integer(
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;
}
{
if (fc instanceof GraduatedColor)
{
- return ((GraduatedColor) fc).getMinColor();
+ 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;
}
}
git://source.jalview.org / jalview.git / blobdiff