/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
- *
- * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import java.awt.event.*;
-
-import jalview.appletgui.FeatureSettings.MyCheckbox;
import jalview.datamodel.*;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer
+public class FeatureRenderer implements jalview.api.FeatureRenderer
{
AlignViewport av;
String[] renderOrder;
FontMetrics fm;
+
int charOffset;
float transparency = 1f;
/**
* Creates a new FeatureRenderer object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * 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;
+
static String lastFeatureGroupAdded;
+
static String lastDescriptionAdded;
int featureIndex = 0;
+
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(MessageManager.getString("error.invalid_colour_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(MessageManager.getString("label.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,
- final AlignmentPanel ap)
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
{
Panel bigPanel = new Panel(new BorderLayout());
final TextField name = new TextField(16);
Button deleteButton = new Button("Delete");
deleteFeature = false;
- colourPanel = new Panel(null);
- colourPanel.setSize(110,15);
+ 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;
- ///////////////////////////////////////
- ///MULTIPLE FEATURES AT SELECTED RESIDUE
- if(!newFeatures && features.length>1)
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
{
- panel = new Panel(new GridLayout(4, 1));
- tmp = new Panel();
- tmp.add(new Label("Select Feature: "));
- overlaps = new Choice();
- for(int i=0; i<features.length; i++)
- {
- String item = features[i].getType()
- +"/"+features[i].getBegin()+"-"+features[i].getEnd();
-
- if(features[i].getFeatureGroup()!=null)
- item += " ("+features[i].getFeatureGroup()+")";
+ panel = new Panel(new GridLayout(4, 1));
+ tmp = new Panel();
+ tmp.add(new Label("Select Feature: "));
+ overlaps = new Choice();
+ for (int i = 0; i < features.length; i++)
+ {
+ String item = features[i].getType() + "/" + features[i].getBegin()
+ + "-" + features[i].getEnd();
- overlaps.addItem(item);
- }
+ if (features[i].getFeatureGroup() != null)
+ item += " (" + features[i].getFeatureGroup() + ")";
- tmp.add(overlaps);
+ overlaps.addItem(item);
+ }
- overlaps.addItemListener(new java.awt.event.ItemListener()
- {
- public void itemStateChanged(java.awt.event.ItemEvent e)
- {
- int index = overlaps.getSelectedIndex();
- if (index != -1)
- {
- featureIndex = index;
- name.setText(features[index].getType());
- description.setText(features[index].getDescription());
- source.setText(features[index].getFeatureGroup());
- start.setText(features[index].getBegin()+"");
- end.setText(features[index].getEnd()+"");
+ tmp.add(overlaps);
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0],
- features[index].getBegin(),
- features[index].getEnd());
+ overlaps.addItemListener(new java.awt.event.ItemListener()
+ {
+ public void itemStateChanged(java.awt.event.ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ name.setText(features[index].getType());
+ description.setText(features[index].getDescription());
+ source.setText(features[index].getFeatureGroup());
+ start.setText(features[index].getBegin() + "");
+ end.setText(features[index].getEnd() + "");
- ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
- }
- Color col = getColour(name.getText());
- if (col == null)
- {
- col = new
- jalview.schemes.UserColourScheme()
- .createColourFromName(name.getText());
- }
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
- colourPanel.setBackground(col);
- }
- });
+ }
+ Object col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+ colourPanel.updateColor(col);
+ }
+ });
- panel.add(tmp);
+ panel.add(tmp);
}
- //////////
- //////////////////////////////////////
-
+ // ////////
+ // ////////////////////////////////////
tmp = new Panel();
panel.add(tmp);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label("Group: ",Label.RIGHT));
+ tmp.add(new Label("Group: ", Label.RIGHT));
tmp.add(source);
tmp = new Panel();
}
}
+ String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
- String title = newFeatures ? "Create New Sequence Feature(s)" :
- "Amend/Delete Features for "
- + sequences[0].getName();
-
- final JVDialog dialog = new JVDialog(ap.alignFrame,
- title,
- true,
- 385,240);
+ final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+ 240);
dialog.setMainPanel(bigPanel);
- if(newFeatures)
+ if (newFeatures)
{
name.setText(lastFeatureAdded);
source.setText(lastFeatureGroupAdded);
}
else
{
- dialog.ok.setLabel("Amend");
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
dialog.buttonPanel.add(deleteButton, 1);
deleteButton.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- deleteFeature = true;
- dialog.setVisible(false);
- }
- });
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ deleteFeature = true;
+ dialog.setVisible(false);
+ }
+ });
name.setText(features[0].getType());
source.setText(features[0].getFeatureGroup());
}
- start.setText(features[0].getBegin()+"");
- end.setText(features[0].getEnd()+"");
+ 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());
+ 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 (dialog.accept)
{
- //This ensures that the last sequence
- //is refreshed and new features are rendered
+ // This ensures that the last sequence
+ // is refreshed and new features are rendered
lastSeq = null;
lastFeatureAdded = name.getText().trim();
lastFeatureGroupAdded = source.getText().trim();
lastDescriptionAdded = description.getText().replace('\n', ' ');
}
- if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)
+ if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
lastFeatureGroupAdded = null;
-
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());
- sf.end = Integer.parseInt(end.getText());
+ sf.end = Integer.parseInt(end.getText());
+ } catch (NumberFormatException ex)
+ {
}
- catch (NumberFormatException ex)
- {}
ffile.parseDescriptionHTML(sf, false);
}
}
else
{
- if (dialog.accept && name.getText().length()>0)
+ if (dialog.accept && name.getText().length() > 0)
{
for (int i = 0; i < sequences.length; i++)
{
}
col = colourPanel.getBackground();
- setColour(lastFeatureAdded, col);
+ // setColour(lastFeatureAdded, fcol);
- if(lastFeatureGroupAdded!=null)
+ 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);
+ 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);
return true;
}
-
public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
{
overview = true;
return initialCol;
}
- return new Color( ( (Integer) currentColour).intValue());
+ return new Color(((Integer) currentColour).intValue());
}
/**
- * This is used by the Molecule Viewer to get the accurate colour
- * of the rendered sequence
+ * This is used by the Molecule Viewer to get the accurate colour of the
+ * rendered sequence
*/
boolean overview = false;
-
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param seq DOCUMENT ME!
- * @param sg DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
- * @param x1 DOCUMENT ME!
- * @param y1 DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param height DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ * @param sg
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
+ * @param x1
+ * DOCUMENT ME!
+ * @param y1
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param height
+ * DOCUMENT ME!
*/
// String type;
// SequenceFeature sf;
-
SequenceI lastSeq;
+
SequenceFeature[] sequenceFeatures;
+
int sfSize, sfindex, spos, epos;
synchronized public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
+ int start, int end, int y1)
{
if (seq.getSequenceFeatures() == null
- || seq.getSequenceFeatures().length == 0)
+ || seq.getSequenceFeatures().length == 0)
{
return;
}
transparencySetter.setTransparency(g, transparency);
}
- if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())
+ if (lastSeq == null || seq != lastSeq
+ || sequenceFeatures != seq.getSequenceFeatures())
{
lastSeq = seq;
sequenceFeatures = seq.getSequenceFeatures();
}
if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
+ && sequenceFeatures[sfindex].featureGroup != null
+ && featureGroups
+ .containsKey(sequenceFeatures[sfindex].featureGroup)
+ && !((Boolean) featureGroups
+ .get(sequenceFeatures[sfindex].featureGroup))
+ .booleanValue())
{
continue;
}
- if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
+ if (!overview
+ && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+ .getEnd() < spos))
{
continue;
}
if (overview)
{
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
+ if (sequenceFeatures[sfindex].begin <= start
+ && sequenceFeatures[sfindex].end >= start)
{
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
+ currentColour = new Integer(
+ getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type);
}
}
{
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);
+ 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,
- new Color( ( (Integer) av.featuresDisplayed.get(
- sequenceFeatures[sfindex].type)).intValue()),
- start, end, y1);
+ 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.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- 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);
+ }
}
}
}
char s;
+
int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
+
+ void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
+ Color featureColour, int start, int end, int y1)
{
- if ( ( (fstart <= end) && (fend >= start)))
+ if (((fstart <= end) && (fend >= start)))
{
if (fstart < start)
{ // fix for if the feature we have starts before the sequence start,
g.setColor(featureColour);
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+ g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
+ av.charHeight);
if (!av.validCharWidth)
{
g.setColor(Color.white);
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+ g.drawString(String.valueOf(s), charOffset
+ + (av.charWidth * (i - start)), (y1 + av.charHeight)
+ - av.charHeight / 5); // pady = height / 5;
}
}
}
+ 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();
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
av.featuresDisplayed = new Hashtable();
Vector allfeatures = new Vector();
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ minmax = new Hashtable();
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- SequenceFeature[] features = av.alignment.getSequenceAt(i).
- getSequenceFeatures();
+ SequenceFeature[] features = alignment.getSequenceAt(i)
+ .getSequenceFeatures();
if (features == null)
{
int index = 0;
while (index < features.length)
{
+ if (features[index].begin == 0 && features[index].end == 0)
+ {
+ index++;
+ continue;
+ }
if (!av.featuresDisplayed.containsKey(features[index].getType()))
{
if (getColour(features[index].getType()) == null)
{
featureColours.put(features[index].getType(),
- ucs.createColourFromName(features[index].
- getType()));
+ ucs.createColourFromName(features[index].getType()));
}
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
+ av.featuresDisplayed.put(features[index].getType(), new Integer(
+ getColour(features[index].getType()).getRGB()));
allfeatures.addElement(features[index].getType());
}
+ 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[][]
+ { null, null };
+ minmax.put(features[index].getType(), mm);
+ }
+ if (mm[nonpos] == null)
+ {
+ mm[nonpos] = new float[]
+ { features[index].score, features[index].score };
+
+ }
+ else
+ {
+ if (mm[nonpos][0] > features[index].score)
+ {
+ mm[nonpos][0] = features[index].score;
+ }
+ if (mm[nonpos][1] < features[index].score)
+ {
+ mm[nonpos][1] = features[index].score;
+ }
+ }
+ }
+
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)
{
- if (!featureColours.containsKey(featureType))
+ Object fc = featureColours.get(featureType);
+ if (fc == null)
{
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
+ 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;
+ }
+
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().getCanonicalName(),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 (Color) featureColours.get(featureType);
+ {
+ return true;
+ }
}
+ /**
+ * implement graduated colouring for features with scores
+ *
+ * @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());
+ }
- 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)
av.featuresDisplayed.clear();
}
- /* if (visibleNew)
- {
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
- }
- if (data == null)
- {
- return;
- }*/
-
+ /*
+ * if (visibleNew) { if (av.featuresDisplayed != null) {
+ * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new
+ * Hashtable(); } } if (data == null) { return; }
+ */
renderOrder = new String[data.length];
for (int i = 0; i < data.length; i++)
{
String type = data[i][0].toString();
- setColour(type, (Color) data[i][1]);
- if ( ( (Boolean) data[i][2]).booleanValue())
+ setColour(type, data[i][1]);
+ if (((Boolean) data[i][2]).booleanValue())
{
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+ av.featuresDisplayed.put(type, new Integer(getColour(type)
+ .getRGB()));
}
renderOrder[data.length - i - 1] = type;
}
}
}
+
/**
- * @return a simple list of feature group names or null
+ * @return a simple list of feature group names or null
*/
public String[] getGroups()
{
buildGroupHash();
- if (featureGroups!=null)
+ if (featureGroups != null)
{
String[] gps = new String[featureGroups.size()];
Enumeration gn = featureGroups.keys();
- int i=0;
+ int i = 0;
while (gn.hasMoreElements())
{
- gps[i++] = (String) gn.nextElement();
+ gps[i++] = (String) gn.nextElement();
}
return gps;
}
return null;
}
+
/**
* get visible or invisible groups
- * @param visible true to return visible groups, false to return hidden ones.
+ *
+ * @param visible
+ * true to return visible groups, false to return hidden ones.
* @return list of groups
*/
- public String[] getGroups(boolean visible)
+ public String[] getGroups(boolean visible)
{
buildGroupHash();
- if (featureGroups!=null)
+ if (featureGroups != null)
{
Vector gp = new Vector();
-
+
Enumeration gn = featureGroups.keys();
while (gn.hasMoreElements())
{
String nm = (String) gn.nextElement();
Boolean state = (Boolean) featureGroups.get(nm);
- if (state.booleanValue()==visible)
+ if (state.booleanValue() == visible)
{
gp.addElement(nm);
}
}
String[] gps = new String[gp.size()];
gp.copyInto(gps);
-
- int i=0;
+
+ int i = 0;
while (gn.hasMoreElements())
{
- gps[i++] = (String) gn.nextElement();
+ gps[i++] = (String) gn.nextElement();
}
return gps;
}
return null;
}
+
/**
* set all feature groups in toset to be visible or invisible
- * @param toset group names
- * @param visible the state of the named groups to set
+ *
+ * @param toset
+ * group names
+ * @param visible
+ * the state of the named groups to set
*/
public void setGroupState(String[] toset, boolean visible)
{
buildGroupHash();
- if (toset!=null && toset.length>0 && featureGroups!=null)
+ if (toset != null && toset.length > 0 && featureGroups != null)
{
boolean rdrw = false;
- for (int i=0;i<toset.length; i++)
+ for (int i = 0; i < toset.length; i++)
{
Object st = featureGroups.get(toset[i]);
- if (st!=null)
+ featureGroups.put(toset[i], new Boolean(visible));
+ if (st != null)
{
- featureGroups.put(toset[i], new Boolean(visible));
- rdrw = rdrw || (visible!=((Boolean) st).booleanValue());
+ rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
}
}
if (rdrw)
{
- if (this.av!=null)
- if (this.av.featureSettings!=null)
+ if (this.av != null)
+ if (this.av.featureSettings != null)
{
av.featureSettings.rebuildGroups();
this.av.featureSettings.resetTable(true);
- } else {
- buildFeatureHash();
}
- if (av!=null)
+ else
{
- av.alignmentChanged(null);
+ buildFeatureHash();
}
+ if (av != null)
+ {
+ av.alignmentChanged(null);
+ }
}
}
}
+
+ ArrayList<String> hiddenGroups = new ArrayList<String>();
+
/**
- * analyse alignment for groups and hash tables
- * (used to be embedded in FeatureSettings.setTableData)
+ * analyse alignment for groups and hash tables (used to be embedded in
+ * FeatureSettings.setTableData)
+ *
* @return true if features are on the alignment
*/
public boolean buildGroupHash()
{
- boolean alignmentHasFeatures=false;
+ boolean alignmentHasFeatures = false;
if (featureGroups == null)
{
featureGroups = new Hashtable();
}
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
+ hiddenGroups = new ArrayList<String>();
+ hiddenGroups.addAll(featureGroups.keySet());
+ ArrayList allFeatures = new ArrayList();
+ ArrayList allGroups = new ArrayList();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
if (tmpfeatures[index].getFeatureGroup() != null)
{
group = tmpfeatures[index].featureGroup;
+ // Remove group from the hiddenGroup list
+ hiddenGroups.remove(group);
if (!allGroups.contains(group))
{
- allGroups.addElement(group);
+ allGroups.add(group);
boolean visible = true;
if (featureGroups.containsKey(group))
{
- visible = ( (Boolean) featureGroups.get(group)).booleanValue();
- } else {
+ visible = ((Boolean) featureGroups.get(group)).booleanValue();
+ }
+ else
+ {
featureGroups.put(group, new Boolean(visible));
}
}
if (!allFeatures.contains(tmpfeatures[index].getType()))
{
- allFeatures.addElement(tmpfeatures[index].getType());
+ allFeatures.add(tmpfeatures[index].getType());
}
index++;
}
}
-
+
return alignmentHasFeatures;
}
+
/**
- * rebuild the featuresDisplayed and renderorder list based on the featureGroups hash and any existing display state
- * and force a repaint if necessary
+ * rebuild the featuresDisplayed and renderorder list based on the
+ * featureGroups hash and any existing display state and force a repaint if
+ * necessary
+ *
* @return true if alignment has visible features
*/
- public boolean buildFeatureHash() {
- boolean alignmentHasFeatures=false;
- if (featureGroups==null)
+ public boolean buildFeatureHash()
+ {
+ boolean alignmentHasFeatures = false;
+ if (featureGroups == null)
{
alignmentHasFeatures = buildGroupHash();
}
Vector allFeatures = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
{
continue;
}
alignmentHasFeatures = true;
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
{
group = tmpfeatures[index].featureGroup;
if (featureGroups.containsKey(group))
{
- visible = ( (Boolean) featureGroups.get(group)).booleanValue();
+ visible = ((Boolean) featureGroups.get(group)).booleanValue();
}
}
-
+
if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
{
allFeatures.addElement(tmpfeatures[index].getType());
index++;
}
}
- if (allFeatures.size()>0)
+ if (allFeatures.size() > 0)
{
String[] neworder = new String[allFeatures.size()];
- int p=neworder.length-1;
- for (int i=renderOrder.length-1; i>=0; i--)
+ int p = neworder.length - 1;
+ for (int i = renderOrder.length - 1; i >= 0; i--)
{
if (allFeatures.contains(renderOrder[i]))
{
neworder[p--] = renderOrder[i];
allFeatures.removeElement(renderOrder[i]);
- } else {
+ }
+ else
+ {
av.featuresDisplayed.remove(renderOrder[i]);
}
}
- for (int i=allFeatures.size()-1; i>0; i++)
+ for (int i = allFeatures.size() - 1; i > 0; i++)
{
Object e = allFeatures.elementAt(i);
- if (e!=null)
+ if (e != null)
{
neworder[p--] = (String) e;
- av.featuresDisplayed.put(e, getColour((String)e));
+ av.featuresDisplayed.put(e, getColour((String) e));
}
}
renderOrder = neworder;
return true;
}
-
+
return alignmentHasFeatures;
}
+
+ /**
+ *
+ * @return the displayed feature type as an array of strings
+ */
+ protected String[] getDisplayedFeatureTypes()
+ {
+ String[] typ = null;
+ synchronized (renderOrder)
+ {
+ typ = new String[renderOrder.length];
+ System.arraycopy(renderOrder, 0, typ, 0, typ.length);
+ for (int i = 0; i < typ.length; i++)
+ {
+ if (av.featuresDisplayed.get(typ[i]) == null)
+ {
+ typ[i] = null;
+ }
+ }
+ }
+ return typ;
+ }
}
class TransparencySetter
{
void setTransparency(Graphics g, float value)
{
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, value));
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ value));
}
}
git://source.jalview.org / jalview.git / blobdiff