/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * A class that manages drawing of sequence features for the Swing gui
*/
public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
{
- AlignViewport av;
- Color resBoxColour;
- float transparency = 1.0f;
- FontMetrics fm;
- int charOffset;
-
- Hashtable featureColours = new Hashtable();
-
- // A higher level for grouping features of a
- // particular type
- Hashtable featureGroups = null;
-
- // This is actually an Integer held in the hashtable,
- // Retrieved using the key feature type
- Object currentColour;
-
- String[] renderOrder;
+ AlignmentPanel ap;
/**
- * Creates a new FeatureRenderer object.
- *
- * @param av DOCUMENT ME!
+ * Creates a new FeatureRenderer object
+ *
+ * @param alignPanel
*/
- public FeatureRenderer(AlignViewport av)
- {
- this.av = av;
- }
-
- public void transferSettings(FeatureRenderer fr)
- {
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
- }
-
- BufferedImage offscreenImage;
- boolean offscreenRender = false;
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
- {
- return new Color(findFeatureColour(initialCol.getRGB(),
- seq, res));
- }
-
- /**
- * 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)
- {
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
-
- if (seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures == null)
- {
- return initialCol;
- }
-
- sfSize = sequenceFeatures.length;
- }
-
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
- {
- return Color.white.getRGB();
- }
-
- //Only bother making an offscreen image if transparency is applied
- if (transparency != 1.0f && offscreenImage == null)
- {
- offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
- }
-
- currentColour = null;
-
- offscreenRender = true;
-
- if (offscreenImage != null)
- {
- offscreenImage.setRGB(0, 0, initialCol);
- drawSequence(offscreenImage.getGraphics(),
- lastSeq,
- column, column, 0);
-
- return offscreenImage.getRGB(0, 0);
- }
- else
- {
- drawSequence(null,
- lastSeq,
- lastSeq.findPosition(column),
- -1, -1);
-
- if (currentColour == null)
- {
- return initialCol;
- }
- else
- {
- return ( (Integer) currentColour).intValue();
- }
- }
-
- }
-
- /**
- * 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;
-
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int y1)
- {
- if (seq.getDatasetSequence().getSequenceFeatures() == null
- || seq.getDatasetSequence().getSequenceFeatures().length == 0)
- {
- return;
- }
-
- if (g != null)
- {
- fm = g.getFontMetrics();
- }
-
- if (av.featuresDisplayed == null
- || renderOrder == null
- || newFeatureAdded)
- {
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
- {
- return;
- }
-
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
-
- if (lastSeq == null || seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
- }
-
- if (transparency != 1 && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, transparency));
- }
-
- if (!offscreenRender)
- {
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
- }
-
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
-
- if (type == null || !av.featuresDisplayed.containsKey(type))
- {
- continue;
- }
-
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
- {
- if (sequenceFeatures.length <= sfindex)
- {
- continue;
- }
- if (!sequenceFeatures[sfindex].type.equals(type))
- {
- continue;
- }
-
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
- {
- continue;
- }
-
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
- {
- continue;
- }
-
- if (offscreenRender && offscreenImage == null)
- {
- if (sequenceFeatures[sfindex].begin <= start &&
- sequenceFeatures[sfindex].end >= start)
- {
- currentColour = 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);
-
- }
- else
- {
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex].type),
- start, end, y1);
- }
-
- }
-
- }
-
- if (transparency != 1.0f && g != null)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, 1.0f));
- }
- }
-
- char s;
- int i;
- 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 < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
-
- if (fend >= end)
- {
- fend = end;
- }
- int pady = (y1 + av.charHeight) - av.charHeight / 5;
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
-
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
-
- if (offscreenRender || !av.validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- pady);
-
- }
- }
- }
-
- boolean newFeatureAdded = false;
-
- public void featuresAdded()
- {
- lastSeq=null;
- findAllFeatures();
- }
-
- boolean findingFeatures = false;
- synchronized void findAllFeatures()
- {
- newFeatureAdded = false;
-
- if (findingFeatures)
- {
- newFeatureAdded = true;
- return;
- }
-
- findingFeatures = true;
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- av.featuresDisplayed.clear();
-
- Vector allfeatures = new Vector();
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceFeature[] features
- = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
- {
- if (! (features[index].begin == 0 && features[index].end == 0))
- {
- // If beginning and end are 0, the feature is for the whole sequence
- // and we don't want to render the feature in the normal way
-
- if (getColour(features[index].getType()) == null)
- {
- 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());
- }
- }
- index++;
- }
- }
-
- renderOrder = new String[allfeatures.size()];
- Enumeration en = allfeatures.elements();
- int i = allfeatures.size() - 1;
- while (en.hasMoreElements())
- {
- renderOrder[i] = en.nextElement().toString();
- i--;
- }
-
- findingFeatures = false;
- }
-
- public Color getColour(String featureType)
+ public FeatureRenderer(AlignmentPanel alignPanel)
{
- Color colour = (Color) featureColours.get(featureType);
- return colour;
- }
-
- static String lastFeatureAdded;
- static String lastFeatureGroupAdded;
- static String lastDescriptionAdded;
-
- public boolean createNewFeatures(SequenceI[] sequences,
- SequenceFeature[] features)
- {
- return amendFeatures(sequences, features, true, null);
- }
-
- int featureIndex = 0;
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features,
- boolean newFeatures,
- final AlignmentPanel ap)
- {
- JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox name = new JComboBox();
- final JComboBox source = new JComboBox();
- final JTextArea description = new JTextArea(3, 25);
- final JSpinner start = new JSpinner();
- 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));
- colour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- colour.setBackground(
- JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground()));
- }
- });
-
- JPanel panel = new JPanel(new GridLayout(3, 2));
- panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT));
- panel.add(name);
- panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
- panel.add(source);
- panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
- JPanel tmp = new JPanel();
- tmp.add(colour);
- colour.setPreferredSize(new Dimension(150, 15));
- panel.add(tmp);
- name.setEditable(true);
- source.setEditable(true);
-
- 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.setLineWrap(true);
- panel.add(new JScrollPane(description));
-
- if (!newFeatures)
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
{
- bigPanel.add(panel, BorderLayout.SOUTH);
-
- panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
- panel.add(start);
- panel.add(new JLabel(" End:", JLabel.RIGHT));
- panel.add(end);
- bigPanel.add(panel, BorderLayout.CENTER);
- }
- else
- {
- bigPanel.add(panel, BorderLayout.CENTER);
- }
-
- if (lastFeatureAdded == null)
- {
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
- {
- lastFeatureAdded = "feature_1";
- }
- }
-
- if (lastFeatureGroupAdded == null)
- {
- if (features[0].featureGroup != null)
- {
- lastFeatureGroupAdded = features[0].featureGroup;
- }
- else
- {
- lastFeatureAdded = "Jalview";
- }
- }
-
- Enumeration en;
- if (featureGroups != null)
- {
- en = featureGroups.keys();
- while (en.hasMoreElements())
- {
- source.addItem(en.nextElement().toString());
- }
- }
-
- if (newFeatures)
- {
- if (av.featuresDisplayed != null)
- {
- en = av.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- name.addItem(en.nextElement().toString());
- }
- }
-
- name.setSelectedItem(lastFeatureAdded);
- source.setSelectedItem(lastFeatureGroupAdded);
- description.setText(
- lastDescriptionAdded == null ?
- features[0].description : lastDescriptionAdded);
-
- if (getColour(lastFeatureAdded) != null)
- {
- colour.setBackground(getColour(lastFeatureAdded));
- }
- else
- {
- colour.setBackground(new Color(60, 160, 115));
- }
-
- }
- else if (!newFeatures)
- {
- featureIndex = 0;
- for (int f = 0; f < features.length; f++)
- {
- name.addItem(features[f].getType().toString());
- }
-
- description.setText(features[0].getDescription());
- source.setSelectedItem(features[0].getFeatureGroup());
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- colour.setBackground(
- getColour(name.getSelectedItem().toString()));
- name.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- int index = name.getSelectedIndex();
- if (index != -1)
- {
- featureIndex = index;
- description.setText(features[index].getDescription());
- source.setSelectedItem(features[index].getFeatureGroup());
- start.setValue(new Integer(features[index].getBegin()));
- end.setValue(new Integer(features[index].getEnd()));
- colour.setBackground(
- getColour(name.getSelectedItem().toString()));
-
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0],
- features[index].getBegin(),
- features[index].getEnd());
-
- ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
-
- }
- Color col = getColour(name.getSelectedItem().toString());
- if (col == null)
- {
- col = new
- jalview.schemes.UserColourScheme()
- .createColourFromName(name.getSelectedItem().toString());
- }
-
- colour.setBackground(col);
- }
- });
-
+ transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
}
-
- Object[] options;
- if (!newFeatures)
- {
- options = new Object[]
- {
- "Amend", "Delete", "Cancel"};
- }
- else
- {
- options = new Object[]
- {
- "OK", "Cancel"};
- }
-
- String title = newFeatures ? "Create New Sequence Feature(s)" :
- "Amend/Delete Features for "
- + sequences[0].getName();
-
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel,
- title,
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options, "OK");
-
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
-
- if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
- {
- //This ensures that the last sequence
- //is refreshed and new features are rendered
- lastSeq = null;
- lastFeatureAdded = name.getSelectedItem().toString();
- lastFeatureGroupAdded = source.getSelectedItem().toString();
- lastDescriptionAdded = description.getText().replaceAll("\n", " ");
- }
-
- if (!newFeatures)
- {
- SequenceFeature sf = features[featureIndex];
-
- if (reply == JOptionPane.NO_OPTION)
- {
- sequences[0].getDatasetSequence().deleteFeature(sf);
- }
- else if (reply == JOptionPane.YES_OPTION)
- {
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
- setColour(sf.type, colour.getBackground());
- try
- {
- sf.begin = ( (Integer) start.getValue()).intValue();
- sf.end = ( (Integer) end.getValue()).intValue();
- }
- catch (NumberFormatException ex)
- {}
-
- ffile.parseDescriptionHTML(sf, false);
- }
- }
- else
- {
- if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
- {
- for (int i = 0; i < sequences.length; i++)
- {
- features[i].type = lastFeatureAdded;
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
- sequences[i].addSequenceFeature(features[i]);
- ffile.parseDescriptionHTML(features[i], false);
- }
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- if (featureGroups == null)
- {
- featureGroups = new Hashtable();
- }
-
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
-
- av.featuresDisplayed.put(lastFeatureGroupAdded,
- new Integer(col.getRGB()));
-
- findAllFeatures();
-
- return true;
- }
- else
- {
- return false;
- }
- }
-
- if (name.getSelectedIndex() == -1)
- {
- findAllFeatures();
- }
-
- return true;
- }
-
- public void setColour(String featureType, Color col)
- {
- featureColours.put(featureType, col);
- }
-
- public void setTransparency(float value)
- {
- transparency = value;
- }
-
- public float getTransparency()
- {
- return transparency;
- }
-
- public void setFeaturePriority(Object[][] data)
- {
- // The feature table will display high priority
- // features at the top, but theses are the ones
- // we need to render last, so invert the data
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- renderOrder = new String[data.length];
-
- if (data.length > 0)
- {
- 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())
- {
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
- }
-
- renderOrder[data.length - i - 1] = type;
- }
- }
-
}
-
}
git://source.jalview.org / jalview.git / blobdiff