+/*
+ * 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
+ * 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.
+ *
+ * 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
+ */
+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 $Revision$
+ */
+public class 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;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ 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.getSequenceFeatures()!=sequenceFeatures)
+ {
+ 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)
+ {
+ 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)
+ {
+ 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);
+ }
+ });
+
+ }
+
+ 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();
+ }
+ if (data!=null)
+ return;
+ 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;
+ }
+ }
+
+ }
+
+}