X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=0284105f5a3a63999c6226ed5fc8befe4e7f2092;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=d21b39e433171a8ba1f6ae05496fe088ec7242d2;hpb=8c6a0091158548409984e31ffbb9d52516b95fa5;p=jalview.git
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index d21b39e..0284105
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,76 +1,459 @@
-package jalview.gui;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
-import java.util.*;
-
-public class FeatureRenderer implements RendererI
-{
- AlignViewport av;
-
- SequenceGroup currentSequenceGroup = null;
- SequenceGroup [] allGroups = null;
- Color resBoxColour;
- Graphics graphics;
-
- public FeatureRenderer(AlignViewport av)
- {
- this.av = av;
- }
-
-
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
- {
- Vector features = seq.getSequenceFeatures();
- Enumeration e = features.elements();
- while( e.hasMoreElements() )
- {
- SequenceFeature sf = (SequenceFeature)e.nextElement();
- int fstart = seq.findIndex(sf.getStart())-1;
- int fend = seq.findIndex(sf.getEnd())-1;
-
- if( (fstart<=end && fend>=start) )
- {
- if(fstart<0) // fix for if the feature we have starts before the sequence start,
- fstart = 0;// but the feature end is still valid!!
-
- if(fstart==fend)
- {
- g.setColor(Color.red);
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
- g.setColor(Color.white);
-
- char s = seq.getSequence().charAt(fstart);
- FontMetrics fm = g.getFontMetrics();
- int charOffset = (width - fm.charWidth(s))/2;
- int pady = height/5;
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
-
- }
- else
- {
- for (int i = fstart; i <= fend; i++)
- {
- try{
- g.setColor(Color.blue);
- g.fillRect( (i-start) * width, y1, width, height);
-
- g.setColor(Color.white);
- char s = seq.getSequence().charAt(i);
- FontMetrics fm = g.getFontMetrics();
- int charOffset = (width - fm.charWidth(s)) / 2;
- int pady = height / 5;
- g.drawString(String.valueOf(s),
- charOffset + x1 + width * (i-start),
- y1 + height - pady);
-
- }catch(Exception ex){System.out.println(i+" "+fstart+" "+fend+" " +sf.getDescription()+" "+seq.getName()+" "+seq.getLength()); }
- }
- }
- }
-
- }
- }
-
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Arrays;
+import java.util.Comparator;
+
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer implements
+ jalview.api.FeatureRenderer
+{
+ Color resBoxColour;
+
+ AlignmentPanel ap;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public FeatureRenderer(AlignmentPanel ap)
+ {
+ super();
+ this.ap = ap;
+ this.av = ap.av;
+ if (ap != null && ap.getSeqPanel() != null
+ && ap.getSeqPanel().seqCanvas != null
+ && ap.getSeqPanel().seqCanvas.fr != null)
+ {
+ transferSettings(ap.getSeqPanel().seqCanvas.fr);
+ }
+ }
+
+ // // /////////////
+ // // Feature Editing Dialog
+ // // Will be refactored in next release.
+
+ static String lastFeatureAdded;
+
+ static String lastFeatureGroupAdded;
+
+ static String lastDescriptionAdded;
+
+ FeatureColourI oldcol, fcol;
+
+ int featureIndex = 0;
+
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
+ {
+
+ featureIndex = 0;
+
+ final JPanel bigPanel = new JPanel(new BorderLayout());
+ final JComboBox overlaps;
+ final JTextField name = new JTextField(25);
+ final JTextField source = new JTextField(25);
+ 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 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;
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (fcol.isSimpleColour())
+ {
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ MessageManager.getString("label.select_feature_colour"),
+ ColorUtils.getColor(fcol.getColour()));
+ if (col != null)
+ {
+ fcol = new FeatureColour(new Colour(col));
+ updateColourButton(bigPanel, colour, fcol);
+ }
+ }
+ else
+ {
+ if (fcc == null)
+ {
+ final String type = features[featureIndex].getType();
+ fcc = new FeatureColourChooser(me, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+
+ fcc.addActionListener(new ActionListener()
+ {
+
+ @Override
+ 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));
+
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
+ {
+ panel = new JPanel(new GridLayout(4, 1));
+ tmp = new JPanel();
+ tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
+ overlaps = new JComboBox();
+ for (int i = 0; i < features.length; i++)
+ {
+ overlaps.addItem(features[i].getType() + "/"
+ + features[i].getBegin() + "-" + features[i].getEnd()
+ + " (" + features[i].getFeatureGroup() + ")");
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(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.setValue(new Integer(features[index].getBegin()));
+ end.setValue(new Integer(features[index].getEnd()));
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
+
+ }
+ FeatureColourI col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new FeatureColour(new Colour(UserColourScheme
+ .createColourFromName(name.getText())));
+ }
+ oldcol = fcol = col;
+ updateColourButton(bigPanel, colour, col);
+ }
+ });
+
+ panel.add(tmp);
+ }
+ // ////////
+ // ////////////////////////////////////
+
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
+ tmp.add(name);
+
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
+ JLabel.RIGHT));
+ tmp.add(source);
+
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel(MessageManager.getString("label.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(MessageManager.getString("label.description"),
+ JLabel.RIGHT));
+ description.setFont(JvSwingUtils.getTextAreaFont());
+ description.setLineWrap(true);
+ panel.add(new JScrollPane(description));
+
+ if (!newFeatures)
+ {
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new JPanel();
+ panel.add(new JLabel(MessageManager.getString("label.start"),
+ JLabel.RIGHT));
+ panel.add(start);
+ panel.add(new JLabel(MessageManager.getString("label.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
+ {
+ lastFeatureGroupAdded = "Jalview";
+ }
+ }
+
+ if (newFeatures)
+ {
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
+ }
+ else
+ {
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
+ }
+
+ start.setValue(new Integer(features[0].getBegin()));
+ end.setValue(new Integer(features[0].getEnd()));
+ description.setText(features[0].getDescription());
+ updateColourButton(bigPanel, colour,
+ (oldcol = fcol = getFeatureStyle(name.getText())));
+ Object[] options;
+ if (!newFeatures)
+ {
+ options = new Object[] { "Amend", "Delete", "Cancel" };
+ }
+ else
+ {
+ options = new Object[] { "OK", "Cancel" };
+ }
+
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[] { sequences[0].getName() });
+
+ int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+ bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
+
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+ if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
+ {
+ // 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().replaceAll("\n", " ");
+ // TODO: determine if the null feature group is valid
+ if (lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
+ }
+
+ 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, fcol);
+ getFeaturesDisplayed().setVisible(sf.type);
+
+ try
+ {
+ sf.begin = ((Integer) start.getValue()).intValue();
+ sf.end = ((Integer) end.getValue()).intValue();
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ ffile.parseDescriptionHTML(sf, false);
+ }
+ }
+ else
+ // NEW FEATURES ADDED
+ {
+ if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+ {
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features[i].type = lastFeatureAdded;
+ // fix for JAL-1538 - always set feature group here
+ features[i].featureGroup = lastFeatureGroupAdded;
+ features[i].description = lastDescriptionAdded;
+ sequences[i].addSequenceFeature(features[i]);
+ ffile.parseDescriptionHTML(features[i], false);
+ }
+
+ if (lastFeatureGroupAdded != null)
+ {
+ setGroupVisibility(lastFeatureGroupAdded, true);
+ }
+ setColour(lastFeatureAdded, fcol);
+ setVisible(lastFeatureAdded);
+
+ findAllFeatures(false);
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+
+ /**
+ * update the amend feature button dependent on the given style
+ *
+ * @param bigPanel
+ * @param colour
+ * @param col
+ */
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ FeatureColourI col)
+ {
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
+
+ if (col.isSimpleColour())
+ {
+ colour.setBackground(ColorUtils.getColor(col.getColour()));
+ }
+ else
+ {
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, col);
+ }
+ }
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
+}