/*
- * 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 java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
+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
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer implements
+ jalview.api.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;
- PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+ AlignmentPanel ap;
/**
* 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;
- featureOrder = fr.featureOrder;
- }
-
- 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)
+ public FeatureRenderer(AlignmentPanel ap)
{
- if (!av.showSequenceFeatures)
+ super(ap.av);
+ this.ap = ap;
+ if (ap != null && ap.getSeqPanel() != null
+ && ap.getSeqPanel().seqCanvas != null
+ && ap.getSeqPanel().seqCanvas.fr != null)
{
- return initialCol;
- }
-
- if (seq != lastSeq)
- {
- lastSeq = seq;
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures!=null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
- }
-
- if (sequenceFeatures == null)
- {
- return initialCol;
- }
-
-
- 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);
+ transferSettings(ap.getSeqPanel().seqCanvas.fr);
}
+ }
- currentColour = null;
+ // // /////////////
+ // // Feature Editing Dialog
+ // // Will be refactored in next release.
- offscreenRender = true;
+ static String lastFeatureAdded;
- if (offscreenImage != null)
- {
- offscreenImage.setRGB(0, 0, initialCol);
- drawSequence(offscreenImage.getGraphics(),
- lastSeq,
- column, column, 0);
+ static String lastFeatureGroupAdded;
- return offscreenImage.getRGB(0, 0);
- }
- else
- {
- drawSequence(null,
- lastSeq,
- lastSeq.findPosition(column),
- -1, -1);
+ static String lastDescriptionAdded;
- if (currentColour == null)
- {
- return initialCol;
- }
- else
- {
- return ( (Integer) currentColour).intValue();
- }
- }
+ FeatureColourI oldcol, fcol;
- }
+ int featureIndex = 0;
- /**
- * 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)
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
{
- 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;
- }
+ featureIndex = 0;
- if (lastSeq == null || seq != lastSeq
- || seq.getDatasetSequence().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++)
+ 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()
{
- type = renderOrder[renderIndex];
+ FeatureColourChooser fcc = null;
- 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++)
+ @Override
+ public void mousePressed(MouseEvent evt)
{
- if (sequenceFeatures.length <= sfindex)
- {
- continue;
- }
- if (!sequenceFeatures[sfindex].type.equals(type))
+ if (fcol.isSimpleColour())
{
- 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)
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ MessageManager.getString("label.select_feature_colour"),
+ fcol.getColour());
+ if (col != null)
{
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
- type);
+ fcol = new FeatureColour(col);
+ updateColourButton(bigPanel, colour, new FeatureColour(col));
}
}
- 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;
- }
+ if (fcc == null)
+ {
+ final String type = features[featureIndex].getType();
+ fcc = new FeatureColourChooser(me, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
- g.setColor(featureColour);
+ fcc.addActionListener(new ActionListener()
+ {
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fcol = fcc.getLastColour();
+ fcc = null;
+ setColour(type, fcol);
+ updateColourButton(bigPanel, colour, fcol);
+ }
+ });
- 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;
- /**
- * Called when alignment in associated view has new/modified features
- * to discover and display.
- *
- */
- public void featuresAdded()
- {
- lastSeq=null;
- findAllFeatures();
- }
-
- boolean findingFeatures = false;
- /**
- * search the alignment for all new features, give them a colour and display
- * them. Then fires a PropertyChangeEvent on the changeSupport object.
- *
- */
- synchronized void findAllFeatures()
- {
- findAllFeatures(true); // add all new features as visible
- if (!firing) {
- firing=true;
- changeSupport.firePropertyChange("changeSupport",null,null);
- firing=false;
- }
- }
- /**
- * Searches alignment for all features and updates colours
- *
- * @param newMadeVisible
- * if true newly added feature types will be rendered immediatly
- */
- synchronized void findAllFeatures(boolean newMadeVisible) {
- newFeatureAdded = false;
-
- if (findingFeatures)
- {
- newFeatureAdded = true;
- return;
- }
-
- findingFeatures = true;
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
+ });
+ JPanel tmp = new JPanel();
+ JPanel panel = new JPanel(new GridLayout(3, 1));
- Vector allfeatures = new Vector();
- Vector oldfeatures = new Vector();
- if (renderOrder!=null)
- {
- for (int i=0; i<renderOrder.length; i++) {
- if (renderOrder[i]!=null)
- {
- oldfeatures.addElement(renderOrder[i]);
- }
- }
- }
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
{
- SequenceFeature[] features
- = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
-
- if (features == null)
+ 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++)
{
- continue;
+ overlaps.addItem(features[i].getType() + "/"
+ + features[i].getBegin() + "-" + features[i].getEnd()
+ + " (" + features[i].getFeatureGroup() + ")");
}
- int index = 0;
- while (index < features.length)
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new ItemListener()
{
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
+ @Override
+ public void itemStateChanged(ItemEvent e)
{
- if (! (features[index].begin == 0 && features[index].end == 0))
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
{
- // 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 (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
- // this is a new feature type on the alignment. Mark it for
- // display.
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
- setOrder(features[index].getType(),0);
- }
- }
- }
- if (!allfeatures.contains(features[index].getType()))
- {
- allfeatures.addElement(features[index].getType());
- }
- index++;
- }
- }
- updateRenderOrder(allfeatures);
- findingFeatures = false;
- }
- protected boolean firing=false;
- /**
- * replaces the current renderOrder with the unordered features in allfeatures.
- * The ordering of any types in both renderOrder and allfeatures is preserved,
- * and all new feature types are rendered on top of the existing types, in
- * the order given by getOrder or the order given in allFeatures.
- * Note. this operates directly on the featureOrder hash for efficiency. TODO:
- * eliminate the float storage for computing/recalling the persistent ordering
- *
- * @param allFeatures
- */
- private void updateRenderOrder(Vector allFeatures) {
- Vector allfeatures = new Vector(allFeatures);
- String[] oldRender = renderOrder;
- renderOrder = new String[allfeatures.size()];
- boolean initOrders=(featureOrder==null);
- int opos=0;
- if (oldRender!=null && oldRender.length>0)
- {
- for (int j=0; j<oldRender.length; j++)
- {
- if (oldRender[j]!=null)
+ 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)
{
- if (initOrders)
- {
- setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
- }
- if (allfeatures.contains(oldRender[j])) {
- renderOrder[opos++] = oldRender[j]; // existing features always
- // appear below new features
- allfeatures.removeElement(oldRender[j]);
- }
+ col = new FeatureColour(UserColourScheme
+ .createColourFromName(name.getText()));
}
+ oldcol = fcol = col;
+ updateColourButton(bigPanel, colour, col);
}
- }
- if (allfeatures.size()==0) {
- // no new features - leave order unchanged.
- return;
- }
- int i=allfeatures.size()-1;
- int iSize=i;
- boolean sort=false;
- String[] newf = new String[allfeatures.size()];
- float[] sortOrder = new float[allfeatures.size()];
- Enumeration en = allfeatures.elements();
- // sort remaining elements
- while (en.hasMoreElements())
- {
- newf[i] = en.nextElement().toString();
- if (initOrders || !featureOrder.containsKey(newf[i]))
- {
- int denom = initOrders ? allfeatures.size() : featureOrder.size();
- // new unordered feature - compute persistent ordering at head of
- // existing features.
- setOrder(newf[i], i/(float) denom);
- }
- // set order from newly found feature from persisted ordering.
- sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
- if (i<iSize)
- {
- // only sort if we need to
- sort = sort || sortOrder[i]>sortOrder[i+1];
- }
- i--;
- }
- if (iSize>1 && sort)
- jalview.util.QuickSort.sort(sortOrder, newf);
- sortOrder=null;
- System.arraycopy(newf, 0, renderOrder, opos, newf.length);
- }
- public Color getColour(String featureType)
- {
- Color colour = (Color) featureColours.get(featureType);
- if (colour == null)
- {
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
- featureColours.put(featureType,
- colour=ucs.createColourFromName(featureType));
- }
- return colour;
- }
+ });
- static String lastFeatureAdded;
- static String lastFeatureGroupAdded;
- static String lastDescriptionAdded;
+ panel.add(tmp);
+ }
+ // ////////
+ // ////////////////////////////////////
- public boolean createNewFeatures(SequenceI[] sequences,
- SequenceFeature[] features)
- {
- return amendFeatures(sequences, features, true, null);
- }
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel(MessageManager.getString("label.name:"),
+ JLabel.RIGHT));
+ tmp.add(name);
- 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()));
- }
- });
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel(MessageManager.getString("label.group:"),
+ JLabel.RIGHT));
+ tmp.add(source);
- 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 = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel(MessageManager.getString("label.colour"),
+ JLabel.RIGHT));
tmp.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
- panel.add(tmp);
- name.setEditable(true);
- source.setEditable(true);
-
+ 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("Description: ", JLabel.RIGHT));
- description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ panel.add(new JLabel(MessageManager.getString("label.description:"),
+ JLabel.RIGHT));
+ description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
panel.add(new JScrollPane(description));
bigPanel.add(panel, BorderLayout.SOUTH);
panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.start"),
+ JLabel.RIGHT));
panel.add(start);
- panel.add(new JLabel(" End:", JLabel.RIGHT));
+ panel.add(new JLabel(MessageManager.getString("label.end"),
+ JLabel.RIGHT));
panel.add(end);
bigPanel.add(panel, BorderLayout.CENTER);
}
}
else
{
- lastFeatureAdded = "Jalview";
- }
- }
-
- Enumeration en;
- if (featureGroups != null)
- {
- en = featureGroups.keys();
- while (en.hasMoreElements())
- {
- source.addItem(en.nextElement().toString());
+ lastFeatureGroupAdded = "Jalview";
}
}
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));
- }
-
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
}
- else if (!newFeatures)
+ else
{
- 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);
- }
- });
-
+ 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"};
+ options = new Object[] { "Amend", "Delete", "Cancel" };
}
else
{
- options = new Object[]
- {
- "OK", "Cancel"};
+ options = new Object[] { "OK", "Cancel" };
}
- String title = newFeatures ? "Create New Sequence Feature(s)" :
- "Amend/Delete Features for "
- + sequences[0].getName();
+ 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, "OK");
+ 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.getSelectedItem() != null
- && source.getSelectedItem() != null)
+ 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.getSelectedItem().toString();
- lastFeatureGroupAdded = source.getSelectedItem().toString();
+ 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)
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
- setColour(sf.type, colour.getBackground());
+
+ setColour(sf.type, fcol);
+ getFeaturesDisplayed().setVisible(sf.type);
+
try
{
- sf.begin = ( (Integer) start.getValue()).intValue();
- sf.end = ( (Integer) end.getValue()).intValue();
+ sf.begin = ((Integer) start.getValue()).intValue();
+ sf.end = ((Integer) end.getValue()).intValue();
+ } catch (NumberFormatException ex)
+ {
}
- catch (NumberFormatException ex)
- {}
ffile.parseDescriptionHTML(sf, false);
}
}
else
+ // NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
+ 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 (av.featuresDisplayed == null)
+ if (lastFeatureGroupAdded != null)
{
- av.featuresDisplayed = new Hashtable();
+ setGroupVisibility(lastFeatureGroupAdded, true);
}
+ setColour(lastFeatureAdded, fcol);
+ setVisible(lastFeatureAdded);
- if (featureGroups == null)
- {
- featureGroups = new Hashtable();
- }
+ findAllFeatures(false);
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
-
- av.featuresDisplayed.put(lastFeatureGroupAdded,
- new Integer(col.getRGB()));
-
- findAllFeatures();
+ ap.paintAlignment(true);
return true;
}
}
}
- if (name.getSelectedIndex() == -1)
- {
- findAllFeatures();
- }
+ ap.paintAlignment(true);
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;
- }
- /**
- * Replace current ordering with new ordering
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
- */
- public void setFeaturePriority(Object[][] data)
- {
- setFeaturePriority(data, true);
- }
/**
+ * update the amend feature button dependent on the given style
*
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
- * @param visibleNew when true current featureDisplay list will be cleared
+ * @param bigPanel
+ * @param col
+ * @param col
*/
- public void setFeaturePriority(Object[][] data, boolean visibleNew)
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ FeatureColourI col)
{
- if (visibleNew)
- {
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
- }
- if (data==null)
- {
- return;
- }
-
- // 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
- 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()));
- }
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
- renderOrder[data.length - i - 1] = type;
- }
- }
-
- }
- Hashtable featureOrder=null;
- /**
- * analogous to colour - store a normalized ordering for all feature types in
- * this rendering context.
- *
- * @param type
- * Feature type string
- * @param position
- * normalized priority - 0 means always appears on top, 1 means
- * always last.
- */
- public float setOrder(String type, float position)
- {
- if (featureOrder==null)
+ if (col.isSimpleColour())
{
- featureOrder = new Hashtable();
+ colour.setBackground(col.getColour());
}
- featureOrder.put(type, new Float(position));
- return position;
- }
- /**
- * get the global priority (0 (top) to 1 (bottom))
- *
- * @param type
- * @return [0,1] or -1 for a type without a priority
- */
- public float getOrder(String type) {
- if (featureOrder!=null)
+ else
{
- if (featureOrder.containsKey(type))
- {
- return ((Float)featureOrder.get(type)).floatValue();
- }
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, col);
}
- return -1;
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
}
/**
- * @param listener
- * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
*/
- public void removePropertyChangeListener(PropertyChangeListener listener)
+ public void orderFeatures(Comparator<String> order)
{
- changeSupport.removePropertyChangeListener(listener);
+ Arrays.sort(renderOrder, order);
}
}
git://source.jalview.org / jalview.git / blobdiff