X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=17f5a7186000150e0a72803bdbbccdc23fd4a2ba;hb=833fafa77f2f63bea98ce1d6e1e4ee3e46e7bd53;hp=a1de62e32e04b55c9a784222d380eaad92610fe4;hpb=97d6516fd717d0daddcbc8154c4de29a812982e5;p=jalview.git
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index a1de62e..17f5a71
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,872 +1,493 @@
/*
- * 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 .
+ * 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.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.FeatureColour;
+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.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSpinner;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
{
- AlignmentPanel ap;
- 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 = new Hashtable();
+ /*
+ * defaults for creating a new feature are the last created
+ * feature type and group
+ */
+ static String lastFeatureAdded = "feature_1";
- // This is actually an Integer held in the hashtable,
- // Retrieved using the key feature type
- Object currentColour;
+ static String lastFeatureGroupAdded = "Jalview";
- String[] renderOrder;
- PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+ Color resBoxColour;
- Vector allfeatures;
+ AlignmentPanel ap;
/**
- * Creates a new FeatureRenderer object.
- *
- * @param av
- * DOCUMENT ME!
+ * Creates a new FeatureRenderer object
+ *
+ * @param alignPanel
*/
- public FeatureRenderer(AlignmentPanel ap)
+ public FeatureRenderer(AlignmentPanel alignPanel)
{
- this.ap = ap;
- this.av = ap.av;
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
+ {
+ transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
+ }
}
+ FeatureColourI oldcol, fcol;
- public void transferSettings(FeatureRenderer fr)
- {
- this.renderOrder = fr.renderOrder;
- this.featureGroups = fr.featureGroups;
- this.featureColours = fr.featureColours;
- this.transparency = fr.transparency;
- this.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));
- }
+ int featureIndex = 0;
/**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
+ * Presents a dialog allowing the user to add new features, or amend or delete
+ * existing features. Currently this can be on
+ *
+ * - double-click on a sequence - Amend/Delete features at position
+ * - Create sequence feature from pop-up menu on selected region
+ * - Create features for pattern matches from Find
+ *
+ * If the supplied feature type is null, show (and update on confirm) the type
+ * and group of the last new feature created (with initial defaults of
+ * "feature_1" and "Jalview").
+ *
+ * @param sequences
+ * the sequences features are to be created on (if creating
+ * features), or a single sequence (if amending features)
+ * @param features
+ * the current features at the position (if amending), or template
+ * new feature(s) with start/end position set (if creating)
+ * @param create
+ * true to create features, false to amend or delete
+ * @param alignPanel
+ * @return
*/
- public int findFeatureColour(int initialCol, SequenceI seq, int column)
+ protected boolean amendFeatures(final List sequences,
+ final List features, boolean create,
+ final AlignmentPanel alignPanel)
{
- if (!av.showSequenceFeatures)
- {
- return initialCol;
- }
+ featureIndex = 0;
+
+ final JPanel mainPanel = new JPanel(new BorderLayout());
- if (seq != lastSeq)
+ final JTextField name = new JTextField(25);
+ name.getDocument().addDocumentListener(new DocumentListener()
{
- lastSeq = seq;
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures!=null)
+ @Override
+ public void insertUpdate(DocumentEvent e)
{
- sfSize = sequenceFeatures.length;
+ warnIfTypeHidden(mainPanel, name.getText());
}
- }
- if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures != null)
+ @Override
+ public void removeUpdate(DocumentEvent e)
{
- sfSize = sequenceFeatures.length;
+ warnIfTypeHidden(mainPanel, name.getText());
}
- }
-
- if (sequenceFeatures == null || sfSize==0)
- {
- 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);
- }
-
- 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)
+ @Override
+ public void changedUpdate(DocumentEvent e)
{
- return initialCol;
+ warnIfTypeHidden(mainPanel, name.getText());
}
- 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;
-
- synchronized 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)
+ final JTextField group = new JTextField(25);
+ group.getDocument().addDocumentListener(new DocumentListener()
{
- findAllFeatures();
- if (av.featuresDisplayed.size() < 1)
+ @Override
+ public void insertUpdate(DocumentEvent e)
{
- return;
+ warnIfGroupHidden(mainPanel, group.getText());
}
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- if (lastSeq == null || seq != lastSeq
- || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
- {
- lastSeq = seq;
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- }
-
- 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);
- }
-
- sfSize = sequenceFeatures.length;
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
-
- if (type == null || !av.featuresDisplayed.containsKey(type))
+ @Override
+ public void removeUpdate(DocumentEvent e)
{
- continue;
+ warnIfGroupHidden(mainPanel, group.getText());
}
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
+ @Override
+ public void changedUpdate(DocumentEvent e)
{
- if (!sequenceFeatures[sfindex].type.equals(type))
- {
- continue;
- }
-
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- &&
- sequenceFeatures[sfindex].featureGroup.length()!=0
- && featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
- &&
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
- featureGroup)).
- booleanValue())
- {
- continue;
- }
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+ });
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
- || sequenceFeatures[sfindex].getEnd() < spos))
- {
- continue;
- }
+ 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;
- if (offscreenRender && offscreenImage == null)
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (fcol.isSimpleColour())
{
- 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(mainPanel, colour, fcol);
}
}
- 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));
- }
- }
+ if (fcc == null)
+ {
+ final String ft = features.get(featureIndex).getType();
+ final String type = ft == null ? lastFeatureAdded : ft;
+ fcc = new FeatureColourChooser(me, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
- char s;
- int i;
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, Color featureColour, int start,
- int end, int y1)
- {
+ fcc.addActionListener(new ActionListener()
+ {
- 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!!
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fcol = fcc.getLastColour();
+ fcc = null;
+ setColour(type, fcol);
+ updateColourButton(mainPanel, colour, fcol);
+ }
+ });
- if (fend >= end)
- {
- fend = end;
+ }
+ }
}
- int pady = (y1 + av.charHeight) - av.charHeight / 5;
- for (i = fstart; i <= fend; i++)
+ });
+ JPanel gridPanel = new JPanel(new GridLayout(3, 1));
+
+ if (!create && features.size() > 1)
+ {
+ /*
+ * more than one feature at selected position -
+ * add a drop-down to choose the feature to amend
+ * space pad text if necessary to make entries distinct
+ */
+ gridPanel = new JPanel(new GridLayout(4, 1));
+ JPanel choosePanel = new JPanel();
+ choosePanel.add(new JLabel(
+ MessageManager.getString("label.select_feature") + ":"));
+ final JComboBox overlaps = new JComboBox();
+ List added = new ArrayList<>();
+ for (SequenceFeature sf : features)
{
- 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)
+ String text = String.format("%s/%d-%d (%s)", sf.getType(),
+ sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
+ while (added.contains(text))
{
- continue;
+ text += " ";
}
-
- g.setColor(Color.white);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + (av.charWidth * (i - start)),
- pady);
-
+ overlaps.addItem(text);
+ added.add(text);
}
- }
- }
+ choosePanel.add(overlaps);
- 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.
- *
- */
- void findAllFeatures()
- {
- synchronized (firing)
- {
- if (firing.equals(Boolean.FALSE)) {
- firing=Boolean.TRUE;
- findAllFeatures(true); // add all new features as visible
- changeSupport.firePropertyChange("changeSupport",null,null);
- firing=Boolean.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();
- }
-
- allfeatures = new Vector();
- Vector oldfeatures = new Vector();
- if (renderOrder!=null)
- {
- for (int i=0; i0)
- {
- for (int j=0; jsortOrder[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)
- {
- if (!featureColours.containsKey(featureType))
- {
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, col);
- return col;
- }
- else
- return (Color) featureColours.get(featureType);
- }
+ });
- static String lastFeatureAdded;
- static String lastFeatureGroupAdded;
- static String lastDescriptionAdded;
-
- int featureIndex = 0;
- boolean amendFeatures(final SequenceI[] sequences,
- final SequenceFeature[] features,
- boolean newFeatures,
- final AlignmentPanel ap)
- {
-
- featureIndex = 0;
-
- 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 JPanel colour = new JPanel();
- colour.setBorder(BorderFactory.createEtchedBorder());
- colour.setMaximumSize(new Dimension(40, 10));
- colour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- Color col = JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground());
- if (col != null)
- colour.setBackground(col);
+ gridPanel.add(choosePanel);
+ }
- }
- });
+ JPanel namePanel = new JPanel();
+ gridPanel.add(namePanel);
+ namePanel.add(new JLabel(MessageManager.getString("label.name:"),
+ JLabel.RIGHT));
+ namePanel.add(name);
- JPanel tmp = new JPanel();
- JPanel panel = new JPanel(new GridLayout(3, 1));
+ JPanel groupPanel = new JPanel();
+ gridPanel.add(groupPanel);
+ groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
+ JLabel.RIGHT));
+ groupPanel.add(group);
- ///////////////////////////////////////
- ///MULTIPLE FEATURES AT SELECTED RESIDUE
- if(!newFeatures && features.length>1)
- {
- panel = new JPanel(new GridLayout(4, 1));
- tmp = new JPanel();
- tmp.add(new JLabel("Select Feature: "));
- overlaps = new JComboBox();
- for(int i=0; i0)
+ if (reply == JvOptionPane.OK_OPTION && enteredType.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", " ");
-
- if(lastFeatureGroupAdded.length()<1)
- lastFeatureGroupAdded = null;
+ /*
+ * update default values only if creating using default values
+ */
+ if (useLastDefaults)
+ {
+ lastFeatureAdded = enteredType;
+ lastFeatureGroupAdded = enteredGroup;
+ // TODO: determine if the null feature group is valid
+ if (lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
+ }
}
- if (!newFeatures)
+ if (!create)
{
- SequenceFeature sf = features[featureIndex];
+ SequenceFeature sf = features.get(featureIndex);
- if (reply == JOptionPane.NO_OPTION)
+ if (reply == JvOptionPane.NO_OPTION)
{
- sequences[0].getDatasetSequence().deleteFeature(sf);
+ /*
+ * NO_OPTION corresponds to the Delete button
+ */
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
+ // update Feature Settings for removal of feature / group
+ featuresAdded();
}
- else if (reply == JOptionPane.YES_OPTION)
+ else if (reply == JvOptionPane.YES_OPTION)
{
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
-
- setColour(sf.type, colour.getBackground());
- av.featuresDisplayed.put(sf.type,
- new Integer(colour.getBackground().getRGB()));
-
+ /*
+ * YES_OPTION corresponds to the Amend button
+ * need to refresh Feature Settings if type, group or colour changed;
+ * note we don't force the feature to be visible - the user has been
+ * warned if a hidden feature type or group was entered
+ */
+ boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
+ .equals(enteredGroup));
+ refreshSettings |= (fcol != oldcol);
+ setColour(enteredType, fcol);
+ int newBegin = sf.begin;
+ int newEnd = sf.end;
try
{
- sf.begin = ( (Integer) start.getValue()).intValue();
- sf.end = ( (Integer) end.getValue()).intValue();
+ newBegin = ((Integer) start.getValue()).intValue();
+ newEnd = ((Integer) end.getValue()).intValue();
+ } catch (NumberFormatException ex)
+ {
+ // JSpinner doesn't accept invalid format data :-)
}
- catch (NumberFormatException ex)
- {}
- ffile.parseDescriptionHTML(sf, false);
+ /*
+ * replace the feature by deleting it and adding a new one
+ * (to ensure integrity of SequenceFeatures data store)
+ */
+ sequences.get(0).deleteFeature(sf);
+ SequenceFeature newSf = new SequenceFeature(sf, enteredType,
+ newBegin, newEnd, enteredGroup, sf.getScore());
+ newSf.setDescription(enteredDescription);
+ ffile.parseDescriptionHTML(newSf, false);
+ // amend features dialog only updates one sequence at a time
+ sequences.get(0).addSequenceFeature(newSf);
+
+ if (refreshSettings)
+ {
+ featuresAdded();
+ }
}
}
- else //NEW FEATURES ADDED
+ else
+ // NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION
- && lastFeatureAdded.length()>0)
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
{
- for (int i = 0; i < sequences.length; i++)
- {
- features[i].type = lastFeatureAdded;
- if (lastFeatureGroupAdded!=null)
- 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 (lastFeatureGroupAdded != null)
+ for (int i = 0; i < sequences.size(); i++)
{
- if (featureGroups == null)
- featureGroups = new Hashtable();
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+ SequenceFeature sf = features.get(i);
+ SequenceFeature sf2 = new SequenceFeature(enteredType,
+ enteredDescription, sf.getBegin(), sf.getEnd(),
+ enteredGroup);
+ ffile.parseDescriptionHTML(sf2, false);
+ sequences.get(i).addSequenceFeature(sf2);
}
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
- av.featuresDisplayed.put(lastFeatureAdded,
- new Integer(col.getRGB()));
-
- findAllFeatures(false);
+ setColour(enteredType, fcol);
- ap.paintAlignment(true);
+ featuresAdded();
+ alignPanel.paintAlignment(true);
return true;
}
@@ -876,129 +497,83 @@ public class FeatureRenderer
}
}
- ap.paintAlignment(true);
+ alignPanel.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);
- }
/**
- *
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
- * @param visibleNew when true current featureDisplay list will be cleared
+ * Show a warning message if the entered type is one that is currently hidden
+ *
+ * @param panel
+ * @param type
*/
- public void setFeaturePriority(Object[][] data, boolean visibleNew)
+ protected void warnIfTypeHidden(JPanel panel, String type)
{
- if (visibleNew)
- {
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
- }
- if (data==null)
+ if (getRenderOrder().contains(type))
{
- 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++)
+ if (!showFeatureOfType(type))
{
- 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;
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
}
}
-
}
- 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.
+ * Show a warning message if the entered group is one that is currently hidden
+ *
+ * @param panel
+ * @param group
*/
- public float setOrder(String type, float position)
+ protected void warnIfGroupHidden(JPanel panel, String group)
{
- if (featureOrder==null)
- {
- featureOrder = new Hashtable();
- }
- 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)
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
{
- if (featureOrder.containsKey(type))
- {
- return ((Float)featureOrder.get(type)).floatValue();
- }
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
}
- return -1;
}
/**
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
+ * update the amend feature button dependent on the given style
+ *
+ * @param bigPanel
+ * @param col
+ * @param col
*/
- public void addPropertyChangeListener(PropertyChangeListener listener)
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ FeatureColourI col)
{
- changeSupport.addPropertyChangeListener(listener);
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
+
+ if (col.isSimpleColour())
+ {
+ colour.setBackground(col.getColour());
+ }
+ else
+ {
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, col);
+ }
}
/**
- * @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 order)
{
- changeSupport.removePropertyChangeListener(listener);
+ Arrays.sort(renderOrder, order);
}
}