X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=17f5a7186000150e0a72803bdbbccdc23fd4a2ba;hb=53b99b41ed7f26f2724f3ed87d524eb83c5208f4;hp=3f332b5fddfe0e32bd1bb09a8794938947d53bab;hpb=d03971168d7f0192862cf5b57602ecf3e341b457;p=jalview.git
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
old mode 100755
new mode 100644
index 3f332b5..17f5a71
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,315 +1,579 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 jalview.datamodel.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-import java.awt.image.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FeatureRenderer
-{
- AlignViewport av;
- Color resBoxColour;
- float transparency = 1.0f;
- FontMetrics fm;
- int charOffset;
- boolean drawText = true;
-
- // The following vector holds the features which are
- // to be added, in the correct order or rendering
- Vector featuresDisplayed = null;
-
- /**
- * Creates a new FeatureRenderer object.
- *
- * @param av DOCUMENT ME!
- */
- public FeatureRenderer(AlignViewport av)
- {
- this.av = av;
- initColours();
- }
-
- /**
- * This is used by the Molecule Viewer to get the accurate colour
- * of the rendered sequence
- */
- BufferedImage bi;
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
- {
- if(!av.showSequenceFeatures)
- return initialCol;
-
- if (bi == null)
- bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
-
- bi.setRGB(0,0, initialCol.getRGB());
-
- drawText = false;
-
- drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
- drawText = true;
-
- return new Color(bi.getRGB(0, 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!
- */
- public void drawSequence(Graphics g, SequenceI seq,
- int start, int end, int x1, int y1, int width, int height)
- {
-
-//System.out.println(start+" "+end+" "+x1+" "+y1);
- if (seq.getDatasetSequence().getSequenceFeatures() == null
- || seq.getDatasetSequence().getSequenceFeatures().size()==0)
- return;
-
- fm = g.getFontMetrics();
-
- if (transparency != 1)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, transparency));
- }
-
- String type;
- SequenceFeature sf;
- if (featuresDisplayed == null)
- findAllFeatures();
-
- Enumeration e = featuresDisplayed.elements(), e2;
-
- // Loop through each visible feature
- while (e.hasMoreElements())
- {
-
- type = e.nextElement().toString();
- e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
- // loop through all features in sequence to find
- // current feature to render
- while (e2.hasMoreElements())
- {
-
- sf = (SequenceFeature) e2.nextElement();
- if (!type.equals(sf.getType()))
- continue;
-
- if (sf.getBegin() > seq.getEnd())
- continue;
-
- if (type.equals("disulfide bond"))
- {
-
- renderFeature(g, seq,
- seq.findIndex(sf.getBegin()) - 1,
- seq.findIndex(sf.getBegin()) - 1,
- type, start, end, x1, y1, width, height);
- renderFeature(g, seq,
- seq.findIndex(sf.getEnd()) - 1,
- seq.findIndex(sf.getEnd()) - 1,
- type, start, end, x1, y1, width, height);
-
- }
- else
- renderFeature(g, seq,
- seq.findIndex(sf.getBegin()) - 1,
- seq.findIndex(sf.getEnd()) - 1,
- type, start, end, x1, y1, width, height);
- }
- }
-
- if(transparency!=1.0f)
- {
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(
- AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, 1.0f));
- }
- }
-
-
- void renderFeature(Graphics g, SequenceI seq,
- int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)
- {
-
- 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;
- }
- for (int i = fstart; i <= fend; i++)
- {
- char s = seq.getSequence().charAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(getColour(type));
-
- g.fillRect( (i - start) * width, y1, width, height);
-
- if(drawText)
- {
- g.setColor(Color.white);
- charOffset = (width - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s),
- charOffset + x1 + (width * (i - start)),
- (y1 + height) - height / 5); //pady = height / 5;
- }
- }
- }
- }
-
- void findAllFeatures()
- {
- Vector features = new Vector();
- SequenceFeature sf;
- featuresDisplayed = new Vector();
- Enumeration e;
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- features = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
- if (features == null)
- continue;
-
- e = features.elements();
- while (e.hasMoreElements())
- {
- sf = (SequenceFeature) e.nextElement();
- if (!featuresDisplayed.contains(sf.getType()))
- {
- featuresDisplayed.addElement(sf.getType());
- }
- }
- }
- }
-
- public Color getColour(String featureType)
- {
- return (Color)featureColours.get(featureType);
- }
-
- 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
- featuresDisplayed.clear();
- for(int i=data.length-1; i>-1; i--)
- {
- String type = data[i][0].toString();
- setColour(type, (Color)data[i][1]);
- if( ((Boolean)data[i][2]).booleanValue() )
- featuresDisplayed.addElement(type);
- }
- }
-
- Hashtable featureColours = new Hashtable();
- void initColours()
- {
- featureColours.put("active site", new Color(255, 75, 0));
- featureColours.put("binding site", new Color(245, 85, 0));
- featureColours.put("calcium-binding region", new Color(235, 95, 0));
- featureColours.put("chain", new Color(225, 105, 0));
- featureColours.put("coiled-coil region", new Color(215, 115, 0));
- featureColours.put("compositionally biased region", new Color(205, 125, 0));
- featureColours.put("cross-link", new Color(195, 135, 0));
- featureColours.put("disulfide bond", new Color(230,230,0));
- featureColours.put("DNA-binding region", new Color(175, 155, 0));
- featureColours.put("domain", new Color(165, 165, 0));
- featureColours.put("glycosylation site", new Color(155, 175, 0));
- featureColours.put("helix", new Color(145, 185, 0));
- featureColours.put("initiator methionine", new Color(135, 195, 5));
- featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));
- featureColours.put("metal ion-binding site", new Color(115, 215, 25));
- featureColours.put("modified residue", new Color(105, 225, 35));
- featureColours.put("mutagenesis site", new Color(95, 235, 45));
- featureColours.put("non-consecutive residues", new Color(85, 245, 55));
- featureColours.put("non-terminal residue", new Color(75, 255, 65));
- featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));
- featureColours.put("peptide", new Color(55, 235, 85));
- featureColours.put("propeptide", new Color(45, 225, 95));
- featureColours.put("region of interest", new Color(35, 215, 105));
- featureColours.put("repeat", new Color(25, 205, 115));
- featureColours.put("selenocysteine", new Color(15, 195, 125));
- featureColours.put("sequence conflict", new Color(5, 185, 135));
- featureColours.put("sequence variant", new Color(0, 175, 145));
- featureColours.put("short sequence motif", new Color(0, 165, 155));
- featureColours.put("signal peptide", new Color(0, 155, 165));
- featureColours.put("site", new Color(0, 145, 175));
- featureColours.put("splice variant", new Color(0, 135, 185));
- featureColours.put("strand", new Color(0, 125, 195));
- featureColours.put("topological domain", new Color(0, 115, 205));
- featureColours.put("transit peptide", new Color(0, 105, 215));
- featureColours.put("transmembrane region", new Color(0, 95, 225));
- featureColours.put("turn", new Color(0, 85, 235));
- featureColours.put("unsure residue", new Color(0, 75, 245));
- featureColours.put("zinc finger region", new Color(0, 65, 255));
- }
-
-}
+/*
+ * 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.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
+{
+ /*
+ * defaults for creating a new feature are the last created
+ * feature type and group
+ */
+ static String lastFeatureAdded = "feature_1";
+
+ static String lastFeatureGroupAdded = "Jalview";
+
+ Color resBoxColour;
+
+ AlignmentPanel ap;
+
+ /**
+ * Creates a new FeatureRenderer object
+ *
+ * @param alignPanel
+ */
+ public FeatureRenderer(AlignmentPanel alignPanel)
+ {
+ 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;
+
+ int featureIndex = 0;
+
+ /**
+ * 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
+ */
+ protected boolean amendFeatures(final List sequences,
+ final List features, boolean create,
+ final AlignmentPanel alignPanel)
+ {
+ featureIndex = 0;
+
+ final JPanel mainPanel = new JPanel(new BorderLayout());
+
+ final JTextField name = new JTextField(25);
+ name.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ warnIfTypeHidden(mainPanel, name.getText());
+ }
+ });
+
+ final JTextField group = new JTextField(25);
+ group.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ warnIfGroupHidden(mainPanel, group.getText());
+ }
+ });
+
+ 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"),
+ fcol.getColour());
+ if (col != null)
+ {
+ fcol = new FeatureColour(col);
+ updateColourButton(mainPanel, colour, fcol);
+ }
+ }
+ else
+ {
+ 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();
+
+ fcc.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fcol = fcc.getLastColour();
+ fcc = null;
+ setColour(type, fcol);
+ updateColourButton(mainPanel, colour, fcol);
+ }
+ });
+
+ }
+ }
+ }
+ });
+ 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)
+ {
+ String text = String.format("%s/%d-%d (%s)", sf.getType(),
+ sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
+ while (added.contains(text))
+ {
+ text += " ";
+ }
+ overlaps.addItem(text);
+ added.add(text);
+ }
+ choosePanel.add(overlaps);
+
+ overlaps.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ SequenceFeature sf = features.get(index);
+ name.setText(sf.getType());
+ description.setText(sf.getDescription());
+ group.setText(sf.getFeatureGroup());
+ start.setValue(new Integer(sf.getBegin()));
+ end.setValue(new Integer(sf.getEnd()));
+
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequences.get(0), sf.getBegin(),
+ sf.getEnd());
+
+ alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
+ highlight, false);
+ }
+ FeatureColourI col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new FeatureColour(
+ ColorUtils.createColourFromName(name.getText()));
+ }
+ oldcol = fcol = col;
+ updateColourButton(mainPanel, colour, 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 groupPanel = new JPanel();
+ gridPanel.add(groupPanel);
+ groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
+ JLabel.RIGHT));
+ groupPanel.add(group);
+
+ JPanel colourPanel = new JPanel();
+ gridPanel.add(colourPanel);
+ colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
+ JLabel.RIGHT));
+ colourPanel.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);
+ mainPanel.add(gridPanel, BorderLayout.NORTH);
+
+ JPanel descriptionPanel = new JPanel();
+ descriptionPanel.add(new JLabel(
+ MessageManager.getString("label.description:"), JLabel.RIGHT));
+ description.setFont(JvSwingUtils.getTextAreaFont());
+ description.setLineWrap(true);
+ descriptionPanel.add(new JScrollPane(description));
+
+ if (!create)
+ {
+ mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
+
+ JPanel startEndPanel = new JPanel();
+ startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
+ JLabel.RIGHT));
+ startEndPanel.add(start);
+ startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
+ JLabel.RIGHT));
+ startEndPanel.add(end);
+ mainPanel.add(startEndPanel, BorderLayout.CENTER);
+ }
+ else
+ {
+ mainPanel.add(descriptionPanel, BorderLayout.CENTER);
+ }
+
+ /*
+ * default feature type and group to that of the first feature supplied,
+ * or to the last feature created if not supplied (null value)
+ */
+ SequenceFeature firstFeature = features.get(0);
+ boolean useLastDefaults = firstFeature.getType() == null;
+ final String featureType = useLastDefaults ? lastFeatureAdded
+ : firstFeature.getType();
+ final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
+ : firstFeature.getFeatureGroup();
+ name.setText(featureType);
+ group.setText(featureGroup);
+
+ start.setValue(new Integer(firstFeature.getBegin()));
+ end.setValue(new Integer(firstFeature.getEnd()));
+ description.setText(firstFeature.getDescription());
+ updateColourButton(mainPanel, colour,
+ (oldcol = fcol = getFeatureStyle(featureType)));
+ Object[] options;
+ if (!create)
+ {
+ options = new Object[] { MessageManager.getString("label.amend"),
+ MessageManager.getString("action.delete"),
+ MessageManager.getString("action.cancel") };
+ }
+ else
+ {
+ options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ }
+
+ String title = create
+ ? MessageManager.getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[]
+ { sequences.get(0).getName() });
+
+ /*
+ * show the dialog
+ */
+ int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.QUESTION_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
+
+ FeaturesFile ffile = new FeaturesFile();
+
+ final String enteredType = name.getText().trim();
+ final String enteredGroup = group.getText().trim();
+ final String enteredDescription = description.getText().replaceAll("\n", " ");
+
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
+ {
+ /*
+ * 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 (!create)
+ {
+ SequenceFeature sf = features.get(featureIndex);
+
+ if (reply == JvOptionPane.NO_OPTION)
+ {
+ /*
+ * 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 == JvOptionPane.YES_OPTION)
+ {
+ /*
+ * 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
+ {
+ newBegin = ((Integer) start.getValue()).intValue();
+ newEnd = ((Integer) end.getValue()).intValue();
+ } catch (NumberFormatException ex)
+ {
+ // JSpinner doesn't accept invalid format data :-)
+ }
+
+ /*
+ * 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
+ {
+ if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
+ {
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ 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);
+ }
+
+ setColour(enteredType, fcol);
+
+ featuresAdded();
+
+ alignPanel.paintAlignment(true);
+
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ alignPanel.paintAlignment(true);
+
+ return true;
+ }
+
+ /**
+ * Show a warning message if the entered type is one that is currently hidden
+ *
+ * @param panel
+ * @param type
+ */
+ protected void warnIfTypeHidden(JPanel panel, String type)
+ {
+ if (getRenderOrder().contains(type))
+ {
+ if (!showFeatureOfType(type))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.feature_type"), type);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
+ }
+ }
+ }
+
+ /**
+ * Show a warning message if the entered group is one that is currently hidden
+ *
+ * @param panel
+ * @param group
+ */
+ protected void warnIfGroupHidden(JPanel panel, String group)
+ {
+ if (featureGroups.containsKey(group) && !featureGroups.get(group))
+ {
+ String msg = MessageManager.formatMessage("label.warning_hidden",
+ MessageManager.getString("label.group"), group);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
+ }
+ }
+
+ /**
+ * update the amend feature button dependent on the given style
+ *
+ * @param bigPanel
+ * @param col
+ * @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(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);
+ }
+}