-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-import javax.swing.JOptionPane;\r
-import java.awt.event.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
- Color resBoxColour;\r
- float transparency = 1.0f;\r
- FontMetrics fm;\r
- int charOffset;\r
-\r
- Hashtable featureColours = new Hashtable();\r
-\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\r
- // This is actually an Integer held in the hashtable,\r
- // Retrieved using the key feature type\r
- Object currentColour;\r
-\r
- String [] renderOrder;\r
-\r
- /**\r
- * Creates a new FeatureRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void transferSettings(FeatureRenderer fr)\r
- {\r
- renderOrder = fr.renderOrder;\r
- featureGroups = fr.featureGroups;\r
- featureColours = fr.featureColours;\r
- transparency = fr.transparency;\r
- }\r
-\r
- BufferedImage offscreenImage;\r
- boolean offscreenRender = false;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
- {\r
- return new Color( findFeatureColour (initialCol.getRGB(),\r
- seq, res ));\r
- }\r
-\r
- /**\r
- * This is used by the Molecule Viewer and Overview to\r
- * get the accurate colourof the rendered sequence\r
- */\r
- public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if(seq!=lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
- return Color.white.getRGB();\r
-\r
-\r
- //Only bother making an offscreen image if transparency is applied\r
- if(transparency!=1.0f && offscreenImage==null)\r
- {\r
- offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
- }\r
-\r
- currentColour = null;\r
-\r
- offscreenRender = true;\r
-\r
- if(offscreenImage!=null)\r
- {\r
- offscreenImage.setRGB(0,0,initialCol);\r
- drawSequence(offscreenImage.getGraphics(),\r
- lastSeq,\r
- column,column,0);\r
-\r
- return offscreenImage.getRGB(0,0);\r
- }\r
- else\r
- {\r
- drawSequence(null,\r
- lastSeq,\r
- lastSeq.findPosition(column),\r
- -1, -1);\r
-\r
- if (currentColour == null)\r
- return initialCol;\r
- else\r
- return ((Integer)currentColour).intValue();\r
- }\r
-\r
-\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param sg DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- // String type;\r
- // SequenceFeature sf;\r
- SequenceI lastSeq;\r
- SequenceFeature [] sequenceFeatures;\r
- int sfSize, sfindex, spos, epos;\r
-\r
- public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1)\r
- {\r
- if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
- return;\r
-\r
- if(g!=null)\r
- fm = g.getFontMetrics();\r
-\r
-\r
- if (av.featuresDisplayed == null\r
- || renderOrder==null\r
- || newFeatureAdded)\r
- {\r
- findAllFeatures();\r
- if(av.featuresDisplayed.size()<1)\r
- return;\r
-\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(lastSeq==null || seq!=lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
-\r
- if (transparency != 1 && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, transparency));\r
- }\r
-\r
- if(!offscreenRender)\r
- {\r
- spos = lastSeq.findPosition(start);\r
- epos = lastSeq.findPosition(end);\r
- }\r
-\r
-\r
- String type;\r
- for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
-\r
- if(!av.featuresDisplayed.containsKey(type))\r
- continue;\r
-\r
- // loop through all features in sequence to find\r
- // current feature to render\r
- for (sfindex = 0; sfindex < sfSize; sfindex++)\r
- {\r
- if(sequenceFeatures.length<=sfindex)\r
- {\r
- continue;\r
- }\r
- if (!sequenceFeatures[sfindex].type.equals(type))\r
- continue;\r
-\r
- if (featureGroups != null\r
- && sequenceFeatures[sfindex].featureGroup != null\r
- &&\r
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
- &&\r
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
- booleanValue())\r
- {\r
- continue;\r
- }\r
-\r
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- continue;\r
-\r
- if (offscreenRender && offscreenImage==null)\r
- {\r
- if (sequenceFeatures[sfindex].begin <= start &&\r
- sequenceFeatures[sfindex].end >= start)\r
- {\r
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
- type);\r
- }\r
- }\r
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
- {\r
-\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1);\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1);\r
-\r
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- getColour(sequenceFeatures[sfindex].type),\r
- start, end, y1);\r
-\r
-\r
- }\r
-\r
- }\r
-\r
- if(transparency!=1.0f && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, 1.0f));\r
- }\r
- }\r
-\r
-\r
- char s;\r
- int i;\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, Color featureColour, int start, int end, int y1)\r
- {\r
-\r
- if (((fstart <= end) && (fend >= start)))\r
- {\r
- if (fstart < start)\r
- { // fix for if the feature we have starts before the sequence start,\r
- fstart = start; // but the feature end is still valid!!\r
- }\r
-\r
- if (fend >= end)\r
- {\r
- fend = end;\r
- }\r
- int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
- for (i = fstart; i <= fend; i++)\r
- {\r
- s = seq.getSequence().charAt(i);\r
-\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
-\r
- g.setColor(featureColour);\r
-\r
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
-\r
- if(offscreenRender || !av.validCharWidth)\r
- continue;\r
-\r
- g.setColor(Color.white);\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + (av.charWidth * (i - start)),\r
- pady);\r
-\r
- }\r
- }\r
- }\r
-\r
-\r
- boolean newFeatureAdded = false;\r
-\r
- public void featuresAdded()\r
- {\r
- findAllFeatures();\r
- }\r
-\r
- boolean findingFeatures = false;\r
- synchronized void findAllFeatures()\r
- {\r
- newFeatureAdded = false;\r
-\r
- if(findingFeatures)\r
- {\r
- newFeatureAdded = true;\r
- return;\r
- }\r
-\r
- findingFeatures = true;\r
- jalview.schemes.UserColourScheme ucs = new\r
- jalview.schemes.UserColourScheme();\r
-\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- av.featuresDisplayed.clear();\r
-\r
- Vector allfeatures = new Vector();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature [] features\r
- = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
-\r
- if (features == null)\r
- continue;\r
-\r
- int index = 0;\r
- while (index < features.length)\r
- {\r
- if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
- {\r
- if(!(features[index].begin == 0 && features[index].end ==0))\r
- {\r
- // If beginning and end are 0, the feature is for the whole sequence\r
- // and we don't want to render the feature in the normal way\r
-\r
- if (getColour(features[index].getType()) == null)\r
- {\r
- featureColours.put(features[index].getType(),\r
- ucs.createColourFromName(features[index].\r
- getType()));\r
- }\r
-\r
- av.featuresDisplayed.put(features[index].getType(),\r
- new Integer(getColour(features[index].\r
- getType()).getRGB()));\r
- allfeatures.addElement(features[index].getType());\r
- }\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- renderOrder = new String[allfeatures.size()];\r
- Enumeration en = allfeatures.elements();\r
- int i = allfeatures.size()-1;\r
- while(en.hasMoreElements())\r
- {\r
- renderOrder[i] = en.nextElement().toString();\r
- i--;\r
- }\r
-\r
- findingFeatures = false;\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- Color colour = (Color)featureColours.get(featureType);\r
- return colour;\r
- }\r
-\r
-\r
- static String lastFeatureAdded;\r
- static String lastFeatureGroupAdded;\r
- static String lastDescriptionAdded;\r
-\r
- public boolean createNewFeatures(SequenceI[] sequences,\r
- SequenceFeature [] features)\r
- {\r
- return amendFeatures(sequences, features, true);\r
- }\r
-\r
- int featureIndex = 0;\r
- boolean amendFeatures(SequenceI[] sequences,\r
- final SequenceFeature [] features,\r
- boolean newFeatures)\r
- {\r
- JPanel bigPanel = new JPanel(new BorderLayout());\r
- final JComboBox name = new JComboBox();\r
- final JComboBox source = new JComboBox();\r
- final JTextArea description = new JTextArea(3,25);\r
- final JSpinner start = new JSpinner();\r
- final JSpinner end = new JSpinner();\r
- final JPanel colour = new JPanel();\r
- colour.setBorder(BorderFactory.createEtchedBorder());\r
- colour.setMaximumSize(new Dimension(40,10));\r
- colour.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- colour.setBackground(\r
- JColorChooser.showDialog(Desktop.desktop,\r
- "Select Feature Colour",\r
- colour.getBackground()));\r
- }\r
- });\r
-\r
- JPanel panel = new JPanel(new GridLayout(3, 2));\r
- panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));\r
- panel.add(name);\r
- panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
- panel.add(source);\r
- panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));\r
- JPanel tmp = new JPanel();\r
- tmp.add(colour);\r
- colour.setPreferredSize(new Dimension(150,15));\r
- panel.add(tmp);\r
- name.setEditable(true);\r
- source.setEditable(true);\r
-\r
- bigPanel.add(panel, BorderLayout.NORTH);\r
- panel = new JPanel();\r
- panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
- description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- description.setLineWrap(true);\r
- panel.add(new JScrollPane(description));\r
-\r
- if(!newFeatures)\r
- {\r
- bigPanel.add(panel, BorderLayout.SOUTH);\r
-\r
- panel = new JPanel();\r
- panel.add(new JLabel(" Start: ", JLabel.RIGHT));\r
- panel.add(start);\r
- panel.add(new JLabel(" End: ", JLabel.RIGHT));\r
- panel.add(end);\r
- bigPanel.add(panel, BorderLayout.CENTER);\r
- }\r
- else\r
- bigPanel.add(panel, BorderLayout.CENTER);\r
-\r
- if (lastFeatureAdded == null)\r
- if (features[0].type != null)\r
- lastFeatureAdded = features[0].type;\r
- else\r
- lastFeatureAdded = "feature_1";\r
-\r
- if (lastFeatureGroupAdded == null)\r
- if (features[0].featureGroup != null)\r
- lastFeatureGroupAdded = features[0].featureGroup;\r
- else\r
- lastFeatureAdded = "Jalview";\r
-\r
-\r
- Enumeration en;\r
- if (featureGroups != null)\r
- {\r
- en = featureGroups.keys();\r
- while (en.hasMoreElements())\r
- {\r
- source.addItem(en.nextElement().toString());\r
- }\r
- }\r
-\r
- if (newFeatures)\r
- {\r
- if(av.featuresDisplayed != null)\r
- {\r
- en = av.featuresDisplayed.keys();\r
- while (en.hasMoreElements())\r
- {\r
- name.addItem(en.nextElement().toString());\r
- }\r
- }\r
-\r
- name.setSelectedItem(lastFeatureAdded);\r
- source.setSelectedItem(lastFeatureGroupAdded);\r
- description.setText(\r
- lastDescriptionAdded == null ?\r
- features[0].description : lastDescriptionAdded);\r
-\r
- if (getColour(lastFeatureAdded) != null)\r
- {\r
- colour.setBackground(getColour(lastFeatureAdded));\r
- colour.setForeground(getColour(lastFeatureAdded));\r
- }\r
- else\r
- {\r
- colour.setBackground(new Color(60, 160, 115));\r
- colour.setForeground(new Color(60, 160, 115));\r
- }\r
-\r
- }\r
- else if (!newFeatures)\r
- {\r
- featureIndex = 0;\r
- for(int f=0; f<features.length; f++)\r
- {\r
- name.addItem(features[f].getType().toString());\r
- }\r
-\r
- description.setText(features[0].getDescription());\r
- source.setSelectedItem(features[0].getFeatureGroup());\r
- start.setValue(new Integer(features[0].getBegin()));\r
- end.setValue(new Integer(features[0].getEnd()));\r
- colour.setBackground(\r
- getColour(name.getSelectedItem().toString()));\r
- name.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- int index = name.getSelectedIndex();\r
- if(index!=-1)\r
- {\r
- featureIndex = index;\r
- description.setText(features[index].getDescription());\r
- source.setSelectedItem(features[index].getFeatureGroup());\r
- start.setValue(new Integer(features[index].getBegin()));\r
- end.setValue(new Integer(features[index].getEnd()));\r
- colour.setBackground(\r
- getColour(name.getSelectedItem().toString()));\r
- colour.setForeground(\r
- getColour(name.getSelectedItem().toString()));\r
- }\r
- }\r
- });\r
-\r
- }\r
-\r
-\r
- Object [] options;\r
- if(!newFeatures)\r
- options = new Object[]{"Amend", "Delete", "Cancel"};\r
- else\r
- options = new Object[]{"OK", "Cancel"};\r
-\r
- String title = newFeatures ? "Create New Sequence Feature(s)" :\r
- "Amend/Delete Features";\r
-\r
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
- bigPanel,\r
- title,\r
- JOptionPane.YES_NO_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- options, "OK");\r
-\r
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
-\r
- if (reply == JOptionPane.OK_OPTION\r
- && name.getSelectedItem() != null\r
- && source.getSelectedItem() != null)\r
- {\r
- lastFeatureAdded = name.getSelectedItem().toString();\r
- lastFeatureGroupAdded = source.getSelectedItem().toString();\r
- lastDescriptionAdded = description.getText().replaceAll("\n", " ");\r
- }\r
-\r
- if(!newFeatures)\r
- {\r
- SequenceFeature sf = features[featureIndex];\r
-\r
- if(reply==JOptionPane.NO_OPTION)\r
- sequences[0].getDatasetSequence().deleteFeature(sf);\r
- else if(reply==JOptionPane.YES_OPTION)\r
- {\r
- sf.type = lastFeatureAdded;\r
- sf.featureGroup = lastFeatureGroupAdded;\r
- sf.description = lastDescriptionAdded;\r
- setColour(sf.type, colour.getBackground());\r
- try{\r
- sf.begin = ((Integer)start.getValue()).intValue();\r
- sf.end = ((Integer)end.getValue()).intValue();\r
- }catch(NumberFormatException ex)\r
- {}\r
-\r
- ffile.parseDescriptionHTML(sf, false);\r
- }\r
- }\r
- else\r
- {\r
- if (reply == JOptionPane.OK_OPTION\r
- && name.getSelectedItem() != null\r
- && source.getSelectedItem() != null)\r
- {\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- features[i].type = lastFeatureAdded;\r
- features[i].featureGroup = lastFeatureGroupAdded;\r
- features[i].description = lastDescriptionAdded;\r
- sequences[i].addSequenceFeature(features[i]);\r
- ffile.parseDescriptionHTML(features[i], false);\r
- }\r
-\r
- if (av.featuresDisplayed == null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- if (featureGroups == null)\r
- featureGroups = new Hashtable();\r
-\r
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
-\r
- Color col = colour.getBackground();\r
- setColour(lastFeatureAdded, colour.getBackground());\r
-\r
- av.featuresDisplayed.put(lastFeatureGroupAdded,\r
- new Integer(col.getRGB()));\r
-\r
- findAllFeatures();\r
-\r
- return true;\r
- }\r
- else\r
- return false;\r
- }\r
-\r
- if(name.getSelectedIndex()==-1)\r
- findAllFeatures();\r
-\r
-\r
- return true;\r
- }\r
-\r
- public void setColour(String featureType, Color col)\r
- {\r
- featureColours.put(featureType, col);\r
- }\r
-\r
- public void setTransparency(float value)\r
- {\r
- transparency = value;\r
- }\r
-\r
- public float getTransparency()\r
- {\r
- return transparency;\r
- }\r
-\r
- public void setFeaturePriority(Object [][] data)\r
- {\r
- // The feature table will display high priority\r
- // features at the top, but theses are the ones\r
- // we need to render last, so invert the data\r
- if(av.featuresDisplayed!=null)\r
- av.featuresDisplayed.clear();\r
- else\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- renderOrder = new String[data.length];\r
-\r
- if (data.length > 0)\r
- for (int i = 0; i < data.length; i++)\r
- {\r
- String type = data[i][0].toString();\r
- setColour(type, (Color) data[i][1]);\r
- if ( ( (Boolean) data[i][2]).booleanValue())\r
- {\r
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
- }\r
-\r
- renderOrder[data.length - i - 1] = type;\r
- }\r
-\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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.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
+ * <ul>
+ * <li>double-click on a sequence - Amend/Delete features at position</li>
+ * <li>Create sequence feature from pop-up menu on selected region</li>
+ * <li>Create features for pattern matches from Find</li>
+ * </ul>
+ * 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<SequenceI> sequences,
+ final List<SequenceFeature> 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
+ */
+ gridPanel = new JPanel(new GridLayout(4, 1));
+ JPanel choosePanel = new JPanel();
+ choosePanel.add(new JLabel(MessageManager
+ .getString("label.select_feature")
+ + ":"));
+ final JComboBox<String> overlaps = new JComboBox<String>();
+ for (SequenceFeature sf : features)
+ {
+ String text = sf.getType() + "/" + sf.getBegin() + "-"
+ + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
+ overlaps.addItem(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);
+
+ }
+ 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, newBegin, newEnd,
+ enteredGroup, sf.getScore());
+ sf.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<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff