-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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 java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-\r
-import jalview.datamodel.*;\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
- // 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
- {\r
- return initialCol;\r
- }\r
-\r
- if (seq != lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
- if (sequenceFeatures == null)\r
- {\r
- return initialCol;\r
- }\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
- {\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
- {\r
- return initialCol;\r
- }\r
- else\r
- {\r
- return ( (Integer) currentColour).intValue();\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
- {\r
- return;\r
- }\r
-\r
- if (g != null)\r
- {\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
- {\r
- return;\r
- }\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
- 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
- String type;\r
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
-\r
- if (type == null || !av.featuresDisplayed.containsKey(type))\r
- {\r
- continue;\r
- }\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
- {\r
- continue;\r
- }\r
-\r
- if (featureGroups != null\r
- && sequenceFeatures[sfindex].featureGroup != null\r
- &&\r
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
- &&\r
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].\r
- featureGroup)).\r
- booleanValue())\r
- {\r
- continue;\r
- }\r
-\r
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- {\r
- continue;\r
- }\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
- {\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
- char s;\r
- int i;\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, Color featureColour, int start,\r
- 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.getCharAt(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
- {\r
- continue;\r
- }\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
- 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
- {\r
- av.featuresDisplayed = new Hashtable();\r
- }\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().\r
- getSequenceFeatures();\r
-\r
- if (features == null)\r
- {\r
- continue;\r
- }\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
- 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, null);\r
- }\r
-\r
- int featureIndex = 0;\r
- boolean amendFeatures(final SequenceI[] sequences,\r
- final SequenceFeature[] features,\r
- boolean newFeatures,\r
- final AlignmentPanel ap)\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
- start.setPreferredSize(new Dimension(80, 20));\r
- end.setPreferredSize(new Dimension(80, 20));\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
- {\r
- bigPanel.add(panel, BorderLayout.CENTER);\r
- }\r
-\r
- if (lastFeatureAdded == null)\r
- {\r
- if (features[0].type != null)\r
- {\r
- lastFeatureAdded = features[0].type;\r
- }\r
- else\r
- {\r
- lastFeatureAdded = "feature_1";\r
- }\r
- }\r
-\r
- if (lastFeatureGroupAdded == null)\r
- {\r
- if (features[0].featureGroup != null)\r
- {\r
- lastFeatureGroupAdded = features[0].featureGroup;\r
- }\r
- else\r
- {\r
- lastFeatureAdded = "Jalview";\r
- }\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
- }\r
- else\r
- {\r
- colour.setBackground(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
-\r
- SearchResults highlight = new SearchResults();\r
- highlight.addResult(sequences[0],\r
- features[index].getBegin(),\r
- features[index].getEnd());\r
-\r
- ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
-\r
- }\r
- Color col = getColour(name.getSelectedItem().toString());\r
- if (col == null)\r
- {\r
- col = new\r
- jalview.schemes.UserColourScheme()\r
- .createColourFromName(name.getSelectedItem().toString());\r
- }\r
-\r
- colour.setBackground(col);\r
- }\r
- });\r
-\r
- }\r
-\r
- Object[] options;\r
- if (!newFeatures)\r
- {\r
- options = new Object[]\r
- {\r
- "Amend", "Delete", "Cancel"};\r
- }\r
- else\r
- {\r
- options = new Object[]\r
- {\r
- "OK", "Cancel"};\r
- }\r
-\r
- String title = newFeatures ? "Create New Sequence Feature(s)" :\r
- "Amend/Delete Features for "\r
- + sequences[0].getName();\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
- //This ensures that the last sequence\r
- //is refreshed and new features are rendered\r
- lastSeq = null;\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
- {\r
- sequences[0].getDatasetSequence().deleteFeature(sf);\r
- }\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
- {\r
- sf.begin = ( (Integer) start.getValue()).intValue();\r
- sf.end = ( (Integer) end.getValue()).intValue();\r
- }\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
- {\r
- av.featuresDisplayed = new Hashtable();\r
- }\r
-\r
- if (featureGroups == null)\r
- {\r
- featureGroups = new Hashtable();\r
- }\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
- {\r
- return false;\r
- }\r
- }\r
-\r
- if (name.getSelectedIndex() == -1)\r
- {\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
- {\r
- av.featuresDisplayed.clear();\r
- }\r
- else\r
- {\r
- av.featuresDisplayed = new Hashtable();\r
- }\r
-\r
- renderOrder = new String[data.length];\r
-\r
- if (data.length > 0)\r
- {\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
+/*
+ * 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
+ * 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 java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class 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;
+
+ /**
+ * 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;
+ }
+
+ 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)
+ {
+ if (!av.showSequenceFeatures)
+ {
+ return initialCol;
+ }
+
+ if (seq != lastSeq)
+ {
+ lastSeq = seq;
+ sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+ if (sequenceFeatures == null)
+ {
+ return initialCol;
+ }
+
+ sfSize = sequenceFeatures.length;
+ }
+
+ 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)
+ {
+ return initialCol;
+ }
+ 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;
+
+ 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)
+ {
+ findAllFeatures();
+ if (av.featuresDisplayed.size() < 1)
+ {
+ return;
+ }
+
+ sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+ sfSize = sequenceFeatures.length;
+ }
+
+ if (lastSeq == null || seq != lastSeq)
+ {
+ 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++)
+ {
+ type = renderOrder[renderIndex];
+
+ 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++)
+ {
+ if (sequenceFeatures.length <= sfindex)
+ {
+ continue;
+ }
+ if (!sequenceFeatures[sfindex].type.equals(type))
+ {
+ 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)
+ {
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+ type);
+ }
+ }
+ 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;
+ }
+
+ g.setColor(featureColour);
+
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+
+ 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;
+
+ public void featuresAdded()
+ {
+ lastSeq=null;
+ findAllFeatures();
+ }
+
+ boolean findingFeatures = false;
+ synchronized void findAllFeatures()
+ {
+ newFeatureAdded = false;
+
+ if (findingFeatures)
+ {
+ newFeatureAdded = true;
+ return;
+ }
+
+ findingFeatures = true;
+ jalview.schemes.UserColourScheme ucs = new
+ jalview.schemes.UserColourScheme();
+
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+
+ av.featuresDisplayed.clear();
+
+ Vector allfeatures = new Vector();
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ SequenceFeature[] features
+ = av.alignment.getSequenceAt(i).getDatasetSequence().
+ getSequenceFeatures();
+
+ if (features == null)
+ {
+ continue;
+ }
+
+ int index = 0;
+ while (index < features.length)
+ {
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))
+ {
+ if (! (features[index].begin == 0 && features[index].end == 0))
+ {
+ // 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 (getColour(features[index].getType()) == null)
+ {
+ featureColours.put(features[index].getType(),
+ ucs.createColourFromName(features[index].
+ getType()));
+ }
+
+ av.featuresDisplayed.put(features[index].getType(),
+ new Integer(getColour(features[index].
+ getType()).getRGB()));
+ allfeatures.addElement(features[index].getType());
+ }
+ }
+ index++;
+ }
+ }
+
+ renderOrder = new String[allfeatures.size()];
+ Enumeration en = allfeatures.elements();
+ int i = allfeatures.size() - 1;
+ while (en.hasMoreElements())
+ {
+ renderOrder[i] = en.nextElement().toString();
+ i--;
+ }
+
+ findingFeatures = false;
+ }
+
+ public Color getColour(String featureType)
+ {
+ Color colour = (Color) featureColours.get(featureType);
+ return colour;
+ }
+
+ static String lastFeatureAdded;
+ static String lastFeatureGroupAdded;
+ static String lastDescriptionAdded;
+
+ public boolean createNewFeatures(SequenceI[] sequences,
+ SequenceFeature[] features)
+ {
+ return amendFeatures(sequences, features, true, null);
+ }
+
+ 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()));
+ }
+ });
+
+ 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.add(colour);
+ colour.setPreferredSize(new Dimension(150, 15));
+ panel.add(tmp);
+ name.setEditable(true);
+ source.setEditable(true);
+
+ 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));
+ description.setLineWrap(true);
+ panel.add(new JScrollPane(description));
+
+ if (!newFeatures)
+ {
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new JPanel();
+ panel.add(new JLabel(" Start:", JLabel.RIGHT));
+ panel.add(start);
+ panel.add(new JLabel(" End:", JLabel.RIGHT));
+ panel.add(end);
+ bigPanel.add(panel, BorderLayout.CENTER);
+ }
+ else
+ {
+ bigPanel.add(panel, BorderLayout.CENTER);
+ }
+
+ if (lastFeatureAdded == null)
+ {
+ if (features[0].type != null)
+ {
+ lastFeatureAdded = features[0].type;
+ }
+ else
+ {
+ lastFeatureAdded = "feature_1";
+ }
+ }
+
+ if (lastFeatureGroupAdded == null)
+ {
+ if (features[0].featureGroup != null)
+ {
+ lastFeatureGroupAdded = features[0].featureGroup;
+ }
+ else
+ {
+ lastFeatureAdded = "Jalview";
+ }
+ }
+
+ Enumeration en;
+ if (featureGroups != null)
+ {
+ en = featureGroups.keys();
+ while (en.hasMoreElements())
+ {
+ source.addItem(en.nextElement().toString());
+ }
+ }
+
+ 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));
+ }
+
+ }
+ else if (!newFeatures)
+ {
+ 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);
+ }
+ });
+
+ }
+
+ Object[] options;
+ if (!newFeatures)
+ {
+ options = new Object[]
+ {
+ "Amend", "Delete", "Cancel"};
+ }
+ else
+ {
+ options = new Object[]
+ {
+ "OK", "Cancel"};
+ }
+
+ String title = newFeatures ? "Create New Sequence Feature(s)" :
+ "Amend/Delete Features for "
+ + sequences[0].getName();
+
+ int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+ bigPanel,
+ title,
+ JOptionPane.YES_NO_CANCEL_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options, "OK");
+
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+ if (reply == JOptionPane.OK_OPTION
+ && name.getSelectedItem() != null
+ && source.getSelectedItem() != null)
+ {
+ //This ensures that the last sequence
+ //is refreshed and new features are rendered
+ lastSeq = null;
+ lastFeatureAdded = name.getSelectedItem().toString();
+ lastFeatureGroupAdded = source.getSelectedItem().toString();
+ lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+ }
+
+ if (!newFeatures)
+ {
+ SequenceFeature sf = features[featureIndex];
+
+ if (reply == JOptionPane.NO_OPTION)
+ {
+ sequences[0].getDatasetSequence().deleteFeature(sf);
+ }
+ else if (reply == JOptionPane.YES_OPTION)
+ {
+ sf.type = lastFeatureAdded;
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ setColour(sf.type, colour.getBackground());
+ try
+ {
+ sf.begin = ( (Integer) start.getValue()).intValue();
+ sf.end = ( (Integer) end.getValue()).intValue();
+ }
+ catch (NumberFormatException ex)
+ {}
+
+ ffile.parseDescriptionHTML(sf, false);
+ }
+ }
+ else
+ {
+ if (reply == JOptionPane.OK_OPTION
+ && name.getSelectedItem() != null
+ && source.getSelectedItem() != null)
+ {
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features[i].type = lastFeatureAdded;
+ 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 (featureGroups == null)
+ {
+ featureGroups = new Hashtable();
+ }
+
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+
+ Color col = colour.getBackground();
+ setColour(lastFeatureAdded, colour.getBackground());
+
+ av.featuresDisplayed.put(lastFeatureGroupAdded,
+ new Integer(col.getRGB()));
+
+ findAllFeatures();
+
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ if (name.getSelectedIndex() == -1)
+ {
+ findAllFeatures();
+ }
+
+ 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;
+ }
+
+ 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
+ if (av.featuresDisplayed != null)
+ {
+ av.featuresDisplayed.clear();
+ }
+ else
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+
+ 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()));
+ }
+
+ renderOrder[data.length - i - 1] = type;
+ }
+ }
+
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff