-/*\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.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.awt.event.*;\r
-\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
-\r
- Hashtable featureColours = new Hashtable();\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\r
- // Holds web links for feature groups and feature types\r
- // in the form label|link\r
- Hashtable featureLinks = 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
- FontMetrics fm;\r
- int charOffset;\r
-\r
- float transparency = 1f;\r
-\r
- TransparencySetter transparencySetter = null;\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
- if (!System.getProperty("java.version").startsWith("1.1"))\r
- {\r
- transparencySetter = new TransparencySetter();\r
- }\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
-\r
- static String lastFeatureAdded;\r
- static String lastFeatureGroupAdded;\r
- static String lastDescriptionAdded;\r
-\r
- int featureIndex = 0;\r
- boolean deleteFeature = false;\r
- Panel colourPanel;\r
- boolean amendFeatures(final SequenceI[] sequences,\r
- final SequenceFeature[] features,\r
- boolean newFeatures,\r
- final AlignmentPanel ap)\r
- {\r
- Panel bigPanel = new Panel(new BorderLayout());\r
- final TextField name = new TextField(16);\r
- final TextField source = new TextField(16);\r
- final TextArea description = new TextArea(3, 35);\r
- final TextField start = new TextField(8);\r
- final TextField end = new TextField(8);\r
- final Choice overlaps;\r
- Button deleteButton = new Button("Delete");\r
- deleteFeature = false;\r
-\r
- colourPanel = new Panel(null);\r
- colourPanel.setSize(110,15);\r
- final FeatureRenderer fr = this;\r
-\r
- Panel panel = new Panel(new GridLayout(3, 1));\r
-\r
- Panel tmp;\r
-\r
- ///////////////////////////////////////\r
- ///MULTIPLE FEATURES AT SELECTED RESIDUE\r
- if(!newFeatures && features.length>1)\r
- {\r
- panel = new Panel(new GridLayout(4, 1));\r
- tmp = new Panel();\r
- tmp.add(new Label("Select Feature: "));\r
- overlaps = new Choice();\r
- for(int i=0; i<features.length; i++)\r
- {\r
- String item = features[i].getType()\r
- +"/"+features[i].getBegin()+"-"+features[i].getEnd();\r
-\r
- if(features[i].getFeatureGroup()!=null)\r
- item += " ("+features[i].getFeatureGroup()+")";\r
-\r
- overlaps.addItem(item);\r
- }\r
-\r
- tmp.add(overlaps);\r
-\r
- overlaps.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(java.awt.event.ItemEvent e)\r
- {\r
- int index = overlaps.getSelectedIndex();\r
- if (index != -1)\r
- {\r
- featureIndex = index;\r
- name.setText(features[index].getType());\r
- description.setText(features[index].getDescription());\r
- source.setText(features[index].getFeatureGroup());\r
- start.setText(features[index].getBegin()+"");\r
- end.setText(features[index].getEnd()+"");\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.getText());\r
- if (col == null)\r
- {\r
- col = new\r
- jalview.schemes.UserColourScheme()\r
- .createColourFromName(name.getText());\r
- }\r
-\r
- colourPanel.setBackground(col);\r
- }\r
- });\r
-\r
-\r
- panel.add(tmp);\r
- }\r
- //////////\r
- //////////////////////////////////////\r
-\r
-\r
- tmp = new Panel();\r
- panel.add(tmp);\r
- tmp.add(new Label("Name: ", Label.RIGHT));\r
- tmp.add(name);\r
-\r
- tmp = new Panel();\r
- panel.add(tmp);\r
- tmp.add(new Label("Group: ",Label.RIGHT));\r
- tmp.add(source);\r
-\r
- tmp = new Panel();\r
- panel.add(tmp);\r
- tmp.add(new Label("Colour: ", Label.RIGHT));\r
- tmp.add(colourPanel);\r
-\r
- bigPanel.add(panel, BorderLayout.NORTH);\r
-\r
- panel = new Panel();\r
- panel.add(new Label("Description: ", Label.RIGHT));\r
- panel.add(new ScrollPane().add(description));\r
-\r
- if (!newFeatures)\r
- {\r
- bigPanel.add(panel, BorderLayout.SOUTH);\r
-\r
- panel = new Panel();\r
- panel.add(new Label(" Start:", Label.RIGHT));\r
- panel.add(start);\r
- panel.add(new Label(" End:", Label.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
-\r
- String title = newFeatures ? "Create New Sequence Feature(s)" :\r
- "Amend/Delete Features for "\r
- + sequences[0].getName();\r
-\r
- final JVDialog dialog = new JVDialog(ap.alignFrame,\r
- title,\r
- true,\r
- 385,240);\r
-\r
- dialog.setMainPanel(bigPanel);\r
-\r
- if(newFeatures)\r
- {\r
- name.setText(lastFeatureAdded);\r
- source.setText(lastFeatureGroupAdded);\r
- }\r
- else\r
- {\r
- dialog.ok.setLabel("Amend");\r
- dialog.buttonPanel.add(deleteButton, 1);\r
- deleteButton.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- deleteFeature = true;\r
- dialog.setVisible(false);\r
- }\r
- });\r
- name.setText(features[0].getType());\r
- source.setText(features[0].getFeatureGroup());\r
- }\r
-\r
- start.setText(features[0].getBegin()+"");\r
- end.setText(features[0].getEnd()+"");\r
- description.setText(features[0].getDescription());\r
-\r
- Color col = getColour(name.getText());\r
- if (col == null)\r
- {\r
- col = new\r
- jalview.schemes.UserColourScheme()\r
- .createColourFromName(name.getText());\r
- }\r
-\r
- colourPanel.setBackground(col);\r
-\r
- dialog.setResizable(true);\r
-\r
-\r
- colourPanel.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mousePressed(java.awt.event.MouseEvent evt)\r
- {\r
- new UserDefinedColours(fr, ap.alignFrame);\r
- }\r
- });\r
-\r
- dialog.setVisible(true);\r
-\r
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
-\r
- if (dialog.accept)\r
- {\r
- //This ensures that the last sequence\r
- //is refreshed and new features are rendered\r
- lastSeq = null;\r
- lastFeatureAdded = name.getText().trim();\r
- lastFeatureGroupAdded = source.getText().trim();\r
- lastDescriptionAdded = description.getText().replace('\n', ' ');\r
- }\r
-\r
- if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)\r
- lastFeatureGroupAdded = null;\r
-\r
-\r
- if (!newFeatures)\r
- {\r
- SequenceFeature sf = features[featureIndex];\r
-\r
- if (dialog.accept)\r
- {\r
- sf.type = lastFeatureAdded;\r
- sf.featureGroup = lastFeatureGroupAdded;\r
- sf.description = lastDescriptionAdded;\r
- setColour(sf.type, colourPanel.getBackground());\r
- try\r
- {\r
- sf.begin = Integer.parseInt(start.getText());\r
- sf.end = Integer.parseInt(end.getText());\r
- }\r
- catch (NumberFormatException ex)\r
- {}\r
-\r
- ffile.parseDescriptionHTML(sf, false);\r
- }\r
- if (deleteFeature)\r
- {\r
- sequences[0].deleteFeature(sf);\r
- }\r
-\r
- }\r
- else\r
- {\r
- if (dialog.accept && name.getText().length()>0)\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
- col = colourPanel.getBackground();\r
- setColour(lastFeatureAdded, col);\r
-\r
- if(lastFeatureGroupAdded!=null)\r
- {\r
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
- av.featuresDisplayed.put(lastFeatureGroupAdded,\r
- new Integer(col.getRGB()));\r
- }\r
- findAllFeatures();\r
-\r
- String [] tro = new String[renderOrder.length];\r
- tro[0] = renderOrder[renderOrder.length-1];\r
- System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);\r
- renderOrder = tro;\r
-\r
- ap.paintAlignment(true);\r
-\r
- return true;\r
- }\r
- else\r
- {\r
- return false;\r
- }\r
- }\r
-\r
- findAllFeatures();\r
-\r
- ap.paintAlignment(true);\r
-\r
- return true;\r
- }\r
-\r
-\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
- {\r
- overview = true;\r
- if (!av.showSequenceFeatures)\r
- {\r
- return initialCol;\r
- }\r
-\r
- lastSeq = seq;\r
- sequenceFeatures = lastSeq.getSequenceFeatures();\r
- if (sequenceFeatures == null)\r
- {\r
- return initialCol;\r
- }\r
-\r
- sfSize = sequenceFeatures.length;\r
-\r
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))\r
- {\r
- return Color.white;\r
- }\r
-\r
- currentColour = null;\r
-\r
- drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
-\r
- if (currentColour == null)\r
- {\r
- return initialCol;\r
- }\r
-\r
- return new Color( ( (Integer) currentColour).intValue());\r
- }\r
-\r
- /**\r
- * This is used by the Molecule Viewer to get the accurate colour\r
- * of the rendered sequence\r
- */\r
- boolean overview = false;\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
-\r
- SequenceI lastSeq;\r
- SequenceFeature[] sequenceFeatures;\r
- int sfSize, sfindex, spos, epos;\r
-\r
- synchronized public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1)\r
- {\r
- if (seq.getSequenceFeatures() == null\r
- || seq.getSequenceFeatures().length == 0)\r
- {\r
- return;\r
- }\r
-\r
- if (transparencySetter != null && g != null)\r
- {\r
- transparencySetter.setTransparency(g, transparency);\r
- }\r
-\r
- if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = seq.getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if (av.featuresDisplayed == null || renderOrder == null)\r
- {\r
- findAllFeatures();\r
- if (av.featuresDisplayed.size() < 1)\r
- {\r
- return;\r
- }\r
-\r
- sequenceFeatures = seq.getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
- if (!overview)\r
- {\r
- spos = lastSeq.findPosition(start);\r
- epos = lastSeq.findPosition(end);\r
- if (g != null)\r
- {\r
- fm = g.getFontMetrics();\r
- }\r
- }\r
- String type;\r
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
- if (!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[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 (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- {\r
- continue;\r
- }\r
-\r
- if (overview)\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
- }\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
- if (transparencySetter != null && g != null)\r
- {\r
- transparencySetter.setTransparency(g, 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
-\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 (!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
- (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;\r
-\r
- }\r
- }\r
- }\r
-\r
- void findAllFeatures()\r
- {\r
- jalview.schemes.UserColourScheme ucs = new\r
- jalview.schemes.UserColourScheme();\r
-\r
- av.featuresDisplayed = new Hashtable();\r
- Vector allfeatures = new Vector();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature[] features = av.alignment.getSequenceAt(i).\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 (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
- 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
-\r
- public Color getColour(String featureType)\r
- {\r
- if (!featureColours.containsKey(featureType))\r
- {\r
- jalview.schemes.UserColourScheme ucs = new\r
- jalview.schemes.UserColourScheme();\r
- Color col = ucs.createColourFromName(featureType);\r
- featureColours.put(featureType, col);\r
- return col;\r
- }\r
- else\r
- return (Color) featureColours.get(featureType);\r
- }\r
-\r
-\r
- public void setColour(String featureType, Color col)\r
- {\r
- featureColours.put(featureType, col);\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
-\r
- /* if (visibleNew)\r
- {\r
- if (av.featuresDisplayed != null)\r
- {\r
- av.featuresDisplayed.clear();\r
- }\r
- else\r
- {\r
- av.featuresDisplayed = new Hashtable();\r
- }\r
- }\r
- if (data == null)\r
- {\r
- return;\r
- }*/\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
-class TransparencySetter\r
-{\r
- void setTransparency(Graphics g, float value)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, value));\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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import java.awt.event.*;
+
+
+import jalview.appletgui.FeatureSettings.MyCheckbox;
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+{
+ AlignViewport av;
+
+ Hashtable featureColours = new Hashtable();
+
+ // A higher level for grouping features of a
+ // particular type
+ Hashtable featureGroups = null;
+
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
+
+ // This is actually an Integer held in the hashtable,
+ // Retrieved using the key feature type
+ Object currentColour;
+
+ String[] renderOrder;
+
+ FontMetrics fm;
+ int charOffset;
+
+ float transparency = 1f;
+
+ TransparencySetter transparencySetter = null;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ public FeatureRenderer(AlignViewport av)
+ {
+ this.av = av;
+
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ transparencySetter = new TransparencySetter();
+ }
+ }
+
+ public void transferSettings(FeatureRenderer fr)
+ {
+ renderOrder = fr.renderOrder;
+ featureGroups = fr.featureGroups;
+ featureColours = fr.featureColours;
+ transparency = fr.transparency;
+ }
+
+
+ static String lastFeatureAdded;
+ static String lastFeatureGroupAdded;
+ static String lastDescriptionAdded;
+
+ int featureIndex = 0;
+ boolean deleteFeature = false;
+ Panel colourPanel;
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features,
+ boolean newFeatures,
+ final AlignmentPanel ap)
+ {
+ Panel bigPanel = new Panel(new BorderLayout());
+ final TextField name = new TextField(16);
+ final TextField source = new TextField(16);
+ final TextArea description = new TextArea(3, 35);
+ final TextField start = new TextField(8);
+ final TextField end = new TextField(8);
+ final Choice overlaps;
+ Button deleteButton = new Button("Delete");
+ deleteFeature = false;
+
+ colourPanel = new Panel(null);
+ colourPanel.setSize(110,15);
+ final FeatureRenderer fr = this;
+
+ Panel panel = new Panel(new GridLayout(3, 1));
+
+ Panel tmp;
+
+ ///////////////////////////////////////
+ ///MULTIPLE FEATURES AT SELECTED RESIDUE
+ if(!newFeatures && features.length>1)
+ {
+ panel = new Panel(new GridLayout(4, 1));
+ tmp = new Panel();
+ tmp.add(new Label("Select Feature: "));
+ overlaps = new Choice();
+ for(int i=0; i<features.length; i++)
+ {
+ String item = features[i].getType()
+ +"/"+features[i].getBegin()+"-"+features[i].getEnd();
+
+ if(features[i].getFeatureGroup()!=null)
+ item += " ("+features[i].getFeatureGroup()+")";
+
+ overlaps.addItem(item);
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new java.awt.event.ItemListener()
+ {
+ public void itemStateChanged(java.awt.event.ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ name.setText(features[index].getType());
+ description.setText(features[index].getDescription());
+ source.setText(features[index].getFeatureGroup());
+ start.setText(features[index].getBegin()+"");
+ end.setText(features[index].getEnd()+"");
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0],
+ features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ Color col = getColour(name.getText());
+ if (col == null)
+ {
+ col = new
+ jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+
+ colourPanel.setBackground(col);
+ }
+ });
+
+
+ panel.add(tmp);
+ }
+ //////////
+ //////////////////////////////////////
+
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(name);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Group: ",Label.RIGHT));
+ tmp.add(source);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(colourPanel);
+
+ bigPanel.add(panel, BorderLayout.NORTH);
+
+ panel = new Panel();
+ panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new ScrollPane().add(description));
+
+ if (!newFeatures)
+ {
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new Panel();
+ panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(start);
+ panel.add(new Label(" End:", Label.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";
+ }
+ }
+
+
+ String title = newFeatures ? "Create New Sequence Feature(s)" :
+ "Amend/Delete Features for "
+ + sequences[0].getName();
+
+ final JVDialog dialog = new JVDialog(ap.alignFrame,
+ title,
+ true,
+ 385,240);
+
+ dialog.setMainPanel(bigPanel);
+
+ if(newFeatures)
+ {
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
+ }
+ else
+ {
+ dialog.ok.setLabel("Amend");
+ dialog.buttonPanel.add(deleteButton, 1);
+ deleteButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ deleteFeature = true;
+ dialog.setVisible(false);
+ }
+ });
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
+ }
+
+ start.setText(features[0].getBegin()+"");
+ end.setText(features[0].getEnd()+"");
+ description.setText(features[0].getDescription());
+
+ Color col = getColour(name.getText());
+ if (col == null)
+ {
+ col = new
+ jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+
+ colourPanel.setBackground(col);
+
+ dialog.setResizable(true);
+
+
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ {
+ public void mousePressed(java.awt.event.MouseEvent evt)
+ {
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ });
+
+ dialog.setVisible(true);
+
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+ if (dialog.accept)
+ {
+ //This ensures that the last sequence
+ //is refreshed and new features are rendered
+ lastSeq = null;
+ lastFeatureAdded = name.getText().trim();
+ lastFeatureGroupAdded = source.getText().trim();
+ lastDescriptionAdded = description.getText().replace('\n', ' ');
+ }
+
+ if(lastFeatureGroupAdded !=null && lastFeatureGroupAdded.length()<1)
+ lastFeatureGroupAdded = null;
+
+
+ if (!newFeatures)
+ {
+ SequenceFeature sf = features[featureIndex];
+
+ if (dialog.accept)
+ {
+ sf.type = lastFeatureAdded;
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ setColour(sf.type, colourPanel.getBackground());
+ try
+ {
+ sf.begin = Integer.parseInt(start.getText());
+ sf.end = Integer.parseInt(end.getText());
+ }
+ catch (NumberFormatException ex)
+ {}
+
+ ffile.parseDescriptionHTML(sf, false);
+ }
+ if (deleteFeature)
+ {
+ sequences[0].deleteFeature(sf);
+ }
+
+ }
+ else
+ {
+ if (dialog.accept && name.getText().length()>0)
+ {
+ 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();
+ }
+
+ col = colourPanel.getBackground();
+ setColour(lastFeatureAdded, col);
+
+ if(lastFeatureGroupAdded!=null)
+ {
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+ av.featuresDisplayed.put(lastFeatureGroupAdded,
+ new Integer(col.getRGB()));
+ }
+ findAllFeatures();
+
+ String [] tro = new String[renderOrder.length];
+ tro[0] = renderOrder[renderOrder.length-1];
+ System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);
+ renderOrder = tro;
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ findAllFeatures();
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+
+
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+ {
+ overview = true;
+ if (!av.showSequenceFeatures)
+ {
+ return initialCol;
+ }
+
+ lastSeq = seq;
+ sequenceFeatures = lastSeq.getSequenceFeatures();
+ if (sequenceFeatures == null)
+ {
+ return initialCol;
+ }
+
+ sfSize = sequenceFeatures.length;
+
+ if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))
+ {
+ return Color.white;
+ }
+
+ currentColour = null;
+
+ drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);
+
+ if (currentColour == null)
+ {
+ return initialCol;
+ }
+
+ return new Color( ( (Integer) currentColour).intValue());
+ }
+
+ /**
+ * This is used by the Molecule Viewer to get the accurate colour
+ * of the rendered sequence
+ */
+ boolean overview = false;
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ * @param sg DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ // String type;
+ // SequenceFeature sf;
+
+ SequenceI lastSeq;
+ SequenceFeature[] sequenceFeatures;
+ int sfSize, sfindex, spos, epos;
+
+ synchronized public void drawSequence(Graphics g, SequenceI seq,
+ int start, int end, int y1)
+ {
+ if (seq.getSequenceFeatures() == null
+ || seq.getSequenceFeatures().length == 0)
+ {
+ return;
+ }
+
+ if (transparencySetter != null && g != null)
+ {
+ transparencySetter.setTransparency(g, transparency);
+ }
+
+ if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())
+ {
+ lastSeq = seq;
+ sequenceFeatures = seq.getSequenceFeatures();
+ sfSize = sequenceFeatures.length;
+ }
+
+ if (av.featuresDisplayed == null || renderOrder == null)
+ {
+ findAllFeatures();
+ if (av.featuresDisplayed.size() < 1)
+ {
+ return;
+ }
+
+ sequenceFeatures = seq.getSequenceFeatures();
+ sfSize = sequenceFeatures.length;
+ }
+ if (!overview)
+ {
+ spos = lastSeq.findPosition(start);
+ epos = lastSeq.findPosition(end);
+ if (g != null)
+ {
+ fm = g.getFontMetrics();
+ }
+ }
+ String type;
+ for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+ {
+ type = renderOrder[renderIndex];
+ if (!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[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 (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+ || sequenceFeatures[sfindex].getEnd() < spos))
+ {
+ continue;
+ }
+
+ if (overview)
+ {
+ 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 (transparencySetter != null && g != null)
+ {
+ transparencySetter.setTransparency(g, 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;
+ }
+
+ 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 (!av.validCharWidth)
+ {
+ continue;
+ }
+
+ g.setColor(Color.white);
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s),
+ charOffset + (av.charWidth * (i - start)),
+ (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+
+ }
+ }
+ }
+
+ void findAllFeatures()
+ {
+ jalview.schemes.UserColourScheme ucs = new
+ jalview.schemes.UserColourScheme();
+
+ av.featuresDisplayed = new Hashtable();
+ Vector allfeatures = new Vector();
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ SequenceFeature[] features = av.alignment.getSequenceAt(i).
+ getSequenceFeatures();
+
+ if (features == null)
+ {
+ continue;
+ }
+
+ int index = 0;
+ while (index < features.length)
+ {
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))
+ {
+ 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--;
+ }
+ }
+
+ public Color getColour(String featureType)
+ {
+ if (!featureColours.containsKey(featureType))
+ {
+ jalview.schemes.UserColourScheme ucs = new
+ jalview.schemes.UserColourScheme();
+ Color col = ucs.createColourFromName(featureType);
+ featureColours.put(featureType, col);
+ return col;
+ }
+ else
+ return (Color) featureColours.get(featureType);
+ }
+
+
+ public void setColour(String featureType, Color col)
+ {
+ featureColours.put(featureType, col);
+ }
+
+ 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();
+ }
+
+ /* if (visibleNew)
+ {
+ if (av.featuresDisplayed != null)
+ {
+ av.featuresDisplayed.clear();
+ }
+ else
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+ }
+ if (data == null)
+ {
+ return;
+ }*/
+
+
+ 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;
+ }
+ }
+ }
+ /**
+ * @return a simple list of feature group names or null
+ */
+ public String[] getGroups()
+ {
+ buildGroupHash();
+ if (featureGroups!=null)
+ {
+ String[] gps = new String[featureGroups.size()];
+ Enumeration gn = featureGroups.keys();
+ int i=0;
+ while (gn.hasMoreElements())
+ {
+ gps[i++] = (String) gn.nextElement();
+ }
+ return gps;
+ }
+ return null;
+ }
+ /**
+ * get visible or invisible groups
+ * @param visible true to return visible groups, false to return hidden ones.
+ * @return list of groups
+ */
+ public String[] getGroups(boolean visible)
+ {
+ buildGroupHash();
+ if (featureGroups!=null)
+ {
+ Vector gp = new Vector();
+
+ Enumeration gn = featureGroups.keys();
+ while (gn.hasMoreElements())
+ {
+ String nm = (String) gn.nextElement();
+ Boolean state = (Boolean) featureGroups.get(nm);
+ if (state.booleanValue()==visible)
+ {
+ gp.addElement(nm);
+ }
+ }
+ String[] gps = new String[gp.size()];
+ gp.copyInto(gps);
+
+ int i=0;
+ while (gn.hasMoreElements())
+ {
+ gps[i++] = (String) gn.nextElement();
+ }
+ return gps;
+ }
+ return null;
+ }
+ /**
+ * set all feature groups in toset to be visible or invisible
+ * @param toset group names
+ * @param visible the state of the named groups to set
+ */
+ public void setGroupState(String[] toset, boolean visible)
+ {
+ buildGroupHash();
+ if (toset!=null && toset.length>0 && featureGroups!=null)
+ {
+ boolean rdrw = false;
+ for (int i=0;i<toset.length; i++)
+ {
+ Object st = featureGroups.get(toset[i]);
+ if (st!=null)
+ {
+ featureGroups.put(toset[i], new Boolean(visible));
+ rdrw = rdrw || (visible!=((Boolean) st).booleanValue());
+ }
+ }
+ if (rdrw)
+ {
+ if (this.av!=null)
+ if (this.av.featureSettings!=null)
+ {
+ av.featureSettings.rebuildGroups();
+ this.av.featureSettings.resetTable(true);
+ } else {
+ buildFeatureHash();
+ }
+ if (av!=null)
+ {
+ av.alignmentChanged(null);
+ }
+ }
+ }
+ }
+ /**
+ * analyse alignment for groups and hash tables
+ * (used to be embedded in FeatureSettings.setTableData)
+ * @return true if features are on the alignment
+ */
+ public boolean buildGroupHash()
+ {
+ boolean alignmentHasFeatures=false;
+ if (featureGroups == null)
+ {
+ featureGroups = new Hashtable();
+ }
+ Vector allFeatures = new Vector();
+ Vector allGroups = new Vector();
+ SequenceFeature[] tmpfeatures;
+ String group;
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ {
+ continue;
+ }
+
+ alignmentHasFeatures = true;
+
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ int index = 0;
+ while (index < tmpfeatures.length)
+ {
+ if (tmpfeatures[index].getFeatureGroup() != null)
+ {
+ group = tmpfeatures[index].featureGroup;
+ if (!allGroups.contains(group))
+ {
+ allGroups.addElement(group);
+
+ boolean visible = true;
+ if (featureGroups.containsKey(group))
+ {
+ visible = ( (Boolean) featureGroups.get(group)).booleanValue();
+ } else {
+ featureGroups.put(group, new Boolean(visible));
+ }
+ }
+ }
+
+ if (!allFeatures.contains(tmpfeatures[index].getType()))
+ {
+ allFeatures.addElement(tmpfeatures[index].getType());
+ }
+ index++;
+ }
+ }
+
+ return alignmentHasFeatures;
+ }
+ /**
+ * rebuild the featuresDisplayed and renderorder list based on the featureGroups hash and any existing display state
+ * and force a repaint if necessary
+ * @return true if alignment has visible features
+ */
+ public boolean buildFeatureHash() {
+ boolean alignmentHasFeatures=false;
+ if (featureGroups==null)
+ {
+ alignmentHasFeatures = buildGroupHash();
+ }
+ if (!alignmentHasFeatures)
+ return false;
+ Hashtable fdisp = av.featuresDisplayed;
+ Vector allFeatures = new Vector();
+ SequenceFeature[] tmpfeatures;
+ String group;
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ {
+ continue;
+ }
+
+ alignmentHasFeatures = true;
+
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ int index = 0;
+ while (index < tmpfeatures.length)
+ {
+ boolean visible = true;
+ if (tmpfeatures[index].getFeatureGroup() != null)
+ {
+ group = tmpfeatures[index].featureGroup;
+ if (featureGroups.containsKey(group))
+ {
+ visible = ( (Boolean) featureGroups.get(group)).booleanValue();
+ }
+ }
+
+ if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
+ {
+ allFeatures.addElement(tmpfeatures[index].getType());
+ }
+ index++;
+ }
+ }
+ if (allFeatures.size()>0)
+ {
+ String[] neworder = new String[allFeatures.size()];
+ int p=neworder.length-1;
+ for (int i=renderOrder.length-1; i>=0; i--)
+ {
+ if (allFeatures.contains(renderOrder[i]))
+ {
+ neworder[p--] = renderOrder[i];
+ allFeatures.removeElement(renderOrder[i]);
+ } else {
+ av.featuresDisplayed.remove(renderOrder[i]);
+ }
+ }
+ for (int i=allFeatures.size()-1; i>0; i++)
+ {
+ Object e = allFeatures.elementAt(i);
+ if (e!=null)
+ {
+ neworder[p--] = (String) e;
+ av.featuresDisplayed.put(e, getColour((String)e));
+ }
+ }
+ renderOrder = neworder;
+ return true;
+ }
+
+ return alignmentHasFeatures;
+ }
+}
+
+class TransparencySetter
+{
+ void setTransparency(Graphics g, float value)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(
+ AlphaComposite.getInstance(
+ AlphaComposite.SRC_OVER, value));
+ }
+}
-/*\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.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class FeatureSettings\r
- extends Panel implements ItemListener,\r
- MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
-{\r
- FeatureRenderer fr;\r
- AlignmentPanel ap;\r
- AlignViewport av;\r
- Frame frame;\r
- Panel groupPanel;\r
- Panel featurePanel = new Panel();\r
- ScrollPane scrollPane;\r
- boolean alignmentHasFeatures = false;\r
- Image linkImage;\r
- Scrollbar transparency;\r
-\r
- public FeatureSettings(final AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- this.av = ap.av;\r
- fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
-\r
- transparency = new Scrollbar(Scrollbar.HORIZONTAL,\r
- 100 - (int) (fr.transparency * 100), 1, 1, 100);\r
-\r
- if (fr.transparencySetter != null)\r
- {\r
- transparency.addAdjustmentListener(this);\r
- }\r
- else\r
- {\r
- transparency.setEnabled(false);\r
- }\r
-\r
- java.net.URL url = getClass().getResource("/images/link.gif");\r
- if (url != null)\r
- {\r
- linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);\r
- }\r
-\r
- if (av.featuresDisplayed == null)\r
- {\r
- fr.findAllFeatures();\r
- }\r
-\r
- setTableData();\r
-\r
- this.setLayout(new BorderLayout());\r
- scrollPane = new ScrollPane();\r
- scrollPane.add(featurePanel);\r
- if (alignmentHasFeatures)\r
- {\r
- add(scrollPane, BorderLayout.CENTER);\r
- }\r
-\r
- Button invert = new Button("Invert Selection");\r
- invert.addActionListener(this);\r
-\r
- Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));\r
- lowerPanel.add(invert);\r
-\r
- Panel tPanel = new Panel(new BorderLayout());\r
-\r
- if (fr.transparencySetter != null)\r
- {\r
- tPanel.add(transparency, BorderLayout.CENTER);\r
- tPanel.add(new Label("Transparency"), BorderLayout.EAST);\r
- }\r
- else\r
- {\r
- tPanel.add(new Label("Transparency not available in this web browser"),\r
- BorderLayout.CENTER);\r
- }\r
-\r
- lowerPanel.add(tPanel, BorderLayout.SOUTH);\r
-\r
- add(lowerPanel, BorderLayout.SOUTH);\r
-\r
- if (groupPanel != null)\r
- {\r
- groupPanel.setLayout(\r
- new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
- groupPanel.validate();\r
-\r
- add(groupPanel, BorderLayout.NORTH);\r
- }\r
- frame = new Frame();\r
- frame.add(this);\r
- int height = featurePanel.getComponentCount() * 50 + 60;\r
-\r
- height = Math.max(200, height);\r
- height = Math.min(400, height);\r
-\r
- jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 280,\r
- height);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- g.setColor(Color.black);\r
- g.drawString("No Features added to this alignment!!", 10, 20);\r
- g.drawString("(Features can be added from searches or", 10, 40);\r
- g.drawString("from Jalview / GFF features files)", 10, 60);\r
- }\r
-\r
- void setTableData()\r
- {\r
- alignmentHasFeatures = false;\r
-\r
- if (fr.featureGroups == null)\r
- {\r
- fr.featureGroups = new Hashtable();\r
- }\r
-\r
- Vector allFeatures = new Vector();\r
- Vector allGroups = new Vector();\r
- SequenceFeature[] tmpfeatures;\r
- String group;\r
-\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
- {\r
- continue;\r
- }\r
-\r
- alignmentHasFeatures = true;\r
-\r
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
- int index = 0;\r
- while (index < tmpfeatures.length)\r
- {\r
- if (tmpfeatures[index].getFeatureGroup() != null)\r
- {\r
- group = tmpfeatures[index].featureGroup;\r
- if (!allGroups.contains(group))\r
- {\r
- allGroups.addElement(group);\r
-\r
- boolean visible = true;\r
- if (fr.featureGroups.containsKey(group))\r
- {\r
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
- }\r
-\r
- fr.featureGroups.put(group, new Boolean(visible));\r
-\r
- if (groupPanel == null)\r
- {\r
- groupPanel = new Panel();\r
- }\r
-\r
- Checkbox check = new MyCheckbox(\r
- group,\r
- visible,\r
- (fr.featureLinks != null && fr.featureLinks.containsKey(group))\r
- );\r
-\r
- check.addMouseListener(this);\r
- check.setFont(new Font("Serif", Font.BOLD, 12));\r
- check.addItemListener(this);\r
- groupPanel.add(check);\r
- }\r
- }\r
-\r
- if (!allFeatures.contains(tmpfeatures[index].getType()))\r
- {\r
- allFeatures.addElement(tmpfeatures[index].getType());\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- resetTable(false);\r
- }\r
-\r
- //This routine adds and removes checkboxes depending on\r
- //Group selection states\r
- void resetTable(boolean groupsChanged)\r
- {\r
- SequenceFeature[] tmpfeatures;\r
- String group = null, type;\r
- Vector visibleChecks = new Vector();\r
-\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
- {\r
- continue;\r
- }\r
-\r
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
- int index = 0;\r
- while (index < tmpfeatures.length)\r
- {\r
- group = tmpfeatures[index].featureGroup;\r
-\r
- if (group == null || fr.featureGroups.get(group) == null ||\r
- ( (Boolean) fr.featureGroups.get(group)).booleanValue())\r
- {\r
- type = tmpfeatures[index].getType();\r
- if (!visibleChecks.contains(type))\r
- {\r
- visibleChecks.addElement(type);\r
- }\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- Component[] comps;\r
- int cSize = featurePanel.getComponentCount();\r
- Checkbox check;\r
- //This will remove any checkboxes which shouldn't be\r
- //visible\r
- for (int i = 0; i < cSize; i++)\r
- {\r
- comps = featurePanel.getComponents();\r
- check = (Checkbox) comps[i];\r
- if (!visibleChecks.contains(check.getLabel()))\r
- {\r
- featurePanel.remove(i);\r
- cSize--;\r
- i--;\r
- }\r
- }\r
-\r
- if (fr.renderOrder != null)\r
- {\r
- //First add the checks in the previous render order,\r
- //in case the window has been closed and reopened\r
- for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)\r
- {\r
- String item = fr.renderOrder[ro];\r
-\r
- if (!visibleChecks.contains(item))\r
- {\r
- continue;\r
- }\r
-\r
- visibleChecks.removeElement(item);\r
-\r
- addCheck(false, item);\r
- }\r
- }\r
-\r
- // now add checkboxes which should be visible,\r
- // if they have not already been added\r
- Enumeration en = visibleChecks.elements();\r
-\r
- while (en.hasMoreElements())\r
- {\r
- addCheck(groupsChanged, en.nextElement().toString());\r
- }\r
-\r
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,\r
- 10, 5));\r
- featurePanel.validate();\r
-\r
- if (scrollPane != null)\r
- {\r
- scrollPane.validate();\r
- }\r
-\r
- itemStateChanged(null);\r
- }\r
-\r
- void addCheck(boolean groupsChanged, String type)\r
- {\r
- boolean addCheck;\r
- Component[] comps = featurePanel.getComponents();\r
- Checkbox check;\r
- addCheck = true;\r
- for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
- {\r
- check = (Checkbox) comps[i];\r
- if (check.getLabel().equals(type))\r
- {\r
- addCheck = false;\r
- break;\r
- }\r
- }\r
-\r
- if (addCheck)\r
- {\r
- boolean selected = false;\r
- if (groupsChanged || av.featuresDisplayed.containsKey(type))\r
- {\r
- selected = true;\r
- }\r
-\r
- check = new MyCheckbox(type,\r
- selected,\r
- (fr.featureLinks != null &&\r
- fr.featureLinks.containsKey(type))\r
- );\r
-\r
- check.addMouseListener(this);\r
- check.addMouseMotionListener(this);\r
- check.setBackground(fr.getColour(type));\r
- check.addItemListener(this);\r
- featurePanel.add(check);\r
- }\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
- {\r
- Checkbox check = (Checkbox) featurePanel.getComponent(i);\r
- check.setState(!check.getState());\r
- }\r
- selectionChanged();\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt != null)\r
- {\r
- //Is the source a top level featureGroup?\r
- Checkbox source = (Checkbox) evt.getSource();\r
- if (fr.featureGroups.containsKey(source.getLabel()))\r
- {\r
- fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));\r
- ap.seqPanel.seqCanvas.repaint();\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
-\r
- resetTable(true);\r
- return;\r
- }\r
- }\r
- selectionChanged();\r
- }\r
-\r
- void selectionChanged()\r
- {\r
- Component[] comps = featurePanel.getComponents();\r
- int cSize = comps.length;\r
-\r
- Object[][] tmp = new Object[cSize][3];\r
- int tmpSize = 0;\r
- for (int i = 0; i < cSize; i++)\r
- {\r
- Checkbox check = (Checkbox) comps[i];\r
- tmp[tmpSize][0] = check.getLabel();\r
- tmp[tmpSize][1] = fr.getColour(check.getLabel());\r
- tmp[tmpSize][2] = new Boolean(check.getState());\r
- tmpSize++;\r
- }\r
-\r
- Object[][] data = new Object[tmpSize][3];\r
- System.arraycopy(tmp, 0, data, 0, tmpSize);\r
-\r
- fr.setFeaturePriority(data);\r
-\r
- ap.paintAlignment(true);\r
- }\r
-\r
- MyCheckbox selectedCheck;\r
- boolean dragging = false;\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
-\r
- selectedCheck = (MyCheckbox) evt.getSource();\r
-\r
- if (fr.featureLinks != null\r
- && fr.featureLinks.containsKey(selectedCheck.getLabel())\r
- )\r
- {\r
- if (evt.getX() > selectedCheck.stringWidth + 20)\r
- {\r
- evt.consume();\r
- }\r
- }\r
-\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if ( ( (Component) evt.getSource()).getParent() != featurePanel)\r
- {\r
- return;\r
- }\r
- dragging = true;\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if ( ( (Component) evt.getSource()).getParent() != featurePanel)\r
- {\r
- return;\r
- }\r
-\r
- Component comp = null;\r
- Checkbox target = null;\r
-\r
- int height = evt.getY() + evt.getComponent().getLocation().y;\r
-\r
- if (height > featurePanel.getSize().height)\r
- {\r
-\r
- comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);\r
- }\r
- else if (height < 0)\r
- {\r
- comp = featurePanel.getComponent(0);\r
- }\r
- else\r
- {\r
- comp = featurePanel.getComponentAt(evt.getX(),\r
- evt.getY() +\r
- evt.getComponent().getLocation().y);\r
- }\r
-\r
- if (comp != null && comp instanceof Checkbox)\r
- {\r
- target = (Checkbox) comp;\r
- }\r
-\r
- if (selectedCheck != null\r
- && target != null\r
- && selectedCheck != target)\r
- {\r
- int targetIndex = -1;\r
- for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
- {\r
- if (target == featurePanel.getComponent(i))\r
- {\r
- targetIndex = i;\r
- break;\r
- }\r
- }\r
-\r
- featurePanel.remove(selectedCheck);\r
- featurePanel.add(selectedCheck, targetIndex);\r
- featurePanel.validate();\r
- itemStateChanged(null);\r
- }\r
- }\r
-\r
- public void setUserColour(String feature, Color col)\r
- {\r
- fr.setColour(feature, col);\r
- featurePanel.removeAll();\r
- resetTable(false);\r
- ap.paintAlignment(true);\r
- }\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
-\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- MyCheckbox check = (MyCheckbox) evt.getSource();\r
-\r
- if (fr.featureLinks != null\r
- && fr.featureLinks.containsKey(check.getLabel()))\r
- {\r
- if (evt.getX() > check.stringWidth + 20)\r
- {\r
- evt.consume();\r
- String link = fr.featureLinks.get(check.getLabel()).toString();\r
- ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),\r
- link.substring(0, link.indexOf("|")));\r
- }\r
- }\r
-\r
- if (check.getParent() != featurePanel)\r
- {\r
- return;\r
- }\r
-\r
- if (evt.getClickCount() > 1)\r
- {\r
- new UserDefinedColours(this, check.getLabel(),\r
- fr.getColour(check.getLabel()));\r
- }\r
- }\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {}\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);\r
- ap.seqPanel.seqCanvas.repaint();\r
-\r
- }\r
-\r
- class MyCheckbox\r
- extends Checkbox\r
- {\r
- public int stringWidth;\r
- boolean hasLink;\r
- public MyCheckbox(String label, boolean checked, boolean haslink)\r
- {\r
- super(label, checked);\r
-\r
- FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());\r
- stringWidth = fm.stringWidth(label);\r
- this.hasLink = haslink;\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- if (hasLink)\r
- {\r
- g.drawImage(linkImage, stringWidth + 25, (\r
- getSize().height - linkImage.getHeight(this)) / 2,\r
- this);\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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+
+public class FeatureSettings
+ extends Panel implements ItemListener,
+ MouseListener, MouseMotionListener, ActionListener, AdjustmentListener
+{
+ FeatureRenderer fr;
+ AlignmentPanel ap;
+ AlignViewport av;
+ Frame frame;
+ Panel groupPanel;
+ Panel featurePanel = new Panel();
+ ScrollPane scrollPane;
+ boolean alignmentHasFeatures = false;
+ Image linkImage;
+ Scrollbar transparency;
+
+ public FeatureSettings(final AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ ap.av.featureSettings = this;
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
+
+ transparency = new Scrollbar(Scrollbar.HORIZONTAL,
+ 100 - (int) (fr.transparency * 100), 1, 1, 100);
+
+ if (fr.transparencySetter != null)
+ {
+ transparency.addAdjustmentListener(this);
+ }
+ else
+ {
+ transparency.setEnabled(false);
+ }
+
+ java.net.URL url = getClass().getResource("/images/link.gif");
+ if (url != null)
+ {
+ linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
+ }
+
+ if (av.featuresDisplayed == null)
+ {
+ fr.findAllFeatures();
+ }
+
+ setTableData();
+
+ this.setLayout(new BorderLayout());
+ scrollPane = new ScrollPane();
+ scrollPane.add(featurePanel);
+ if (alignmentHasFeatures)
+ {
+ add(scrollPane, BorderLayout.CENTER);
+ }
+
+ Button invert = new Button("Invert Selection");
+ invert.addActionListener(this);
+
+ Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
+ lowerPanel.add(invert);
+
+ Panel tPanel = new Panel(new BorderLayout());
+
+ if (fr.transparencySetter != null)
+ {
+ tPanel.add(transparency, BorderLayout.CENTER);
+ tPanel.add(new Label("Transparency"), BorderLayout.EAST);
+ }
+ else
+ {
+ tPanel.add(new Label("Transparency not available in this web browser"),
+ BorderLayout.CENTER);
+ }
+
+ lowerPanel.add(tPanel, BorderLayout.SOUTH);
+
+ add(lowerPanel, BorderLayout.SOUTH);
+
+ if (groupPanel != null)
+ {
+ groupPanel.setLayout(
+ new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+ groupPanel.validate();
+
+ add(groupPanel, BorderLayout.NORTH);
+ }
+ frame = new Frame();
+ frame.add(this);
+ final FeatureSettings me = this;
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ if (me.av.featureSettings==me)
+ {
+ me.av.featureSettings = null;
+ me.ap = null;
+ me.av = null;
+ }
+ }
+ }
+ );
+ int height = featurePanel.getComponentCount() * 50 + 60;
+
+ height = Math.max(200, height);
+ height = Math.min(400, height);
+ int width = 300;
+ jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", width,
+ height);
+ }
+
+ public void paint(Graphics g)
+ {
+ g.setColor(Color.black);
+ g.drawString("No Features added to this alignment!!", 10, 20);
+ g.drawString("(Features can be added from searches or", 10, 40);
+ g.drawString("from Jalview / GFF features files)", 10, 60);
+ }
+
+ public void setTableData()
+ {
+ alignmentHasFeatures = fr.buildGroupHash();
+ if (alignmentHasFeatures)
+ {
+ rebuildGroups();
+
+ }
+ resetTable(false);
+ }
+ /**
+ * rebuilds the group panel
+ */
+ public void rebuildGroups()
+ {
+ boolean rdrw = false;
+ if (groupPanel == null)
+ {
+ groupPanel = new Panel();
+ } else {
+ rdrw = true;
+ groupPanel.removeAll();
+ }
+
+ Enumeration gps = fr.featureGroups.keys();
+ while (gps.hasMoreElements())
+ {
+ String group = (String) gps.nextElement();
+ Boolean vis = (Boolean) fr.featureGroups.get(group);
+ Checkbox check = new MyCheckbox(
+ group,
+ vis.booleanValue(),
+ (fr.featureLinks != null && fr.featureLinks.containsKey(group))
+ );
+ check.addMouseListener(this);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(this);
+ groupPanel.add(check);
+ }
+ if (rdrw)
+ {
+ groupPanel.validate();
+ }
+ }
+
+ //This routine adds and removes checkboxes depending on
+ //Group selection states
+ void resetTable(boolean groupsChanged)
+ {
+ SequenceFeature[] tmpfeatures;
+ String group = null, type;
+ Vector visibleChecks = new Vector();
+
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+ {
+ continue;
+ }
+
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+ int index = 0;
+ while (index < tmpfeatures.length)
+ {
+ group = tmpfeatures[index].featureGroup;
+
+ if (group == null || fr.featureGroups.get(group) == null ||
+ ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+ {
+ type = tmpfeatures[index].getType();
+ if (!visibleChecks.contains(type))
+ {
+ visibleChecks.addElement(type);
+ }
+ }
+ index++;
+ }
+ }
+
+ Component[] comps;
+ int cSize = featurePanel.getComponentCount();
+ Checkbox check;
+ //This will remove any checkboxes which shouldn't be
+ //visible
+ for (int i = 0; i < cSize; i++)
+ {
+ comps = featurePanel.getComponents();
+ check = (Checkbox) comps[i];
+ if (!visibleChecks.contains(check.getLabel()))
+ {
+ featurePanel.remove(i);
+ cSize--;
+ i--;
+ }
+ }
+
+ if (fr.renderOrder != null)
+ {
+ //First add the checks in the previous render order,
+ //in case the window has been closed and reopened
+ for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
+ {
+ String item = fr.renderOrder[ro];
+
+ if (!visibleChecks.contains(item))
+ {
+ continue;
+ }
+
+ visibleChecks.removeElement(item);
+
+ addCheck(false, item);
+ }
+ }
+
+ // now add checkboxes which should be visible,
+ // if they have not already been added
+ Enumeration en = visibleChecks.elements();
+
+ while (en.hasMoreElements())
+ {
+ addCheck(groupsChanged, en.nextElement().toString());
+ }
+
+ featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1,
+ 10, 5));
+ featurePanel.validate();
+
+ if (scrollPane != null)
+ {
+ scrollPane.validate();
+ }
+
+ itemStateChanged(null);
+ }
+ /**
+ * update the checklist of feature types with the given type
+ * @param groupsChanged true means if the type is not in the display list then it will be added and displayed
+ * @param type feature type to be checked for in the list.
+ */
+ void addCheck(boolean groupsChanged, String type)
+ {
+ boolean addCheck;
+ Component[] comps = featurePanel.getComponents();
+ Checkbox check;
+ addCheck = true;
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ check = (Checkbox) comps[i];
+ if (check.getLabel().equals(type))
+ {
+ addCheck = false;
+ break;
+ }
+ }
+
+ if (addCheck)
+ {
+ boolean selected = false;
+ if (groupsChanged || av.featuresDisplayed.containsKey(type))
+ {
+ selected = true;
+ }
+
+ check = new MyCheckbox(type,
+ selected,
+ (fr.featureLinks != null &&
+ fr.featureLinks.containsKey(type))
+ );
+
+ check.addMouseListener(this);
+ check.addMouseMotionListener(this);
+ check.setBackground(fr.getColour(type));
+ check.addItemListener(this);
+ featurePanel.add(check);
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ Checkbox check = (Checkbox) featurePanel.getComponent(i);
+ check.setState(!check.getState());
+ }
+ selectionChanged();
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt != null)
+ {
+ //Is the source a top level featureGroup?
+ Checkbox source = (Checkbox) evt.getSource();
+ if (fr.featureGroups.containsKey(source.getLabel()))
+ {
+ fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
+ ap.seqPanel.seqCanvas.repaint();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+
+ resetTable(true);
+ return;
+ }
+ }
+ selectionChanged();
+ }
+
+ void selectionChanged()
+ {
+ Component[] comps = featurePanel.getComponents();
+ int cSize = comps.length;
+
+ Object[][] tmp = new Object[cSize][3];
+ int tmpSize = 0;
+ for (int i = 0; i < cSize; i++)
+ {
+ Checkbox check = (Checkbox) comps[i];
+ tmp[tmpSize][0] = check.getLabel();
+ tmp[tmpSize][1] = fr.getColour(check.getLabel());
+ tmp[tmpSize][2] = new Boolean(check.getState());
+ tmpSize++;
+ }
+
+ Object[][] data = new Object[tmpSize][3];
+ System.arraycopy(tmp, 0, data, 0, tmpSize);
+
+ fr.setFeaturePriority(data);
+
+ ap.paintAlignment(true);
+ }
+
+ MyCheckbox selectedCheck;
+ boolean dragging = false;
+
+ public void mousePressed(MouseEvent evt)
+ {
+
+ selectedCheck = (MyCheckbox) evt.getSource();
+
+ if (fr.featureLinks != null
+ && fr.featureLinks.containsKey(selectedCheck.getLabel())
+ )
+ {
+ if (evt.getX() > selectedCheck.stringWidth + 20)
+ {
+ evt.consume();
+ }
+ }
+
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+ dragging = true;
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ if ( ( (Component) evt.getSource()).getParent() != featurePanel)
+ {
+ return;
+ }
+
+ Component comp = null;
+ Checkbox target = null;
+
+ int height = evt.getY() + evt.getComponent().getLocation().y;
+
+ if (height > featurePanel.getSize().height)
+ {
+
+ comp = featurePanel.getComponent(featurePanel.getComponentCount() - 1);
+ }
+ else if (height < 0)
+ {
+ comp = featurePanel.getComponent(0);
+ }
+ else
+ {
+ comp = featurePanel.getComponentAt(evt.getX(),
+ evt.getY() +
+ evt.getComponent().getLocation().y);
+ }
+
+ if (comp != null && comp instanceof Checkbox)
+ {
+ target = (Checkbox) comp;
+ }
+
+ if (selectedCheck != null
+ && target != null
+ && selectedCheck != target)
+ {
+ int targetIndex = -1;
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)
+ {
+ if (target == featurePanel.getComponent(i))
+ {
+ targetIndex = i;
+ break;
+ }
+ }
+
+ featurePanel.remove(selectedCheck);
+ featurePanel.add(selectedCheck, targetIndex);
+ featurePanel.validate();
+ itemStateChanged(null);
+ }
+ }
+
+ public void setUserColour(String feature, Color col)
+ {
+ fr.setColour(feature, col);
+ featurePanel.removeAll();
+ resetTable(false);
+ ap.paintAlignment(true);
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {}
+
+ public void mouseExited(MouseEvent evt)
+ {}
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ MyCheckbox check = (MyCheckbox) evt.getSource();
+
+ if (fr.featureLinks != null
+ && fr.featureLinks.containsKey(check.getLabel()))
+ {
+ if (evt.getX() > check.stringWidth + 20)
+ {
+ evt.consume();
+ String link = fr.featureLinks.get(check.getLabel()).toString();
+ ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
+ link.substring(0, link.indexOf("|")));
+ }
+ }
+
+ if (check.getParent() != featurePanel)
+ {
+ return;
+ }
+
+ if (evt.getClickCount() > 1)
+ {
+ new UserDefinedColours(this, check.getLabel(),
+ fr.getColour(check.getLabel()));
+ }
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {}
+
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ fr.transparency = ( (float) (100 - transparency.getValue()) / 100f);
+ ap.seqPanel.seqCanvas.repaint();
+
+ }
+
+ class MyCheckbox
+ extends Checkbox
+ {
+ public int stringWidth;
+ boolean hasLink;
+ public MyCheckbox(String label, boolean checked, boolean haslink)
+ {
+ super(label, checked);
+
+ FontMetrics fm = av.nullFrame.getFontMetrics(av.nullFrame.getFont());
+ stringWidth = fm.stringWidth(label);
+ this.hasLink = haslink;
+ }
+
+ public void paint(Graphics g)
+ {
+ if (hasLink)
+ {
+ g.drawImage(linkImage, stringWidth + 25, (
+ getSize().height - linkImage.getHeight(this)) / 2,
+ this);
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / commitdiff