/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
\r
-import java.util.*;\r
+import java.awt.event.*;\r
+\r
+\r
+import jalview.datamodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class FeatureRenderer\r
{\r
- AlignViewport av;\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
- Graphics graphics;\r
-\r
- // The following vector holds the features which are\r
- // to be added, in the correct order or rendering\r
- Vector featuresDisplayed;\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\r
- Color currentColour = null;\r
-\r
- boolean drawText = true;\r
- FontMetrics fm;\r
- int charOffset;\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
- initColours();\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
- //boolean highlightTransparent = true;\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
- public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int x1, int y1, int width, int height)\r
- {\r
- fm = g.getFontMetrics();\r
-\r
- if(seq.getSequenceFeatures()==null)\r
- return;\r
-\r
- Enumeration e = null, e2;\r
- String type;\r
- if(featuresDisplayed!=null)\r
- e = featuresDisplayed.elements();\r
- else\r
- e = seq.getSequenceFeatures().elements();\r
\r
+ tmp = new Panel();\r
+ panel.add(tmp);\r
+ tmp.add(new Label("Name: ", Label.RIGHT));\r
+ tmp.add(name);\r
\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf=null;\r
- if(featuresDisplayed!=null)\r
- {\r
- e2 = seq.getSequenceFeatures().elements();\r
- type = e.nextElement().toString();\r
- while(e2.hasMoreElements())\r
- {\r
- sf = (SequenceFeature) e2.nextElement();\r
- if(sf.getType().equals(type))\r
- break;\r
- else\r
- sf = null;\r
- }\r
- }\r
- else\r
- {\r
- sf = (SequenceFeature) e.nextElement();\r
- type = sf.getType();\r
- }\r
+ tmp = new Panel();\r
+ panel.add(tmp);\r
+ tmp.add(new Label("Group: ",Label.RIGHT));\r
+ tmp.add(source);\r
\r
- if(sf==null)\r
- continue;\r
+ tmp = new Panel();\r
+ panel.add(tmp);\r
+ tmp.add(new Label("Colour: ", Label.RIGHT));\r
+ tmp.add(colourPanel);\r
\r
- if(featureGroups!=null\r
- && sf.getFeatureGroup()!=null\r
- && featureGroups.containsKey(sf.getFeatureGroup())\r
- && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())\r
- {\r
- continue;\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 (sf.getBegin() > seq.getEnd())\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
- continue;\r
+ deleteFeature = true;\r
+ dialog.setVisible(false);\r
}\r
+ });\r
+ name.setText(features[0].getType());\r
+ source.setText(features[0].getFeatureGroup());\r
+ }\r
\r
- if (type.equals("disulfide bond"))\r
- {\r
+ start.setText(features[0].getBegin()+"");\r
+ end.setText(features[0].getEnd()+"");\r
+ description.setText(features[0].getDescription());\r
\r
- renderFeature(g, seq,\r
- seq.findIndex(sf.getBegin()) - 1,\r
- seq.findIndex(sf.getBegin()) - 1,\r
- type, start, end, x1, y1, width, height);\r
- renderFeature(g, seq,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- type, start, end, x1, y1, width, height);\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
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sf.getBegin()) - 1,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- type, start, end, x1, y1, width, height);\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
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, String type, int start, int end,\r
- int x1, int y1, int width, int height)\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 ( ( (fstart <= end) && (fend >= start)))\r
+ if (dialog.accept && name.getText().length()>0)\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
+ 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 (fend >= end)\r
+ if (av.featuresDisplayed == null)\r
{\r
- fend = end;\r
+ av.featuresDisplayed = new Hashtable();\r
}\r
- for (int i = fstart; i <= fend; i++)\r
+\r
+ if (featureGroups == null)\r
{\r
- char s = seq.getSequence().charAt(i);\r
+ featureGroups = new Hashtable();\r
+ }\r
\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
+ col = colourPanel.getBackground();\r
+ setColour(lastFeatureAdded, col);\r
\r
- currentColour = getColour(type);\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
- g.setColor(currentColour);\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
- g.fillRect( (i - start) * width, y1, width, height);\r
+ ap.paintAlignment(true);\r
\r
- if (drawText)\r
- {\r
- g.setColor(Color.white);\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + (width * (i - start)),\r
- (y1 + height) - height / 5);\r
- }\r
- }\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ return false;\r
}\r
}\r
\r
- Image offscreen;\r
- Frame nullframe;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\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
- currentColour = initialCol;\r
- if(offscreen == null)\r
- {\r
- nullframe = new Frame();\r
- nullframe.addNotify();\r
- offscreen = nullframe.createImage(1, 1);\r
- }\r
+ return initialCol;\r
+ }\r
\r
- drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
- return currentColour;\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
- public Color getColour(String featureType)\r
+ drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
+\r
+ if (currentColour == null)\r
{\r
- return (Color)featureColours.get(featureType);\r
+ return initialCol;\r
}\r
\r
- public void setColour(String featureType, Color col)\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
- featureColours.put(featureType, col);\r
+ return;\r
}\r
\r
- public void addNewFeature(String name, Color col)\r
+ if (transparencySetter != null && g != null)\r
{\r
- setColour(name, col);\r
- if (featuresDisplayed == null)\r
- featuresDisplayed = new Vector();\r
- featuresDisplayed.insertElementAt(name, 0);\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
- /* public void setTransparency(float value)\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
- transparency = value;\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
- public float getTransparency()\r
+ if (transparencySetter != null && g != null)\r
{\r
- return transparency;\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
- public void setFeaturePriority(Object [][] data)\r
+ if ( ( (fstart <= end) && (fend >= start)))\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(featuresDisplayed!=null)\r
- featuresDisplayed.removeAllElements();\r
- else\r
- featuresDisplayed = new Vector();\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
- for(int i=data.length-1; i>-1; i--)\r
+ if (fend >= end)\r
{\r
- String type = data[i][0].toString();\r
- setColour(type, (Color)data[i][1]);\r
- if( ((Boolean)data[i][2]).booleanValue() )\r
- featuresDisplayed.addElement(type);\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
- Hashtable featureColours = new Hashtable();\r
- void initColours()\r
- {\r
- featureColours.put("active site", new Color(255, 75, 0));\r
- featureColours.put("binding site", new Color(245, 85, 0));\r
- featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
- featureColours.put("chain", new Color(225, 105, 0));\r
- featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
- featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
- featureColours.put("cross-link", new Color(195, 135, 0));\r
- featureColours.put("disulfide bond", new Color(185, 145, 0));\r
- featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
- featureColours.put("domain", new Color(165, 165, 0));\r
- featureColours.put("glycosylation site", new Color(155, 175, 0));\r
- featureColours.put("helix", new Color(145, 185, 0));\r
- featureColours.put("initiator methionine", new Color(135, 195, 5));\r
- featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
- featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
- featureColours.put("modified residue", new Color(105, 225, 35));\r
- featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
- featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
- featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
- featureColours.put("nucleotide phosphate-binding region",\r
- new Color(65, 245, 75));\r
- featureColours.put("peptide", new Color(55, 235, 85));\r
- featureColours.put("propeptide", new Color(45, 225, 95));\r
- featureColours.put("region of interest", new Color(35, 215, 105));\r
- featureColours.put("repeat", new Color(25, 205, 115));\r
- featureColours.put("selenocysteine", new Color(15, 195, 125));\r
- featureColours.put("sequence conflict", new Color(5, 185, 135));\r
- featureColours.put("sequence variant", new Color(0, 175, 145));\r
- featureColours.put("short sequence motif", new Color(0, 165, 155));\r
- featureColours.put("signal peptide", new Color(0, 155, 165));\r
- featureColours.put("site", new Color(0, 145, 175));\r
- featureColours.put("splice variant", new Color(0, 135, 185));\r
- featureColours.put("strand", new Color(0, 125, 195));\r
- featureColours.put("topological domain", new Color(0, 115, 205));\r
- featureColours.put("transit peptide", new Color(0, 105, 215));\r
- featureColours.put("transmembrane region", new Color(0, 95, 225));\r
- featureColours.put("turn", new Color(0, 85, 235));\r
- featureColours.put("unsure residue", new Color(0, 75, 245));\r
- featureColours.put("zinc finger region", new Color(0, 65, 255));\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
-}\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