/*\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.gui;\r
\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\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
public class FeatureRenderer\r
{\r
- AlignViewport av;\r
- Color resBoxColour;\r
- float transparency = 1.0f;\r
- FontMetrics fm;\r
- int charOffset;\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\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
- /**\r
- * Creates a new FeatureRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public FeatureRenderer(AlignViewport av)\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
- this.av = av;\r
- initColours();\r
+ return initialCol;\r
}\r
\r
- public void transferSettings(FeatureRenderer fr)\r
+ if (seq != lastSeq)\r
{\r
- renderOrder = fr.renderOrder;\r
- featureGroups = fr.featureGroups;\r
- featureColours = fr.featureColours;\r
- transparency = fr.transparency;\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
- BufferedImage offscreenImage;\r
- boolean offscreenRender = false;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
+ if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
{\r
- int seqindex = av.alignment.findIndex(seq);\r
-\r
- return new Color( findFeatureColour (initialCol.getRGB(),\r
- seqindex, res ));\r
+ return Color.white.getRGB();\r
}\r
\r
- /**\r
- * This is used by the Molecule Viewer to get the accurate colour\r
- * of the rendered sequence\r
- */\r
- public int findFeatureColour(int initialCol, int seqIndex, int column)\r
+ //Only bother making an offscreen image if transparency is applied\r
+ if (transparency != 1.0f && offscreenImage == null)\r
{\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if(seqIndex!=lastSequenceIndex)\r
- {\r
- lastSequence = av.alignment.getSequenceAt(seqIndex);\r
- lastSequenceIndex = seqIndex;\r
- sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
+ offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);\r
+ }\r
\r
- if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
- return Color.white.getRGB();\r
+ currentColour = null;\r
\r
+ offscreenRender = true;\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
+ if (offscreenImage != null)\r
+ {\r
+ offscreenImage.setRGB(0, 0, initialCol);\r
+ drawSequence(offscreenImage.getGraphics(),\r
+ lastSeq,\r
+ column, column, 0);\r
\r
- offscreenRender = true;\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(offscreenImage!=null)\r
+ if (currentColour == null)\r
{\r
- offscreenImage.setRGB(0,0,initialCol);\r
- drawSequence(offscreenImage.getGraphics(),\r
- lastSequence,\r
- column,column,0);\r
-\r
- return offscreenImage.getRGB(0,0);\r
+ return initialCol;\r
}\r
else\r
{\r
- drawSequence(null,\r
- lastSequence,\r
- lastSequence.findPosition(column),\r
- -1, -1);\r
-\r
- if (currentColour == null)\r
- return initialCol;\r
- else\r
- return ((Integer)currentColour).intValue();\r
+ return ( (Integer) currentColour).intValue();\r
}\r
-\r
-\r
}\r
\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ // String type;\r
+ // SequenceFeature sf;\r
+ SequenceI lastSeq;\r
+ SequenceFeature[] sequenceFeatures;\r
+ int sfSize, sfindex, spos, epos;\r
+\r
+ public void drawSequence(Graphics g, SequenceI seq,\r
+ int start, int end, int y1)\r
+ {\r
+ if (seq.getDatasetSequence().getSequenceFeatures() == null\r
+ || seq.getDatasetSequence().getSequenceFeatures().length == 0)\r
+ {\r
+ return;\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
- int lastSequenceIndex=-1;\r
- SequenceI lastSequence;\r
- SequenceFeature [] sequenceFeatures;\r
- int sfSize, sfindex, spos, epos;\r
+ if (g != null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\r
\r
- public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1)\r
+ if (av.featuresDisplayed == null\r
+ || renderOrder == null\r
+ || newFeatureAdded)\r
{\r
- if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().length==0)\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(g!=null)\r
- fm = g.getFontMetrics();\r
-\r
-\r
- if (av.featuresDisplayed == null || renderOrder==null)\r
- {\r
- findAllFeatures();\r
- if(av.featuresDisplayed.size()<1)\r
- return;\r
+ if (lastSeq == null || seq != lastSeq)\r
+ {\r
+ lastSeq = seq;\r
+ sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\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(lastSequence==null || seq!=lastSequence)\r
- {\r
- lastSequence = seq;\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\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 (transparency != 1 && g!=null)\r
+ if (type == null || !av.featuresDisplayed.containsKey(type))\r
{\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, transparency));\r
+ continue;\r
}\r
\r
- if(!offscreenRender)\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ for (sfindex = 0; sfindex < sfSize; sfindex++)\r
{\r
- spos = lastSequence.findPosition(start);\r
- epos = lastSequence.findPosition(end);\r
- }\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
+ if (sequenceFeatures.length <= sfindex)\r
+ {\r
continue;\r
+ }\r
+ if (!sequenceFeatures[sfindex].type.equals(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
+ 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
- if(sequenceFeatures.length<=sfindex)\r
- {\r
- continue;\r
- }\r
- if (!sequenceFeatures[sfindex].type.equals(type))\r
- continue;\r
-\r
- if (featureGroups != null\r
- && sequenceFeatures[sfindex].featureGroup != null\r
- &&\r
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
- &&\r
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
- booleanValue())\r
- {\r
- continue;\r
- }\r
+ continue;\r
+ }\r
\r
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- continue;\r
+ if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
+ {\r
+ continue;\r
+ }\r
\r
- if (offscreenRender && offscreenImage==null)\r
+ if (offscreenRender && offscreenImage == null)\r
+ {\r
+ if (sequenceFeatures[sfindex].begin <= start &&\r
+ sequenceFeatures[sfindex].end >= start)\r
{\r
- if (sequenceFeatures[sfindex].begin <= start &&\r
- sequenceFeatures[sfindex].end >= start)\r
- {\r
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
- type);\r
- }\r
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
+ type);\r
}\r
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
- {\r
-\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1);\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1);\r
-\r
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- getColour(sequenceFeatures[sfindex].type),\r
- start, end, y1);\r
+ }\r
+ 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
- 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
+ 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, int end, int y1)\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 (((fstart <= end) && (fend >= start)))\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
- 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
+ s = seq.getCharAt(i);\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
}\r
\r
- if (fend >= end)\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
- fend = end;\r
+ continue;\r
}\r
- int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
- for (i = fstart; i <= fend; i++)\r
- {\r
- s = seq.getSequence().charAt(i);\r
\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
+ 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
- g.setColor(featureColour);\r
+ }\r
+ }\r
+ }\r
\r
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
+ boolean newFeatureAdded = false;\r
\r
- if(offscreenRender || !av.validCharWidth)\r
- continue;\r
+ public void featuresAdded()\r
+ {\r
+ findAllFeatures();\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
+ boolean findingFeatures = false;\r
+ synchronized void findAllFeatures()\r
+ {\r
+ newFeatureAdded = false;\r
\r
- }\r
- }\r
+ if (findingFeatures)\r
+ {\r
+ newFeatureAdded = true;\r
+ return;\r
}\r
\r
- void findAllFeatures()\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
- Vector allfeatures = new Vector();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature [] features\r
- = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ }\r
\r
- if (features == null)\r
- continue;\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
+ int index = 0;\r
+ while (index < features.length)\r
+ {\r
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
{\r
- if (!av.featuresDisplayed.containsKey(features[index].getType()))\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].getType()).getRGB()) );\r
+ new Integer(getColour(features[index].\r
+ getType()).getRGB()));\r
allfeatures.addElement(features[index].getType());\r
}\r
- index++;\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
+ 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
- renderOrder[i] = en.nextElement().toString();\r
- i--;\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
- public Color getColour(String featureType)\r
+ if (lastFeatureAdded == null)\r
{\r
- return (Color)featureColours.get(featureType);\r
+ if (features[0].type != null)\r
+ {\r
+ lastFeatureAdded = features[0].type;\r
+ }\r
+ else\r
+ {\r
+ lastFeatureAdded = "feature_1";\r
+ }\r
}\r
\r
- public void addNewFeature(String name, Color col, String group)\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
- setColour(name, col);\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\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(group == null)\r
- group = "NOGROUP";\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
- av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
- }\r
+ name.setSelectedItem(lastFeatureAdded);\r
+ source.setSelectedItem(lastFeatureGroupAdded);\r
+ description.setText(\r
+ lastDescriptionAdded == null ?\r
+ features[0].description : lastDescriptionAdded);\r
\r
- public void setColour(String featureType, Color col)\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
- featureColours.put(featureType, col);\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
- public void setTransparency(float value)\r
+ Object[] options;\r
+ if (!newFeatures)\r
+ {\r
+ options = new Object[]\r
+ {\r
+ "Amend", "Delete", "Cancel"};\r
+ }\r
+ else\r
{\r
- transparency = value;\r
+ options = new Object[]\r
+ {\r
+ "OK", "Cancel"};\r
}\r
\r
- public float getTransparency()\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
- return transparency;\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
- public void setFeaturePriority(Object [][] data)\r
+ if (!newFeatures)\r
{\r
- // The feature table will display high priority\r
- // features at the top, but theses are the ones\r
- // we need to render last, so invert the data\r
- if(av.featuresDisplayed!=null)\r
- av.featuresDisplayed.clear();\r
- else\r
- av.featuresDisplayed = new Hashtable();\r
+ SequenceFeature sf = features[featureIndex];\r
\r
- renderOrder = new String[data.length];\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
- if (data.length > 0)\r
- for (int i = 0; i < data.length; i++)\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
- 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
+ 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
- renderOrder[data.length - i - 1] = type;\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
- 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(230,230,0));\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",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
+ 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
git://source.jalview.org / jalview.git / blobdiff