/*\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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
import java.util.*;\r
\r
import java.awt.image.*;\r
+import javax.swing.*;\r
+import javax.swing.JOptionPane;\r
+import java.awt.event.*;\r
\r
\r
/**\r
\r
String [] renderOrder;\r
\r
- boolean newFeatureAdded = false;\r
-\r
-\r
/**\r
* Creates a new FeatureRenderer object.\r
*\r
{\r
type = renderOrder[renderIndex];\r
\r
- if(!av.featuresDisplayed.containsKey(type))\r
+ if(type==null || !av.featuresDisplayed.containsKey(type))\r
continue;\r
\r
// loop through all features in sequence to find\r
int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
for (i = fstart; i <= fend; i++)\r
{\r
- s = seq.getSequence().charAt(i);\r
+ s = seq.getCharAt(i);\r
\r
if (jalview.util.Comparison.isGap(s))\r
{\r
}\r
}\r
\r
- synchronized public void featuresAdded()\r
+\r
+ boolean newFeatureAdded = false;\r
+\r
+ public void featuresAdded()\r
{\r
- newFeatureAdded = true;\r
findAllFeatures();\r
- newFeatureAdded = false;\r
}\r
\r
+ boolean findingFeatures = false;\r
synchronized void findAllFeatures()\r
{\r
+ newFeatureAdded = false;\r
+\r
+ if(findingFeatures)\r
+ {\r
+ newFeatureAdded = true;\r
+ return;\r
+ }\r
+\r
+ findingFeatures = true;\r
jalview.schemes.UserColourScheme ucs = new\r
jalview.schemes.UserColourScheme();\r
\r
renderOrder[i] = en.nextElement().toString();\r
i--;\r
}\r
+\r
+ findingFeatures = false;\r
}\r
\r
public Color getColour(String featureType)\r
}\r
\r
\r
- public void addNewFeature(String name, Color col, String group)\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
- setColour(name, col);\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
+ int featureIndex = 0;\r
+ boolean amendFeatures(final SequenceI[] sequences,\r
+ final SequenceFeature[] features,\r
+ boolean newFeatures,\r
+ final AlignmentPanel ap)\r
+ {\r
+ JPanel bigPanel = new JPanel(new BorderLayout());\r
+ final JComboBox name = new JComboBox();\r
+ final JComboBox source = new JComboBox();\r
+ final JTextArea description = new JTextArea(3,25);\r
+ final JSpinner start = new JSpinner();\r
+ final JSpinner end = new JSpinner();\r
+ start.setPreferredSize(new Dimension(80,20));\r
+ end.setPreferredSize(new Dimension(80,20));\r
+ final JPanel colour = new JPanel();\r
+ colour.setBorder(BorderFactory.createEtchedBorder());\r
+ colour.setMaximumSize(new Dimension(40,10));\r
+ colour.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ colour.setBackground(\r
+ JColorChooser.showDialog(Desktop.desktop,\r
+ "Select Feature Colour",\r
+ colour.getBackground()));\r
+ }\r
+ });\r
+\r
+ JPanel panel = new JPanel(new GridLayout(3, 2));\r
+ panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));\r
+ panel.add(name);\r
+ panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
+ panel.add(source);\r
+ panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));\r
+ JPanel tmp = new JPanel();\r
+ tmp.add(colour);\r
+ colour.setPreferredSize(new Dimension(150,15));\r
+ panel.add(tmp);\r
+ name.setEditable(true);\r
+ source.setEditable(true);\r
+\r
+ bigPanel.add(panel, BorderLayout.NORTH);\r
+ panel = new JPanel();\r
+ panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
+ description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ description.setLineWrap(true);\r
+ panel.add(new JScrollPane(description));\r
+\r
+ if(!newFeatures)\r
+ {\r
+ bigPanel.add(panel, BorderLayout.SOUTH);\r
+\r
+ panel = new JPanel();\r
+ panel.add(new JLabel(" Start:", JLabel.RIGHT));\r
+ panel.add(start);\r
+ panel.add(new JLabel(" End:", JLabel.RIGHT));\r
+ panel.add(end);\r
+ bigPanel.add(panel, BorderLayout.CENTER);\r
+ }\r
+ else\r
+ bigPanel.add(panel, BorderLayout.CENTER);\r
+\r
+ if (lastFeatureAdded == null)\r
+ if (features[0].type != null)\r
+ lastFeatureAdded = features[0].type;\r
+ else\r
+ lastFeatureAdded = "feature_1";\r
+\r
+ if (lastFeatureGroupAdded == null)\r
+ if (features[0].featureGroup != null)\r
+ lastFeatureGroupAdded = features[0].featureGroup;\r
+ else\r
+ lastFeatureAdded = "Jalview";\r
+\r
+\r
+ Enumeration en;\r
+ if (featureGroups != null)\r
+ {\r
+ en = featureGroups.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ source.addItem(en.nextElement().toString());\r
+ }\r
+ }\r
+\r
+ if (newFeatures)\r
+ {\r
+ if(av.featuresDisplayed != null)\r
+ {\r
+ en = av.featuresDisplayed.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ name.addItem(en.nextElement().toString());\r
+ }\r
+ }\r
+\r
+ name.setSelectedItem(lastFeatureAdded);\r
+ source.setSelectedItem(lastFeatureGroupAdded);\r
+ description.setText(\r
+ lastDescriptionAdded == null ?\r
+ features[0].description : lastDescriptionAdded);\r
+\r
+ if (getColour(lastFeatureAdded) != null)\r
+ {\r
+ colour.setBackground(getColour(lastFeatureAdded));\r
+ }\r
+ else\r
+ {\r
+ colour.setBackground(new Color(60, 160, 115));\r
+ }\r
+\r
+ }\r
+ else if (!newFeatures)\r
+ {\r
+ featureIndex = 0;\r
+ for(int f=0; f<features.length; f++)\r
+ {\r
+ name.addItem(features[f].getType().toString());\r
+ }\r
+\r
+ description.setText(features[0].getDescription());\r
+ source.setSelectedItem(features[0].getFeatureGroup());\r
+ start.setValue(new Integer(features[0].getBegin()));\r
+ end.setValue(new Integer(features[0].getEnd()));\r
+ colour.setBackground(\r
+ getColour(name.getSelectedItem().toString()));\r
+ name.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ int index = name.getSelectedIndex();\r
+ if(index!=-1)\r
+ {\r
+ featureIndex = index;\r
+ description.setText(features[index].getDescription());\r
+ source.setSelectedItem(features[index].getFeatureGroup());\r
+ start.setValue(new Integer(features[index].getBegin()));\r
+ end.setValue(new Integer(features[index].getEnd()));\r
+ colour.setBackground(\r
+ getColour(name.getSelectedItem().toString()));\r
+\r
+ SearchResults highlight = new SearchResults();\r
+ highlight.addResult(sequences[0],\r
+ features[index].getBegin(),\r
+ features[index].getEnd());\r
+\r
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
+\r
+ }\r
+ Color col = getColour(name.getSelectedItem().toString());\r
+ if (col == null)\r
+ col = new\r
+ jalview.schemes.UserColourScheme()\r
+ .createColourFromName(name.getSelectedItem().toString());\r
+\r
+ colour.setBackground(col);\r
+ }\r
+ });\r
+\r
+ }\r
+\r
+\r
+ Object [] options;\r
+ if(!newFeatures)\r
+ options = new Object[]{"Amend", "Delete", "Cancel"};\r
+ else\r
+ options = new Object[]{"OK", "Cancel"};\r
+\r
+ String title = newFeatures ? "Create New Sequence Feature(s)" :\r
+ "Amend/Delete Features for "\r
+ +sequences[0].getName();\r
+\r
+ int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
+ bigPanel,\r
+ title,\r
+ JOptionPane.YES_NO_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ options, "OK");\r
+\r
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
+\r
+ if (reply == JOptionPane.OK_OPTION\r
+ && name.getSelectedItem() != null\r
+ && source.getSelectedItem() != null)\r
+ {\r
+ //This ensures that the last sequence\r
+ //is refreshed and new features are rendered\r
+ lastSeq=null;\r
+ lastFeatureAdded = name.getSelectedItem().toString();\r
+ lastFeatureGroupAdded = source.getSelectedItem().toString();\r
+ lastDescriptionAdded = description.getText().replaceAll("\n", " ");\r
+ }\r
+\r
+ if(!newFeatures)\r
+ {\r
+ SequenceFeature sf = features[featureIndex];\r
+\r
+ if(reply==JOptionPane.NO_OPTION)\r
+ sequences[0].getDatasetSequence().deleteFeature(sf);\r
+ else if(reply==JOptionPane.YES_OPTION)\r
+ {\r
+ sf.type = lastFeatureAdded;\r
+ sf.featureGroup = lastFeatureGroupAdded;\r
+ sf.description = lastDescriptionAdded;\r
+ setColour(sf.type, colour.getBackground());\r
+ try{\r
+ sf.begin = ((Integer)start.getValue()).intValue();\r
+ sf.end = ((Integer)end.getValue()).intValue();\r
+ }catch(NumberFormatException ex)\r
+ {}\r
+\r
+ ffile.parseDescriptionHTML(sf, false);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (reply == JOptionPane.OK_OPTION\r
+ && name.getSelectedItem() != null\r
+ && source.getSelectedItem() != null)\r
+ {\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ features[i].type = lastFeatureAdded;\r
+ features[i].featureGroup = lastFeatureGroupAdded;\r
+ features[i].description = lastDescriptionAdded;\r
+ sequences[i].addSequenceFeature(features[i]);\r
+ ffile.parseDescriptionHTML(features[i], false);\r
+ }\r
+\r
+ if (av.featuresDisplayed == null)\r
+ av.featuresDisplayed = new Hashtable();\r
+\r
+ if (featureGroups == null)\r
+ featureGroups = new Hashtable();\r
+\r
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
+\r
+ Color col = colour.getBackground();\r
+ setColour(lastFeatureAdded, colour.getBackground());\r
+\r
+ av.featuresDisplayed.put(lastFeatureGroupAdded,\r
+ new Integer(col.getRGB()));\r
+\r
+ findAllFeatures();\r
+\r
+ return true;\r
+ }\r
+ else\r
+ return false;\r
+ }\r
+\r
+ if(name.getSelectedIndex()==-1)\r
+ findAllFeatures();\r
\r
- if(group == null)\r
- group = "NOGROUP";\r
\r
- av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
+ return true;\r
}\r
\r
public void setColour(String featureType, Color col)\r
git://source.jalview.org / jalview.git / blobdiff