import java.awt.image.*;\r
import javax.swing.*;\r
import javax.swing.JOptionPane;\r
+import java.awt.event.*;\r
\r
\r
/**\r
public boolean createNewFeatures(SequenceI[] sequences,\r
SequenceFeature [] features)\r
{\r
+ return amendFeatures(sequences, features, true);\r
+ }\r
\r
+ boolean amendFeatures(SequenceI[] sequences,\r
+ final SequenceFeature [] features,\r
+ boolean newFeatures)\r
+ {\r
JPanel bigPanel = new JPanel(new BorderLayout());\r
- JComboBox name = new JComboBox();\r
- JComboBox source = new JComboBox();\r
- JTextArea description = new JTextArea(3,25);\r
+ final JComboBox name = new JComboBox();\r
+ final JComboBox source = new JComboBox();\r
+ final JTextArea description = new JTextArea(3,25);\r
+ final JTextField start = new JTextField(6);\r
+ final JTextField end = new JTextField(6);\r
+ final JButton colour = new JButton(" ");\r
+ colour.setMaximumSize(new Dimension(40,10));\r
+ colour.setBackground(new Color(60, 160, 115));\r
+ colour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent 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(2, 2));\r
- panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));\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
description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
description.setLineWrap(true);\r
panel.add(new JScrollPane(description));\r
- bigPanel.add(panel, BorderLayout.CENTER);\r
-\r
\r
- Enumeration en;\r
- if (av.featuresDisplayed != null)\r
+ if(!newFeatures)\r
{\r
- en = av.featuresDisplayed.keys();\r
- while (en.hasMoreElements())\r
- {\r
- name.addItem(en.nextElement().toString());\r
- }\r
- }\r
-\r
- if (featureGroups != null)\r
- {\r
- en = featureGroups.keys();\r
- while (en.hasMoreElements())\r
- {\r
- source.addItem(en.nextElement().toString());\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 = "Jalview";\r
\r
\r
- name.setSelectedItem(lastFeatureAdded);\r
- source.setSelectedItem(lastFeatureGroupAdded);\r
- description.setText(\r
- lastDescriptionAdded == null ?\r
- features[0].description : lastDescriptionAdded);\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
+ else if (!newFeatures)\r
+ {\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.setText(features[0].getBegin()+"");\r
+ end.setText(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
+ description.setText(features[index].getDescription());\r
+ source.setSelectedItem(features[index].getFeatureGroup());\r
+ start.setText(features[index].getBegin() + "");\r
+ end.setText(features[index].getEnd() + "");\r
+ colour.setBackground(\r
+ getColour(name.getSelectedItem().toString()));\r
+ }\r
+ });\r
\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- bigPanel, "Create New Sequence Feature(s)",\r
- JOptionPane.OK_CANCEL_OPTION);\r
+ }\r
\r
\r
- if(reply==JOptionPane.OK_OPTION\r
- && name.getSelectedItem()!=null\r
- && source.getSelectedItem()!=null)\r
+ Object [] options;\r
+ if(!newFeatures)\r
+ options = new Object[]{"Amend", "Delete", "Cancel"};\r
+ else\r
+ options = new Object[]{"OK", "Cancel"};\r
+\r
+ int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
+ bigPanel,\r
+ newFeatures ?\r
+ "Create New Sequence Feature(s)" :\r
+ "Amend/Delete Features",\r
+ JOptionPane.YES_NO_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ options, null);\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
lastFeatureAdded = name.getSelectedItem().toString();\r
lastFeatureGroupAdded = source.getSelectedItem().toString();\r
- lastDescriptionAdded = description.getText().replaceAll("\n"," ");\r
-\r
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
-\r
+ lastDescriptionAdded = description.getText().replaceAll("\n", " ");\r
+ }\r
\r
- for(int i=0; i<sequences.length; i++)\r
+ if(!newFeatures)\r
+ {\r
+ SequenceFeature sf = features[name.getSelectedIndex()];\r
+ if(reply==JOptionPane.NO_OPTION)\r
+ sequences[0].getDatasetSequence().deleteFeature(sf);\r
+ else if(reply==JOptionPane.YES_OPTION)\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
+ sf.type = lastFeatureAdded;\r
+ sf.featureGroup = lastFeatureGroupAdded;\r
+ sf.description = lastDescriptionAdded;\r
+ setColour(sf.type, colour.getBackground());\r
+ try{\r
+ sf.begin = Integer.parseInt( start.getText() );\r
+ sf.end = Integer.parseInt( end.getText() );\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
+ if (av.featuresDisplayed == null)\r
+ av.featuresDisplayed = new Hashtable();\r
\r
- if(featureGroups==null)\r
- featureGroups = new Hashtable();\r
+ if (featureGroups == null)\r
+ featureGroups = new Hashtable();\r
\r
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
\r
- Color col = getColour(lastFeatureAdded);\r
- if(col==null)\r
- {\r
- col = new Color(60, 160, 115);\r
- setColour(lastFeatureAdded, col);\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
- av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));\r
- findAllFeatures();\r
- return true;\r
+ return true;\r
+ }\r
+ else\r
+ return false;\r
}\r
- else\r
- return false;\r
\r
+ return true;\r
}\r
\r
public void setColour(String featureType, Color col)\r
git://source.jalview.org / jalview.git / blobdiff