-package jalview.gui;\r
-\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-import jalview.io.*;\r
-\r
-import jalview.bin.Cache;\r
-import javax.swing.*;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.*;\r
-\r
-\r
-public class Preferences extends GPreferences\r
-{\r
- static boolean preferencesLoaded=false;\r
-\r
- public static boolean showFullscreen=false;\r
- public static boolean showFullId=true;\r
- public static boolean showAnnotation=true;\r
- public static boolean showConservation=true;\r
- public static boolean showQuality=true;\r
- public static boolean showIdentity=true;\r
- public static String fontName="SansSerif";\r
- public static String fontSize="10";\r
- public static String fontStyle=Font.PLAIN+"";\r
- public static char gapSymbol='-';\r
- public static String defaultColour=null;\r
- public static boolean showStartupFile=true;\r
- public static String startupFile = "http://www.compbio.dundee.ac.uk/~andrew/jalviewTEST/fasta";\r
-\r
- JInternalFrame frame;\r
-\r
- public static void initPreferences()\r
- {\r
- String string = Cache.getProperty("SHOW_FULL_ID");\r
- if(string!=null)\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_FULLSCREEN");\r
- if(string!=null)\r
- showFullscreen = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_ANNOTATIONS");\r
- if(string!=null)\r
- showAnnotation = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("SHOW_CONSERVATION");\r
- if(string!=null)\r
- showConservation = Boolean.valueOf(string).booleanValue();\r
- string = Cache.getProperty("SHOW_QUALITY");\r
- if(string!=null)\r
- showQuality = Boolean.valueOf(string).booleanValue();\r
- string = Cache.getProperty("SHOW_IDENTITY");\r
- if(string!=null)\r
- showIdentity = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("GAP_SYMBOL");\r
- if(string!=null)\r
- gapSymbol = string.charAt(0);\r
-\r
- string = Cache.getProperty("SHOW_FULL_ID");\r
- if(string!=null)\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
-\r
- string = Cache.getProperty("FONT_NAME");\r
- if (string != null)\r
- fontName = string;\r
-\r
- string = Cache.getProperty("FONT_STYLE");\r
- if (string != null)\r
- fontStyle = string;\r
-\r
- string = Cache.getProperty("FONT_SIZE");\r
- if (string != null)\r
- fontSize = string;\r
-\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- defaultColour = string;\r
-\r
- string = Cache.getProperty("STARTUP_FILE");\r
- if(string!=null)\r
- startupFile = string;\r
-\r
- string = Cache.getProperty("SHOW_STARTUP_FILE");\r
- if(string!=null)\r
- showStartupFile = Boolean.valueOf(string).booleanValue();\r
-\r
- preferencesLoaded = true;\r
- }\r
-\r
- public Preferences()\r
- {\r
- initPreferences();\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480,390 );\r
-\r
- fullID.setSelected(showFullId);\r
- String string = Cache.getProperty("SHOW_FULLSCREEN");\r
- boolean value = false;\r
- if(string!=null)\r
- value = Boolean.valueOf(string).booleanValue();\r
-\r
- fullScreen.setSelected(value);\r
- annotations.setSelected(showAnnotation);\r
-\r
- conservation.setEnabled(showAnnotation);\r
- quality.setEnabled(showAnnotation);\r
- identity.setEnabled(showAnnotation);\r
-\r
- conservation.setSelected(showConservation);\r
- quality.setSelected(showQuality);\r
- identity.setSelected(showIdentity);\r
-\r
- for(int i=0; i<12; i++)\r
- colour.addItem( ColourSchemeProperty.getColourName(i) );\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- colour.setSelectedItem( string );\r
- else\r
- colour.setSelectedIndex( 11 );\r
-\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
- for(int i=0; i<fonts.length; i++)\r
- fontNameCB.addItem(fonts[i]);\r
-\r
- for(int i=1; i<31; i++)\r
- fontSizeCB.addItem(i+"");\r
-\r
- fontStyleCB.addItem("plain");\r
- fontStyleCB.addItem("bold");\r
- fontStyleCB.addItem("italic");\r
-\r
- fontNameCB.setSelectedItem(fontName);\r
- fontSizeCB.setSelectedItem(fontSize);\r
- fontStyleCB.setSelectedItem(fontStyle);\r
-\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
-\r
- gapSymbolCB.setSelectedItem( gapSymbol+"" );\r
-\r
- startupCheckbox.setSelected(showStartupFile);\r
- startupFileTextfield.setText(startupFile);\r
-\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- showFullId = fullID.isSelected() ;\r
- showFullscreen = fullScreen.isSelected();\r
- showAnnotation = annotations.isSelected();\r
- showConservation = conservation.isSelected();\r
- showQuality = quality.isSelected();\r
- showIdentity = identity.isSelected();\r
- defaultColour = colour.getSelectedItem().toString();\r
- gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);\r
- fontName = fontNameCB.getSelectedItem().toString();\r
- fontSize = fontSizeCB.getSelectedItem().toString();\r
- fontStyle = fontStyleCB.getSelectedItem().toString();\r
- startupFile = startupFileTextfield.getText();\r
- showStartupFile = startupCheckbox.isSelected();\r
-\r
- Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));\r
- Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( showFullscreen ) );\r
-\r
- Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( showAnnotation ));\r
- Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( showConservation ));\r
- Cache.setProperty("SHOW_QUALITY", Boolean.toString( showQuality ));\r
- Cache.setProperty("SHOW_IDENTITY", Boolean.toString( showIdentity ));\r
-\r
- Cache.setProperty("DEFAULT_COLOUR", defaultColour);\r
- Cache.setProperty("GAP_SYMBOL", gapSymbol+"");\r
-\r
- Cache.setProperty("FONT_NAME", fontName);\r
- Cache.setProperty("FONT_STYLE", fontStyle);\r
- Cache.setProperty("FONT_SIZE", fontSize);\r
-\r
- Cache.setProperty("STARTUP_FILE", startupFile);\r
- Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));\r
-\r
-\r
-\r
- try {\r
- frame.setClosed(true);\r
- } catch (Exception ex) {}\r
-\r
- }\r
-\r
- public void startupFileTextfield_mouseClicked()\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}\r
- ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select startup file");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());\r
- startupFileTextfield.setText( chooser.getSelectedFile().getAbsolutePath() );\r
- }\r
- }\r
-\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
- conservation.setEnabled(annotations.isSelected());\r
- quality.setEnabled(annotations.isSelected());\r
- identity.setEnabled(annotations.isSelected());\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.gui;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import java.util.*;
+
+import jalview.bin.Cache;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+ /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
+ public static Vector sequenceURLLinks;
+ static
+ {
+ String string = Cache.getDefault("SEQUENCE_LINKS",
+ "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ sequenceURLLinks = new Vector();
+
+ try
+ {
+ StringTokenizer st = new StringTokenizer(string, "|");
+ while (st.hasMoreElements())
+ {
+ sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
+ }
+ }
+ catch (Exception ex)
+ {
+ System.out.println(ex + "\nError parsing sequence links");
+ }
+ }
+ Vector nameLinks, urlLinks;
+
+ JInternalFrame frame;
+
+ DasSourceBrowser dasSource;
+
+
+ /**
+ * Creates a new Preferences object.
+ */
+ public Preferences()
+ {
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ dasSource = new DasSourceBrowser();
+ dasPanel.add(dasSource, BorderLayout.CENTER);
+
+ int width = 500, height = 420;
+ if(System.getProperty("os.name").startsWith("Mac"))
+ {
+ width = 570;
+ height = 460;
+ }
+
+ Desktop.addInternalFrame(frame, "Preferences", width, height);
+ frame.setMinimumSize(new Dimension(width, height));
+
+ seqLimit.setSelected( Cache.getDefault("SHOW_JVSUFFIX", true));
+ fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));
+ annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
+ quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+ identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
+ quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
+ identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+
+ for (int i = 0; i < 13; i++)
+ {
+ colour.addItem(ColourSchemeProperty.getColourName(i));
+ }
+
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+
+ colour.setSelectedItem(string);
+
+ String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+ .getAvailableFontFamilyNames();
+
+ for (int i = 0; i < fonts.length; i++)
+ {
+ fontNameCB.addItem(fonts[i]);
+ }
+
+ for (int i = 1; i < 31; i++)
+ {
+ fontSizeCB.addItem(i + "");
+ }
+
+ fontStyleCB.addItem("plain");
+ fontStyleCB.addItem("bold");
+ fontStyleCB.addItem("italic");
+
+ fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+ fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
+
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
+ gapSymbolCB.addItem("-");
+ gapSymbolCB.addItem(".");
+
+ gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
+
+ startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ "http://www.jalview.org/examples/exampleFile.jar"));
+
+ sortby.addItem("No sort");
+ sortby.addItem("Id");
+ sortby.addItem("Pairwise Identity");
+ sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+
+ epsRendering.addItem("Prompt each time");
+ epsRendering.addItem("Lineart");
+ epsRendering.addItem("Text");
+ epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
+
+ blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
+ clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
+ fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
+ msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
+ pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
+ pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
+ pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
+
+ modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
+ autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+
+ /****************************************************
+ * Set up Connections
+ */
+ nameLinks = new Vector();
+ urlLinks = new Vector();
+ for(int i=0; i<sequenceURLLinks.size(); i++)
+ {
+ String link = sequenceURLLinks.elementAt(i).toString();
+ nameLinks.addElement(link.substring(0, link.indexOf("|")) );
+ urlLinks.addElement(link.substring(link.indexOf("|")+1));
+ }
+
+ updateLinkData();
+
+ useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
+ proxyServerTB.setEnabled(useProxy.isSelected());
+ proxyPortTB.setEnabled(useProxy.isSelected());
+ proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
+ proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+ defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void ok_actionPerformed(ActionEvent e)
+ {
+
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
+
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
+
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
+
+ Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
+
+ Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
+
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));
+
+ Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));
+
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
+
+ if(epsRendering.getSelectedItem().equals("Prompt each time"))
+ Cache.applicationProperties.remove("EPS_RENDERING");
+ else
+ Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
+
+ if(defaultBrowser.getText().trim().length()<1)
+ Cache.applicationProperties.remove("DEFAULT_BROWSER");
+ else
+ Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+ defaultBrowser.getText());
+
+ jalview.util.BrowserLauncher.resetBrowser();
+
+ if(nameLinks.size()>0)
+ {
+ StringBuffer links = new StringBuffer();
+ sequenceURLLinks = new Vector();
+ for (int i = 0; i < nameLinks.size(); i++)
+ {
+ sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
+ links.append(sequenceURLLinks.elementAt(i).toString());
+ links.append("|");
+ }
+ // remove last "|"
+ links.setLength( links.length()-1 );
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
+ }
+ else
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");
+
+
+ Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
+
+ if (proxyServerTB.getText().trim().length() < 1)
+ Cache.applicationProperties.remove("PROXY_SERVER");
+ else
+ Cache.applicationProperties.setProperty("PROXY_SERVER",
+ proxyServerTB.getText());
+
+ if (proxyPortTB.getText().trim().length() < 1)
+ Cache.applicationProperties.remove("PROXY_PORT");
+ else
+ Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+
+ if(useProxy.isSelected())
+ {
+ System.setProperty("http.proxyHost", proxyServerTB.getText());
+ System.setProperty("http.proxyPort", proxyPortTB.getText());
+ }
+ else
+ {
+ System.setProperty("http.proxyHost","");
+ System.setProperty("http.proxyPort","");
+ }
+
+
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+ Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+ Boolean.toString(autoCalculateConsCheck.isSelected()));
+ Cache.applicationProperties.setProperty("PAD_GAPS",
+ Boolean.toString(padGaps.isSelected()));
+
+ dasSource.saveProperties(Cache.applicationProperties);
+
+ Cache.saveProperties();
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void startupFileTextfield_mouseClicked()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"),
+ new String[]
+ {
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+ "jar"
+ },
+ new String[]
+ {
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Select startup file");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+ chooser.getSelectedFormat());
+ startupFileTextfield.setText(chooser.getSelectedFile()
+ .getAbsolutePath());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void annotations_actionPerformed(ActionEvent e)
+ {
+ conservation.setEnabled(annotations.isSelected());
+ quality.setEnabled(annotations.isSelected());
+ identity.setEnabled(annotations.isSelected());
+ }
+
+
+ public void newLink_actionPerformed(ActionEvent e) {
+
+ GSequenceLink link = new GSequenceLink();
+ boolean valid = false;
+ while( !valid )
+ {
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ "New sequence URL link",
+ JOptionPane.OK_CANCEL_OPTION
+ ,-1, null)
+ == JOptionPane.OK_OPTION)
+ {
+ if (link.checkValid())
+ {
+ nameLinks.addElement(link.getName());
+ urlLinks.addElement(link.getURL());
+ updateLinkData();
+ valid = true;
+ }
+ }
+ else
+ break;
+ }
+ }
+
+ public void editLink_actionPerformed(ActionEvent e) {
+ GSequenceLink link = new GSequenceLink();
+
+ int index = linkNameList.getSelectedIndex();
+ if(index==-1)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
+ ,"No link selected", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ link.setName( nameLinks.elementAt(index).toString() );
+ link.setURL( urlLinks.elementAt(index).toString() );
+
+ boolean valid = false;
+ while (!valid)
+ {
+
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ "New sequence URL link",
+ JOptionPane.OK_CANCEL_OPTION
+ ,-1, null)
+ == JOptionPane.OK_OPTION)
+ {
+ if (link.checkValid())
+ {
+ nameLinks.setElementAt(link.getName(), index);
+ urlLinks.setElementAt(link.getURL(), index);
+ updateLinkData();
+ valid = true;
+ }
+ }
+
+ else
+ break;
+ }
+ }
+
+ public void deleteLink_actionPerformed(ActionEvent e) {
+ int index = linkNameList.getSelectedIndex();
+ if(index==-1)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
+ ,"No link selected", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+ nameLinks.removeElementAt(index);
+ urlLinks.removeElementAt(index);
+ updateLinkData();
+ }
+
+ void updateLinkData()
+ {
+ linkNameList.setListData(nameLinks);
+ linkURLList.setListData(urlLinks);
+ }
+
+ public void defaultBrowser_mouseClicked(MouseEvent e)
+ {
+ JFileChooser chooser = new JFileChooser(".");
+ chooser.setDialogTitle("Select default web browser");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ }
+
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ }
+}
git://source.jalview.org / jalview.git / blobdiff