X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=e69492c605f42a6460e6ce696aefeb9a77c21471;hb=d0b7395c10aec7c5da5a5662fc69783ec78fae8d;hp=b16ae32d6a5ab9ab3f4fae4575adf3836ac8e753;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index b16ae32..e69492c 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -18,6 +18,8 @@ */ package jalview.gui; +import java.util.*; + import java.awt.*; import java.awt.event.*; import javax.swing.*; @@ -27,70 +29,86 @@ import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class Preferences extends GPreferences { - static boolean preferencesLoaded = false; - public static boolean showFullscreen = false; - public static boolean showFullId = true; - public static boolean showAnnotation = true; - public static boolean showConservation = true; - public static boolean showQuality = true; - public static boolean showIdentity = true; - public static String fontName = "SansSerif"; - public static String fontSize = "10"; - public static String fontStyle = Font.PLAIN + ""; - public static char gapSymbol = '-'; - public static String defaultColour = null; - public static boolean showStartupFile = true; - public static String startupFile = - "http://www.jalview.org/examples/exampleFile.jar"; + /** 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() { - initPreferences(); frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Preferences", 480, 390); - - fullID.setSelected(showFullId); - - String string = Cache.getProperty("SHOW_FULLSCREEN"); - boolean value = false; + dasSource = new DasSourceBrowser(); + dasPanel.add(dasSource, BorderLayout.CENTER); - if (string != null) + int width = 500, height = 420; + if (System.getProperty("os.name").startsWith("Mac")) { - value = Boolean.valueOf(string).booleanValue(); + width = 570; + height = 460; } - fullScreen.setSelected(value); - annotations.setSelected(showAnnotation); + Desktop.addInternalFrame(frame, "Preferences", width, height); + frame.setMinimumSize(new Dimension(width, height)); - conservation.setEnabled(showAnnotation); - quality.setEnabled(showAnnotation); - identity.setEnabled(showAnnotation); + seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true)); + rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false)); + fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false)); + annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true)); - conservation.setSelected(showConservation); - quality.setSelected(showQuality); - identity.setSelected(showIdentity); + conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true)); + quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true)); + identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true)); - for (int i = 0; i < 12; i++) + conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true)); + quality.setSelected(Cache.getDefault("SHOW_QUALITY", true)); + identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true)); + openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false)); + + for (int i = 0; i < 13; i++) { colour.addItem(ColourSchemeProperty.getColourName(i)); } - string = Cache.getProperty("DEFAULT_COLOUR"); + String string = Cache.getDefault("DEFAULT_COLOUR", "None"); - if (string != null) - { - colour.setSelectedItem(string); - } - else - { - colour.setSelectedIndex(11); - } + colour.setSelectedItem(string); String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment() .getAvailableFontFamilyNames(); @@ -109,157 +127,256 @@ public class Preferences fontStyleCB.addItem("bold"); fontStyleCB.addItem("italic"); - fontNameCB.setSelectedItem(fontName); - fontSizeCB.setSelectedItem(fontSize); - fontStyleCB.setSelectedItem(fontStyle); + fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif")); + fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10")); + fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "")); - gapSymbolCB.addItem("-"); - gapSymbolCB.addItem("."); + smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false)); - gapSymbolCB.setSelectedItem(gapSymbol + ""); + idItalics.setSelected(Cache.getDefault("ID_ITALICS", true)); - startupCheckbox.setSelected(showStartupFile); - startupFileTextfield.setText(startupFile); - } + wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false)); - public static void initPreferences() - { - String string = Cache.getProperty("SHOW_FULL_ID"); + gapSymbolCB.addItem("-"); + gapSymbolCB.addItem("."); - if (string != null) + 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++) { - showFullId = Boolean.valueOf(string).booleanValue(); + String link = sequenceURLLinks.elementAt(i).toString(); + nameLinks.addElement(link.substring(0, link.indexOf("|"))); + urlLinks.addElement(link.substring(link.indexOf("|") + 1)); } - string = Cache.getProperty("SHOW_FULLSCREEN"); + 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", "")); - if (string != null) + defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", "")); + try { - showFullscreen = Boolean.valueOf(string).booleanValue(); + jbInit(); } - - string = Cache.getProperty("SHOW_ANNOTATIONS"); - - if (string != null) + catch (Exception ex) { - showAnnotation = Boolean.valueOf(string).booleanValue(); + ex.printStackTrace(); } - string = Cache.getProperty("SHOW_CONSERVATION"); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void ok_actionPerformed(ActionEvent e) + { - if (string != null) + Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", + Boolean.toString(seqLimit. + isSelected())); + Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", + Boolean.toString(rightAlign. + isSelected())); + Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", + Boolean.toString(fullScreen. + isSelected())); + Cache.applicationProperties.setProperty("SHOW_OVERVIEW", + Boolean.toString(openoverv. + 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("ID_ITALICS", + Boolean.toString(idItalics. + isSelected())); + + 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")) { - showConservation = Boolean.valueOf(string).booleanValue(); + Cache.applicationProperties.remove("EPS_RENDERING"); } - - string = Cache.getProperty("SHOW_QUALITY"); - - if (string != null) + else { - showQuality = Boolean.valueOf(string).booleanValue(); + Cache.applicationProperties.setProperty("EPS_RENDERING", + epsRendering.getSelectedItem(). + toString()); } - string = Cache.getProperty("SHOW_IDENTITY"); - - if (string != null) + if (defaultBrowser.getText().trim().length() < 1) { - showIdentity = Boolean.valueOf(string).booleanValue(); + Cache.applicationProperties.remove("DEFAULT_BROWSER"); } - - string = Cache.getProperty("GAP_SYMBOL"); - - if (string != null) + else { - gapSymbol = string.charAt(0); + Cache.applicationProperties.setProperty("DEFAULT_BROWSER", + defaultBrowser.getText()); } - string = Cache.getProperty("SHOW_FULL_ID"); + jalview.util.BrowserLauncher.resetBrowser(); - if (string != null) + if (nameLinks.size() > 0) { - showFullId = Boolean.valueOf(string).booleanValue(); + 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()); } - - string = Cache.getProperty("FONT_NAME"); - - if (string != null) + else { - fontName = string; + Cache.applicationProperties.remove("SEQUENCE_LINKS"); } - string = Cache.getProperty("FONT_STYLE"); + Cache.applicationProperties.setProperty("USE_PROXY", + Boolean.toString(useProxy. + isSelected())); - if (string != null) + if (proxyServerTB.getText().trim().length() < 1) { - fontStyle = string; + Cache.applicationProperties.remove("PROXY_SERVER"); } - - string = Cache.getProperty("FONT_SIZE"); - - if (string != null) + else { - fontSize = string; + Cache.applicationProperties.setProperty("PROXY_SERVER", + proxyServerTB.getText()); } - string = Cache.getProperty("DEFAULT_COLOUR"); - - if (string != null) + if (proxyPortTB.getText().trim().length() < 1) { - defaultColour = string; + Cache.applicationProperties.remove("PROXY_PORT"); } - - string = Cache.getProperty("STARTUP_FILE"); - - if (string != null) + else { - startupFile = string; + Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText()); } - string = Cache.getProperty("SHOW_STARTUP_FILE"); - - if (string != null) + if (useProxy.isSelected()) { - showStartupFile = Boolean.valueOf(string).booleanValue(); + System.setProperty("http.proxyHost", proxyServerTB.getText()); + System.setProperty("http.proxyPort", proxyPortTB.getText()); + } + else + { + System.setProperty("http.proxyHost", ""); + System.setProperty("http.proxyPort", ""); } - preferencesLoaded = true; - } - - public void ok_actionPerformed(ActionEvent e) - { - showFullId = fullID.isSelected(); - showFullscreen = fullScreen.isSelected(); - showAnnotation = annotations.isSelected(); - showConservation = conservation.isSelected(); - showQuality = quality.isSelected(); - showIdentity = identity.isSelected(); - defaultColour = colour.getSelectedItem().toString(); - gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0); - fontName = fontNameCB.getSelectedItem().toString(); - fontSize = fontSizeCB.getSelectedItem().toString(); - fontStyle = fontStyleCB.getSelectedItem().toString(); - startupFile = startupFileTextfield.getText(); - showStartupFile = startupCheckbox.isSelected(); - - Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId)); - Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen)); - - Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation)); - Cache.setProperty("SHOW_CONSERVATION", - Boolean.toString(showConservation)); - Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality)); - Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity)); - - Cache.setProperty("DEFAULT_COLOUR", defaultColour); - Cache.setProperty("GAP_SYMBOL", gapSymbol + ""); - - Cache.setProperty("FONT_NAME", fontName); - Cache.setProperty("FONT_STYLE", fontStyle); - Cache.setProperty("FONT_SIZE", fontSize); - - Cache.setProperty("STARTUP_FILE", startupFile); - Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile)); - + 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); @@ -269,6 +386,9 @@ public class Preferences } } + /** + * DOCUMENT ME! + */ public void startupFileTextfield_mouseClicked() { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. @@ -290,13 +410,18 @@ public class Preferences if (value == JalviewFileChooser.APPROVE_OPTION) { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - chooser.getSelectedFormat()); + 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 @@ -308,10 +433,127 @@ public class Preferences } } + /** + * 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 + { + } }