X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=e69492c605f42a6460e6ce696aefeb9a77c21471;hb=5c57814f95e73a63e012479651b919fdc4099f53;hp=6c07d23623c6e83307ca91f0619bc3ea6b2839ae;hpb=aee942d972498d3e51334fc890221b1827e0b255;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6c07d23..e69492c 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,108 +1,443 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * 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.jbgui.*;
-import jalview.schemes.*;
+import java.util.*;
 
-import jalview.bin.Cache;
-import javax.swing.*;
-import java.awt.event.ActionEvent;
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
 
-public class Preferences extends GPreferences
+import jalview.bin.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences
+    extends GPreferences
 {
-  AlignViewport av;
+  /** 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;
-  public Preferences(AlignViewport av)
+
+  DasSourceBrowser dasSource;
+
+  /**
+   * Creates a new Preferences object.
+   */
+  public Preferences()
   {
-    this.av = av;
+
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Preferences", 480,350 );
+    dasSource = new DasSourceBrowser();
+    dasPanel.add(dasSource, BorderLayout.CENTER);
 
+    int width = 500, height = 420;
+    if (System.getProperty("os.name").startsWith("Mac"))
+    {
+      width = 570;
+      height = 460;
+    }
 
-    fullID.setSelected(av.getShowFullId());
-    String string = Cache.getProperty("SHOW_FULLSCREEN");
-    boolean value = false;
-    if(string!=null)
-      value =  Boolean.valueOf(string).booleanValue();
+    Desktop.addInternalFrame(frame, "Preferences", width, height);
+    frame.setMinimumSize(new Dimension(width, height));
 
-    fullScreen.setSelected(value);
-    annotations.setSelected(av.getShowAnnotation());
+    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.setEnabled(av.getShowAnnotation());
-    quality.setEnabled(av.getShowAnnotation());
-    identity.setEnabled(av.getShowAnnotation());
+    conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+    quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+    identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
 
-    conservation.setSelected(av.showConservation);
-    quality.setSelected(av.showQuality);
-    identity.setSelected(av.showIdentity);
+    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<12; i++)
-      colour.addItem( ColourSchemeProperty.getColourName(i) );
+    for (int i = 0; i < 13; i++)
+    {
+      colour.addItem(ColourSchemeProperty.getColourName(i));
+    }
 
-    string = Cache.getProperty("DEFAULT_COLOUR");
-    if(string!=null)
-      colour.setSelectedItem( string );
-    else
-      colour.setSelectedIndex( 11 );
+    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");
 
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-    for(int i=0; i<fonts.length; i++)
-      fontName.addItem(fonts[i]);
+    fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+    fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+    fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
-    for(int i=1; i<31; i++)
-      fontSize.addItem(i+"");
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
-   fontStyle.addItem("plain");
-   fontStyle.addItem("bold");
-   fontStyle.addItem("italic");
+    idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
-   Font oldFont = av.getFont();
-   fontName.setSelectedItem(oldFont.getName());
-   fontSize.setSelectedItem(oldFont.getSize() + "");
-   fontStyle.setSelectedIndex(oldFont.getStyle());
+    wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 
-   gapSymbol.addItem("-");
-   gapSymbol.addItem(".");
+    gapSymbolCB.addItem("-");
+    gapSymbolCB.addItem(".");
 
-   gapSymbol.setSelectedItem( av.getGapCharacter()+"" );
+    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.setProperty("SHOW_FULL_ID", Boolean.toString( fullID.isSelected() ));
-    Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( fullScreen.isSelected() ));
 
-    Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( annotations.isSelected() ));
-    Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( conservation.isSelected() ));
-    Cache.setProperty("SHOW_QUALITY", Boolean.toString( quality.isSelected() ));
-    Cache.setProperty("SHOW_IDENTITY", Boolean.toString( identity.isSelected() ));
+    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.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString() );
-    Cache.setProperty("GAP_SYMBOL", gapSymbol.getSelectedItem().toString());
+    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"))
+    {
+      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());
+    }
 
-    Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());
-    Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex()+"");
-    Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
+    jalview.util.BrowserLauncher.resetBrowser();
 
-    try    {
+    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)  {}
+    }
+    catch (Exception ex)
+    {
+    }
+  }
 
-    av.updateFromPreferences();
+  /**
+   * 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");
 
-    repaint();
+    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{
+    try
+    {
       frame.setClosed(true);
-    }catch(Exception ex){}
+    }
+    catch (Exception ex)
+    {
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void annotations_actionPerformed(ActionEvent e)
   {
     conservation.setEnabled(annotations.isSelected());
@@ -110,4 +445,115 @@ public class Preferences extends GPreferences
     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
+  {
+  }
 }