X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=dfe08edd68b37fe19781da67e0602b7251d7326b;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=a4c03bed0bb70473b8431b779349076042f3284b;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index a4c03be..dfe08ed 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -21,6 +21,8 @@
 package jalview.jbgui;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.MemorySetting;
 import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.service.pdb.PDBFTSRestClient;
@@ -35,6 +37,7 @@ import jalview.io.BackupFilesPresetEntry;
 import jalview.io.IntKeyStringValueEntry;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.StringUtils;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -73,6 +76,7 @@ import javax.swing.JPanel;
 import javax.swing.JPasswordField;
 import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
+import javax.swing.JSlider;
 import javax.swing.JSpinner;
 import javax.swing.JTabbedPane;
 import javax.swing.JTable;
@@ -93,6 +97,8 @@ import javax.swing.event.DocumentListener;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 
+import net.miginfocom.swing.MigLayout;
+
 /**
  * Base class for the Preferences panel.
  * 
@@ -181,7 +187,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox structFromPdb = new JCheckBox();
 
-
   protected JCheckBox addSecondaryStructure = new JCheckBox();
 
   protected JCheckBox addTempFactor = new JCheckBox();
@@ -403,6 +408,30 @@ public class GPreferences extends JPanel
   private final JTabbedPane tabbedPane = new JTabbedPane();
 
   private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+
+  /*
+   * Startup tab components
+   */
+
+  protected JCheckBox customiseMemorySetting = new JCheckBox();
+
+  protected JLabel exampleMemoryLabel = new JLabel();
+
+  protected JTextArea exampleMemoryMessageTextArea = new JTextArea();
+
+  protected JLabel maxMemoryLabel = new JLabel();
+
+  protected JLabel jvmMemoryPercentLabel = new JLabel();
+
+  protected JSlider jvmMemoryPercentSlider = new JSlider();
+
+  protected JLabel jvmMemoryPercentDisplay = new JLabel();
+
+  protected JLabel jvmMemoryMaxLabel = new JLabel();
+
+  protected JTextField jvmMemoryMaxTextField = new JTextField(null, 8);
+
+  protected JComboBox<Object> lafCombo = new JComboBox<>();
   /**
    * Creates a new GPreferences object.
    */
@@ -426,8 +455,10 @@ public class GPreferences extends JPanel
   {
     // final JTabbedPane tabbedPane = new JTabbedPane();
     this.setLayout(new BorderLayout());
+
     // message label at top
     this.add(messageLabel, BorderLayout.NORTH);
+
     JPanel okCancelPanel = initOkCancelPanel();
     this.add(tabbedPane, BorderLayout.CENTER);
     this.add(okCancelPanel, BorderLayout.SOUTH);
@@ -462,12 +493,14 @@ public class GPreferences extends JPanel
     tabbedPane.add(initEditingTab(),
             MessageManager.getString("label.editing"));
 
-    tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
     /*
      * See WsPreferences for the real work of configuring this tab.
      */
     if (!Platform.isJS())
     {
+      tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+      tabbedPane.add(initStartupTab(),
+              MessageManager.getString("label.startup"));
       wsTab.setLayout(new BorderLayout());
       tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
     }
@@ -497,6 +530,7 @@ public class GPreferences extends JPanel
           }
         }
         lastTab = tabbedPane.getSelectedComponent();
+
         clearMessage();
       }
 
@@ -861,44 +895,10 @@ public class GPreferences extends JPanel
     connectTab = new JPanel();
     connectTab.setLayout(new GridBagLayout());
 
-    // Label for browser text box
-    JLabel browserLabel = new JLabel();
-    browserLabel.setFont(LABEL_FONT);
-    browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
-    browserLabel.setText(
-            MessageManager.getString("label.default_browser_unix"));
-    defaultBrowser.setFont(LABEL_FONT);
-    defaultBrowser.setText("");
-    final String tooltip = JvSwingUtils.wrapTooltip(true,
-            MessageManager.getString("label.double_click_to_browse"));
-    defaultBrowser.setToolTipText(tooltip);
-    defaultBrowser.addMouseListener(new MouseAdapter()
-    {
-      @Override
-      public void mouseClicked(MouseEvent e)
-      {
-        if (e.getClickCount() > 1)
-        {
-          defaultBrowser_mouseClicked(e);
-        }
-      }
-    });
 
     JPanel proxyPanel = initConnTabProxyPanel();
     initConnTabCheckboxes();
 
-    // Add default Browser text box
-    connectTab.add(browserLabel,
-            new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
-                    GridBagConstraints.WEST, GridBagConstraints.NONE,
-                    new Insets(10, 0, 5, 5), 5, 1));
-    defaultBrowser.setFont(LABEL_FONT);
-    defaultBrowser.setText("");
-
-    connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
-            0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
-            new Insets(10, 0, 5, 10), 30, 1));
-
     // Add proxy server panel
     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
@@ -1273,6 +1273,7 @@ public class GPreferences extends JPanel
         proxyAuth_actionPerformed();
       }
     });
+
     setCustomProxyEnabled();
 
     // Make proxy server panel
@@ -1809,7 +1810,6 @@ public class GPreferences extends JPanel
     structureTab.add(structFromPdb);
 
     // indent checkboxes that are conditional on the first one
-
     ypos += lineSpacing;
     addSecondaryStructure.setFont(LABEL_FONT);
     addSecondaryStructure
@@ -1878,35 +1878,7 @@ public class GPreferences extends JPanel
       {
         if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
         {
-          structureViewer_actionPerformed(
-                  (String) structViewer.getSelectedItem());
-        }
-      });
-      structureTab.add(structViewer);
-      ypos += lineSpacing;
-      structureViewerPathLabel = new JLabel();
-      structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
-                                                   // 11));
-      structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
-      structureViewerPathLabel.setText(MessageManager
-              .formatMessage("label.viewer_path", "Chimera(X)"));
-      structureViewerPathLabel
-              .setBounds(new Rectangle(10, ypos, 170, height));
-      structureViewerPathLabel.setEnabled(false);
-      structureTab.add(structureViewerPathLabel);
- 
-      structureViewerPath.setFont(LABEL_FONT);
-      structureViewerPath.setText("");
-      structureViewerPath.setEnabled(false);
-      final String tooltip = JvSwingUtils.wrapTooltip(true,
-              MessageManager.getString("label.viewer_path_tip"));
-      structureViewerPath.setToolTipText(tooltip);
-      structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
-      structureViewerPath.addMouseListener(new MouseAdapter()
-      {
-        if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
-        {
-          String chosen = openFileChooser();
+          String chosen = openFileChooser(false);
           if (chosen != null)
           {
             structureViewerPath.setText(chosen);
@@ -1953,6 +1925,7 @@ public class GPreferences extends JPanel
       viewerLabel.setVisible(false);
       structViewer.setVisible(false);
     }
+
     return structureTab;
   }
 
@@ -1988,7 +1961,6 @@ public class GPreferences extends JPanel
     {
       chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
     }
-
     // chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.open_local_file"));
@@ -2342,12 +2314,14 @@ public class GPreferences extends JPanel
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
+
     
     if (Platform.isJS())
     {
       startupCheckbox.setVisible(false);
       startupFileTextfield.setVisible(false);
     }
+
     
     return visualTab;
   }
@@ -2385,6 +2359,18 @@ public class GPreferences extends JPanel
     updateBackupFilesExampleLabel();
   }
 
+  /*
+   * Load the saved Memory settings
+   */
+  protected void loadLastSavedMemorySettings()
+  {
+    customiseMemorySetting.setSelected(
+            Cache.getDefault(MemorySetting.CUSTOMISED_SETTINGS, false));
+    jvmMemoryPercentSlider
+            .setValue(Cache.getDefault(MemorySetting.MEMORY_JVMMEMPC, 90));
+    jvmMemoryMaxTextField.setText(
+            Cache.getDefault(MemorySetting.MEMORY_JVMMEMMAX, "32g"));
+  }
   private boolean warnAboutSuffixReverseChange()
   {
     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
@@ -2402,6 +2388,285 @@ public class GPreferences extends JPanel
             && nowSuffixTemplate.equals(savedSuffixTemplate);
   }
 
+  /* Initialises the Startup tabbed panel.
+   * 
+   * @return
+   * */
+
+  private JPanel initStartupTab()
+  {
+    JPanel startupTab = new JPanel();
+    startupTab.setBorder(
+            new TitledBorder(MessageManager.getString("label.memory")));
+    startupTab.setLayout(new GridBagLayout());
+
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 0.0;
+    gbc.weighty = 0.0;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+    gbc.fill = GridBagConstraints.NONE;
+
+    initMemoryPanel();
+
+    gbc.gridheight = 1;
+    gbc.gridwidth = 3;
+
+    gbc.gridy = 0; // row 1
+    gbc.gridx = 0;
+    JLabel memoryText = new JLabel();
+    memoryText.setFont(LABEL_FONT_ITALIC);
+    memoryText
+            .setText(MessageManager.getString("label.memory_setting_text"));
+    startupTab.add(memoryText, gbc);
+
+    gbc.gridy++; // row 2
+    gbc.gridx = 0;
+    JPanel exampleMemoryPanel = new JPanel();
+    exampleMemoryPanel
+            .setLayout(new BoxLayout(exampleMemoryPanel, BoxLayout.Y_AXIS));
+    exampleMemoryPanel.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.memory_example_tooltip")));
+    JLabel exampleTextLabel = new JLabel();
+    exampleTextLabel
+            .setText(MessageManager.getString("label.memory_example_text"));
+    exampleTextLabel.setForeground(Color.GRAY);
+    exampleTextLabel.setFont(LABEL_FONT);
+    exampleMemoryPanel.add(exampleTextLabel);
+    exampleMemoryPanel.add(exampleMemoryLabel);
+    exampleMemoryPanel.setBackground(Color.WHITE);
+    exampleMemoryPanel.setBorder(BorderFactory.createEtchedBorder());
+    startupTab.add(exampleMemoryPanel, gbc);
+
+    gbc.gridy++; // row 3
+    gbc.gridx = 0;
+    startupTab.add(customiseMemorySetting, gbc);
+
+    gbc.gridy += 2; // row 4 with a gap
+    gbc.gridx = 0;
+    startupTab.add(maxMemoryLabel, gbc);
+
+    gbc.gridy += 2; // row 5
+    gbc.gridx = 0;
+    gbc.gridwidth = 1;
+    startupTab.add(jvmMemoryPercentLabel, gbc);
+    gbc.gridx++;
+    startupTab.add(jvmMemoryPercentSlider, gbc);
+    gbc.gridx++;
+    // gbc.weightx = 0.1;
+    startupTab.add(jvmMemoryPercentDisplay, gbc);
+    // gbc.weightx = 1.0;
+    gbc.gridwidth = 3;
+
+    gbc.gridy++; // row 6
+    gbc.gridx = 0;
+    startupTab.add(jvmMemoryMaxLabel, gbc);
+    gbc.gridx++;
+    startupTab.add(jvmMemoryMaxTextField, gbc);
+
+    gbc.gridy++; // row 7
+    gbc.gridx = 0;
+    gbc.gridwidth = 4;
+    exampleMemoryMessageTextArea.setBackground(startupTab.getBackground());
+    JScrollPane sp = new JScrollPane(exampleMemoryMessageTextArea);
+    sp.setBorder(BorderFactory.createEmptyBorder());
+    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
+    startupTab.add(sp, gbc);
+
+    // fill empty space to push widget to top left
+    gbc.gridy++;
+    gbc.weighty = 1.0;
+    gbc.gridx = 100;
+    gbc.gridwidth = 1;
+    gbc.weightx = 1.0;
+    startupTab.add(new JPanel(), gbc);
+
+    setMemoryPercentDisplay();
+    memoryOptionsSetEnabled();
+    return startupTab;
+  }
+
+  private void initMemoryPanel()
+  {
+    // Enable memory settings checkbox
+    customiseMemorySetting.setFont(LABEL_FONT_BOLD);
+    customiseMemorySetting.setText(
+            MessageManager.getString("label.customise_memory_settings"));
+    customiseMemorySetting.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        memoryOptionsSetEnabled();
+      }
+    });
+
+    loadLastSavedMemorySettings();
+
+    exampleMemoryLabel.setFont(LABEL_FONT_BOLD);
+    exampleMemoryLabel.setBackground(Color.WHITE);
+
+    maxMemoryLabel = new JLabel(
+            MessageManager.getString("label.maximum_memory_used"));
+    maxMemoryLabel.setFont(LABEL_FONT_BOLD);
+
+    // Maximum memory percentage slider
+    jvmMemoryPercentLabel.setFont(LABEL_FONT);
+    jvmMemoryPercentLabel.setText(
+            MessageManager.getString("label.percent_of_physical_memory"));
+    jvmMemoryPercentSlider.setPaintLabels(true);
+    jvmMemoryPercentSlider.setPaintTicks(true);
+    jvmMemoryPercentSlider.setPaintTrack(true);
+    jvmMemoryPercentSlider.setMajorTickSpacing(50);
+    jvmMemoryPercentSlider.setMinorTickSpacing(10);
+    jvmMemoryPercentSlider.addChangeListener(new ChangeListener()
+    {
+      @Override
+      public void stateChanged(ChangeEvent e)
+      {
+        setMemoryPercentDisplay();
+      }
+    });
+    jvmMemoryPercentDisplay.setFont(LABEL_FONT);
+    setMemoryPercentDisplay();
+
+    // Maximum memory cap textbox
+    jvmMemoryMaxLabel.setFont(LABEL_FONT);
+    jvmMemoryMaxLabel
+            .setText(MessageManager.getString("label.maximum_memory"));
+    initMemoryMaxTextField();
+
+    exampleMemoryMessageTextArea.setFont(LABEL_FONT_ITALIC);
+    exampleMemoryMessageTextArea.setForeground(Color.GRAY);
+    exampleMemoryMessageTextArea.setEditable(false);
+    exampleMemoryMessageTextArea.setLineWrap(true);
+    exampleMemoryMessageTextArea.setWrapStyleWord(true);
+    exampleMemoryMessageTextArea.setText(" ");
+    exampleMemoryMessageTextArea.setRows(2);
+    exampleMemoryMessageTextArea.setColumns(40);
+
+    setExampleMemoryLabel();
+  }
+
+  private void initMemoryMaxTextField()
+  {
+    jvmMemoryMaxTextField.setToolTipText(
+            MessageManager.getString("label.maximum_memory_tooltip"));
+    jvmMemoryMaxTextField.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        validateMemoryMaxTextField();
+        setExampleMemoryLabel();
+      }
+    });
+
+    jvmMemoryMaxTextField.addKeyListener(new KeyListener()
+    {
+      @Override
+      public void keyReleased(KeyEvent e)
+      {
+        validateMemoryMaxTextField();
+        setExampleMemoryLabel();
+      }
+
+      @Override
+      public void keyPressed(KeyEvent e)
+      {
+      }
+
+      // try and stop invalid typing
+      @Override
+      public void keyTyped(KeyEvent e)
+      {
+        char c = Character.toLowerCase(e.getKeyChar());
+        String text = jvmMemoryMaxTextField.getText();
+        String suffixes = "tgmkb";
+        int pos = jvmMemoryMaxTextField.getCaretPosition();
+        int suffixPos = StringUtils.firstCharPosIgnoreCase(text, suffixes);
+        if (!((('0' <= c && c <= '9')
+                && (suffixPos == -1 || pos <= suffixPos)) // digits only allowed
+                // before suffix
+                || (suffixes.indexOf(Character.toLowerCase(c)) >= 0 // valid
+                                                                    // suffix
+                        && pos == text.length() // at end of text and
+                        && suffixPos == -1) // there isn't already one
+        ))
+        {
+          // don't process
+          e.consume();
+        }
+      }
+    });
+  }
+
+  private boolean isMemoryMaxTextFieldValid()
+  {
+    return MemorySetting
+            .isValidMemoryString(jvmMemoryMaxTextField.getText());
+  }
+
+  private void validateMemoryMaxTextField()
+  {
+    if (isMemoryMaxTextFieldValid())
+    {
+      jvmMemoryMaxTextField.setBackground(Color.WHITE);
+    }
+    else
+    {
+      jvmMemoryMaxTextField.setBackground(Color.PINK);
+    }
+  }
+
+  private void setMemoryPercentDisplay()
+  {
+    jvmMemoryPercentDisplay
+            .setText(jvmMemoryPercentSlider.getValue() + "%");
+    setExampleMemoryLabel();
+  }
+
+  private void setExampleMemoryLabel()
+  {
+    boolean selected = customiseMemorySetting.isSelected();
+    int jvmmempc = jvmMemoryPercentSlider.getValue();
+    String jvmmemmax = jvmMemoryMaxTextField.getText();
+
+    long mem;
+    if (selected && (0 <= jvmmempc && jvmmempc <= 100)
+            && MemorySetting.isValidMemoryString(jvmmemmax))
+    {
+      mem = MemorySetting.getMemorySetting(jvmmemmax,
+              String.valueOf(jvmmempc), false, true);
+    }
+    else
+    {
+      mem = MemorySetting.getMemorySetting(null, null, false, true);
+    }
+    exampleMemoryLabel.setText(MemorySetting.memoryLongToString(mem));
+    String message = MemorySetting.getAdjustmentMessage();
+    exampleMemoryMessageTextArea.setText(
+            MessageManager.getString("label.adjustments_for_this_computer")
+                    + ": "
+                    + (message == null
+                            ? MessageManager.getString("label.none")
+                            : message));
+  }
+
+  private void memoryOptionsSetEnabled()
+  {
+    boolean enabled = customiseMemorySetting.isSelected();
+    // leave exampleMemoryLabel enabled always
+    maxMemoryLabel.setEnabled(enabled);
+    jvmMemoryPercentLabel.setEnabled(enabled);
+    jvmMemoryPercentSlider.setEnabled(enabled);
+    jvmMemoryPercentDisplay.setEnabled(enabled);
+    jvmMemoryMaxLabel.setEnabled(enabled);
+    jvmMemoryMaxTextField.setEnabled(enabled);
+    exampleMemoryMessageTextArea.setEnabled(enabled);
+    setExampleMemoryLabel();
+  }
+
   /**
    * Initialises the Backups tabbed panel.
    * 
@@ -2438,7 +2703,6 @@ public class GPreferences extends JPanel
       }
     });
 
-
     // enable checkbox 1 col
     gbc.gridwidth = 1;
     gbc.gridheight = 1;
@@ -2624,7 +2888,6 @@ public class GPreferences extends JPanel
     exampleFilesPanel.setBorder(tb);
     exampleFilesPanel.setLayout(new GridBagLayout());
 
-
     backupfilesExampleLabel.setEditable(false);
     backupfilesExampleLabel
             .setBackground(exampleFilesPanel.getBackground());
@@ -2657,7 +2920,7 @@ public class GPreferences extends JPanel
     }
     else
     {
-      Cache.log.error(
+      Console.error(
               "Preset '" + value + "' [key:" + key + "] not implemented");
     }
 
@@ -2677,7 +2940,7 @@ public class GPreferences extends JPanel
               .getSelectedItem();
     } catch (Exception ex)
     {
-      Cache.log.error(
+      Console.error(
               "Problem casting Combo entry to IntKeyStringValueEntry.");
       e = null;
     }
@@ -2696,7 +2959,7 @@ public class GPreferences extends JPanel
         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
       } catch (Exception ex)
       {
-        Cache.log.error(
+        Console.error(
                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
         continue;
       }
@@ -3144,7 +3407,7 @@ public class GPreferences extends JPanel
         i = ((Integer) s.getValue()).intValue();
       } catch (Exception e)
       {
-        Cache.log.error(
+        Console.error(
                 "Exception casting the initial value of s.getValue()");
       }
     }
@@ -3180,7 +3443,7 @@ public class GPreferences extends JPanel
       i = (Integer) s.getValue();
     } catch (Exception e)
     {
-      Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+      Console.error("Failed casting (Integer) JSpinner s.getValue()");
     }
     return i;
   }
@@ -3559,4 +3822,3 @@ public class GPreferences extends JPanel
     panel.validate();
   }
 }
-