JAL-1528 new Preference CHIMERA_PATH (Preferences | Structure)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 9eee9cc..511e5e9 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -248,6 +248,9 @@ label.use_rnaview = Use RNAView for secondary structure
 label.autoadd_secstr = Add secondary structure annotation to alignment
 label.autoadd_temp = Add Temperature Factor annotation to alignment
 label.structure_viewer = Default structure viewer
+label.chimera_path = Path to Chimera program
+label.chimera_path_tip = Jalview will try standard locations, plus any path entered here.
+label.invalid_path = File not found or not executable
 label.min_colour = Minimum Colour
 label.max_colour = Maximum Colour
 label.use_original_colours = Use Original Colours

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index ec956d7..1208638 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -1,12 +1,14 @@
 package ext.edu.ucsf.rbvi.strucviz2;
 
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
+
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
@@ -32,10 +34,6 @@ public class StructureManager
   static final String[] defaultResidueKeys =
   { "FunctionalResidues", "ResidueList", "Residues" };
 
-  private final String chimeraPropertyName = "chimera";
-
-  private final String chimeraPathPropertyKey = "LastChimeraPath";
-
   public enum ModelType
   {
     PDB_MODEL, MODBASE_MODEL, SMILES
@@ -494,7 +492,9 @@ public class StructureManager
       // we do not care about the model anymore
       selSpec = selSpec.concat(nodeInfo.toSpec());
       if (i < chimSelectionList.size() - 1)
+      {
         selSpec.concat("|");
+      }
     }
     if (selSpec.length() > 0)
     {
@@ -665,7 +665,9 @@ public class StructureManager
     for (ChimeraStructuralObject cso : chimSelectionList)
     {
       if (cso != null)
+      {
         cso.setSelected(false);
+      }
     }
     chimSelectionList.clear();
   }
@@ -879,17 +881,16 @@ public class StructureManager
       }
     }
 
-    // if no network settings, check if the last chimera path is saved in the
-    // session
-    // String lastPath = CytoUtils.getDefaultChimeraPath(registrar,
-    // chimeraPropertyName,
-    // chimeraPathPropertyKey);
-    // if (lastPath != null && !lastPath.equals("")) {
-    // pathList.add(lastPath);
-    // return pathList;
-    // }
+    /*
+     * Jalview addition: check if path set in user preferences.
+     */
+    String userPath = Cache.getDefault(Preferences.CHIMERA_PATH, null);
+    if (userPath != null)
+    {
+      pathList.add(userPath);
+    }
 
-    // if no user settings and no last path, get default system's settings
+    // Add default installation paths
     String os = System.getProperty("os.name");
     if (os.startsWith("Linux"))
     {

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a48b750..24ed1b4 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -173,6 +173,7 @@ import org.apache.log4j.SimpleLayout;
  * display</li>
  * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
  * display</li>
+ * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
  * 
  * </ul>
  * Deprecated settings:
@@ -906,4 +907,27 @@ public class Cache
     }
     return sourceRegistry;
   }
+
+  /**
+   * Set the specified value, or remove it if null or empty. Does not save the
+   * properties file.
+   * 
+   * @param propName
+   * @param value
+   */
+  public static void setOrRemove(String propName, String value)
+  {
+    if (propName == null)
+    {
+      return;
+    }
+    if (value == null || value.trim().length() < 1)
+    {
+      Cache.applicationProperties.remove(propName);
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty(propName, value);
+    }
+  }
 }

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 2e8aa89..ab4f94f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -35,7 +35,9 @@ import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
+import java.io.File;
 import java.util.Collection;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -65,6 +67,8 @@ public class Preferences extends GPreferences
 
   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 
+  public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
@@ -281,6 +285,25 @@ public class Preferences extends GPreferences
     addTempFactor.setEnabled(structSelected);
     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
             Viewer.JMOL.name()));
+    chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+    chimeraPath.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (chimeraPath.getText().trim().length() > 0)
+        {
+          File f = new File(chimeraPath.getText());
+          if (!f.canExecute())
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    MessageManager.getString("label.invalid_path"),
+                    MessageManager.getString("label.invalid_name"),
+                    JOptionPane.ERROR_MESSAGE);
+          }
+        }
+      }
+    });
 
     /*
      * Set Connections tab defaults
@@ -449,6 +472,7 @@ public class Preferences extends GPreferences
             Boolean.toString(structFromPdb.isSelected()));
     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
             .getSelectedItem().toString());
+    Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 
     /*
      * Save Output settings
@@ -466,15 +490,7 @@ public class Preferences extends GPreferences
     /*
      * Save Connections settings
      */
-    if (defaultBrowser.getText().trim().length() < 1)
-    {
-      Cache.applicationProperties.remove("DEFAULT_BROWSER");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
-              defaultBrowser.getText());
-    }
+    Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 
     jalview.util.BrowserLauncher.resetBrowser();
 
@@ -502,25 +518,9 @@ public class Preferences extends GPreferences
     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());
-    }
+    Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 
-    if (proxyPortTB.getText().trim().length() < 1)
-    {
-      Cache.applicationProperties.remove("PROXY_PORT");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("PROXY_PORT",
-              proxyPortTB.getText());
-    }
+    Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 
     if (useProxy.isSelected())
     {

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index cd3064e..a232377 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -140,6 +140,8 @@ public class GPreferences extends JPanel
 
   protected JComboBox<String> structViewer = new JComboBox<String>();
 
+  protected JTextField chimeraPath = new JTextField();
+
   /*
    * Colours tab components
    */
@@ -744,11 +746,26 @@ public class GPreferences extends JPanel
     structureTab.add(viewerLabel);
 
     structViewer.setFont(verdana11);
-    structViewer.setBounds(new Rectangle(150, ypos, 120, height));
+    structViewer.setBounds(new Rectangle(160, ypos, 120, height));
     structViewer.addItem(Viewer.JMOL.name());
     structViewer.addItem(Viewer.CHIMERA.name());
     structureTab.add(structViewer);
 
+    ypos += lineSpacing;
+    JLabel pathLabel = new JLabel();
+    pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
+    pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    pathLabel.setText(MessageManager.getString("label.chimera_path"));
+    pathLabel.setToolTipText(MessageManager
+            .getString("label.chimera_path_tip"));
+    pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
+    structureTab.add(pathLabel);
+
+    chimeraPath.setFont(verdana11);
+    chimeraPath.setText("");
+    chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+    structureTab.add(chimeraPath);
+
     return structureTab;
   }