X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=a368e74cdb9eb9e18d909907b3ebd3536de9a76d;hb=bffd5239316cc37765480e532ed8f153d512732b;hp=cfc464ed066e661f98c3b42d2558831686b5948e;hpb=3f719e5608ad146997cfa48b5f7005137fb2d1a6;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index cfc464e..a368e74 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -43,16 +43,11 @@ import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.FileOutputStream;
-import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.SortedMap;
-import java.util.StringTokenizer;
-import java.util.TreeMap;
 
 import javax.swing.JButton;
 import javax.swing.JInternalFrame;
@@ -71,7 +66,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 {
   private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
 
-  private static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+  public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
 
   private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
 
@@ -81,8 +76,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
 
-  static SortedMap<String, UserColourScheme> userColourSchemes;
-
   AlignmentPanel ap;
 
   SequenceGroup seqGroup;
@@ -116,7 +109,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -125,7 +118,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (oldColourScheme instanceof UserColourScheme)
     {
-      schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
+      schemeName.setText(oldColourScheme.getSchemeName());
       if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
       {
         caseSensitive.setSelected(true);
@@ -181,7 +174,15 @@ public class UserDefinedColours extends GUserDefinedColours implements
     }
   }
 
-  void resetButtonPanel(boolean caseSensitive)
+  /**
+   * Rebuilds the panel with coloured buttons for residues. If not case
+   * sensitive colours, show 3-letter amino acid code as button text. If case
+   * sensitive, just show the single letter code, in order to make space for the
+   * additional buttons.
+   * 
+   * @param isCaseSensitive
+   */
+  void resetButtonPanel(boolean isCaseSensitive)
   {
     buttonPanel.removeAll();
 
@@ -190,23 +191,13 @@ public class UserDefinedColours extends GUserDefinedColours implements
       upperCaseButtons = new ArrayList<JButton>();
     }
 
-    JButton button;
-    String label;
     for (int i = 0; i < 20; i++)
     {
-      if (caseSensitive)
-      {
-        label = ResidueProperties.aa[i];
-      }
-      else
-      {
-        label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
-                .toString();
-      }
-
-      button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
-              i);
-
+      String label = isCaseSensitive ? ResidueProperties.aa[i]
+              : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+                      .toString();
+      JButton button = makeButton(label, ResidueProperties.aa[i],
+              upperCaseButtons, i);
       buttonPanel.add(button);
     }
 
@@ -215,7 +206,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
     buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
 
-    if (!caseSensitive)
+    if (!isCaseSensitive)
     {
       gridLayout.setRows(6);
       gridLayout.setColumns(4);
@@ -235,14 +226,14 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         int row = i / cols + 1;
         int index = (row * cols) + i;
-        button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+        JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
                 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
 
         buttonPanel.add(button, index);
       }
     }
 
-    if (caseSensitive)
+    if (isCaseSensitive)
     {
       buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
       buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
@@ -253,7 +244,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     // codes
     if (this.frame != null)
     {
-      int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+      int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
               : MY_FRAME_WIDTH;
       this.frame.setSize(newWidth, this.frame.getHeight());
     }
@@ -437,15 +428,15 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
       buttons.add(button);
 
+      /*
+       * make initial button colour that of the current colour scheme,
+       * if it is a simple per-residue colouring, else white
+       */
       col = Color.white;
-      if (oldColourScheme != null)
+      if (oldColourScheme != null && oldColourScheme.isSimple())
       {
-        try
-        {
-          col = oldColourScheme.findColour(residue.charAt(0), -1, null);
-        } catch (Exception ex)
-        {
-        }
+        col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+                0f);
       }
     }
 
@@ -528,11 +519,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     }
     UserColourScheme ucs = getSchemeFromButtons();
-    ucs.setName(schemeName.getText());
 
     if (seqGroup != null)
     {
-      seqGroup.cs = ucs;
+      seqGroup.setColourScheme(ucs);
       ap.paintAlignment(true);
     }
     else if (ap != null)
@@ -570,6 +560,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
+    ucs.setName(schemeName.getText());
 
     if (caseSensitive.isSelected())
     {
@@ -595,10 +586,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     return ucs;
   }
@@ -631,7 +622,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     File choice = chooser.getSelectedFile();
     Cache.setProperty(LAST_DIRECTORY, choice.getParent());
 
-    UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
     Color[] colors = ucs.getColours();
     schemeName.setText(ucs.getSchemeName());
 
@@ -663,9 +654,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Loads the user-defined colour scheme from the first file listed in property
+   * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme.
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   public static UserColourScheme loadDefaultColours()
   {
@@ -678,18 +670,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         colours = colours.substring(0, colours.indexOf("|"));
       }
-
-      ret = loadColours(colours);
+      ret = ColourSchemes.loadColourScheme(colours);
     }
 
     if (ret == null)
     {
-      Color[] newColours = new Color[24];
-      for (int i = 0; i < 24; i++)
-      {
-        newColours[i] = Color.white;
-      }
-      ret = new UserColourScheme(newColours);
+      ret = new UserColourScheme("white");
     }
 
     return ret;
@@ -698,125 +684,14 @@ public class UserDefinedColours extends GUserDefinedColours implements
   /**
    * DOCUMENT ME!
    * 
-   * @param file
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  static UserColourScheme loadColours(String file)
-  {
-    UserColourScheme ucs = null;
-    Color[] newColours = null;
-    try
-    {
-      InputStreamReader in = new InputStreamReader(
-              new FileInputStream(file), "UTF-8");
-
-      jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-
-      org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
-              jucs);
-      jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
-              .unmarshal(in);
-
-      newColours = new Color[24];
-
-      Color[] lowerCase = null;
-      boolean caseSensitive = false;
-
-      String name;
-      int index;
-      for (int i = 0; i < jucs.getColourCount(); i++)
-      {
-        name = jucs.getColour(i).getName();
-        if (ResidueProperties.aa3Hash.containsKey(name))
-        {
-          index = ResidueProperties.aa3Hash.get(name).intValue();
-        }
-        else
-        {
-          index = ResidueProperties.aaIndex[name.charAt(0)];
-        }
-        if (index == -1)
-        {
-          continue;
-        }
-
-        if (name.toLowerCase().equals(name))
-        {
-          if (lowerCase == null)
-          {
-            lowerCase = new Color[23];
-          }
-          caseSensitive = true;
-          lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
-                  .getRGB(), 16));
-        }
-        else
-        {
-          newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
-                  .getRGB(), 16));
-        }
-      }
-
-      if (newColours != null)
-      {
-        ucs = new UserColourScheme(newColours);
-        ucs.setName(jucs.getSchemeName());
-        if (caseSensitive)
-        {
-          ucs.setLowerCaseColours(lowerCase);
-        }
-      }
-
-    } catch (Exception ex)
-    {
-      // Could be Archive Jalview format
-      try
-      {
-        InputStreamReader in = new InputStreamReader(new FileInputStream(
-                file), "UTF-8");
-
-        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-
-        jucs = jucs.unmarshal(in);
-
-        newColours = new Color[jucs.getColourCount()];
-
-        for (int i = 0; i < 24; i++)
-        {
-          newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
-                  .getRGB(), 16));
-        }
-        if (newColours != null)
-        {
-          ucs = new UserColourScheme(newColours);
-          ucs.setName(jucs.getSchemeName());
-        }
-      } catch (Exception ex2)
-      {
-        ex2.printStackTrace();
-      }
-
-      if (newColours == null)
-      {
-        System.out.println("Error loading User ColourFile\n" + ex);
-      }
-    }
-
-    return ucs;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param e
    *          DOCUMENT ME!
    */
   @Override
   protected void savebutton_actionPerformed(ActionEvent e)
   {
-    if (schemeName.getText().trim().length() < 1)
+    String name = schemeName.getText().trim();
+    if (name.length() < 1)
     {
       JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("label.user_colour_scheme_must_have_name"),
@@ -825,27 +700,26 @@ public class UserDefinedColours extends GUserDefinedColours implements
       return;
     }
 
-    if (userColourSchemes != null
-            && userColourSchemes.containsKey(schemeName.getText()))
+    if (ColourSchemes.getInstance().nameExists(name))
     {
       int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
               MessageManager.formatMessage(
                       "label.colour_scheme_exists_overwrite", new Object[] {
-                          schemeName.getText(), schemeName.getText() }),
+                          name, name }),
               MessageManager.getString("label.duplicate_scheme_name"),
               JvOptionPane.YES_NO_OPTION);
       if (reply != JvOptionPane.YES_OPTION)
       {
         return;
       }
-
-      userColourSchemes.remove(schemeName.getText());
+      ColourSchemes.getInstance().removeColourScheme(name);
     }
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty(LAST_DIRECTORY), "jc",
             "Jalview User Colours");
 
-    chooser.setFileView(new JalviewFileView());
+    JalviewFileView fileView = new JalviewFileView();
+    chooser.setFileView(fileView);
     chooser.setDialogTitle(MessageManager
             .getString("label.save_colour_scheme"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -854,9 +728,9 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      addNewColourScheme(choice);
-      saveToFile(choice);
+      File file = chooser.getSelectedFile();
+      addNewColourScheme(file.getPath());
+      saveToFile(file);
     }
   }
 
@@ -887,12 +761,9 @@ public class UserDefinedColours extends GUserDefinedColours implements
     Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
 
     /*
-     * add to the cache in this object
+     * construct and register the colour scheme
      */
     UserColourScheme ucs = getSchemeFromButtons();
-    String name = schemeName.getText();
-    userColourSchemes.put(name, ucs);
-
     ColourSchemes.getInstance().registerColourScheme(ucs);
 
     /*
@@ -907,9 +778,9 @@ public class UserDefinedColours extends GUserDefinedColours implements
   /**
    * Saves the colour scheme to file in XML format
    * 
-   * @param filePath
+   * @param path
    */
-  protected void saveToFile(String filePath)
+  protected void saveToFile(File toFile)
   {
     /*
      * build a Java model of colour scheme as XML, and 
@@ -920,7 +791,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     try
     {
       PrintWriter out = new PrintWriter(new OutputStreamWriter(
-              new FileOutputStream(filePath), "UTF-8"));
+              new FileOutputStream(toFile), "UTF-8"));
 
       for (int i = 0; i < buttonPanel.getComponentCount(); i++)
       {
@@ -950,7 +821,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = oldColourScheme;
+        seqGroup.setColourScheme(oldColourScheme);
       }
       else
       {
@@ -972,103 +843,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
     }
   }
 
-  public static SortedMap<String, UserColourScheme> getUserColourSchemes()
-  {
-    return userColourSchemes;
-  }
-
-  public static void initUserColourSchemes(String files)
-  {
-    userColourSchemes = new TreeMap<String, UserColourScheme>();
-
-    if (files == null || files.length() == 0)
-    {
-      return;
-    }
-
-    // In case colours can't be loaded, we'll remove them
-    // from the default list here.
-    StringBuffer coloursFound = new StringBuffer();
-    StringTokenizer st = new StringTokenizer(files, "|");
-    while (st.hasMoreElements())
-    {
-      String file = st.nextToken();
-      try
-      {
-        UserColourScheme ucs = loadColours(file);
-        if (ucs != null)
-        {
-          if (coloursFound.length() > 0)
-          {
-            coloursFound.append("|");
-          }
-          coloursFound.append(file);
-          String name = ucs.getName();
-          userColourSchemes.put(name, ucs);
-          ColourSchemes.getInstance().registerColourScheme(ucs);
-        }
-      } catch (Exception ex)
-      {
-        System.out.println("Error loading User ColourFile\n" + ex);
-      }
-    }
-    if (!files.equals(coloursFound.toString()))
-    {
-      if (coloursFound.toString().length() > 1)
-      {
-        Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString());
-      }
-      else
-      {
-        Cache.applicationProperties.remove(USER_DEFINED_COLOURS);
-      }
-    }
-  }
-
-  public static void removeColourFromDefaults(String target)
-  {
-    // The only way to find colours by name is to load them in
-    // In case colours can't be loaded, we'll remove them
-    // from the default list here.
-
-    userColourSchemes = new TreeMap<String, UserColourScheme>();
-
-    StringBuffer coloursFound = new StringBuffer();
-    StringTokenizer st = new StringTokenizer(
-            Cache.getProperty(USER_DEFINED_COLOURS), "|");
-
-    while (st.hasMoreElements())
-    {
-      String file = st.nextToken();
-      try
-      {
-        UserColourScheme ucs = loadColours(file);
-        if (ucs != null && !ucs.getSchemeName().equals(target))
-        {
-          if (coloursFound.length() > 0)
-          {
-            coloursFound.append("|");
-          }
-          coloursFound.append(file);
-          userColourSchemes.put(ucs.getSchemeName(), ucs);
-        }
-      } catch (Exception ex)
-      {
-        System.out.println("Error loading User ColourFile\n" + ex);
-      }
-    }
-
-    if (coloursFound.toString().length() > 1)
-    {
-      Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString());
-    }
-    else
-    {
-      Cache.applicationProperties.remove(USER_DEFINED_COLOURS);
-    }
-
-  }
-
   @Override
   public void caseSensitive_actionPerformed(ActionEvent e)
   {