apply version 2.7 copyright

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index e863d0b..27c455e 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -137,7 +137,7 @@ public class Preferences extends GPreferences
             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
             true));
-
+    sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
     {
       colour.addItem(ColourSchemeProperty.getColourName(i));
@@ -147,6 +147,12 @@ public class Preferences extends GPreferences
 
     colour.setSelectedItem(string);
 
+    /**
+     * default min-max colours for annotation shading
+     */
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+
     String[] fonts = java.awt.GraphicsEnvironment
             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 
@@ -183,7 +189,7 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org","http://www.jalview.org")+"/examples/exampleFile_2_3.jar"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
@@ -270,22 +276,22 @@ public class Preferences extends GPreferences
   public void ok_actionPerformed(ActionEvent e)
   {
 
-    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("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());
@@ -299,36 +305,39 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
             .getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
-            .toString(idItalics.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean
-            .toString(showUnconserved.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean
-            .toString(showGroupConsensus.isSelected()));
+    Cache.applicationProperties.setProperty("ID_ITALICS",
+            Boolean.toString(idItalics.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+            Boolean.toString(showUnconserved.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+            Boolean.toString(showGroupConsensus.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
             Boolean.toString(showGroupConservation.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
             Boolean.toString(showConsensHistogram.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean
-            .toString(showConsensLogo.isSelected()));
-    Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
-            .toString(smoothFont.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean
-            .toString(showNpTooltip.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean
-            .toString(showDbRefTooltip.isSelected()));
-
-    Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
-            .toString(wrap.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+            Boolean.toString(showConsensLogo.isSelected()));
+    Cache.applicationProperties.setProperty("ANTI_ALIAS",
+            Boolean.toString(smoothFont.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+            Boolean.toString(showNpTooltip.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+            Boolean.toString(showDbRefTooltip.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("SHOW_STARTUP_FILE",
+            Boolean.toString(startupCheckbox.isSelected()));
 
     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
             .getSelectedItem().toString());
 
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground());
+    
     if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
       Cache.applicationProperties.remove("EPS_RENDERING");
@@ -364,16 +373,16 @@ public class Preferences extends GPreferences
       }
       // remove last "|"
       links.setLength(links.length() - 1);
-      Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
-              .toString());
+      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+              links.toString());
     }
     else
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
 
-    Cache.applicationProperties.setProperty("USE_PROXY", Boolean
-            .toString(useProxy.isSelected()));
+    Cache.applicationProperties.setProperty("USE_PROXY",
+            Boolean.toString(useProxy.isSelected()));
 
     if (proxyServerTB.getText().trim().length() < 1)
     {
@@ -381,8 +390,8 @@ public class Preferences extends GPreferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
-              .getText());
+      Cache.applicationProperties.setProperty("PROXY_SERVER",
+              proxyServerTB.getText());
     }
 
     if (proxyPortTB.getText().trim().length() < 1)
@@ -391,8 +400,8 @@ public class Preferences extends GPreferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
-              .getText());
+      Cache.applicationProperties.setProperty("PROXY_PORT",
+              proxyPortTB.getText());
     }
 
     if (useProxy.isSelected())
@@ -405,13 +414,13 @@ public class Preferences extends GPreferences
       System.setProperty("http.proxyHost", "");
       System.setProperty("http.proxyPort", "");
     }
-    Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck
-            .isSelected()));
+    Cache.setProperty("VERSION_CHECK",
+            Boolean.toString(versioncheck.isSelected()));
     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
     {
       // default is false - we only set this if the user has actively agreed
-      Cache.setProperty("USAGESTATS", Boolean.toString(usagestats
-              .isSelected()));
+      Cache.setProperty("USAGESTATS",
+              Boolean.toString(usagestats.isSelected()));
     }
     if (!questionnaire.isSelected())
     {
@@ -423,31 +432,33 @@ public class Preferences extends GPreferences
       // by just adding the given line
       Cache.removeProperty("NOQUESTIONNAIRES");
     }
-    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()));
+    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()));
+    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+            Boolean.toString(autoCalculateConsCheck.isSelected()));
+    Cache.applicationProperties.setProperty("SORT_BY_TREE",
+            Boolean.toString(sortByTree.isSelected()));
+    Cache.applicationProperties.setProperty("PAD_GAPS",
+            Boolean.toString(padGaps.isSelected()));
 
     dasSource.saveProperties(Cache.applicationProperties);
-    wsPrefs.updateWsMenuConfig(false);
+    wsPrefs.updateAndRefreshWsMenuConfig(false);
     Cache.saveProperties();
     try
     {
@@ -462,9 +473,10 @@ public class Preferences extends GPreferences
    */
   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" },
+    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"));
@@ -493,6 +505,7 @@ public class Preferences extends GPreferences
     try
     {
       wsPrefs.updateWsMenuConfig(true);
+      wsPrefs.refreshWs_actionPerformed(e);
       frame.setClosed(true);
     } catch (Exception ex)
     {
@@ -640,4 +653,26 @@ public class Preferences extends GPreferences
   {
     return groupURLLinks;
   }
+  public void minColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Minimum Value", minColour.getBackground());
+    if (col != null)
+    {
+      minColour.setBackground(col);
+    }
+    minColour.repaint();
+  }
+
+  public void maxColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Maximum Value", maxColour.getBackground());
+    if (col != null)
+    {
+      maxColour.setBackground(col);
+    }
+    maxColour.repaint();
+  }
+
 }