ID_ITALICS option in preferences

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8b929c7..6c8e0e4 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,6 +61,7 @@ public class AlignViewport
     boolean validCharWidth;
     int wrappedWidth;
     Font font;
+    boolean seqNameItalics;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -170,6 +171,8 @@ public class AlignViewport
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
        int style = 0;
 
        if (fontStyle.equals("bold"))

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4047ac8..4a21781 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -711,9 +711,8 @@ public class AlignmentPanel extends GAlignmentPanel
     Color currentColor = null;\r
     Color currentTextColor = null;\r
 \r
-    pg.setFont(new Font(av.getFont().getName(),\r
-                        Font.ITALIC,\r
-                        av.getFont().getSize()));\r
+    pg.setFont(idPanel.idCanvas.idfont);\r
+\r
     SequenceI seq;\r
     for (int i = startSeq; i < endSeq; i++)\r
     {\r
@@ -827,20 +826,20 @@ public class AlignmentPanel extends GAlignmentPanel
     pg.setClip(0, pi * pheight, pwidth, pheight);\r
 \r
     int ypos = hgap;\r
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
-                           av.getFont().getSize());\r
-    pg.setFont(italic);\r
+\r
+\r
 \r
     do\r
     {\r
       for (int i = 0; i < av.alignment.getHeight(); i++)\r
       {\r
+        pg.setFont(idPanel.idCanvas.idfont);\r
         SequenceI s = av.alignment.getSequenceAt(i);\r
         String string = s.getDisplayId( av.getShowJVSuffix());\r
         int xPos = 0;\r
         if (av.rightAlignIds)\r
         {\r
-          FontMetrics fm = getFontMetrics(italic);\r
+          FontMetrics fm = getFontMetrics(idPanel.idCanvas.idfont);\r
           xPos = idWidth - fm.stringWidth( string ) - 4;\r
         }\r
         pg.drawString(string, xPos,\r
@@ -855,7 +854,6 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         pg.setFont(av.getFont());\r
         labels.drawComponent(pg, idWidth);\r
-        pg.setFont(italic);\r
         pg.translate(+3,\r
                      -ypos -\r
                      (av.getAlignment().getHeight() * av.charHeight));\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 168b50d..71cc483 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -46,6 +46,7 @@ public class IdCanvas extends JPanel
     FontMetrics fm;\r
     AnnotationLabels labels = null;\r
     AnnotationPanel ap;\r
+    Font idfont;\r
 \r
     /**\r
      * Creates a new IdCanvas object.\r
@@ -219,10 +220,13 @@ public class IdCanvas extends JPanel
      */\r
     void drawIds(int starty, int endy)\r
     {\r
-      Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+     if(av.seqNameItalics)\r
+      idfont = new Font(av.getFont().getName(), Font.ITALIC,\r
                              av.getFont().getSize());\r
+    else\r
+      idfont = av.getFont();\r
 \r
-      gg.setFont(italic);\r
+      gg.setFont(idfont);\r
       fm = gg.getFontMetrics();\r
 \r
       if (av.antiAlias)\r
@@ -277,7 +281,7 @@ public class IdCanvas extends JPanel
                   setHiddenFont(s);\r
                 }\r
                 else\r
-                  gg.setFont(italic);\r
+                  gg.setFont(idfont);\r
 \r
                 drawIdString(gg, s, i, 0, ypos);\r
               }\r
@@ -421,8 +425,6 @@ public class IdCanvas extends JPanel
 \r
     void setHiddenFont(SequenceI seq)\r
     {\r
-      Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
-                             av.getFont().getSize());\r
       Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
                            av.getFont().getSize());\r
 \r
@@ -431,7 +433,7 @@ public class IdCanvas extends JPanel
           av.hiddenRepSequences.containsKey(seq))\r
         gg.setFont(bold);\r
       else\r
-        gg.setFont(italic);\r
+        gg.setFont(idfont);\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 840598b..b58c72d 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -136,6 +136,8 @@ public class Preferences extends GPreferences
 \r
         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 \r
+        idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
+\r
         wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
 \r
         gapSymbolCB.addItem("-");\r
@@ -227,6 +229,8 @@ public class Preferences extends GPreferences
       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
 \r
+      Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected()));\r
+\r
       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 \r
       Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index bc4a37b..2b194bf 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -114,6 +114,7 @@ public class GPreferences extends JPanel
   BorderLayout borderLayout4 = new BorderLayout();\r
   protected JCheckBox wrap = new JCheckBox();\r
   protected JCheckBox rightAlign = new JCheckBox();\r
+  protected JCheckBox idItalics = new JCheckBox();\r
   /**\r
      * Creates a new GPreferences object.\r
      */\r
@@ -193,7 +194,7 @@ public class GPreferences extends JPanel
         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         gapLabel.setText("Gap Symbol ");\r
     colour.setFont(verdana11);\r
-        colour.setBounds(new Rectangle(172, 203, 155, 21));\r
+        colour.setBounds(new Rectangle(172, 225, 155, 21));\r
         colourLabel.setFont(verdana11);\r
         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         colourLabel.setText("Colour ");\r
@@ -207,14 +208,14 @@ public class GPreferences extends JPanel
         fontNameCB.setFont(verdana11);\r
         fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));\r
         gapSymbolCB.setFont(verdana11);\r
-        gapSymbolCB.setBounds(new Rectangle(172, 179, 69, 21));\r
+        gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));\r
         startupCheckbox.setText("Open file");\r
     startupCheckbox.setFont(verdana11);\r
         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
         startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
         startupCheckbox.setSelected(true);\r
         startupFileTextfield.setFont(verdana11);\r
-        startupFileTextfield.setBounds(new Rectangle(172, 249, 270, 20));\r
+        startupFileTextfield.setBounds(new Rectangle(172, 273, 270, 20));\r
         startupFileTextfield.addMouseListener(new MouseAdapter()\r
             {\r
                 public void mouseClicked(MouseEvent e)\r
@@ -312,14 +313,14 @@ public class GPreferences extends JPanel
     jPanel1.setBorder(titledBorder1);\r
     jPanel1.setLayout(gridBagLayout1);\r
     sortby.setFont(verdana11);\r
-    sortby.setBounds(new Rectangle(172, 225, 155, 21));\r
+    sortby.setBounds(new Rectangle(172, 249, 155, 21));\r
     sortLabel.setFont(verdana11);\r
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
     sortLabel.setText("Sort by ");\r
-    jPanel2.setBounds(new Rectangle(7, 17, 158, 257));\r
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 278));\r
     jPanel2.setLayout(gridLayout2);\r
-    gridLayout2.setRows(11);\r
-    jPanel3.setBounds(new Rectangle(169, 39, 274, 26));\r
+    gridLayout2.setRows(12);\r
+    jPanel3.setBounds(new Rectangle(173, 35, 274, 26));\r
     exportTab.setLayout(null);\r
     epsLabel.setFont(verdana11);\r
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -385,26 +386,30 @@ public class GPreferences extends JPanel
     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);\r
     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);\r
     rightAlign.setText("Right Align Ids");\r
+    idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    idItalics.setHorizontalAlignment(SwingConstants.RIGHT);\r
+    idItalics.setHorizontalTextPosition(SwingConstants.LEADING);\r
+    idItalics.setText("Sequence Name Italics");\r
     jPanel2.add(fullScreen);\r
-\r
     jPanel2.add(annotations);\r
     jPanel2.add(seqLimit);\r
     jPanel2.add(rightAlign);\r
     jPanel2.add(fontLabel);\r
+    jPanel2.add(idItalics);\r
     jPanel2.add(smoothFont);\r
     jPanel2.add(wrap);\r
     jPanel2.add(gapLabel);\r
     jPanel2.add(colourLabel);\r
     jPanel2.add(sortLabel);\r
     jPanel2.add(startupCheckbox);\r
-    visualTab.add(fontNameCB);\r
-    visualTab.add(fontSizeCB);\r
-    visualTab.add(fontStyleCB);\r
     visualTab.add(startupFileTextfield);\r
-    visualTab.add(gapSymbolCB);\r
-    visualTab.add(colour);\r
     visualTab.add(sortby);\r
+    visualTab.add(colour);\r
+    visualTab.add(gapSymbolCB);\r
     visualTab.add(jPanel3);\r
+    visualTab.add(fontNameCB);\r
+    visualTab.add(fontSizeCB);\r
+    visualTab.add(fontStyleCB);\r
     jPanel3.add(conservation);\r
     jPanel3.add(identity);\r
     jPanel3.add(quality);\r
@@ -543,4 +548,5 @@ public class GPreferences extends JPanel
       proxyServerTB.setEnabled(useProxy.isSelected());\r
       proxyPortTB.setEnabled(useProxy.isSelected());\r
   }\r
+\r
 }\r