Wrap alignment added to preferences

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c61c799..7921ed2 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1308,7 +1308,7 @@ public class AlignFrame
    *\r
    * @param e DOCUMENT ME!\r
    */\r
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+  public void wrapMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index ba1e85e..d89d3be 100755 (executable)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -166,6 +166,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                                      AlignFrame.NEW_WINDOW_HEIGHT);\r
             af.statusBar.setText("Successfully pasted alignment file");\r
 \r
+            if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
+            {\r
+              af.wrapMenuItem.setSelected(true);\r
+              af.wrapMenuItem_actionPerformed(null);\r
+            }\r
             try\r
             {\r
               af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 09f4b3a..6ac9b76 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -624,7 +624,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 \r
     public void inputSequence_actionPerformed(ActionEvent e)\r
     {\r
-      SequenceFetcher sf = new SequenceFetcher(null);\r
+      new SequenceFetcher(null);\r
     }\r
 }\r
 \r

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 92f1f5b..b7905e3 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -128,6 +128,8 @@ public class Preferences extends GPreferences
 \r
         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
 \r
+        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
+\r
         gapSymbolCB.addItem("-");\r
         gapSymbolCB.addItem(".");\r
 \r
@@ -218,6 +220,8 @@ public class Preferences extends GPreferences
 \r
       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
 \r
+      Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r
+\r
       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));\r
 \r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 19ee273..79d55fd 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -552,7 +552,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                       sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +\r
                                      features[i].getEnd());\r
                       if (features[i].links != null)\r
-                      sbuffer.append("<img src=\"" + linkImageURL + "\">");\r
+                      sbuffer.append(" <img src=\"" + linkImageURL + "\">");\r
                     }\r
                   }\r
                   else\r
@@ -574,7 +574,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                       sbuffer.append("; (" + features[i].getStatus() + ")");\r
                     }\r
                     if (features[i].links != null)\r
-                      sbuffer.append("<img src=\"" + linkImageURL + "\">");\r
+                      sbuffer.append(" <img src=\"" + linkImageURL + "\">");\r
 \r
                   }\r
                 }\r

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 7b25531..6bdba4a 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -373,6 +373,12 @@ public class SequenceFetcher
                                    AlignFrame.NEW_WINDOW_WIDTH,\r
                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
           af.statusBar.setText("Successfully pasted alignment file");\r
+          if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
+          {\r
+            af.wrapMenuItem.setSelected(true);\r
+            af.wrapMenuItem_actionPerformed(null);\r
+          }\r
+\r
           try\r
           {\r
             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3aaba9e..f720804 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -164,6 +164,11 @@ public class FileLoader
             Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
                                      AlignFrame.NEW_WINDOW_HEIGHT);\r
 \r
+            if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
+            {\r
+              af.wrapMenuItem.setSelected(true);\r
+              af.wrapMenuItem_actionPerformed(null);\r
+            }\r
             try\r
             {\r
               af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 3ca4c79..8c1eea1 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -24,7 +24,8 @@ import javax.swing.*;
 import javax.swing.border.TitledBorder;\r
 import java.awt.event.*;\r
 import javax.swing.event.*;\r
-\r
+import java.awt.Font;\r
+import java.awt.Rectangle;\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -110,6 +111,7 @@ public class GPreferences extends JPanel
   protected JCheckBox modellerOutput = new JCheckBox();\r
   protected JPanel dasPanel = new JPanel();\r
   BorderLayout borderLayout4 = new BorderLayout();\r
+  protected JCheckBox wrap = new JCheckBox();\r
   /**\r
      * Creates a new GPreferences object.\r
      */\r
@@ -191,7 +193,7 @@ public class GPreferences extends JPanel
         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         gapLabel.setText("Gap Symbol ");\r
     colour.setFont(verdana11);\r
-        colour.setBounds(new Rectangle(171, 180, 155, 21));\r
+        colour.setBounds(new Rectangle(172, 188, 155, 21));\r
         colourLabel.setFont(verdana11);\r
         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         colourLabel.setText("Colour ");\r
@@ -199,13 +201,13 @@ public class GPreferences extends JPanel
         fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         fontLabel.setText("Font ");\r
     fontSizeCB.setFont(verdana11);\r
-        fontSizeCB.setBounds(new Rectangle(318, 100, 49, 21));\r
+        fontSizeCB.setBounds(new Rectangle(317, 92, 49, 21));\r
         fontStyleCB.setFont(verdana11);\r
-        fontStyleCB.setBounds(new Rectangle(366, 100, 70, 21));\r
+        fontStyleCB.setBounds(new Rectangle(364, 92, 70, 21));\r
         fontNameCB.setFont(verdana11);\r
-        fontNameCB.setBounds(new Rectangle(171, 100, 147, 21));\r
+        fontNameCB.setBounds(new Rectangle(171, 92, 147, 21));\r
         gapSymbolCB.setFont(verdana11);\r
-        gapSymbolCB.setBounds(new Rectangle(171, 153, 69, 21));\r
+        gapSymbolCB.setBounds(new Rectangle(172, 163, 69, 21));\r
         startupCheckbox.setText("Open file");\r
     startupCheckbox.setFont(verdana11);\r
         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -310,14 +312,14 @@ public class GPreferences extends JPanel
     jPanel1.setBorder(titledBorder1);\r
     jPanel1.setLayout(gridBagLayout1);\r
     sortby.setFont(verdana11);\r
-    sortby.setBounds(new Rectangle(171, 208, 155, 21));\r
+    sortby.setBounds(new Rectangle(171, 213, 155, 21));\r
     sortLabel.setFont(verdana11);\r
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
     sortLabel.setText("Sort by ");\r
     jPanel2.setBounds(new Rectangle(7, 17, 158, 245));\r
     jPanel2.setLayout(gridLayout2);\r
-    gridLayout2.setRows(9);\r
-    jPanel3.setBounds(new Rectangle(167, 41, 274, 26));\r
+    gridLayout2.setRows(10);\r
+    jPanel3.setBounds(new Rectangle(169, 39, 274, 26));\r
     exportTab.setLayout(null);\r
     epsLabel.setFont(verdana11);\r
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -374,24 +376,29 @@ public class GPreferences extends JPanel
     modellerOutput.setText("Use Modeller Output");\r
     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));\r
     dasPanel.setLayout(borderLayout4);\r
+    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    wrap.setHorizontalAlignment(SwingConstants.TRAILING);\r
+    wrap.setHorizontalTextPosition(SwingConstants.LEADING);\r
+    wrap.setText("Wrap Alignment");\r
     jPanel2.add(fullScreen);\r
 \r
     jPanel2.add(annotations);\r
     jPanel2.add(seqLimit);\r
     jPanel2.add(fontLabel);\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(colour);\r
-    visualTab.add(gapSymbolCB);\r
-    visualTab.add(startupFileTextfield);\r
     visualTab.add(sortby);\r
+    visualTab.add(gapSymbolCB);\r
+    visualTab.add(colour);\r
     visualTab.add(fontNameCB);\r
     visualTab.add(fontSizeCB);\r
     visualTab.add(fontStyleCB);\r
     visualTab.add(jPanel3);\r
+    visualTab.add(startupFileTextfield);\r
     jPanel3.add(conservation);\r
     jPanel3.add(identity);\r
     jPanel3.add(quality);\r