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No more dbprefix
[jalview.git]
/
src
/
jalview
/
jbgui
/
GPreferences.java
diff --git
a/src/jalview/jbgui/GPreferences.java
b/src/jalview/jbgui/GPreferences.java
index
7cca77c
..
2001efd
100755
(executable)
--- a/
src/jalview/jbgui/GPreferences.java
+++ b/
src/jalview/jbgui/GPreferences.java
@@
-42,8
+42,7
@@
public class GPreferences extends JPanel
BorderLayout borderLayout1 = new BorderLayout();
\r
protected JCheckBox quality = new JCheckBox();
\r
JPanel visualTab = new JPanel();
\r
BorderLayout borderLayout1 = new BorderLayout();
\r
protected JCheckBox quality = new JCheckBox();
\r
JPanel visualTab = new JPanel();
\r
- protected JCheckBox dbRef = new JCheckBox();
\r
- protected JCheckBox fullScreen = new JCheckBox();
\r
+ protected JCheckBox fullScreen = new JCheckBox();
\r
protected JCheckBox conservation = new JCheckBox();
\r
protected JCheckBox identity = new JCheckBox();
\r
protected JCheckBox annotations = new JCheckBox();
\r
protected JCheckBox conservation = new JCheckBox();
\r
protected JCheckBox identity = new JCheckBox();
\r
protected JCheckBox annotations = new JCheckBox();
\r
@@
-98,7
+97,6
@@
public class GPreferences extends JPanel
protected JCheckBox msfjv = new JCheckBox();
\r
protected JCheckBox fastajv = new JCheckBox();
\r
protected JCheckBox pfamjv = new JCheckBox();
\r
protected JCheckBox msfjv = new JCheckBox();
\r
protected JCheckBox fastajv = new JCheckBox();
\r
protected JCheckBox pfamjv = new JCheckBox();
\r
- JLabel jLabel11 = new JLabel();
\r
FlowLayout flowLayout1 = new FlowLayout();
\r
protected JCheckBox pirjv = new JCheckBox();
\r
JPanel jPanel11 = new JPanel();
\r
FlowLayout flowLayout1 = new FlowLayout();
\r
protected JCheckBox pirjv = new JCheckBox();
\r
JPanel jPanel11 = new JPanel();
\r
@@
-152,11
+150,6
@@
public class GPreferences extends JPanel
quality.setText("Quality");
\r
visualTab.setBorder(new TitledBorder("Open new alignment"));
\r
visualTab.setLayout(null);
\r
quality.setText("Quality");
\r
visualTab.setBorder(new TitledBorder("Open new alignment"));
\r
visualTab.setLayout(null);
\r
- dbRef.setFont(verdana11);
\r
- dbRef.setHorizontalAlignment(SwingConstants.RIGHT);
\r
- dbRef.setHorizontalTextPosition(SwingConstants.LEFT);
\r
- dbRef.setMargin(new Insets(4, 2, 2, 0));
\r
- dbRef.setText("DB prefix (DB|AccNo)");
\r
fullScreen.setFont(verdana11);
\r
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
\r
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
\r
fullScreen.setFont(verdana11);
\r
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
\r
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
\r
@@
-327,13
+320,10
@@
public class GPreferences extends JPanel
epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
\r
jLabel1.setFont(verdana11);
\r
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
\r
epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
\r
jLabel1.setFont(verdana11);
\r
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
\r
- jLabel1.setText("/start-end suffix");
\r
+ jLabel1.setText("Append /start-end (/15-380)");
\r
jLabel1.setFont(verdana11);
\r
fastajv.setFont(verdana11);
\r
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
\r
jLabel1.setFont(verdana11);
\r
fastajv.setFont(verdana11);
\r
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
\r
- jLabel11.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
\r
- jLabel11.setHorizontalAlignment(SwingConstants.CENTER);
\r
- jLabel11.setText("(/15-380)");
\r
clustaljv.setText("Clustal ");
\r
blcjv.setText("BLC ");
\r
fastajv.setText("Fasta ");
\r
clustaljv.setText("Clustal ");
\r
blcjv.setText("BLC ");
\r
fastajv.setText("Fasta ");
\r
@@
-345,7
+335,7
@@
public class GPreferences extends JPanel
pirjv.setText("PIR ");
\r
jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
jPanel11.setBorder(titledBorder2);
\r
pirjv.setText("PIR ");
\r
jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
jPanel11.setBorder(titledBorder2);
\r
- jPanel11.setBounds(new Rectangle(63, 70, 137, 182));
\r
+ jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
\r
jPanel11.setLayout(gridLayout3);
\r
blcjv.setFont(verdana11);
\r
blcjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
jPanel11.setLayout(gridLayout3);
\r
blcjv.setFont(verdana11);
\r
blcjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
@@
-358,13
+348,13
@@
public class GPreferences extends JPanel
pirjv.setFont(verdana11);
\r
pirjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
pirjv.setFont(verdana11);
\r
pirjv.setHorizontalAlignment(SwingConstants.LEFT);
\r
seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
\r
seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);
\r
seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);
\r
- seqLimit.setText("Sequence Limits (/1-350)");
\r
- seqLimit.setBounds(new Rectangle(172, 82, 195, 23));
\r
- gridLayout3.setRows(9);
\r
+ seqLimit.setText("Full Sequence Id");
\r
+ gridLayout3.setRows(8);
\r
jPanel2.add(fullScreen);
\r
jPanel2.add(annotations);
\r
jPanel2.add(fullScreen);
\r
jPanel2.add(annotations);
\r
- jPanel2.add(dbRef);
\r
+ jPanel2.add(seqLimit);
\r
jPanel2.add(fontLabel);
\r
jPanel2.add(gapLabel);
\r
jPanel2.add(colourLabel);
\r
jPanel2.add(fontLabel);
\r
jPanel2.add(gapLabel);
\r
jPanel2.add(colourLabel);
\r
@@
-372,7
+362,6
@@
public class GPreferences extends JPanel
jPanel2.add(startupCheckbox);
\r
visualTab.add(gapSymbolCB);
\r
visualTab.add(colour);
\r
jPanel2.add(startupCheckbox);
\r
visualTab.add(gapSymbolCB);
\r
visualTab.add(colour);
\r
- visualTab.add(seqLimit);
\r
visualTab.add(jPanel3);
\r
jPanel3.add(conservation);
\r
jPanel3.add(identity);
\r
visualTab.add(jPanel3);
\r
jPanel3.add(conservation);
\r
jPanel3.add(identity);
\r
@@
-436,7
+425,6
@@
public class GPreferences extends JPanel
tabbedPane.add(connectTab,"Connections");
\r
tabbedPane.add(exportTab, "Output");
\r
jPanel11.add(jLabel1);
\r
tabbedPane.add(connectTab,"Connections");
\r
tabbedPane.add(exportTab, "Output");
\r
jPanel11.add(jLabel1);
\r
- jPanel11.add(jLabel11);
\r
jPanel11.add(blcjv);
\r
jPanel11.add(clustaljv);
\r
jPanel11.add(fastajv);
\r
jPanel11.add(blcjv);
\r
jPanel11.add(clustaljv);
\r
jPanel11.add(fastajv);
\r