ID tooltip preference settings and doc

diff --git a/help/html/releases.html b/help/html/releases.html
index a43909f..ea95696 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -19,7 +19,7 @@
        <tr>
 
                <td>
-               <div align="center"><strong>2.4.1</strong><br>
+               <div align="center"><strong>2.5</strong><br>
                <em>Not Yet Released</em></div>
                </td>
                <td>
@@ -65,6 +65,7 @@
                        <li>Optional automatic sort of associated alignment view when a
                        new tree is opened.</li>
                        <li>Jalview Java Console</li>
+                       <li>New preference items for sequence ID tooltip and consensus annotation</li>
                </ul>
                <em>Applet</em>
                <ul>
@@ -77,8 +78,7 @@
                <ul>
                        <li>Features format: graduated colour definitions and
                        specification of feature scores</li>
-                       <li>XML formats extended to support graduated feature colourschemes</li>
-                       <li>
+                       <li>XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.</li>
                </td>
                <td>
                <ul>

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index f8ad900..ac2c59c 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -127,6 +127,8 @@ public class Preferences extends GPreferences
     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
     showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+    showNpTooltip.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 
     for (int i = 0; i < 13; i++)
     {
@@ -288,6 +290,8 @@ public class Preferences extends GPreferences
     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()));

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4f102ad..77b8938 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -694,7 +694,8 @@ public class SeqCanvas extends JComponent
     for (int i = startSeq; i < endSeq; i++)
     {
       nextSeq = av.alignment.getSequenceAt(i);
-
+      if (nextSeq==null)
+        continue;
       sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
               startRes, endRes, offset + ((i - startSeq) * av.charHeight));
 

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 7bd8f53..98bf8b6 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -193,6 +193,8 @@ public class GPreferences extends JPanel
   protected JCheckBox rightAlign = new JCheckBox();
 
   protected JCheckBox showUnconserved = new JCheckBox();
+  protected JCheckBox showDbRefTooltip = new JCheckBox();
+  protected JCheckBox showNpTooltip = new JCheckBox();
 
   protected JCheckBox idItalics = new JCheckBox();
 
@@ -305,6 +307,18 @@ public class GPreferences extends JPanel
     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
     showGroupConservation.setSelected(true);
     showGroupConservation.setText("Conservation");
+    showNpTooltip.setEnabled(true);
+    showNpTooltip.setFont(verdana11);
+    showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+    showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+    showNpTooltip.setSelected(true);
+    showNpTooltip.setText("Non-positional Features");
+    showDbRefTooltip.setEnabled(true);
+    showDbRefTooltip.setFont(verdana11);
+    showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+    showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+    showDbRefTooltip.setSelected(true);
+    showDbRefTooltip.setText("Database References");
     annotations.setFont(verdana11);
     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
@@ -335,7 +349,6 @@ public class GPreferences extends JPanel
     showUnconserved.setFont(verdana11);
     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
-    //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
     showUnconserved.setSelected(true);
     showUnconserved.setText("Show Unconserved");
     showUnconserved.addActionListener(new ActionListener()
@@ -348,7 +361,6 @@ public class GPreferences extends JPanel
     shareSelections.setFont(verdana11);
     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
-    //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
     shareSelections.setSelected(true);
     shareSelections.setText("Share selection across views");
     followHighlight.setFont(verdana11);
@@ -506,11 +518,6 @@ public class GPreferences extends JPanel
     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
     jPanel2.setLayout(gridLayout2);
     gridLayout2.setRows(13);
-  //  jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
-    //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
-    //jPanel3.setLayout(new GridLayout(3,3));
-//    autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
-//    autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
     exportTab.setLayout(null);
     epsLabel.setFont(verdana11);
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -613,12 +620,9 @@ public class GPreferences extends JPanel
     annsettingsPanel.add(autoAnnotSettings2);
     annsettingsPanel.add(autoAnnotSettings3);
     autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
-//  autoAnnotSettings1.setPreferredSize(new Dimensions())
   autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
   autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
     visualTab.add(annsettingsPanel);
-    //visualTab.add(autoAnnotSettings1);
-    //visualTab.add(autoAnnotSettings2);
     Border jb = new EmptyBorder(1,1,4,5);
     quality.setBorder(jb);
     conservation.setBorder(jb);
@@ -633,19 +637,20 @@ public class GPreferences extends JPanel
     autoAnnotSettings2.add(conservation);
     autoAnnotSettings1.add(quality);
     autoAnnotSettings3.add(identity);
-
-    /*FlowLayout fl = new FlowLayout();
-    fl.setAlignment(FlowLayout.LEFT);
-    autoAnnotSettings1.setLayout(fl);
-    fl = new FlowLayout();
-    fl.setAlignment(FlowLayout.LEFT);
-    autoAnnotSettings2.setLayout(fl); */
-    autoAnnotSettings1.add(showGroupbits);
+autoAnnotSettings1.add(showGroupbits);
     autoAnnotSettings3.add(showGroupConsensus);
     autoAnnotSettings2.add(showGroupConservation);
     autoAnnotSettings1.add(showConsensbits);
     autoAnnotSettings2.add(showConsensHistogram);
     autoAnnotSettings3.add(showConsensLogo);
+
+    JPanel tooltipSettings = new JPanel();
+    tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
+    tooltipSettings.setBounds(173, 130, 200,62);
+    tooltipSettings.setLayout(new GridLayout(2,1));
+    tooltipSettings.add(showDbRefTooltip);
+    tooltipSettings.add(showNpTooltip);
+    visualTab.add(tooltipSettings);
     visualTab.add(jPanel2);
 
     linkPanel.add(editLinkButtons, BorderLayout.EAST);