merge Jan and Lauren's RNA GUI changes into develop (JAL-826)

diff --git a/.externalToolBuilders/Jalview Release indices [Builder].launch b/.externalToolBuilders/Jalview Release indices [Builder].launch
index a5659a6..4c0c7dd 100644 (file)
--- a/.externalToolBuilders/Jalview Release indices [Builder].launch
+++ b/.externalToolBuilders/Jalview Release indices [Builder].launch
@@ -15,7 +15,7 @@
 <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="jalview"/>
 <stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_ANT_TARGETS" value="buildindices,"/>
-<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="false"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="true"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LAUNCH_CONFIGURATION_BUILD_SCOPE" value="${none}"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${build_project}/build.xml"/>
 <stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="full,incremental,"/>

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b61d44b..6a5ab9b 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -662,11 +662,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
+    rnahelicesColour.setEnabled(nucleotide);
+    purinePyrimidineColour.setEnabled(nucleotide);
     // Remember AlignFrame always starts as protein
-    if (!nucleotide)
-    {
-      calculateMenu.remove(calculateMenu.getItemCount() - 2);
-    }
+    //if (!nucleotide)
+   // {
+   //   showTr
+   //   calculateMenu.remove(calculateMenu.getItemCount() - 2);
+   // }
   }
 
   /**
@@ -719,7 +722,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     autoCalculate.setSelected(av.autoCalculateConsensus);
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
-    
+    rnahelicesColour.setEnabled(av.alignment.hasRNAStructure());
+    rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
 
     updateEditMenuBar();

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1cc4cd7..c751494 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -70,6 +70,11 @@ public class PopupMenu extends JPopupMenu
 
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+  // protected JRadioButtonMenuItem covariationColour = new
+  // JRadioButtonMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
@@ -80,7 +85,7 @@ public class PopupMenu extends JPopupMenu
 
   JMenuItem sequenceName = new JMenuItem();
 
-  Sequence sequence;
+  SequenceI sequence;
 
   JMenuItem unGroupMenuItem = new JMenuItem();
 
@@ -157,7 +162,7 @@ public class PopupMenu extends JPopupMenu
    * @param links
    * @param groupLinks
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
+  public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
           Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
@@ -183,6 +188,8 @@ public class PopupMenu extends JPopupMenu
     colours.add(userDefinedColour);
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
+    colours.add(purinePyrimidineColour);
+    // colours.add(covariationColour);
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
@@ -248,10 +255,67 @@ public class PopupMenu extends JPopupMenu
       }
       else
       {
+        if (ap.av.alignment.isNucleotide() == false)
+        {
         structureMenu.remove(viewStructureMenu);
+        }
         // structureMenu.remove(colStructureMenu);
       }
 
+      if (ap.av.alignment.isNucleotide() == true)
+      {
+        AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+        for (int i = 0; i < aa.length; i++)
+        {
+          if (aa[i].getRNAStruc() != null)
+          {
+            final String rnastruc = aa[i].getRNAStruc();
+            
+            menuItem = new JMenuItem();
+            menuItem.setText("RNA structure - consensus");
+            menuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                        .getName(), ap);
+              }
+            });
+            viewStructureMenu.add(menuItem);
+          }
+        }
+
+        // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+        if (seq.getAnnotation() != null)
+        {
+          AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+          for (int i = 0; i < seqAnno.length; i++)
+          {
+            if (seqAnno[i].getRNAStruc() != null)
+            {
+              final String rnastruc = seqAnno[i].getRNAStruc();
+              
+           // TODO: make rnastrucF a bit more nice
+              menuItem = new JMenuItem();
+              menuItem.setText("RNA structure - "+seq.getName());
+              menuItem.addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  // TODO: VARNA does'nt print gaps in the sequence
+                  new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+                          .getName(), ap);
+                }
+              });
+              viewStructureMenu.add(menuItem);
+            }
+          }
+        }
+
+        
+      }
+
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
       {
@@ -371,6 +435,14 @@ public class PopupMenu extends JPopupMenu
       {
         clustalColour.setSelected(true);
       }
+      else if (sg.cs instanceof PurinePyrimidineColourScheme)
+      {
+        purinePyrimidineColour.setSelected(true);
+      }
+      /*
+       * else if (sg.cs instanceof CovariationColourScheme) {
+       * covariationColour.setSelected(true); }
+       */
       else
       {
         noColourmenuItem.setSelected(true);
@@ -1009,6 +1081,10 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
+    if (ap.getAlignment().isNucleotide()) {
+       colourMenu.add(purinePyrimidineColour);
+    }
+    // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
@@ -1160,6 +1236,21 @@ public class PopupMenu extends JPopupMenu
         BLOSUM62Colour_actionPerformed();
       }
     });
+    purinePyrimidineColour.setText("Purine/Pyrimidine");
+    purinePyrimidineColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                purinePyrimidineColour_actionPerformed();
+              }
+            });
+    /*
+     * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+     * public void actionPerformed(ActionEvent e) {
+     * covariationColour_actionPerformed(); } });
+     */
+
     conservationMenuItem.setText("Conservation");
     conservationMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -1299,6 +1390,16 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
+  protected void purinePyrimidineColour_actionPerformed()
+  {
+    getGroup().cs = new PurinePyrimidineColourScheme();
+    refresh();
+  }
+
+  /*
+   * protected void covariationColour_actionPerformed() { getGroup().cs = new
+   * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+   */
   /**
    * DOCUMENT ME!
    * 
@@ -1782,7 +1883,7 @@ public class PopupMenu extends JPopupMenu
   public void discoverPDB_actionPerformed()
   {
 
-    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[]
     { sequence }
             : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
     Thread discpdb = new Thread(new Runnable()

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4f60de3..ab72009 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -222,7 +222,7 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem annotationColour = new JMenuItem();
 
-  JMenuItem rnahelicesColour = new JMenuItem();
+  protected JMenuItem rnahelicesColour = new JMenuItem();
 
   JMenuItem associatedData = new JMenuItem();