JAL-1152 prototype of new Annotations menu with sort options

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d9c0c6a..a048721 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter;
 import jalview.analysis.Conservation;
 import jalview.analysis.CrossRef;
 import jalview.analysis.NJTree;
@@ -377,7 +378,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
                 && Character.isDigit(evt.getKeyChar()))
+        {
           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+        }
 
         switch (evt.getKeyCode())
         {
@@ -389,32 +392,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         case KeyEvent.VK_DOWN:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             moveSelectedSequences(false);
+          }
           if (viewport.cursorMode)
+          {
             alignPanel.seqPanel.moveCursor(0, 1);
+          }
           break;
 
         case KeyEvent.VK_UP:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             moveSelectedSequences(true);
+          }
           if (viewport.cursorMode)
+          {
             alignPanel.seqPanel.moveCursor(0, -1);
+          }
 
           break;
 
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+          }
           else
+          {
             alignPanel.seqPanel.moveCursor(-1, 0);
+          }
 
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+          }
           else
+          {
             alignPanel.seqPanel.moveCursor(1, 0);
+          }
           break;
 
         case KeyEvent.VK_SPACE:
@@ -551,14 +570,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
+          }
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
+          }
           break;
         }
       }
@@ -1458,7 +1481,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.historyList.empty())
+    {
       return;
+    }
     CommandI command = (CommandI) viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand(getViewAlignments());
@@ -1611,37 +1636,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
     {
       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+      {
         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+      }
     }
 
     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
 
     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
     for (int i = 0; i < invertGroup.size(); i++)
+    {
       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+    }
 
     SlideSequencesCommand ssc;
     if (right)
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
               size, viewport.getGapCharacter());
+    }
     else
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
               size, viewport.getGapCharacter());
+    }
 
     int groupAdjustment = 0;
     if (ssc.getGapsInsertedBegin() && right)
     {
       if (viewport.cursorMode)
+      {
         alignPanel.seqPanel.moveCursor(size, 0);
+      }
       else
+      {
         groupAdjustment = size;
+      }
     }
     else if (!ssc.getGapsInsertedBegin() && !right)
     {
       if (viewport.cursorMode)
+      {
         alignPanel.seqPanel.moveCursor(-size, 0);
+      }
       else
+      {
         groupAdjustment = -size;
+      }
     }
 
     if (groupAdjustment != 0)
@@ -1662,7 +1703,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (!appendHistoryItem)
+    {
       addHistoryItem(ssc);
+    }
 
     repaint();
   }
@@ -1997,7 +2040,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
             if (sann == null)
+            {
               continue;
+            }
             for (int avnum = 0; avnum < alview.length; avnum++)
             {
               if (alview[avnum] != alignment)
@@ -4643,7 +4688,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               if (ds.getSequences() == null
                       || !ds.getSequences().contains(
                               sprods[s].getDatasetSequence()))
+              {
                 ds.addSequence(sprods[s].getDatasetSequence());
+              }
               sprods[s].updatePDBIds();
             }
             Alignment al = new Alignment(sprods);
@@ -5734,6 +5781,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     this.alignPanel.paintAlignment(true);
   }
+
+  @Override
+  protected void sortAnnotationsByType_actionPerformed()
+  {
+    AnnotationSorter sorter = new AnnotationSorter(
+            this.alignPanel.getAlignment());
+    sorter.sortByTypeAndSequence(this.alignPanel.getAlignment()
+            .getAlignmentAnnotation());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  @Override
+  protected void sortAnnotationsBySequence_actionPerformed()
+  {
+    AnnotationSorter sorter = new AnnotationSorter(
+            this.alignPanel.getAlignment());
+    sorter.sortBySequenceAndType(this.alignPanel.getAlignment()
+            .getAlignmentAnnotation());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
 }
 
 class PrintThread extends Thread