Merge branch 'develop' into features/r2_11_2_alphafold/JAL-2349_JAL-3855

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 9976604..804ab7b 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,23 +20,6 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
-import jalview.analysis.AlignSeq;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Dimension;
@@ -56,6 +39,7 @@ import java.awt.geom.AffineTransform;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Iterator;
+import java.util.Locale;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenuItem;
@@ -64,6 +48,21 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * The panel that holds the labels for alignment annotations, providing
  * tooltips, context menus, drag to reorder rows, and drag to adjust panel
@@ -293,25 +292,21 @@ public class AnnotationLabels extends JPanel
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, name, description);
 
-    dialog.showDialog(ap.alignFrame, title, new Runnable()
-    {
-      @Override
-      public void run()
+    dialog.showDialog(ap.alignFrame, title, () -> {
+      annotation.label = dialog.getName();
+      String text = dialog.getDescription();
+      if (text != null && text.length() == 0)
       {
-        annotation.label = dialog.getName();
-        String text = dialog.getDescription();
-        if (text != null && text.length() == 0)
-        {
-          text = null;
-        }
-        annotation.description = text;
-        if (addNew)
-        {
-          ap.av.getAlignment().addAnnotation(annotation);
-          ap.av.getAlignment().setAnnotationIndex(annotation, 0);
-        }
-        ap.refresh(true);
+        text = null;
+      }
+      annotation.description = text;
+      if (addNew)
+      {
+        ap.av.getAlignment().addAnnotation(annotation);
+        ap.av.getAlignment().setAnnotationIndex(annotation, 0);
       }
+      ap.refresh(true);
+      return null;
     });
   }
 
@@ -1060,7 +1055,7 @@ public class AnnotationLabels extends JPanel
 
     g.translate(0, getScrollOffset());
     g.setColor(Color.black);
-
+    SequenceI lastSeqRef = null;
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
@@ -1139,8 +1134,22 @@ public class AnnotationLabels extends JPanel
         {
           offset += fm.getDescent();
         }
-
-        x = width - fm.stringWidth(aa[i].label) - 3;
+        String label = aa[i].label;
+        boolean vertBar = false;
+        if (aa[i].sequenceRef != null)
+        {
+          if (aa[i].sequenceRef != lastSeqRef)
+          {
+            label = aa[i].sequenceRef.getName() + " " + label;
+            // TODO record relationship between sequence and this annotation and
+            // display it here
+          }
+          else
+          {
+            vertBar = true;
+          }
+        }
+        x = width - fm.stringWidth(label) - 3;
 
         if (aa[i].graphGroup > -1)
         {
@@ -1208,16 +1217,26 @@ public class AnnotationLabels extends JPanel
         }
         else
         {
-          g.drawString(aa[i].label, x, y + offset);
+          if (vertBar)
+          {
+            g.drawLine(20, y + offset, 20, y - aa[i].height);
+            g.drawLine(20, y + offset, x - 20, y + offset);
+
+          }
+          g.drawString(label, x, y + offset);
         }
+        lastSeqRef = aa[i].sequenceRef;
       }
     }
 
     if (!resizePanel && dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
-      g.drawString(aa[selectedRow].label, dragEvent.getX(),
-              dragEvent.getY() - getScrollOffset());
+      g.drawString(
+              (aa[selectedRow].sequenceRef == null ? ""
+                      : aa[selectedRow].sequenceRef.getName())
+                      + aa[selectedRow].label,
+              dragEvent.getX(), dragEvent.getY() - getScrollOffset());
     }
 
     if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))