finer column label format control and new 'scale label to column' format for annotati...

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index a34f8f5..3ea788b 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -38,6 +38,8 @@ import jalview.io.*;
 public class AnnotationLabels extends JPanel implements MouseListener,
         MouseMotionListener, ActionListener
 {
+  static String TOGGLE_LABELSCALE = "Scale Label to Column";
+
   static String ADDNEW = "Add New Row";
 
   static String EDITNAME = "Edit Label/Description";
@@ -227,6 +229,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       }
 
     }
+    else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+    {
+      aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; 
+    }
 
     ap.annotationPanel.adjustPanelHeight();
     ap.annotationScroller.validate();
@@ -491,46 +497,72 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     item.addActionListener(this);
     pop.add(item);
     // TODO: annotation object should be typed for autocalculated/derived property methods
-    if (selectedRow < aa.length && aa[selectedRow].autoCalculated && aa[selectedRow].label.indexOf("Consensus")>-1)
-    {
-      pop.addSeparator();
-      // av and sequencegroup need to implement same interface for 
-      final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-              "Ignore Gaps In Consensus", (aa[selectedRow].groupRef!=null) ? aa[selectedRow].groupRef.getIgnoreGapsConsensus() : ap.av.getIgnoreGapsConsensus());
-      final AlignmentAnnotation aaa = aa[selectedRow];
-      cbmi.addActionListener(new ActionListener()
+    if (selectedRow < aa.length)
+    {
+      if (!aa[selectedRow].autoCalculated)
       {
-        public void actionPerformed(ActionEvent e)
-        {
-          if (aaa.groupRef!=null)
-          {
-            aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); // TODO: pass on reference to ap so the view can be updated.
-            ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-          } else {
-            ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
-          }
-        }
-      });
-      pop.add(cbmi);
-      // av and sequencegroup need to implement same interface for 
-      if (aaa.groupRef!=null) {
-        final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                "Show Full Profile", aa[selectedRow].groupRef.isIncludeAllConsSymbols());
-        cprof.addActionListener(new ActionListener()
+        // display settings for this row.
+        pop.addSeparator();
+        // av and sequencegroup need to implement same interface for
+        item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+                aa[selectedRow].scaleColLabel);
+        item.addActionListener(this);
+        pop.add(item);
+      }
+      else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+      {
+        pop.addSeparator();
+        // av and sequencegroup need to implement same interface for
+        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+                "Ignore Gaps In Consensus",
+                (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+                        .getIgnoreGapsConsensus()
+                        : ap.av.getIgnoreGapsConsensus());
+        final AlignmentAnnotation aaa = aa[selectedRow];
+        cbmi.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent e)
           {
-            aaa.groupRef.setIncludeAllConsSymbols(cprof.getState()); // TODO: pass on reference to ap so the view can be updated.
-            ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            if (aaa.groupRef != null)
+            {
+           // TODO: pass on reference to ap so the view can be updated.
+              aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); 
+              ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+            else
+            {
+              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+            }
           }
         });
-        pop.add(cprof);
+        pop.add(cbmi);
+        // av and sequencegroup need to implement same interface for
+        if (aaa.groupRef != null)
+        {
+          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+                  "Show Full Profile", aa[selectedRow].groupRef
+                          .isIncludeAllConsSymbols());
+          cprof.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+              ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprof);
+        }
+        final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+        consclipbrd.addActionListener(this);
+        pop.add(consclipbrd);
       }
-      final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
-      consclipbrd.addActionListener(this);
-      pop.add(consclipbrd);
     }
-
     pop.show(this, evt.getX(), evt.getY());
   }
 

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index c3984f2..42ca1b6 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -335,7 +335,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 || label2.equals(LABEL))
         {
           tlabel = anot[index].description;
-          if (tlabel == null)
+          if (tlabel == null || tlabel.length()<1)
           {
             if (label2.equals(HELIX) || label2.equals(SHEET))
             {
@@ -771,8 +771,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     int iconOffset = 0;
     boolean validRes = false;
     boolean validEnd = false;
+    boolean labelAllCols = false;
+    boolean centreColLabels,centreColLabelsDef = av.getCentreColumnLabels();
+    boolean scaleColLabel=false;
     boolean[] graphGroupDrawn = new boolean[aa.length];
-
+    int charOffset = 0; // offset for a label
+    float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a column.
+    Font ofont = g.getFont();
     // \u03B2 \u03B1
     for (int i = 0; i < aa.length; i++)
     {
@@ -782,7 +787,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       {
         continue;
       }
-
+      centreColLabels = row.centreColLabels || centreColLabelsDef;
+      labelAllCols = row.showAllColLabels;
+      scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
       lastSSX = 0;
 
@@ -899,15 +906,31 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 && row.annotations[column].displayCharacter != null
                 && (row.annotations[column].displayCharacter.length() > 0))
         {
-
-          int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm
-                  .charsWidth(row.annotations[column].displayCharacter
-                          .toCharArray(), 0,
-                          row.annotations[column].displayCharacter.length())) / 2)
-                  : (av.charWidth - fm
-                          .charWidth(row.annotations[column].displayCharacter
-                                  .charAt(0))) / 2;
-
+          
+          if (centreColLabels || scaleColLabel)
+          {
+            fmWidth = (float) fm
+            .charsWidth(row.annotations[column].displayCharacter
+                    .toCharArray(), 0,
+                    row.annotations[column].displayCharacter.length());
+
+            if ( scaleColLabel ) { 
+              // justify the label and scale to fit in column
+              if (fmWidth > av.charWidth) {
+                // scale only if the current font isn't already small enough
+                fmScaling = av.charWidth;
+                fmScaling /= fmWidth;
+                g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(fmScaling, 1.0)));
+                // and update the label's width to reflect the scaling.
+                fmWidth = av.charWidth;
+              }
+            }
+          } else {
+            fmWidth = (float) fm
+            .charWidth(row.annotations[column].displayCharacter.charAt(0));
+          }
+          charOffset =  (int) ((av.charWidth - fmWidth) / 2f);
+          
           if (row.annotations[column].colour == null)
             g.setColor(Color.black);
           else
@@ -919,13 +942,14 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     (x * av.charWidth) + charOffset, y + iconOffset);
           }
           else if (row.annotations[column - 1] == null
-                  || (!row.annotations[column].displayCharacter
+                  || (labelAllCols||!row.annotations[column].displayCharacter
                           .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
                           .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
           {
             g.drawString(row.annotations[column].displayCharacter, x
                     * av.charWidth + charOffset, y + iconOffset);
           }
+          g.setFont(ofont);
         }
 
         if (row.hasIcons)