JAL-244 Added light grey marks to indicate regions to resize the margins

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 26276ae..6006026 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -88,7 +88,7 @@ public class AnnotationLabels extends JPanel
   /**
    * height in pixels for allowing height adjuster to be active
    */
-  private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+  public static int HEIGHT_ADJUSTER_HEIGHT = 10;
 
   private static final Font font = new Font("Arial", Font.PLAIN, 11);
 
@@ -138,6 +138,8 @@ public class AnnotationLabels extends JPanel
 
   private int annotationIdWidth = -1;
 
+  public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK";
+
   /**
    * Creates a new AnnotationLabels object
    * 
@@ -515,8 +517,10 @@ public class AnnotationLabels extends JPanel
           public void actionPerformed(ActionEvent e)
           {
             sel_row.setShowGroupsForContactMatrix(chitem.getState());
-            ap.getAnnotationPanel()
-                    .paint(ap.getAnnotationPanel().getGraphics());
+            // so any annotation colour changes are propagated - though they
+            // probably won't be unless the annotation row colours are removed
+            // too!
+            ap.alignmentChanged();
           }
         });
         pop.add(chitem);
@@ -562,7 +566,10 @@ public class AnnotationLabels extends JPanel
                                 "action.clustering_matrix_for",
                                 cm.getAnnotDescr(), 5f),
                         progBar = System.currentTimeMillis());
-                cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
+                cm.setGroupSet(GroupSet.makeGroups(cm, true));
+                cm.randomlyReColourGroups();
+                cm.transferGroupColorsTo(alignmentAnnotation);
+                ap.alignmentChanged();
                 ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
                 ap.alignFrame.setProgressBar(null, progBar);
               }
@@ -1162,7 +1169,6 @@ public class AnnotationLabels extends JPanel
     }
 
     drawComponent(g2, true, width);
-
   }
 
   /**
@@ -1195,37 +1201,53 @@ public class AnnotationLabels extends JPanel
   public void drawComponent(Graphics g, boolean clip, int givenWidth)
   {
     int width = givenWidth;
-    IdwidthAdjuster iwa = ap.idwidthAdjuster;
-    if ((Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true)
-            || Jalview.isHeadlessMode()))
+    IdwidthAdjuster iwa = null;
+    if (ap != null)
     {
-      Graphics2D g2d = (Graphics2D) g;
-      Graphics dummy = g2d.create();
-      int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
-              null);
-      Dimension d = ap.calculateDefaultAlignmentIdWidth();
-      int alignmentIdWidth = d.width;
-      if (!iwa.manuallyAdjusted())
-      {
-        // If no manual adjustment to ID column with has been made then adjust
-        // width match widest of alignment or annotation id widths
-        width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
-      }
-      else if (newAnnotationIdWidth != annotationIdWidth
-              && newAnnotationIdWidth > givenWidth
-              && newAnnotationIdWidth > alignmentIdWidth)
+      iwa = ap.idwidthAdjuster;
+      if ((Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true)
+              || Jalview.isHeadlessMode()))
       {
-        // otherwise if the annotation id width has become larger than the
-        // current id width, increase
-        width = newAnnotationIdWidth;
-        annotationIdWidth = newAnnotationIdWidth;
-      }
-      // set the width if it's changed
-      if (width != ap.av.getIdWidth())
-      {
-        iwa.setWidth(width);
+        Graphics2D g2d = (Graphics2D) g;
+        Graphics dummy = g2d.create();
+        int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+                null);
+        dummy.dispose();
+        Dimension d = ap.calculateDefaultAlignmentIdWidth();
+        int alignmentIdWidth = d.width;
+        if (iwa != null && !iwa.manuallyAdjusted())
+        {
+          // If no manual adjustment to ID column with has been made then adjust
+          // width match widest of alignment or annotation id widths
+          boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH",
+                  false);
+          width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
+          if (clip && width < givenWidth && !allowShrink)
+          {
+            width = givenWidth;
+          }
+        }
+        else if (newAnnotationIdWidth != annotationIdWidth
+                && newAnnotationIdWidth > givenWidth
+                && newAnnotationIdWidth > alignmentIdWidth)
+        {
+          // otherwise if the annotation id width has become larger than the
+          // current id width, increase
+          width = newAnnotationIdWidth;
+          annotationIdWidth = newAnnotationIdWidth;
+        }
+        // set the width if it's changed
+        if (width != ap.av.getIdWidth())
+        {
+          iwa.setWidth(width);
+        }
       }
     }
+    else
+    {
+      int newAnnotationIdWidth = drawLabels(g, clip, width, false, null);
+      width = Math.max(newAnnotationIdWidth, givenWidth);
+    }
     drawLabels(g, clip, width, true, null);
   }
 
@@ -1247,11 +1269,30 @@ public class AnnotationLabels extends JPanel
    * @param fmetrics
    *          FontMetrics if Graphics object g is null
    */
-  public int drawLabels(Graphics g, boolean clip, int width,
+  public int drawLabels(Graphics g0, boolean clip, int width,
           boolean actuallyDraw, FontMetrics fmetrics)
   {
+    if (clip)
+    {
+      clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS",
+              true);
+    }
+    Graphics g = null;
+    // create a dummy Graphics object if not drawing and one is supplied
+    if (g0 != null)
+    {
+      if (!actuallyDraw)
+      {
+        Graphics2D g2d = (Graphics2D) g0;
+        g = g2d.create();
+      }
+      else
+      {
+        g = g0;
+      }
+    }
     int actualWidth = 0;
-    if (actuallyDraw && g != null)
+    if (g != null)
     {
       if (av.getFont().getSize() < 10)
       {
@@ -1269,6 +1310,17 @@ public class AnnotationLabels extends JPanel
     {
       g.setColor(Color.white);
       g.fillRect(0, 0, getWidth(), getHeight());
+
+      if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false)
+              && !av.getWrapAlignment())
+      {
+        g.setColor(Color.LIGHT_GRAY);
+        g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4,
+                HEIGHT_ADJUSTER_HEIGHT / 4);
+        g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4,
+                HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4);
+
+      }
     }
 
     if (actuallyDraw)