X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=31277319d6333abfe6c5be9e65270eb2f8942a8c;hb=f6d1305378fa256a42caf7d284b13d5a084bc471;hp=ce87c01785119785c4123c42961e5653e8c4bd98;hpb=772387bbccde43cd52ccfadb854d45b1c27f3324;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ce87c01..3127731 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -302,7 +302,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * Calculate the width of the alignment labels based on the displayed names
-   * and any bounds on label width set in preferences.
+   * and any bounds on label width set in preferences. Also includes annotations
+   * not actually visible.
+   * 
+   * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation
+   * label decorators and only called during tests
    * 
    * @param maxwidth
    *          -1 or maximum width allowed for IdWidth
@@ -313,7 +317,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return calculateIdWidth(maxwidth, true, false);
   }
-
+  /**
+   * Calculate the width of the alignment labels based on the displayed names
+   * and any bounds on label width set in preferences.
+   * 
+   * @param maxwidth
+   *          -1 or maximum width allowed for IdWidth
+   * @param includeAnnotations - when true includes width of any additional marks in annotation id panel 
+   * @param visibleOnly -  
+   * @return Dimension giving the maximum width of the alignment label panel
+   *         that should be used.
+   */
   public Dimension calculateIdWidth(int maxwidth,
           boolean includeAnnotations, boolean visibleOnly)
   {
@@ -338,28 +352,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // Also check annotation label widths
     if (includeAnnotations && al.getAlignmentAnnotation() != null)
     {
-      if (Jalview.isHeadlessMode())
-      {
-        AnnotationLabels aal = getAlabels();
-        int stringWidth = aal.drawLabels(null, false, idWidth, false, false, fm);
-        idWidth = Math.max(idWidth, stringWidth);
-      }
-      else
-      {
-        fm = c.getFontMetrics(getAlabels().getFont());
-
-        for (i = 0; i < al.getAlignmentAnnotation().length; i++)
-        {
-          AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
-          if (visibleOnly && !aa.visible)
-          {
-            continue;
-          }
-          String label = aa.label;
-          int stringWidth = fm.stringWidth(label);
-          idWidth = Math.max(idWidth, stringWidth);
-        }
-      }
+      AnnotationLabels aal = getAlabels();
+      int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
+              fm, !visibleOnly);
+      idWidth = Math.max(idWidth, stringWidth);
     }
 
     int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
@@ -997,8 +993,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
           Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
-    final int idWidth = getVisibleIdWidth(false);
-
+    final int idWidth, idWidthForGui;
+    // otherwise calculate it
+    idWidth = getVisibleIdWidth(false);
+//    if (getIdPanel()!=null && getIdPanel().getWidth()>0)
+//    {
+//      // use the current IdPanel's width, if its set and non-zero
+//      idWidthForGui = getIdPanel().getWidth();
+//    } else {
+//      idWidthForGui=0;
+//    }
     /*
      * Get the horizontal offset to where we draw the sequences.
      * This is idWidth if using a single Graphics context, else zero.
@@ -1047,6 +1051,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
 
+    alignmentGraphics.setColor(Color.white);
+    alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight+scaleHeight);
+
     /*
      * draw the Scale at horizontal offset, then reset to top left (0, 0)
      */
@@ -1063,8 +1070,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     IdCanvas idCanvas = getIdPanel().getIdCanvas();
     List<SequenceI> selection = av.getSelectionGroup() == null ? null
             : av.getSelectionGroup().getSequences(null);
+    
     idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
-            selection, false);
+            selection, false,idWidth);
 
     idGraphics.setFont(av.getFont());
     idGraphics.translate(0, -scaleHeight);
@@ -1211,7 +1219,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // see if rendering offscreen - check preferences and calc width accordingly
     if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
     {
-      return calculateIdWidth(-1).width;
+      return calculateIdWidth(-1,true,true).width;
     }
     Integer idwidth = onscreen ? null
             : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
@@ -1229,7 +1237,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           throws ImageOutputException
   {
     makeAlignmentImage(type, file, renderer,
-            BitmapImageSizing.nullBitmapImageSizing());
+            BitmapImageSizing.defaultBitmapImageSizing());
   }
 
   /**