Merge branch 'develop' into patch/JAL-4281_idwidthandannotHeight_in_project

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c5c7ae9..fe6477e 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -313,7 +313,11 @@ 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
@@ -324,14 +328,13 @@ 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, annotation label widths are also accounted for
+   * @param includeAnnotations - when true includes width of any additional marks in annotation id panel 
    * @param visibleOnly - when true, ignore label widths for hidden annotation rows 
    * @return Dimension giving the maximum width of the alignment label panel
    *         that should be used.
@@ -379,7 +382,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (!legacy || Jalview.isHeadlessMode())
       {
         AnnotationLabels aal = getAlabels();
-        int stringWidth = aal.drawLabels(null, false, idWidth, false, false, fm);
+        int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
+                fm, !visibleOnly);
         idWidth = Math.max(idWidth, stringWidth);
       }
       else
@@ -1033,8 +1037,16 @@ 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.
@@ -1083,6 +1095,9 @@ 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)
      */
@@ -1099,8 +1114,9 @@ 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);
@@ -1247,7 +1263,7 @@ 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");
@@ -1265,7 +1281,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           throws ImageOutputException
   {
     makeAlignmentImage(type, file, renderer,
-            BitmapImageSizing.nullBitmapImageSizing());
+            BitmapImageSizing.defaultBitmapImageSizing());
   }
 
   /**