X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fe6477e9b5bff1b8c348a03ba342027aaf9db6a4;hb=1140532d01b32b648e7e5b17ea717ae790625f8f;hp=baf9e2654d8a8223fd16460d20490f6986d98e9e;hpb=56b3e093761bc8b409ffc66fae03d5be40edea89;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index baf9e26..fe6477e 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -256,8 +256,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * Calculates the width of the alignment labels based on the displayed names
-   * and any bounds on label width set in preferences. The calculated width is
-   * also set as a property of the viewport.
+   * and any bounds on label width set in preferences.
+   * 
+   * The calculated width is set as a property of the viewport and the layout is
+   * updated.
    * 
    * @return Dimension giving the maximum width of the alignment label panel
    *         that should be used.
@@ -294,10 +296,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public Dimension calculateDefaultAlignmentIdWidth()
   {
+    return calculateIdWidth(-1, false, false);
+  }
+  /**
+   * pre 2.11.3 Id width calculation - used when importing old projects only
+   * @return
+   */
+  public int getLegacyIdWidth()
+  {
     int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
     int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
     int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
-    return calculateIdWidth(-1, false, false);
+    Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false);
+    return w.width;
   }
 
   /**
@@ -324,13 +335,27 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @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 -  
+   * @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.
    */
   public Dimension calculateIdWidth(int maxwidth,
           boolean includeAnnotations, boolean visibleOnly)
   {
+    return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, visibleOnly);
+  }
+  
+  /**
+   * legacy mode or post 2.11.3 ID width calculation
+   * @param legacy - uses annotation labels, not rendered label width (excludes additional decorators)
+   * @param maxwidth
+   * @param includeAnnotations
+   * @param visibleOnly
+   * @return
+   */
+  private Dimension calculateIdWidthOrLegacy(boolean legacy, int maxwidth,
+          boolean includeAnnotations, boolean visibleOnly)
+  {
     Container c = new Container();
 
     FontMetrics fm = c.getFontMetrics(
@@ -352,17 +377,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // Also check annotation label widths
     if (includeAnnotations && al.getAlignmentAnnotation() != null)
     {
-      if (Jalview.isHeadlessMode())
+      fm = c.getFontMetrics(getAlabels().getFont());
+
+      if (!legacy || Jalview.isHeadlessMode())
       {
         AnnotationLabels aal = getAlabels();
         int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
-                fm,false);
+                fm, !visibleOnly);
         idWidth = Math.max(idWidth, stringWidth);
       }
       else
       {
-        fm = c.getFontMetrics(getAlabels().getFont());
-
         for (i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
           AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
@@ -581,7 +606,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // this is called after loading new annotation onto alignment
     if (alignFrame.getHeight() == 0)
     {
-      jalview.bin.Console.outPrintln("NEEDS FIXING");
+      jalview.bin.Console.error("adjustAnnotationHeight called with zero height alignment window");
     }
     validateAnnotationDimensions(true);
     addNotify();
@@ -614,7 +639,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     int idWidth = e.width;
     boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
-            .manuallyAdjusted();
+            .isManuallyAdjusted();
     annotationScroller.setPreferredSize(new Dimension(
             manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
             annotationHeight));
@@ -1012,16 +1037,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
           Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
-    final int idWidth;
-    if (getIdPanel()!=null && getIdPanel().getWidth()>0)
-    {
-      // use the current IdPanel's width, if its set and non-zero
-      idWidth = getIdPanel().getWidth();
-    } else { 
-      // otherwise calculate it
-      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.
@@ -1070,6 +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)
      */
@@ -1086,8 +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);
@@ -1234,7 +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");
@@ -1244,7 +1273,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
 
     int w = getIdPanel().getWidth();
-    w = this.calculateIdWidth(-1, true, true).width;
+    w = calculateIdWidth(-1, true, true).width;
     return (w > 0 ? w : calculateIdWidth().width);
   }
 
@@ -1872,5 +1901,4 @@ public class AlignmentPanel extends GAlignmentPanel implements
       overviewPanel = null;
     }
   }
-
 }