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 3127731..fe6477e 100644 (file)
--- 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(
@@ -352,10 +377,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // Also check annotation label widths
     if (includeAnnotations && al.getAlignmentAnnotation() != null)
     {
-      AnnotationLabels aal = getAlabels();
-      int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
-              fm, !visibleOnly);
-      idWidth = Math.max(idWidth, stringWidth);
+      fm = c.getFontMetrics(getAlabels().getFont());
+
+      if (!legacy || Jalview.isHeadlessMode())
+      {
+        AnnotationLabels aal = getAlabels();
+        int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
+                fm, !visibleOnly);
+        idWidth = Math.max(idWidth, stringWidth);
+      }
+      else
+      {
+        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);
+        }
+      }
     }
 
     int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
@@ -562,7 +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();
@@ -595,7 +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));
@@ -1229,7 +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);
   }
 
@@ -1857,5 +1901,4 @@ public class AlignmentPanel extends GAlignmentPanel implements
       overviewPanel = null;
     }
   }
-
 }