JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index bfbaf4d..330620c 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -173,15 +173,28 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public Dimension calculateIdWidth()
   {
+    // calculate sensible default width when no preference is available
+    
+    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+    int maxwidth = Math.max(20,
+            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
+    return calculateIdWidth(maxwidth);
+  }
+  /**
+   * 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
+   * @return Dimension giving the maximum width of the alignment label panel
+   *         that should be used.
+   */
+  public Dimension calculateIdWidth(int maxwidth)
+  {
     Container c = new Container();
 
     FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
             Font.ITALIC, av.font.getSize()));
 
     AlignmentI al = av.getAlignment();
-    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-    int maxwidth = Math.max(20,
-            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
     int i = 0;
     int idWidth = 0;
     String id;
@@ -220,7 +233,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    return new Dimension(Math.min(maxwidth, idWidth), 12);
+    return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12);
   }
 
   /**
@@ -788,7 +801,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
           throws PrinterException
   {
-    int idWidth = getVisibleIdWidth();
+    int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
@@ -955,7 +968,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
             + annotationHeight;
 
-    int idWidth = getVisibleIdWidth();
+    int idWidth = getVisibleIdWidth(false);
 
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
@@ -1028,11 +1041,33 @@ public class AlignmentPanel extends GAlignmentPanel implements
       return Printable.NO_SUCH_PAGE;
     }
   }
-
+  /**
+   * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
+   * @return
+   */
   int getVisibleIdWidth()
   {
-    return idPanel.getWidth() > 0 ? idPanel.getWidth()
-            : calculateIdWidth().width + 4;
+    return getVisibleIdWidth(true);
+  }
+
+  /**
+   * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
+   * @param onscreen indicate if the Id width for onscreen or offscreen display should be returned
+   * @return
+   */
+  int getVisibleIdWidth(boolean onscreen)
+  {
+    // see if rendering offscreen - check preferences and calc width accordingly
+    if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
+    {
+      return calculateIdWidth(-1).width+4;
+    }
+    Integer idwidth=null;
+    if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) {
+      return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+            : calculateIdWidth().width + 4);
+    }
+    return idwidth.intValue()+4;
   }
 
   void makeAlignmentImage(int type, File file)
@@ -1045,7 +1080,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
             + scalePanel.getHeight();
-    int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
+    int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
 
     if (av.getWrapAlignment())
     {
@@ -1053,14 +1088,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (System.getProperty("java.awt.headless") != null
               && System.getProperty("java.awt.headless").equals("true"))
       {
-        // TODO: JAL-244
+        // need to obtain default alignment width and then add in any additional allowance for id margin
+        // this duplicates the calculation in getWrappedHeight but adjusts for offscreen idWith
         width = alignFrame.getWidth() - vscroll.getPreferredSize().width
                 - alignFrame.getInsets().left
-                - alignFrame.getInsets().right;
+                - alignFrame.getInsets().right
+                - getVisibleIdWidth()+getVisibleIdWidth(false);
       }
       else
       {
-        width = seqPanel.getWidth() + getVisibleIdWidth();
+        width = seqPanel.getWidth() + getVisibleIdWidth(false);
       }
 
     }
@@ -1135,7 +1172,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
-    int idWidth = getVisibleIdWidth();
+    int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
@@ -1363,7 +1400,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // remove old automatic annotation
     // add any new annotation
 
-    Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.getAlignment().getSequencesArray());
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
@@ -1380,13 +1416,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
       }
     }
-    SequenceGroup sg;
-    if (gr != null)
+    if (av.getAlignment().getGroups()!=null)
     {
-      for (int g = 0; g < gr.size(); g++)
+      for (SequenceGroup sg:av.getAlignment().getGroups())
       {
         updateCalcs = false;
-        sg = (SequenceGroup) gr.elementAt(g);
         if (applyGlobalSettings || !oldrfs.containsKey(sg))
         {
           // set defaults for this group's conservation/consensus