X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1ac553668f2a9230ae5af6b1c3cb40fd6835755d;hb=3a206ee73908f2339e44fae78d2a7d1f5e384158;hp=2c5684a8a168c5ccd0876b20f2614d83447a66a2;hpb=6f153aac5d457ab69f994d71df1cf30b69d07af5;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2c5684a..1ac5536 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -48,6 +48,7 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
@@ -942,30 +943,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param pg
-   *          DOCUMENT ME!
-   * @param pwidth
-   *          DOCUMENT ME!
-   * @param pheight
-   *          DOCUMENT ME!
-   * @param pi
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   * 
-   * @throws PrinterException
-   *           DOCUMENT ME!
-   */
-  /**
    * Draws the alignment image, including sequence ids, sequences, and
    * annotation labels and annotations if shown, on either one or two Graphics
-   * context.
+   * contexts.
    * 
    * @param pageWidth
+   *          in pixels
    * @param pageHeight
-   * @param pi
+   *          in pixels
+   * @param pageIndex
+   *          (0, 1, ...)
    * @param idGraphics
    *          the graphics context for sequence ids and annotation labels
    * @param alignmentGraphics
@@ -974,7 +961,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return
    * @throws PrinterException
    */
-  public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+  public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
           Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
@@ -988,8 +975,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             : idWidth;
 
     FontMetrics fm = getFontMetrics(av.getFont());
-    int charHeight = av.getCharHeight();
-    int scaleHeight = charHeight + fm.getDescent();
+    final int charHeight = av.getCharHeight();
+    final int scaleHeight = charHeight + fm.getDescent();
 
     idGraphics.setColor(Color.white);
     idGraphics.fillRect(0, 0, pageWidth, pageHeight);
@@ -998,29 +985,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     /*
      * How many sequences and residues can we fit on a printable page?
      */
-    int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+    final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
 
-    int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+    final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    int alignmentWidth = av.getAlignment().getWidth();
-    int pagesWide = (alignmentWidth / totalRes) + 1;
+    final int alignmentWidth = av.getAlignment().getWidth();
+    final int pagesWide = (alignmentWidth / totalRes) + 1;
 
-    final int startRes = (pi % pagesWide) * totalRes;
-    int endRes = (startRes + totalRes) - 1;
+    final int startRes = (pageIndex % pagesWide) * totalRes;
+    final int endRes = Math.min(startRes + totalRes - 1,
+            alignmentWidth - 1);
 
-    if (endRes > (alignmentWidth - 1))
-    {
-      endRes = alignmentWidth - 1;
-    }
-
-    final int startSeq = (pi / pagesWide) * totalSeq;
-    int endSeq = startSeq + totalSeq;
-
-    int alignmentHeight = av.getAlignment().getHeight();
-    if (endSeq > alignmentHeight)
-    {
-      endSeq = alignmentHeight;
-    }
+    final int startSeq = (pageIndex / pagesWide) * totalSeq;
+    final int alignmentHeight = av.getAlignment().getHeight();
+    final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
 
     int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
 
@@ -1031,7 +1009,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pagesHigh /= pageHeight;
 
-    if (pi >= (pagesWide * pagesHigh))
+    if (pageIndex >= (pagesWide * pagesHigh))
     {
       return Printable.NO_SUCH_PAGE;
     }
@@ -1050,47 +1028,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * then reset to top left (0, 0)
      */
     idGraphics.translate(0, scaleHeight);
-    idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
-    Color currentColor = null;
-    Color currentTextColor = null;
+    IdCanvas idCanvas = getIdPanel().getIdCanvas();
+    List<SequenceI> selection = av.getSelectionGroup() == null ? null
+            : av.getSelectionGroup().getSequences(null);
+    idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+            selection);
 
-    SequenceI seq;
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      seq = av.getAlignment().getSequenceAt(i);
-      if ((av.getSelectionGroup() != null)
-              && av.getSelectionGroup().getSequences(null).contains(seq))
-      {
-        /*
-         * gray out ids of sequences in selection group (if any)
-         */
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getSequenceColour(seq);
-        currentTextColor = Color.black;
-      }
-
-      idGraphics.setColor(currentColor);
-      idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
-              charHeight);
-
-      idGraphics.setColor(currentTextColor);
-
-      int xPos = 0;
-      String displayId = seq.getDisplayId(av.getShowJVSuffix());
-      if (av.isRightAlignIds())
-      {
-        fm = idGraphics.getFontMetrics();
-        xPos = idWidth - fm.stringWidth(displayId) - 4;
-      }
-
-      idGraphics.drawString(displayId, xPos,
-              (((i - startSeq) * charHeight) + charHeight)
-                      - (charHeight / 5));
-    }
     idGraphics.setFont(av.getFont());
     idGraphics.translate(0, -scaleHeight);
 
@@ -1100,7 +1043,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
     getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq);
+            endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))