X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1c2e91c01824c0f1674a407d90637a9d357b45ff;hb=45b0738d718c18b5507f283b0d4be006594e816e;hp=fa30e0966ab1e524f4896d5063a7d9acba7681d7;hpb=f887a21118fae5bc1f2cadcd4f36ffed4554edc8;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fa30e09..1c2e91c 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -56,6 +56,7 @@ import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
 import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
 import java.awt.print.PageFormat;
 import java.awt.print.Printable;
 import java.awt.print.PrinterException;
@@ -66,10 +67,15 @@ import java.io.FileWriter;
 import java.io.PrintWriter;
 import java.util.List;
 
-import javax.swing.SwingUtilities;
-
 /**
- * DOCUMENT ME!
+ * The main panel of an AlignFrame, containing holders for the IdPanel,
+ * SeqPanel, AnnotationLabels (a JPanel), and AnnotationPanel.
+ * 
+ * Additional holders contain an IdPanelWidthAdjuster space above the idPanel,
+ * AnnotationScroller (JScrollPane for AnnotationPanel), and vertical and
+ * horizontal scrollbars.
+ * 
+ * 
  * 
  * @author $author$
  * @version $Revision: 1.161 $
@@ -136,7 +142,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     annotationScroller.setViewportView(getAnnotationPanel());
     annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
-
+    if (!av.isShowAnnotation())
+    {
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
     scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
     seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
 
@@ -580,7 +590,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void updateLayout()
   {
-    fontChanged();
+    fontChanged(); // fires repaint
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
     ViewportRanges ranges = av.getRanges();
@@ -790,7 +800,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       // This is only called if file loaded is a jar file that
       // was wrapped when saved and user has wrap alignment true
       // as preference setting
-      SwingUtilities.invokeLater(new Runnable()
+      Jalview.execRunnable(new Runnable()
       {
         @Override
         public void run()
@@ -830,7 +840,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     if (updateOverview)
     {
-
       if (overviewPanel != null)
       {
         overviewPanel.updateOverviewImage();
@@ -847,6 +856,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
+
     invalidate(); // needed so that the id width adjuster works correctly
 
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
@@ -1067,6 +1077,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
           Graphics g) throws PrinterException
   {
+
     int annotationHeight = 0;
     if (av.isShowAnnotation())
     {
@@ -1091,6 +1102,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int totalHeight = cHeight * (maxwidth / resWidth + 1);
 
+    g = g.create();
+
     g.setColor(Color.white);
     g.fillRect(0, 0, pageWidth, pageHeight);
     g.setFont(av.getFont());
@@ -1104,7 +1117,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     g.translate(0, -pageNumber * pageHeight);
 
-    g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
+    // BH 2020.03.19 avoiding g.setClip
+    g.clipRect(0, pageNumber * pageHeight, pageWidth, pageHeight);
 
     /*
      * draw sequence ids and annotation labels (if shown)
@@ -1117,6 +1131,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
             totalHeight, 0);
 
+    g.dispose();
     if ((pageNumber * pageHeight) < totalHeight)
     {
       return Printable.PAGE_EXISTS;
@@ -1730,4 +1745,148 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return seqPanel.seqCanvas.getSequenceRenderer();
   }
 
+  public boolean scrollTo(int ostart, int end, int seqIndex,
+          boolean scrollToNearest, boolean redrawOverview)
+  {
+    int startv, endv, starts, ends;// , width;
+
+    int start = -1;
+    if (av.hasHiddenColumns())
+    {
+      AlignmentI al = av.getAlignment();
+      start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+      end = al.getHiddenColumns().absoluteToVisibleColumn(end);
+      if (start == end)
+      {
+        if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
+        {
+          // don't scroll - position isn't visible
+          return false;
+        }
+      }
+    }
+    else
+    {
+      start = ostart;
+    }
+
+    ViewportRanges ranges = av.getRanges();
+    if (!av.getWrapAlignment())
+    {
+      /*
+       * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+       * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+       * setScrollValues(start - 1, seqIndex); } else if ((endv =
+       * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+       * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+       * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+       * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+       * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+       */
+
+      // below is scrolling logic up to Jalview 2.8.2
+      // if ((av.getStartRes() > end)
+      // || (av.getEndRes() < start)
+      // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+      // {
+      // if (start > av.getAlignment().getWidth() - hextent)
+      // {
+      // start = av.getAlignment().getWidth() - hextent;
+      // if (start < 0)
+      // {
+      // start = 0;
+      // }
+      //
+      // }
+      // if (seqIndex > av.getAlignment().getHeight() - vextent)
+      // {
+      // seqIndex = av.getAlignment().getHeight() - vextent;
+      // if (seqIndex < 0)
+      // {
+      // seqIndex = 0;
+      // }
+      // }
+      // setScrollValues(start, seqIndex);
+      // }
+      // logic copied from jalview.gui.AlignmentPanel:
+      if ((startv = ranges.getStartRes()) >= start)
+      {
+        /*
+         * Scroll left to make start of search results visible
+         */
+        setScrollValues(start - 1, seqIndex);
+      }
+      else if ((endv = ranges.getEndRes()) <= end)
+      {
+        /*
+         * Scroll right to make end of search results visible
+         */
+        setScrollValues(startv + 1 + end - endv, seqIndex);
+      }
+      else if ((starts = ranges.getStartSeq()) > seqIndex)
+      {
+        /*
+         * Scroll up to make start of search results visible
+         */
+        setScrollValues(ranges.getStartRes(), seqIndex);
+      }
+      else if ((ends = ranges.getEndSeq()) <= seqIndex)
+      {
+        /*
+         * Scroll down to make end of search results visible
+         */
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
+      }
+      /*
+       * Else results are already visible - no need to scroll
+       */
+    }
+    else
+    {
+      ranges.scrollToWrappedVisible(start);
+    }
+
+    paintAlignment(redrawOverview, false);
+    return true;
+  }
+
+  @Override
+  public void overviewDone(BufferedImage miniMe)
+  {
+    overviewPanel.canvas.finalizeDraw(miniMe);
+  }
+
+
+  private boolean holdRepaint = false;
+
+  public boolean getHoldRepaint()
+  {
+    return holdRepaint;
+  }
+
+  public void setHoldRepaint(boolean b)
+  {
+    if (holdRepaint == b)
+    {
+      return;
+    }
+    holdRepaint = b;
+    if (!b)
+    {
+      repaint();
+    }
+  }
+
+  @Override
+  public void repaint()
+  {
+    if (holdRepaint)
+    {
+      // System.out.println("AP repaint holding");
+      // Platform.stackTrace();
+      return;
+    }
+    super.repaint();
+  }
+
 }