JAL-3269 JAL-3370 JalviewJS interface upgrade

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2aa21bb..f723794 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.AnnotationSorter;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.SequenceRenderer;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
@@ -73,6 +74,7 @@ import javax.swing.SwingUtilities;
  * @author $author$
  * @version $Revision: 1.161 $
  */
+@SuppressWarnings("serial")
 public class AlignmentPanel extends GAlignmentPanel implements
         AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
 {
@@ -116,7 +118,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-//     setBackground(Color.white);  // BH 2019
+    setBackground(Color.white); // BH 2019
+    setOpaque(true);
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
@@ -542,6 +545,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
+    // BH 2018.04.18 comment: addNotify() is not appropriate here. We
+    // are not changing ancestors, and keyboard action listeners do
+    // not need to be reset. addNotify() is a very expensive operation,
+    // requiring a full re-layout of all parents and children.
+    // Note in JComponent:
+    // This method is called by the toolkit internally and should
+    // not be called directly by programs.
+    // I note that addNotify() is called in several areas of Jalview.
+
     int annotationHeight = getAnnotationPanel().adjustPanelHeight();
     annotationHeight = getAnnotationPanel()
             .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
@@ -553,6 +565,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
+
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -1137,13 +1150,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int getVisibleIdWidth(boolean onscreen)
   {
     // see if rendering offscreen - check preferences and calc width accordingly
-    if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
+    if (!onscreen && Cache.getDefault(Preferences.FIGURE_AUTOIDWIDTH, false))
     {
       return calculateIdWidth(-1).width + 4;
     }
     Integer idwidth = null;
     if (onscreen || (idwidth = Cache
-            .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+            .getIntegerProperty(Preferences.FIGURE_FIXEDIDWIDTH)) == null)
     {
       int w = getIdPanel().getWidth();
       return (w > 0 ? w : calculateIdWidth().width + 4);
@@ -1365,8 +1378,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
 
-    if (System.getProperty("java.awt.headless") != null
-            && System.getProperty("java.awt.headless").equals("true"))
+    if (Jalview.isHeadlessMode())
     {
       seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
               - vscroll.getPreferredSize().width
@@ -1711,4 +1723,116 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return calculationDialog;
   }
+
+  @Override
+  public SequenceRenderer getSequenceRenderer()
+  {
+    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;
+  }
+
 }