X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=458ed54f5dfd4ce0ae08811b2a667d98ca2629e3;hb=36e7c887ef91f49f6065dea063180f7de146b3e1;hp=f77d6a1e766e03d3b26e01385064f1c99a441fc7;hpb=ea8826bea12e5d811e47463d22413c33dae3738a;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index f77d6a1..458ed54 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -65,6 +66,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   AnnotationLabels alabels;
 
+  ViewportRanges vpRanges;
+
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
@@ -73,6 +76,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     alignFrame = null;
     av = null;
+    vpRanges = null;
     seqPanel = null;
     seqPanelHolder = null;
     sequenceHolderPanel = null;
@@ -96,6 +100,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     seqPanel = new SeqPanel(av, this);
     idPanel = new IdPanel(av, this);
     scalePanel = new ScalePanel(av, this);
@@ -126,7 +131,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        setScrollValues(av.getStartRes(), av.getStartSeq());
+        setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
         if (getSize().height > 0
                 && annotationPanelHolder.getSize().height > 0)
         {
@@ -383,7 +388,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
        */
       if (centre)
       {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
         end = Math.min(end + offset, seq.getEnd() - 1);
       }
@@ -414,11 +419,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     int start = -1;
     if (av.hasHiddenColumns())
     {
-      start = av.getColumnSelection().findColumnPosition(ostart);
-      end = av.getColumnSelection().findColumnPosition(end);
+      AlignmentI al = av.getAlignment();
+      start = al.getHiddenColumns().findColumnPosition(ostart);
+      end = al.getHiddenColumns().findColumnPosition(end);
       if (start == end)
       {
-        if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
+        if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
         {
           // don't scroll - position isn't visible
           return false;
@@ -468,33 +474,34 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       // setScrollValues(start, seqIndex);
       // }
       // logic copied from jalview.gui.AlignmentPanel:
-      if ((startv = av.getStartRes()) >= start)
+      if ((startv = vpRanges.getStartRes()) >= start)
       {
         /*
          * Scroll left to make start of search results visible
          */
         setScrollValues(start - 1, seqIndex);
       }
-      else if ((endv = av.getEndRes()) <= end)
+      else if ((endv = vpRanges.getEndRes()) <= end)
       {
         /*
          * Scroll right to make end of search results visible
          */
         setScrollValues(startv + 1 + end - endv, seqIndex);
       }
-      else if ((starts = av.getStartSeq()) > seqIndex)
+      else if ((starts = vpRanges.getStartSeq()) > seqIndex)
       {
         /*
          * Scroll up to make start of search results visible
          */
-        setScrollValues(av.getStartRes(), seqIndex);
+        setScrollValues(vpRanges.getStartRes(), seqIndex);
       }
-      else if ((ends = av.getEndSeq()) <= seqIndex)
+      else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
       {
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+        setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -516,10 +523,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     int cwidth = seqPanel.seqCanvas
             .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res <= vpRanges.getStartRes()
+            || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
-      av.startRes = vscroll.getValue() * cwidth;
+      vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
   }
 
@@ -632,8 +640,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   public void setWrapAlignment(boolean wrap)
   {
-    av.startSeq = 0;
-    av.startRes = 0;
+    vpRanges.setStartSeq(0);
+    vpRanges.setStartRes(0);
     scalePanelHolder.setVisible(!wrap);
 
     hscroll.setVisible(!wrap);
@@ -718,13 +726,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (av.hasHiddenColumns())
     {
-      width = av.getColumnSelection().findColumnPosition(width);
+      width = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(width);
     }
     if (x < 0)
     {
       x = 0;
     }
-    ;
+
 
     hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
     vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
@@ -741,8 +750,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if ((hextent + x) > width)
     {
-      System.err.println("hextent was " + hextent + " and x was " + x);
-
+      // System.err.println("hextent was " + hextent + " and x was " + x);
+      //
       x = width - hextent;
     }
 
@@ -762,17 +771,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       x = 0;
     }
 
-    av.setStartSeq(y);
-
-    int endSeq = y + vextent;
-    if (endSeq > av.getAlignment().getHeight())
-    {
-      endSeq = av.getAlignment().getHeight();
-    }
-
-    av.setEndSeq(endSeq);
-    av.setStartRes(x);
-    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+    vpRanges.setStartSeq(y);
+    vpRanges.setEndSeq(y + vextent);
+    vpRanges.setStartRes(x);
+    vpRanges.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
             .getCharWidth())) - 1);
 
     hscroll.setValues(x, hextent, 0, width);
@@ -789,8 +791,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt == null || evt.getSource() == apvscroll)
     {
@@ -804,8 +806,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     if (evt == null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes(x + seqPanel.seqCanvas.getSize().width
               / av.getCharWidth() - 1);
     }
 
@@ -816,14 +818,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         int rowSize = seqPanel.seqCanvas
                 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes((vscroll.getValue() + 1) * rowSize);
+        vpRanges.setStartRes(vscroll.getValue() * rowSize);
+        vpRanges.setEndRes((vscroll.getValue() + 1) * rowSize);
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
-                / av.getCharHeight());
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+                / av.getCharHeight() - 1);
       }
     }
 
@@ -832,8 +834,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
+    int scrollX = vpRanges.getStartRes() - oldX;
+    int scrollY = vpRanges.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
@@ -843,13 +845,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.endRes - av.startRes)
+      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
       {
-        scrollX = av.endRes - av.startRes;
+        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
       }
-      else if (scrollX < av.startRes - av.endRes)
+      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
       {
-        scrollX = av.startRes - av.endRes;
+        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
       }
 
       idPanel.idCanvas.fastPaint(scrollY);
@@ -858,7 +860,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       scalePanel.repaint();
       if (av.isShowAnnotation())
       {
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
+        annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
       }
     }
     sendViewPosition();
@@ -920,7 +922,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
      * mapped), we can make the scroll-to location a sequence above the one
      * actually mapped.
      */
-    SequenceI mappedTo = sr.getResultSequence(0);
+    SequenceI mappedTo = sr.getResults().get(0).getSequence();
     List<SequenceI> seqs = av.getAlignment().getSequences();
 
     /*
@@ -955,8 +957,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   private void sendViewPosition()
   {
     StructureSelectionManager.getStructureSelectionManager(av.applet)
-            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
-                    av.endSeq);
+            .sendViewPosition(this, vpRanges.getStartRes(),
+                    vpRanges.getEndRes(), vpRanges.getStartSeq(),
+                    vpRanges.getEndSeq());
   }
 
   /**
@@ -1008,7 +1011,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
       if (av.hasHiddenColumns())
       {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
       }
 
       int canvasWidth = seqPanel.seqCanvas
@@ -1024,7 +1028,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
 
     seqPanel.seqCanvas.repaint();