X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8ade5d690648ee799b1b4b6c8e31970f63019770;hb=3d2b5edf9ea33c6ebbde4717ccc14f03554fb6f0;hp=921429b5a24ba1f3d0f08d13c2b32acb1ecab175;hpb=4f30cce34289ac0c2dee7b65218f8b98a6a63172;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 921429b..8ade5d6 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,7 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -69,6 +70,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 {
   public AlignViewport av;
 
+  ViewportRanges vpRanges;
+
   OverviewPanel overviewPanel;
 
   private SeqPanel seqPanel;
@@ -91,9 +94,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  int hextent = 0;
+  private int hextent = 0;
 
-  int vextent = 0;
+  private int vextent = 0;
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@ -113,6 +116,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
@@ -297,7 +301,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Highlight the given results on the alignment.
    * 
    */
-  public void highlightSearchResults(SearchResults results)
+  public void highlightSearchResults(SearchResultsI results)
   {
     scrollToPosition(results);
     getSeqPanel().seqCanvas.highlightSearchResults(results);
@@ -309,7 +313,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param results
    */
-  public boolean scrollToPosition(SearchResults results)
+  public boolean scrollToPosition(SearchResultsI results)
   {
     return scrollToPosition(results, 0, true, false);
   }
@@ -322,7 +326,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResults searchResults,
+  public boolean scrollToPosition(SearchResultsI searchResults,
           boolean redrawOverview)
   {
     return scrollToPosition(searchResults, 0, redrawOverview, false);
@@ -342,7 +346,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          if true, try to centre the search results horizontally in the view
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results,
+  public boolean scrollToPosition(SearchResultsI results,
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
@@ -377,7 +381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       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 = end + offset - 1;
       }
@@ -413,7 +417,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
-        if ((startv = av.getStartRes()) >= start)
+        if ((startv = vpRanges.getStartRes()) >= start)
         {
           /*
            * Scroll left to make start of search results visible
@@ -421,7 +425,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
-        else if ((endv = av.getEndRes()) <= end)
+        else if ((endv = vpRanges.getEndRes()) <= end)
         {
           /*
            * Scroll right to make end of search results visible
@@ -429,19 +433,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + 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
@@ -464,10 +469,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int cwidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-    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);
     }
 
   }
@@ -591,7 +597,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    av.startSeq = 0;
+    vpRanges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -688,7 +694,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -698,12 +703,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.hasHiddenColumns())
     {
+      // reset the width to exclude hidden columns
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
-    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-            .getCharWidth())) - 1);
-
     hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
     vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -737,6 +740,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       x = 0;
     }
 
+    // update endRes after x has (possibly) been adjusted
+    vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+            .getCharWidth())) - 1);
+
     /*
      * each scroll adjustment triggers adjustmentValueChanged, which resets the
      * 'do not scroll complement' flag; ensure it is the same for both
@@ -757,14 +764,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
               .getCharWidth())) - 1);
     }
 
@@ -778,8 +785,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           int rowSize = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          av.setStartRes(offy * rowSize);
-          av.setEndRes((offy + 1) * rowSize);
+          vpRanges.setStartRes(offy * rowSize);
+          vpRanges.setEndRes((offy + 1) * rowSize);
         }
         else
         {
@@ -791,16 +798,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
             @Override
             public void run()
             {
-              setScrollValues(av.getStartRes(), av.getStartSeq());
+              setScrollValues(vpRanges.getStartRes(),
+                      vpRanges.getStartSeq());
             }
           });
         }
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy
-                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
+                - 1);
       }
     }
 
@@ -809,8 +818,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       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)
     {
@@ -820,13 +829,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       // 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();
       }
 
       if (scrollX != 0 || scrollY != 0)
@@ -926,7 +935,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
   }
 
@@ -1299,8 +1308,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (onscreen
             || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
     {
-      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
-              : calculateIdWidth().width + 4);
+      int w = getIdPanel().getWidth();
+      return (w > 0 ? w : calculateIdWidth().width + 4);
     }
     return idwidth.intValue() + 4;
   }
@@ -1448,7 +1457,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
-    // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+    // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
     // ////////////////////////////////////////////
     int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
@@ -1462,7 +1471,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
                 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
-        StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
@@ -1478,7 +1486,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
-            text = new StringBuffer();
+            StringBuilder text = new StringBuilder();
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
@@ -1502,18 +1510,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + "," + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                text.append("<area shape=\"rect\" coords=\"")
+                        .append((idWidth + res * av.getCharWidth()))
+                        .append(",").append(sy).append(",")
+                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append(",").append((av.getCharHeight() + sy))
+                        .append("\"").append(" onMouseOver=\"toolTip('")
+                        .append(alIndex).append(" ").append(triplet);
               }
 
               if (groups[g].getStartRes() < res
                       && groups[g].getEndRes() > res)
               {
-                text.append("<br><em>" + groups[g].getName() + "</em>");
+                text.append("<br><em>").append(groups[g].getName())
+                        .append("</em>");
               }
             }
 
@@ -1521,12 +1531,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             {
               if (text.length() < 1)
               {
-                text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.getCharWidth()) + "," + sy
-                        + "," + (idWidth + (res + 1) * av.getCharWidth())
-                        + "," + (av.getCharHeight() + sy) + "\""
-                        + " onMouseOver=\"toolTip('" + alIndex + " "
-                        + triplet);
+                text.append("<area shape=\"rect\" coords=\"")
+                        .append((idWidth + res * av.getCharWidth()))
+                        .append(",").append(sy).append(",")
+                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append(",").append((av.getCharHeight() + sy))
+                        .append("\"").append(" onMouseOver=\"toolTip('")
+                        .append(alIndex).append(" ").append(triplet);
               }
               fSize = features.length;
               for (f = 0; f < fSize; f++)
@@ -1535,15 +1546,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 if ((features[f].getBegin() <= seq.findPosition(res))
                         && (features[f].getEnd() >= seq.findPosition(res)))
                 {
-                  if (features[f].getType().equals("disulfide bond"))
+                  if (features[f].isContactFeature())
                   {
                     if (features[f].getBegin() == seq.findPosition(res)
                             || features[f].getEnd() == seq
                                     .findPosition(res))
                     {
-                      text.append("<br>disulfide bond "
-                              + features[f].getBegin() + ":"
-                              + features[f].getEnd());
+                      text.append("<br>").append(features[f].getType())
+                              .append(" ").append(features[f].getBegin())
+                              .append(":").append(features[f].getEnd());
                     }
                   }
                   else
@@ -1554,13 +1565,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
                             && !features[f].getType().equals(
                                     features[f].getDescription()))
                     {
-                      text.append(" " + features[f].getDescription());
+                      text.append(" ").append(features[f].getDescription());
                     }
 
                     if (features[f].getValue("status") != null)
                     {
-                      text.append(" (" + features[f].getValue("status")
-                              + ")");
+                      text.append(" (").append(features[f].getValue("status"))
+                              .append(")");
                     }
                   }
                 }
@@ -1825,14 +1836,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResults sr, int verticalOffset)
+  public void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
      * 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();
 
     /*
@@ -1873,4 +1884,26 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return this.dontScrollComplement;
   }
+
+  /**
+   * Redraw sensibly.
+   * 
+   * @adjustHeight if true, try to recalculate panel height for visible
+   *               annotations
+   */
+  protected void refresh(boolean adjustHeight)
+  {
+    validateAnnotationDimensions(adjustHeight);
+    addNotify();
+    if (adjustHeight)
+    {
+      // sort, repaint, update overview
+      paintAlignment(true);
+    }
+    else
+    {
+      // lightweight repaint
+      repaint();
+    }
+  }
 }