X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=7f1ce31d11bfcd6f8f88b5eae6763cc8e1e775b2;hb=e4f893546d61b043b3381c9548f0cfbf7084fd78;hp=8619ad0d7deb8abfb3284dcb2c38b96547181739;hpb=9a9de4a2b0432d0c5e65b033f51ac7e95e8bbbda;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 8619ad0..7f1ce31 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,6 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -33,6 +34,7 @@ import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
@@ -104,12 +106,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
-   * true, suppresses invoking the same method recursively.
+   * false, suppresses invoking the same method recursively.
    */
-  private boolean dontScrollComplement;
+  private boolean scrollComplementaryPanel = true;
 
   private PropertyChangeListener propertyChangeListener;
 
+  private CalculationChooser calculationDialog;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -156,19 +160,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           int widthInRes = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          vpRanges.setStartEndRes(vpRanges.getStartRes(),
-                  vpRanges.getStartRes() + widthInRes);
+          vpRanges.setViewportWidth(widthInRes);
         }
         else
         {
-          int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
-                  .getCharWidth()) - 1;
-          int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()) - 1;
+          int widthInRes = getSeqPanel().seqCanvas.getWidth()
+                  / av.getCharWidth();
+          int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+                  / av.getCharHeight();
           
-          vpRanges.setStartEndRes(vpRanges.getStartRes(),
-                  vpRanges.getStartRes() + widthInRes);
-          vpRanges.setStartEndSeq(vpRanges.getStartSeq(),
-                  vpRanges.getStartSeq() + heightInSeq);
+          vpRanges.setViewportWidth(widthInRes);
+          vpRanges.setViewportHeight(heightInSeq);
         }
       }
 
@@ -205,6 +207,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     av.alignmentChanged(this);
 
+    if (getCalculationDialog() != null)
+    {
+      getCalculationDialog().validateCalcTypes();
+    }
+
     alignFrame.updateEditMenuBar();
 
     paintAlignment(true);
@@ -403,9 +410,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // DEBUG
-      // System.err.println(this.av.viewName + " Seq : " + seqIndex
-      // + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -413,7 +417,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       if (centre)
       {
-        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+                - 1;
         start = Math.max(start - offset, 0);
         end = end + offset - 1;
       }
@@ -427,11 +432,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (av.hasHiddenColumns())
       {
-        start = av.getColumnSelection().findColumnPosition(start);
-        end = av.getColumnSelection().findColumnPosition(end);
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        start = hidden.findColumnPosition(start);
+        end = hidden.findColumnPosition(end);
         if (start == end)
         {
-          if (!av.getColumnSelection().isVisible(r[0]))
+          if (!hidden.isVisible(r[0]))
           {
             // don't scroll - position isn't visible
             return false;
@@ -444,9 +450,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       seqIndex = Math.max(0, seqIndex - verticalOffset);
 
-      // System.out.println("start=" + start + ", end=" + end + ", startv="
-      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
-      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = vpRanges.getStartRes()) >= start)
@@ -454,7 +457,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll left to make start of search results visible
            */
-          // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
         else if ((endv = vpRanges.getEndRes()) <= end)
@@ -462,7 +464,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
           /*
            * Scroll right to make end of search results visible
            */
-          // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + end - endv, seqIndex);
         }
         else if ((starts = vpRanges.getStartSeq()) > seqIndex)
@@ -633,8 +634,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int widthInRes = getSeqPanel().seqCanvas
               .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-      vpRanges.setStartEndRes(vpRanges.getStartRes(),
-              vpRanges.getStartRes() + widthInRes - 1);
+      vpRanges.setViewportWidth(widthInRes);
     }
     else
     {
@@ -643,8 +643,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
               .getCharHeight()) - 1;
 
-      vpRanges.setStartEndRes(vpRanges.getStartRes(), widthInRes);
-      vpRanges.setStartEndSeq(vpRanges.getStartSeq(), heightInSeq);
+      vpRanges.setViewportWidth(widthInRes);
+      vpRanges.setViewportHeight(heightInSeq);
     }
 
     idSpaceFillerPanel1.setVisible(!wrap);
@@ -662,8 +662,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          visible row to scroll to
    * 
    */
-  public void setScrollValues(int x, int y)
+  public void setScrollValues(int xpos, int ypos)
   {
+    int x = xpos;
+    int y = ypos;
+
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -675,14 +678,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-
       int width = av.getAlignment().getWidth();
       int height = av.getAlignment().getHeight();
 
       if (av.hasHiddenColumns())
       {
         // reset the width to exclude hidden columns
-        width = av.getColumnSelection().findColumnPosition(width);
+        width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
       }
 
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -725,10 +727,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Respond to adjustment event when horizontal or vertical scrollbar is
+   * changed
    * 
    * @param evt
-   *          DOCUMENT ME!
+   *          adjustment event encoding whether hscroll or vscroll changed
    */
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -759,23 +762,31 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
         else if (offy > -1)
         {
-          vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize - 1);
+          vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
         }
-        else
+      }
+      else
+      {
+        // 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()
         {
-          // 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()
-          {
-            @Override
-            public void run()
-            {
-              setScrollValues(vpRanges.getStartRes(),
-                      vpRanges.getStartSeq());
-            }
-          });
-        }
+          @Override
+          public void run()
+        {
+            // When updating scrolling to use ViewportChange events, this code
+            // could not be validated and it is not clear if it is now being
+            // called. Log warning here in case it is called and unforeseen
+            // problems occur
+            Cache.log
+                    .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+            // scroll to start of panel
+            vpRanges.setStartRes(0);
+            vpRanges.setStartSeq(0);
+          }
+        });
       }
       repaint();
     }
@@ -785,7 +796,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (evt.getSource() == hscroll)
       {
         int x = hscroll.getValue();
-        int width = (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth()) - 1;
+        int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
 
         // if we're scrolling to the position we're already at, stop
         // this prevents infinite recursion of events when the scroll/viewport
@@ -794,13 +805,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           return;
         }
-        vpRanges.setStartEndRes(x, x + width);
+        vpRanges.setViewportStartAndWidth(x, width);
       }
       else if (evt.getSource() == vscroll)
       {
         int y = vscroll.getValue();
-        int height = (getSeqPanel().seqCanvas.getHeight() / av
-                .getCharHeight()) - 1;
+        int height = getSeqPanel().seqCanvas.getHeight()
+                / av.getCharHeight();
 
         // if we're scrolling to the position we're already at, stop
         // this prevents infinite recursion of events when the scroll/viewport
@@ -809,7 +820,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           return;
         }
-        vpRanges.setStartEndSeq(y, y + height);
+        vpRanges.setViewportStartAndHeight(y, height);
       }
       if (!fastPaint)
       {
@@ -876,7 +887,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
     }
 
     // get the width of the canvas in residues
@@ -1161,7 +1173,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
@@ -1355,7 +1368,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1438,11 +1452,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
           sy = s * av.getCharHeight() + scaleHeight;
 
           SequenceI seq = av.getAlignment().getSequenceAt(s);
-          SequenceFeature[] features = seq.getSequenceFeatures();
           SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
-            StringBuilder text = new StringBuilder();
+            StringBuilder text = new StringBuilder(512);
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
@@ -1460,7 +1473,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
               continue;
             }
 
-            int alIndex = seq.findPosition(res);
+            int seqPos = seq.findPosition(res);
             gSize = groups.length;
             for (g = 0; g < gSize; g++)
             {
@@ -1472,7 +1485,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                         .append((idWidth + (res + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
-                        .append(alIndex).append(" ").append(triplet);
+                        .append(seqPos).append(" ").append(triplet);
               }
 
               if (groups[g].getStartRes() < res
@@ -1483,61 +1496,51 @@ public class AlignmentPanel extends GAlignmentPanel implements
               }
             }
 
-            if (features != null)
+            if (text.length() < 1)
             {
-              if (text.length() < 1)
-              {
-                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++)
+              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(seqPos).append(" ").append(triplet);
+            }
+            if (!Comparison.isGap(seq.getCharAt(res)))
+            {
+              List<SequenceFeature> features = seq.findFeatures(seqPos,
+                      seqPos);
+              for (SequenceFeature sf : features)
               {
-
-                if ((features[f].getBegin() <= seq.findPosition(res))
-                        && (features[f].getEnd() >= seq.findPosition(res)))
+                if (sf.isContactFeature())
                 {
-                  if (features[f].isContactFeature())
-                  {
-                    if (features[f].getBegin() == seq.findPosition(res)
-                            || features[f].getEnd() == seq
-                                    .findPosition(res))
-                    {
-                      text.append("<br>").append(features[f].getType())
-                              .append(" ").append(features[f].getBegin())
-                              .append(":").append(features[f].getEnd());
-                    }
-                  }
-                  else
+                  text.append("<br>").append(sf.getType()).append(" ")
+                          .append(sf.getBegin()).append(":")
+                          .append(sf.getEnd());
+                }
+                else
+                {
+                  text.append("<br>");
+                  text.append(sf.getType());
+                  String description = sf.getDescription();
+                  if (description != null
+                          && !sf.getType().equals(description))
                   {
-                    text.append("<br>");
-                    text.append(features[f].getType());
-                    if (features[f].getDescription() != null
-                            && !features[f].getType().equals(
-                                    features[f].getDescription()))
-                    {
-                      text.append(" ").append(features[f].getDescription());
-                    }
-
-                    if (features[f].getValue("status") != null)
-                    {
-                      text.append(" (").append(features[f].getValue("status"))
-                              .append(")");
-                    }
+                    description = description.replace("\"", "&quot;");
+                    text.append(" ").append(description);
                   }
                 }
-
+                String status = sf.getStatus();
+                if (status != null && !"".equals(status))
+                {
+                  text.append(" (").append(status).append(")");
+                }
+              }
+              if (text.length() > 1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
               }
-            }
-            if (text.length() > 1)
-            {
-              text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
-              out.println(text.toString());
             }
           }
         }
@@ -1585,7 +1588,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;
@@ -1603,6 +1607,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
 
+    closeChildFrames();
+
     /*
      * try to ensure references are nulled
      */
@@ -1634,6 +1640,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
+   * Close any open dialogs that would be orphaned when this one is closed
+   */
+  protected void closeChildFrames()
+  {
+    if (calculationDialog != null)
+    {
+      calculationDialog.closeFrame();
+    }
+  }
+
+  /**
    * hides or shows dynamic annotation rows based on groups and av state flags
    */
   public void updateAnnotation()
@@ -1831,14 +1848,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param b
    */
-  protected void setDontScrollComplement(boolean b)
+  protected void setToScrollComplementPanel(boolean b)
   {
-    this.dontScrollComplement = b;
+    this.scrollComplementaryPanel = b;
   }
 
-  protected boolean isDontScrollComplement()
+  /**
+   * Get whether to scroll complement panel
+   * 
+   * @return true if cDNA/protein complement panels should be scrolled
+   */
+  protected boolean isSetToScrollComplementPanel()
   {
-    return this.dontScrollComplement;
+    return this.scrollComplementaryPanel;
   }
 
   /**
@@ -1877,11 +1899,31 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // now update any complementary alignment (its viewport ranges object
     // is different so does not get automatically updated)
-    if (!isDontScrollComplement())
+    if (isSetToScrollComplementPanel())
     {
-      setDontScrollComplement(true);
+      setToScrollComplementPanel(false);
       av.scrollComplementaryAlignment();
-      setDontScrollComplement(false);
+      setToScrollComplementPanel(true);
     }
   }
+
+  /**
+   * Set the reference to the PCA/Tree chooser dialog for this panel. This
+   * reference should be nulled when the dialog is closed.
+   * 
+   * @param calculationChooser
+   */
+  public void setCalculationDialog(CalculationChooser calculationChooser)
+  {
+    calculationDialog = calculationChooser;
+  }
+
+  /**
+   * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+   * if none is open)
+   */
+  public CalculationChooser getCalculationDialog()
+  {
+    return calculationDialog;
+  }
 }