X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=3228372617c5880eb3bba6daeb4d3b265d86f8c9;hb=9c96547bd26c1cfb65877bc3bc1941c3c5d5fe76;hp=922e4810d465c50f080000aa652d828df0b27bf7;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 922e481..3228372 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -30,10 +30,12 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.HTMLOutput;
 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;
@@ -212,7 +214,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     alignFrame.updateEditMenuBar();
 
-    paintAlignment(true);
+    // no idea if we need to update structure
+    paintAlignment(true, true);
 
   }
 
@@ -229,7 +232,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
     idSpaceFillerPanel1.setPreferredSize(
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
-
+    idwidthAdjuster.invalidate();
+    scalePanelHolder.invalidate();
     getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
     getAnnotationPanel().adjustPanelHeight();
@@ -240,11 +244,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
-    if (this.alignFrame.getSplitViewContainer() != null)
-    {
-      ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
-    }
-
     repaint();
   }
 
@@ -340,19 +339,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void highlightSearchResults(SearchResultsI results)
   {
-    scrollToPosition(results);
-    getSeqPanel().seqCanvas.highlightSearchResults(results);
-  }
+    boolean scrolled = scrollToPosition(results, 0, true, false);
 
-  /**
-   * Scroll the view to show the position of the highlighted region in results
-   * (if any) and redraw the overview
-   * 
-   * @param results
-   */
-  public boolean scrollToPosition(SearchResultsI results)
-  {
-    return scrollToPosition(results, 0, true, false);
+    boolean noFastPaint = scrolled && av.getWrapAlignment();
+
+    getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
   }
 
   /**
@@ -370,8 +361,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Scroll the view to show the position of the highlighted region in results
-   * (if any)
+   * Scrolls the view (if necessary) to show the position of the first
+   * highlighted region in results (if any). Answers true if the view was
+   * scrolled, or false if no matched region was found, or it is already
+   * visible.
    * 
    * @param results
    * @param verticalOffset
@@ -381,116 +374,117 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          - when set, the overview will be recalculated (takes longer)
    * @param centre
    *          if true, try to centre the search results horizontally in the view
-   * @return false if results were not found
+   * @return
    */
-  public boolean scrollToPosition(SearchResultsI results,
+  protected boolean scrollToPosition(SearchResultsI results,
           int verticalOffset, boolean redrawOverview, boolean centre)
   {
     int startv, endv, starts, ends;
-    // TODO: properly locate search results in view when large numbers of hidden
-    // columns exist before highlighted region
-    // do we need to scroll the panel?
-    // TODO: tons of nullpointerexceptions raised here.
-    if (results != null && results.getSize() > 0 && av != null
-            && av.getAlignment() != null)
-    {
-      int seqIndex = av.getAlignment().findIndex(results);
-      if (seqIndex == -1)
-      {
-        return false;
-      }
-      SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
 
-      int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
-      if (r == null)
-      {
-        return false;
-      }
-      int start = r[0];
-      int end = r[1];
+    if (results == null || results.isEmpty() || av == null
+            || av.getAlignment() == null)
+    {
+      return false;
+    }
+    int seqIndex = av.getAlignment().findIndex(results);
+    if (seqIndex == -1)
+    {
+      return false;
+    }
+    SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
 
-      /*
-       * To centre results, scroll to positions half the visible width
-       * left/right of the start/end positions
-       */
-      if (centre)
-      {
-        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
-                - 1;
-        start = Math.max(start - offset, 0);
-        end = end + offset - 1;
-      }
-      if (start < 0)
-      {
-        return false;
-      }
-      if (end == seq.getEnd())
-      {
-        return false;
-      }
-      if (av.hasHiddenColumns())
+    int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+    if (r == null)
+    {
+      return false;
+    }
+    int start = r[0];
+    int end = r[1];
+
+    /*
+     * To centre results, scroll to positions half the visible width
+     * left/right of the start/end positions
+     */
+    if (centre)
+    {
+      int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+      start = Math.max(start - offset, 0);
+      end = end + offset - 1;
+    }
+    if (start < 0)
+    {
+      return false;
+    }
+    if (end == seq.getEnd())
+    {
+      return false;
+    }
+
+    if (av.hasHiddenColumns())
+    {
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      start = hidden.findColumnPosition(start);
+      end = hidden.findColumnPosition(end);
+      if (start == end)
       {
-        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        start = hidden.findColumnPosition(start);
-        end = hidden.findColumnPosition(end);
-        if (start == end)
+        if (!hidden.isVisible(r[0]))
         {
-          if (!hidden.isVisible(r[0]))
-          {
-            // don't scroll - position isn't visible
-            return false;
-          }
+          // don't scroll - position isn't visible
+          return false;
         }
       }
+    }
 
-      /*
-       * allow for offset of target sequence (actually scroll to one above it)
-       */
-      seqIndex = Math.max(0, seqIndex - verticalOffset);
+    /*
+     * allow for offset of target sequence (actually scroll to one above it)
+     */
+    seqIndex = Math.max(0, seqIndex - verticalOffset);
+    boolean scrollNeeded = true;
 
-      if (!av.getWrapAlignment())
+    if (!av.getWrapAlignment())
+    {
+      if ((startv = vpRanges.getStartRes()) >= start)
       {
-        if ((startv = vpRanges.getStartRes()) >= start)
-        {
-          /*
-           * Scroll left to make start of search results visible
-           */
-          setScrollValues(start, seqIndex);
-        }
-        else if ((endv = vpRanges.getEndRes()) <= end)
-        {
-          /*
-           * Scroll right to make end of search results visible
-           */
-          setScrollValues(startv + end - endv, seqIndex);
-        }
-        else if ((starts = vpRanges.getStartSeq()) > seqIndex)
-        {
-          /*
-           * Scroll up to make start of search results visible
-           */
-          setScrollValues(vpRanges.getStartRes(), seqIndex);
-        }
-        else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
-        {
-          /*
-           * Scroll down to make end of search results visible
-           */
-          setScrollValues(vpRanges.getStartRes(),
-                  starts + seqIndex - ends + 1);
-        }
         /*
-         * Else results are already visible - no need to scroll
+         * Scroll left to make start of search results visible
          */
+        setScrollValues(start, seqIndex);
       }
-      else
+      else if ((endv = vpRanges.getEndRes()) <= end)
       {
-        vpRanges.scrollToWrappedVisible(start);
+        /*
+         * Scroll right to make end of search results visible
+         */
+        setScrollValues(startv + end - endv, seqIndex);
       }
+      else if ((starts = vpRanges.getStartSeq()) > seqIndex)
+      {
+        /*
+         * Scroll up to make start of search results visible
+         */
+        setScrollValues(vpRanges.getStartRes(), seqIndex);
+      }
+      else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+      {
+        /*
+         * Scroll down to make end of search results visible
+         */
+        setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                + 1);
+      }
+      /*
+       * Else results are already visible - no need to scroll
+       */
+      scrollNeeded = false;
+    }
+    else
+    {
+      scrollNeeded = vpRanges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
-    return true;
+    paintAlignment(redrawOverview, false);
+
+    return scrollNeeded;
   }
 
   /**
@@ -545,7 +539,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     validateAnnotationDimensions(true);
     addNotify();
-    paintAlignment(true);
+    // TODO: many places call this method and also paintAlignment with various
+    // different settings. this means multiple redraws are triggered...
+    paintAlignment(true, false);
   }
 
   /**
@@ -639,9 +635,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       else
       {
-        int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+        int widthInRes = (canvasWidth / av.getCharWidth());
         int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
-                / av.getCharHeight()) - 1;
+                / av.getCharHeight());
 
         vpRanges.setViewportWidth(widthInRes);
         vpRanges.setViewportHeight(heightInSeq);
@@ -844,12 +840,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
-  /**
-   * Repaint the alignment including the annotations and overview panels (if
-   * shown).
+  /* (non-Javadoc)
+   * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
    */
   @Override
-  public void paintAlignment(boolean updateOverview)
+  public void paintAlignment(boolean updateOverview,
+          boolean updateStructures)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
@@ -857,10 +853,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
             av.getSortAnnotationsBy());
     repaint();
 
-    if (updateOverview)
+    if (updateStructures)
     {
-      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
+    }
+    if (updateOverview)
+    {
 
       if (overviewPanel != null)
       {
@@ -1103,8 +1101,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
-            startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
+            endRes, startSeq, endSeq);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1231,7 +1229,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
             totalHeight, 0);
 
     if ((pi * pheight) < totalHeight)
@@ -1437,35 +1435,33 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       try
       {
-        int s, sSize = av.getAlignment().getHeight(), res,
-                alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize,
-                sy;
+        int sSize = av.getAlignment().getHeight();
+        int alwidth = av.getAlignment().getWidth();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
-        out.println(jalview.io.HTMLOutput.getImageMapHTML());
+        out.println(HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
                 + "\" border=\"0\" usemap=\"#Map\" >"
                 + "<map name=\"Map\">");
 
-        for (s = 0; s < sSize; s++)
+        for (int s = 0; s < sSize; s++)
         {
-          sy = s * av.getCharHeight() + scaleHeight;
+          int 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++)
+          for (int column = 0; column < alwidth; column++)
           {
-            StringBuilder text = new StringBuilder();
+            StringBuilder text = new StringBuilder(512);
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              triplet = ResidueProperties.nucleotideName
-                      .get(seq.getCharAt(res) + "");
+              triplet = ResidueProperties.nucleotideName.get(seq
+                      .getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet
-                      .get(seq.getCharAt(res) + "");
+              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
+                      + "");
             }
 
             if (triplet == null)
@@ -1473,84 +1469,73 @@ public class AlignmentPanel extends GAlignmentPanel implements
               continue;
             }
 
-            int alIndex = seq.findPosition(res);
-            gSize = groups.length;
-            for (g = 0; g < gSize; g++)
+            int seqPos = seq.findPosition(column);
+            int gSize = groups.length;
+            for (int g = 0; g < gSize; g++)
             {
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\"")
-                        .append((idWidth + res * av.getCharWidth()))
+                        .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (res + 1) * av.getCharWidth()))
+                        .append((idWidth + (column + 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
-                      && groups[g].getEndRes() > res)
+              if (groups[g].getStartRes() < column
+                      && groups[g].getEndRes() > column)
               {
                 text.append("<br><em>").append(groups[g].getName())
                         .append("</em>");
               }
             }
 
-            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 + column * av.getCharWidth()))
+                      .append(",").append(sy).append(",")
+                      .append((idWidth + (column + 1) * av.getCharWidth()))
+                      .append(",").append((av.getCharHeight() + sy))
+                      .append("\"").append(" onMouseOver=\"toolTip('")
+                      .append(seqPos).append(" ").append(triplet);
+            }
+            if (!Comparison.isGap(seq.getCharAt(column)))
+            {
+              List<SequenceFeature> features = seq.findFeatures(column, column);
+              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());
             }
           }
         }
@@ -1819,7 +1804,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          the number of visible sequences to show above the mapped region
    */
-  public void scrollToCentre(SearchResultsI sr, int verticalOffset)
+  protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
     /*
      * To avoid jumpy vertical scrolling (if some sequences are gapped or not
@@ -1886,7 +1871,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (adjustHeight)
     {
       // sort, repaint, update overview
-      paintAlignment(true);
+      paintAlignment(true, false);
     }
     else
     {