X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=e61b042728f4735e45ab91592db20f2ae4817703;hb=b2b7e99113e1f0962140fc72d989cc826799a2d4;hp=65546556e218a42f45c4c4bb2f7bc80d46cf1294;hpb=608282e79f4dd02c92565235b7946265bdca847d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 6554655..e61b042 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;
@@ -297,7 +297,7 @@ 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 +309,7 @@ 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 +322,7 @@ 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 +342,7 @@ 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;
@@ -1062,7 +1062,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             + 3;
 
     /*
-     * draw the Scale at horizontal offset, then reset to origin
+     * draw the Scale at horizontal offset, then reset to top left (0, 0)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, 0);
     getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
@@ -1071,7 +1071,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     /*
      * Draw the sequence ids, offset for scale height,
-     * then reset to origin
+     * then reset to top left (0, 0)
      */
     idGraphics.translate(0, scaleHeight);
     idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
@@ -1122,7 +1122,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     /*
      * draw the sequences, offset for scale height, and id width (if using a
-     * single graphics context), then reset to origin + scale height
+     * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
     getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
@@ -1132,16 +1132,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
     {
       /*
-       * draw annotation labels, offset for current scroll position
-       * then reset to origin + scale height
+       * draw annotation labels; drawComponent() translates by
+       * getScrollOffset(), so compensate for that first;
+       * then reset to (0, scale height)
        */
-      int offset = -getAlabels().getScrollOffset();
-      idGraphics.translate(0, offset + alignmentDrawnHeight);
+      int offset = getAlabels().getScrollOffset();
+      idGraphics.translate(0, -offset);
+      idGraphics.translate(0, alignmentDrawnHeight);
       getAlabels().drawComponent(idGraphics, idWidth);
-      idGraphics.translate(0, -offset - alignmentDrawnHeight);
+      idGraphics.translate(0, -alignmentDrawnHeight);
 
       /*
-       * draw the annotations
+       * draw the annotations starting at 
+       * (idOffset, alignmentHeight) from (0, scaleHeight)
        */
       alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
       getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
@@ -1296,8 +1299,8 @@ 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;
   }
@@ -1445,7 +1448,7 @@ 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());
@@ -1459,7 +1462,6 @@ 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
@@ -1475,7 +1477,7 @@ 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())
             {
@@ -1499,18 +1501,20 @@ 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>");
               }
             }
 
@@ -1518,12 +1522,13 @@ 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++)
@@ -1532,15 +1537,15 @@ 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
@@ -1551,13 +1556,13 @@ 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(")");
                     }
                   }
                 }
@@ -1822,14 +1827,14 @@ 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();
 
     /*