X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f81e471e67966cb9aed1bb31f35455791399d9e0;hb=7c12f8eb9879172c5c437143ca5eb811a8daf5c7;hp=ed00d3379d6c59bec106afe6b8878f4a64c18a68;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ed00d33..f81e471 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -81,9 +81,7 @@ public class AlignmentPanel extends GAlignmentPanel
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
@@ -242,22 +240,34 @@ public class AlignmentPanel extends GAlignmentPanel
    *
    * @param results DOCUMENT ME!
    */
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
     // do we need to scroll the panel?
     if (results != null)
     {
-      SequenceI seq = av.alignment.getSequenceAt(results[0]);
-      int start = seq.findIndex(results[1]) - 1;
-      int end = seq.findIndex(results[2]) - 1;
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-          ( (av.getStartSeq() > results[0]) ||
-           (av.getEndSeq() < results[0])))
+      if(!av.wrapAlignment)
+      {
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        {
+          setScrollValues(start, seqIndex);
+        }
+      }
+      else
       {
-        setScrollValues(start, results[0]);
+        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
+        {
+          vscroll.setValue(start / cwidth);
+          av.startRes = vscroll.getValue() * cwidth;
+        }
       }
     }
   }
@@ -480,28 +490,33 @@ public class AlignmentPanel extends GAlignmentPanel
       overviewPanel.setBoxPosition();
     }
 
-    int xShift = av.getStartRes() - oldX;
-    int yShift = av.getStartSeq() - oldY;
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
 
-    if ( (xShift != 0 && yShift != 0) ||
-        (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
-         || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
-        || av.getWrapAlignment()
-        || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint)
     {
-      // Either no shift at all, or shift greater than visible amount
       repaint();
     }
     else
     {
-      idPanel.idCanvas.fastPaint(yShift);
-      seqPanel.seqCanvas.fastPaint(xShift, yShift);
-
-      scalePanel.repaint();
-
-      if (av.getShowAnnotation())
+      // Make sure we're not trying to draw a panel
+      // larger than the visible window
+      if(scrollX>av.endRes-av.startRes)
+        scrollX = av.endRes-av.startRes;
+      else if(scrollX<av.startRes-av.endRes)
+        scrollX = av.startRes - av.endRes;
+
+      if(scrollX!=0 || scrollY!=0)
       {
-        annotationPanel.fastPaint(xShift);
+        idPanel.idCanvas.fastPaint(scrollY);
+        seqPanel.seqCanvas.fastPaint(scrollX,
+                                     scrollY);
+        scalePanel.repaint();
+
+        if (av.getShowAnnotation())
+        {
+          annotationPanel.fastPaint(scrollX);
+        }
       }
     }
   }
@@ -657,6 +672,9 @@ public class AlignmentPanel extends GAlignmentPanel
     Color currentColor = null;
     Color currentTextColor = null;
 
+    pg.setFont(new Font(av.getFont().getName(),
+                        Font.ITALIC,
+                        av.getFont().getSize()));
     for (int i = startSeq; i < endSeq; i++)
     {
       if ( (av.getSelectionGroup() != null) &&
@@ -686,6 +704,8 @@ public class AlignmentPanel extends GAlignmentPanel
                     (av.getCharHeight() / 5));
     }
 
+    pg.setFont(av.getFont());
+
     // draw main sequence panel
     pg.translate(idWidth, 0);
     seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
@@ -693,9 +713,9 @@ public class AlignmentPanel extends GAlignmentPanel
 
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
     {
-      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);
+      pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
       alabels.drawComponent( (Graphics2D) pg, idWidth);
-      pg.translate(idWidth, 0);
+      pg.translate(idWidth+3, 0);
       annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
                                     1);
     }
@@ -773,14 +793,14 @@ public class AlignmentPanel extends GAlignmentPanel
       }
       if (labels != null)
       {
-        pg.translate(0,
+        pg.translate(-3,
                      ypos +
                      (av.getAlignment().getHeight() * av.charHeight));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
         pg.setFont(italic);
-        pg.translate(0,
+        pg.translate(+3,
                      -ypos -
                      (av.getAlignment().getHeight() * av.charHeight));
       }
@@ -809,6 +829,11 @@ public class AlignmentPanel extends GAlignmentPanel
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
     int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
+    if (idPanel.getWidth() == 0)
+    {
+      width += calculateIdWidth().getWidth() + 4;
+    }
+
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
@@ -836,15 +861,19 @@ public class AlignmentPanel extends GAlignmentPanel
       if (av.getWrapAlignment())
       {
         if(im.getGraphics()!=null)
+        {
           printWrappedAlignment(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
       }
       else
       {
         if(im.getGraphics()!=null)
+        {
           printUnwrapped(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
       }
-
-      im.writeImage();
     }
     catch (OutOfMemoryError err)
     {
@@ -897,45 +926,107 @@ public class AlignmentPanel extends GAlignmentPanel
     {
       try
       {
+        int s, sSize = av.alignment.getHeight(),
+            res, alwidth = av.alignment.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 +
                     "\" border=\"0\" usemap=\"#Map\" >"
                     + "<map name=\"Map\">");
 
-        for (int s = 0; s < av.alignment.getHeight(); s++)
+        for (s = 0; s < sSize; s++)
         {
+          sy = s * av.charHeight + scaleHeight;
+
           SequenceI seq = av.alignment.getSequenceAt(s);
+          java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();
           SequenceGroup[] groups = av.alignment.findAllGroups(seq);
-          for (int i = 0; i < groups.length; i++)
+          for(res =0; res<alwidth; res++)
           {
-            int sy = s * av.charHeight + scaleHeight;
-            for (int res = groups[i].getStartRes();
-                 res < groups[i].getEndRes() + 1; res++)
-            {
-              int alIndex = seq.findPosition(res);
-              Object obj = ResidueProperties.aa2Triplet.get(
-                  seq.getCharAt(res) + "");
+            text = new StringBuffer();
+            Object obj = null;
+            if(av.alignment.isNucleotide())
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
+            else
+              obj = ResidueProperties.aa2Triplet.get(
+                    seq.getCharAt(res) + "");
+
               if (obj == null)
-                continue;
+                  continue;
 
-              String triplet = obj.toString();
+            String triplet = obj.toString();
+            int alIndex = seq.findPosition(res);
+            gSize = groups.length;
+            for (g = 0; g < gSize; g++)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                  + (idWidth + res * av.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
 
-              out.println(
-                  "<area shape=\"rect\" coords=\""
+              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+            }
+
+            if (features != null)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
                   + (idWidth + res * av.charWidth) + ","
                   + sy + ","
                   + (idWidth + (res + 1) * av.charWidth) + ","
                   + (av.charHeight + sy) + "\""
                   + " onMouseOver=\"toolTip('"
-                  + alIndex + " " + triplet +
-                  "<br><em>" + groups[i].getName() +
-                  "</em>')\"; onMouseOut=\"toolTip()\"; "
-                  + " href=\"#\">");
+                  + alIndex + " " + triplet );
+              }
+                fSize = features.size();
+                for (f = 0; f < fSize; f++)
+                {
+                  SequenceFeature sf = (SequenceFeature) features.elementAt(f);
+
+                  if ( (sf.getBegin() <= seq.findPosition(res)) &&
+                      (sf.getEnd() >= seq.findPosition(res)))
+                  {
+                    if (sf.getType().equals("disulfide bond"))
+                    {
+                      if (sf.getBegin() == seq.findPosition(res)
+                          || sf.getEnd() == seq.findPosition(res))
+                      {
+                        text.append("<br>disulfide bond " + sf.getBegin() + ":" +
+                                       sf.getEnd());
+                      }
+                    }
+                    else
+                    {
+                      text.append("<br>");
+                      text.append(sf.getType());
+                      if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
+                        text.append(" " + sf.getDescription());
+
+                      if (sf.getStatus() != null && sf.getStatus().length()>0)
+                      {
+                        text.append(" (" + sf.getStatus() + ")");
+                      }
+                    }
+                  }
+
+                }
+              }
+              if(text.length()>1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
+              }
             }
           }
-        }
-
         out.println("</map></body></html>");
         out.close();