X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=00f27aaac335738f261495cec9644fc724b1c073;hb=b01c4edc00dbeedd6b53777310d4232a4104a9ec;hp=af24c9ff5c60b9b66c5a906a911109a874c172fb;hpb=df7880a58e6b16d65f9ed8dbe4433efffbe8abec;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index af24c9f..00f27aa 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);
 
@@ -108,6 +106,13 @@ public class AlignmentPanel extends GAlignmentPanel
     {
       public void keyPressed(KeyEvent evt)
       {
+        if(av.cursorMode
+           && evt.getKeyCode()>=KeyEvent.VK_0
+           && evt.getKeyCode()<=KeyEvent.VK_9)
+        {
+          seqPanel.numberPressed(evt.getKeyChar());
+        }
+
         switch (evt.getKeyCode())
         {
           case 27: // escape key
@@ -117,26 +122,128 @@ public class AlignmentPanel extends GAlignmentPanel
             break;
 
           case KeyEvent.VK_DOWN:
-            alignFrame.moveSelectedSequences(false);
-
+            if(av.cursorMode)
+            {
+              seqPanel.moveCursor(0,1);
+            }
+            else
+              alignFrame.moveSelectedSequences(false);
             break;
 
           case KeyEvent.VK_UP:
-            alignFrame.moveSelectedSequences(true);
+            if (av.cursorMode)
+            {
+              seqPanel.moveCursor(0,-1);
+            }
+            else
+              alignFrame.moveSelectedSequences(true);
+            break;
 
+          case KeyEvent.VK_LEFT:
+            if(av.cursorMode)
+            {
+              seqPanel.moveCursor(-1,0);
+            }
+            break;
+
+          case KeyEvent.VK_RIGHT:
+            if (av.cursorMode)
+            {
+              seqPanel.moveCursor(1,0);
+            }
+            break;
+
+          case KeyEvent.VK_SPACE:
+            if(av.cursorMode)
+            {
+              seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+            }
             break;
 
-          case KeyEvent.VK_BACK_SPACE:
           case KeyEvent.VK_DELETE:
-            alignFrame.cut_actionPerformed(null);
+            if(av.cursorMode)
+            {
+              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+            }
             break;
 
+          case KeyEvent.VK_BACK_SPACE:
+            if(!av.cursorMode)
+            {
+              alignFrame.cut_actionPerformed(null);
+              seqPanel.seqCanvas.repaint();
+            }
+            break;
+
+          case KeyEvent.VK_S:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorRow();
+            }
+            break;
+          case KeyEvent.VK_C:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorColumn();
+            }
+            break;
           case KeyEvent.VK_P:
-            seqPanel.seqCanvas.increaseAARatio();
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorPosition();
+            }
             break;
-          case KeyEvent.VK_L:
-            seqPanel.seqCanvas.decreaseAARation();
+
+          case KeyEvent.VK_ENTER:
+          case KeyEvent.VK_COMMA:
+            if(av.cursorMode)
+            {
+              seqPanel.setCursorRowAndColumn();
+            }
             break;
+
+          case KeyEvent.VK_Q:
+            if(av.cursorMode)
+            {
+              seqPanel.setSelectionAreaAtCursor(true);
+            }
+            break;
+          case KeyEvent.VK_M:
+            if(av.cursorMode)
+            {
+              seqPanel.setSelectionAreaAtCursor(false);
+            }
+            break;
+
+         case KeyEvent.VK_F2:
+           av.cursorMode = ! av.cursorMode;
+           alignFrame.statusBar.setText("Keyboard editing mode is "+
+               (av.cursorMode ? "on" : "off"));
+           if(av.cursorMode)
+           {
+             seqPanel.seqCanvas.cursorX = av.startRes;
+             seqPanel.seqCanvas.cursorY = av.startSeq;
+           }
+           seqPanel.seqCanvas.repaint();
+           break;
+
+          case KeyEvent.VK_F1:
+            try
+            {
+              ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+              java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+              javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+              javax.help.HelpBroker hb = hs.createHelpBroker();
+              hb.setCurrentID("home");
+              hb.setDisplayed(true);
+            }
+            catch (Exception ex)
+            {
+              ex.printStackTrace();
+            }
+            break;
+
         }
       }
     });
@@ -242,22 +349,34 @@ 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)
       {
-        setScrollValues(start, results[0]);
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        {
+          setScrollValues(start, seqIndex);
+        }
+      }
+      else
+      {
+        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;
+        }
       }
     }
   }
@@ -363,7 +482,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public boolean scrollRight(boolean right)
   {
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
@@ -397,30 +516,36 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void setScrollValues(int x, int y)
   {
-    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
-                 1);
+
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
+
+    if(av.hasHiddenColumns)
+     width = av.getColumnSelection().findColumnPosition(width);
+
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
 
     hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
     vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if (hextent > av.alignment.getWidth())
+    if (hextent > width)
     {
-      hextent = av.alignment.getWidth();
+      hextent = width;
     }
 
-    if (vextent > av.alignment.getHeight())
+    if (vextent > height)
     {
-      vextent = av.alignment.getHeight();
+      vextent = height;
     }
 
-    if ( (hextent + x) > av.getAlignment().getWidth())
+    if ( (hextent + x) > width)
     {
-      x = av.getAlignment().getWidth() - hextent;
+      x = width - hextent;
     }
 
-    if ( (vextent + y) > av.getAlignment().getHeight())
+    if ( (vextent + y) > height)
     {
-      y = av.getAlignment().getHeight() - vextent;
+      y = height - vextent;
     }
 
     if (y < 0)
@@ -433,8 +558,8 @@ public class AlignmentPanel extends GAlignmentPanel
       x = 0;
     }
 
-    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
-    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
   }
 
   /**
@@ -444,7 +569,6 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -480,28 +604,33 @@ 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);
+        }
       }
     }
   }
@@ -524,6 +653,8 @@ public class AlignmentPanel extends GAlignmentPanel
     {
       int max = av.alignment.getWidth() /
           seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
+
+
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -533,12 +664,10 @@ public class AlignmentPanel extends GAlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-
-    if( this.getVisibleRect().getBounds() == g.getClipBounds() )
-    {
-      if (overviewPanel != null)
+    if( this.getVisibleRect().getBounds() == g.getClipBounds()
+        && overviewPanel != null)
         overviewPanel.updateOverviewImage();
-    }
+
   }
 
   /**
@@ -657,6 +786,9 @@ 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) &&
@@ -686,16 +818,17 @@ 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,
-                                 startRes, startSeq, 0);
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
     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 +906,14 @@ 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));
       }
@@ -841,15 +974,19 @@ 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)
     {
@@ -916,7 +1053,7 @@ public class AlignmentPanel extends GAlignmentPanel
           sy = s * av.charHeight + scaleHeight;
 
           SequenceI seq = av.alignment.getSequenceAt(s);
-          java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();
+          SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
           SequenceGroup[] groups = av.alignment.findAllGroups(seq);
           for(res =0; res<alwidth; res++)
           {
@@ -963,33 +1100,32 @@ public class AlignmentPanel extends GAlignmentPanel
                   + " onMouseOver=\"toolTip('"
                   + alIndex + " " + triplet );
               }
-                fSize = features.size();
+                fSize = features.length;
                 for (f = 0; f < fSize; f++)
                 {
-                  SequenceFeature sf = (SequenceFeature) features.elementAt(f);
 
-                  if ( (sf.getBegin() <= seq.findPosition(res)) &&
-                      (sf.getEnd() >= seq.findPosition(res)))
+                  if ( (features[f].getBegin() <= seq.findPosition(res)) &&
+                      (features[f].getEnd() >= seq.findPosition(res)))
                   {
-                    if (sf.getType().equals("disulfide bond"))
+                    if (features[f].getType().equals("disulfide bond"))
                     {
-                      if (sf.getBegin() == seq.findPosition(res)
-                          || sf.getEnd() == seq.findPosition(res))
+                      if (features[f].getBegin() == seq.findPosition(res)
+                          || features[f].getEnd() == seq.findPosition(res))
                       {
-                        text.append("<br>disulfide bond " + sf.getBegin() + ":" +
-                                       sf.getEnd());
+                        text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
+                                       features[f].getEnd());
                       }
                     }
                     else
                     {
                       text.append("<br>");
-                      text.append(sf.getType());
-                      if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
-                        text.append(" " + sf.getDescription());
+                      text.append(features[f].getType());
+                      if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
+                        text.append(" " + features[f].getDescription());
 
-                      if (sf.getStatus() != null && sf.getStatus().length()>0)
+                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
                       {
-                        text.append(" (" + sf.getStatus() + ")");
+                        text.append(" (" + features[f].getStatus() + ")");
                       }
                     }
                   }