X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8e02a9c3c7cbce6c68e5ada9b25730e11b81d724;hb=d2f3c59deebfd9ea52b0021ab31467c18b9d2c14;hp=fdd01d3d09a8514ddd5083ca334a5a16978a8ab1;hpb=3a455483336b530b45d449270069815a933151d2;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fdd01d3..8e02a9c 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -32,6 +32,8 @@ import java.io.*;
 
 import javax.swing.*;
 
+import org.biojava.dasobert.eventmodel.*;
+
 
 /**
  * DOCUMENT ME!
@@ -40,7 +42,7 @@ import javax.swing.*;
  * @version $Revision$
  */
 public class AlignmentPanel extends GAlignmentPanel
-    implements AdjustmentListener, Printable
+    implements AdjustmentListener, Printable, FeatureListener
 {
   public AlignViewport av;
   OverviewPanel overviewPanel;
@@ -92,11 +94,8 @@ public class AlignmentPanel extends GAlignmentPanel
 
     setScrollValues(0, 0);
 
-    annotationPanel.adjustPanelHeight();
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.
-                                        getPreferredSize());
+    adjustAnnotationHeight();
+
     setAnnotationVisible(av.getShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
@@ -106,6 +105,13 @@ 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
@@ -115,31 +121,146 @@ 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);
+          case KeyEvent.VK_BACK_SPACE:
+            if(!av.cursorMode)
+            {
+              alignFrame.cut_actionPerformed(null);
+              seqPanel.seqCanvas.repaint();
+            }
+            else
+              seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
+
             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;
+
         }
       }
     });
   }
 
+  public void comeBackLater(FeatureEvent evt)
+  {}
+
+  public void newFeatures(FeatureEvent evt)
+  {
+    if (evt.getFeatures().length > 0)
+    {
+      seqPanel.seqCanvas.fr.featuresAdded();
+      repaint();
+    }
+    else
+    {
+      System.out.println("No Features found for "+evt.getDasSource().getNickname());
+    }
+  }
+
   /**
    * DOCUMENT ME!
    */
@@ -240,37 +361,43 @@ 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.wrapAlignment)
       {
-        if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-            ( (av.getStartSeq() > results[0]) ||
-             (av.getEndSeq() < results[0])))
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
         {
-          setScrollValues(start, results[0]);
+          setScrollValues(start, seqIndex);
         }
       }
       else
       {
-        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
-        {
-          vscroll.setValue(start / cwidth);
-        }
+        scrollToWrappedVisible(start);
       }
     }
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -306,6 +433,37 @@ public class AlignmentPanel extends GAlignmentPanel
     repaint();
   }
 
+  public void adjustAnnotationHeight()
+  {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+          while(alignFrame.getHeight()==0)
+          {
+            Thread.yield();
+          }
+
+        int height = annotationPanel.adjustPanelHeight();
+
+        if (height > alignFrame.getHeight() / 2)
+        {
+          height = alignFrame.getHeight() / 2;
+        }
+
+        annotationScroller.setPreferredSize(
+            new Dimension(annotationScroller.getWidth(),
+                          height));
+
+        annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            annotationSpaceFillerHolder.getWidth(),
+            height));
+
+        annotationPanel.repaint();
+      }
+    });
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -372,7 +530,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public boolean scrollRight(boolean right)
   {
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
@@ -406,30 +564,36 @@ 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)
@@ -442,8 +606,8 @@ 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);
   }
 
   /**
@@ -453,7 +617,6 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -538,6 +701,8 @@ 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);
@@ -547,12 +712,10 @@ 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();
-    }
+
   }
 
   /**
@@ -707,8 +870,7 @@ public class AlignmentPanel extends GAlignmentPanel
 
     // 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()))
     {
@@ -827,7 +989,6 @@ 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;
@@ -836,7 +997,15 @@ public class AlignmentPanel extends GAlignmentPanel
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
-      width = seqPanel.getWidth() + idPanel.getWidth();
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        width = alignFrame.getWidth() - 22;
+      }
+      else
+
+        width = seqPanel.getWidth() + idPanel.getWidth();
+
     }
     else if (av.getShowAnnotation())
     {
@@ -939,7 +1108,7 @@ 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++)
           {
@@ -986,33 +1155,32 @@ 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].getValue("status") != null )
                       {
-                        text.append(" (" + sf.getStatus() + ")");
+                        text.append(" (" + features[f].getValue("status") + ")");
                       }
                     }
                   }
@@ -1040,9 +1208,19 @@ public class AlignmentPanel extends GAlignmentPanel
 
   int getWrappedHeight()
   {
+    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+
+    //If headless, seqPanel will have 0 width
+    if (System.getProperty("java.awt.headless") != null
+              && System.getProperty("java.awt.headless").equals("true"))
+    {
+      int idWidth = calculateIdWidth().width + 4;
+      seqPanelWidth = alignFrame.getWidth() - idWidth;
+    }
 
     int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
-        seqPanel.seqCanvas.getWidth());
+        seqPanelWidth
+          );
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)