X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=f2fca589848182a743d78f3228be7d8282fc73ec;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=ba6d8735118473ceab00691f1aa93b8455bd9e4a;hpb=e8ede151da126e8fe205392c64f1604d80adda6d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index ba6d873..f2fca58 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,32 +1,46 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Hashtable;
-import java.util.Vector;
-
 import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
 
-public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+
+public class AlignmentPanel extends Panel implements AdjustmentListener,
+        AlignmentViewPanel
 {
 
   public AlignViewport av;
@@ -49,19 +63,21 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
-  
-  public void finalize() {
-    alignFrame=null;
-    av=null;
-    seqPanel=null;
-    seqPanelHolder=null;
-    sequenceHolderPanel=null;
-    scalePanel=null;
-    scalePanelHolder=null;
-    annotationPanel=null;
-    annotationPanelHolder=null;
-    annotationSpaceFillerHolder=null;
+
+  public void finalize()
+  {
+    alignFrame = null;
+    av = null;
+    seqPanel = null;
+    seqPanelHolder = null;
+    sequenceHolderPanel = null;
+    scalePanel = null;
+    scalePanelHolder = null;
+    annotationPanel = null;
+    annotationPanelHolder = null;
+    annotationSpaceFillerHolder = null;
   }
+
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     try
@@ -82,7 +98,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
 
     sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
-
     alabels = new AnnotationLabels(this);
 
     setAnnotationVisible(av.showAnnotation);
@@ -105,12 +120,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
       public void componentResized(ComponentEvent evt)
       {
         setScrollValues(av.getStartRes(), av.getStartSeq());
-        if (getSize().height>0 && annotationPanelHolder.getSize().height>0) {
+        if (getSize().height > 0
+                && annotationPanelHolder.getSize().height > 0)
+        {
           validateAnnotationDimensions(false);
         }
         repaint();
       }
-      
+
     });
 
     Dimension d = calculateIdWidth();
@@ -134,7 +151,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
         }
       }
     });
-
   }
 
   public SequenceRenderer getSequenceRenderer()
@@ -177,10 +193,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
     alabels.setSize(d.width + 4, ap);
-    
+
     idPanel.idCanvas.setSize(d);
     hscrollFillerPanel.setSize(d);
-    
+
     validateAnnotationDimensions(false);
     annotationPanel.repaint();
     validate();
@@ -196,7 +212,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   {
     idPanel.idCanvas.setSize(w, h);
     idPanelHolder.setSize(w, idPanelHolder.getSize().height);
-    annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
+    annotationSpaceFillerHolder.setSize(w,
+            annotationSpaceFillerHolder.getSize().height);
     alabels.setSize(w, alabels.getSize().height);
     validate();
   }
@@ -282,31 +299,36 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   public boolean scrollToPosition(SearchResults results,
           boolean redrawOverview)
   {
-	  
+
     // do we need to scroll the panel?
     if (results != null && results.getSize() > 0)
     {
-      AlignmentI alignment=av.getAlignment();
+      AlignmentI alignment = av.getAlignment();
       int seqIndex = alignment.findIndex(results);
       if (seqIndex == -1)
       {
         return false;
       }
       SequenceI seq = alignment.getSequenceAt(seqIndex);
-      int[] r = results.getResults(seq, 0,alignment.getWidth());
+      int[] r = results.getResults(seq, 0, alignment.getWidth());
       if (r == null)
       {
-        if (av.applet.debug) {// DEBUG
-          System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
+        if (av.applet.debug)
+        {// DEBUG
+          System.out
+                  .println("DEBUG: scroll didn't happen - results not within alignment : "
+                          + seq.getStart() + "," + seq.getEnd());
         }
         return false;
       }
-      if (av.applet.debug) {
+      if (av.applet.debug)
+      {
         // DEBUG
-        /*System.out.println("DEBUG: scroll: start=" + r[0]
-                + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
-                + " seq.end=" + seq.getEnd() + " av.getEndRes()="
-                + av.getEndRes() + " hextent=" + hextent);
+        /*
+         * System.out.println("DEBUG: scroll: start=" + r[0] +
+         * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
+         * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
+         * " hextent=" + hextent);
          */
       }
       int start = r[0];
@@ -323,11 +345,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     }
     return true;
   }
-  public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview)
+
+  public boolean scrollTo(int ostart, int end, int seqIndex,
+          boolean scrollToNearest, boolean redrawOverview)
   {
-	    int startv, endv, starts, ends, width;
+    int startv, endv, starts, ends, width;
 
-	  int start=-1;
+    int start = -1;
     if (av.hasHiddenColumns())
     {
       start = av.getColumnSelection().findColumnPosition(ostart);
@@ -347,58 +371,47 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     }
     if (!av.wrapAlignment)
     {
-    	  /*
-    	  int spos=av.getStartRes(),sqpos=av.getStartSeq();
-          if ((startv = av.getStartRes()) >= start)
-          {
-        	  spos=start-1;
-//        	  seqIn
-//            setScrollValues(start - 1, seqIndex);
-          }
-          else if ((endv = av.getEndRes()) <= end)
-          {
-//            setScrollValues(spos=startv + 1 + end - endv, seqIndex);
-        	  spos=startv + 1 + end - endv;
-          }
-          else if ((starts = av.getStartSeq()) > seqIndex)
-          {
-            setScrollValues(av.getStartRes(), seqIndex);
-          }
-          else if ((ends = av.getEndSeq()) <= seqIndex)
+      /*
+       * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+       * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+       * setScrollValues(start - 1, seqIndex); } else if ((endv =
+       * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+       * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+       * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+       * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+       * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+       * 
+       * /*
+       */
+      if ((av.getStartRes() > end)
+              || (av.getEndRes() < start)
+              || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+      {
+        if (start > av.getAlignment().getWidth() - hextent)
+        {
+          start = av.getAlignment().getWidth() - hextent;
+          if (start < 0)
           {
-            setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+            start = 0;
           }
 
-    	  /* */
-        if ((av.getStartRes() > end)
-                || (av.getEndRes() < start)
-                || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        }
+        if (seqIndex > av.getAlignment().getHeight() - vextent)
         {
-          if (start > av.getAlignment().getWidth() - hextent)
-          {
-            start = av.getAlignment().getWidth() - hextent;
-            if (start < 0)
-            {
-              start = 0;
-            }
-
-          }
-          if (seqIndex > av.getAlignment().getHeight() - vextent)
+          seqIndex = av.getAlignment().getHeight() - vextent;
+          if (seqIndex < 0)
           {
-            seqIndex = av.getAlignment().getHeight() - vextent;
-            if (seqIndex < 0)
-            {
-              seqIndex = 0;
-            }
+            seqIndex = 0;
           }
-          // System.out.println("trying to scroll to: "+start+" "+seqIndex);
-          setScrollValues(start, seqIndex);
-        }/**/
-      }
-      else
-      {
-        scrollToWrappedVisible(start);
-      }
+        }
+        // System.out.println("trying to scroll to: "+start+" "+seqIndex);
+        setScrollValues(start, seqIndex);
+      }/**/
+    }
+    else
+    {
+      scrollToWrappedVisible(start);
+    }
     if (redrawOverview && overviewPanel != null)
     {
       overviewPanel.setBoxPosition();
@@ -435,10 +448,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
       annotationSpaceFillerHolder.setVisible(b);
       annotationPanelHolder.setVisible(b);
     }
+    else
+    {
+      annotationSpaceFillerHolder.setVisible(false);
+      annotationPanelHolder.setVisible(false);
+    }
     validate();
     repaint();
   }
-  
+
   /**
    * automatically adjust annotation panel height for new annotation whilst
    * ensuring the alignment is still visible.
@@ -458,55 +476,76 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     validate();
     paintAlignment(true);
   }
+
   /**
    * calculate the annotation dimensions and refresh slider values accordingly.
-   * need to do repaints/notifys afterwards. 
+   * need to do repaints/notifys afterwards.
    */
-  protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
-    boolean modified=false;
+  protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+  {
+    boolean modified = false;
     int height = av.calcPanelHeight();
-    int minsize=0;
+    int minsize = 0;
     if (hscroll.isVisible())
     {
-      height += (minsize=hscroll.getPreferredSize().height);
+      height += (minsize = hscroll.getPreferredSize().height);
     }
-    if (apvscroll.isVisible()) {
-      minsize+=apvscroll.getPreferredSize().height;
+    if (apvscroll.isVisible())
+    {
+      minsize += apvscroll.getPreferredSize().height;
     }
     int mheight = height;
-    Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize(); 
-    int seqandannot=d.height-scalePanelHolder.getSize().height;
-    // sets initial preferred height
-    if ((height+40) > seqandannot / 2)
-    {
-      height = seqandannot / 2;
+    Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
+    int seqandannot = d.height - scalePanelHolder.getSize().height;
+
+    if (adjustPanelHeight)
+    {
+      // NOTE: this logic is different in the application. Need a better
+      // algorithm to define behaviour
+      // sets initial preferred height
+      // try and set height according to alignment
+      float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
+              .getHeight()) / (1.0 * mheight));
+      if (sscaling > 0.5)
+      {
+        // if the alignment is too big then
+        // default is 0.5 split
+        height = seqandannot / 2;
+      }
+      else
+      {
+        // otherwise just set the panel so that one row of sequence is visible
+        height = -av.getCharHeight() * 1
+                + (int) (seqandannot * (1 - sscaling));
+      }
     }
-    if (!adjustPanelHeight)
+    else
     {
       // maintain same window layout whilst updating sliders
-      height=annotationPanelHolder.getSize().height;
+      height = annotationPanelHolder.getSize().height;
     }
-            
-    if (seqandannot-height<5)
+
+    if (seqandannot - height < 5)
     {
       height = seqandannot;
     }
-    annotationPanel.setSize(new Dimension(d.width,height));
-    alabels.setSize(new Dimension(e.width,height));
+    annotationPanel.setSize(new Dimension(d.width, height));
+    alabels.setSize(new Dimension(e.width, height));
     annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
     annotationPanelHolder.setSize(new Dimension(d.width, height));
-    seqPanelHolder.setSize(d.width,seqandannot-height);
-    seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-    int s=apvscroll.getValue();
-    if (s>mheight-height)
+    // seqPanelHolder.setSize(d.width, seqandannot - height);
+    seqPanel.seqCanvas
+            .setSize(d.width, seqPanel.seqCanvas.getSize().height);
+    int s = apvscroll.getValue();
+    if (s > mheight - height)
     {
       s = 0;
     }
     apvscroll.setValues(s, height, 0, mheight);
-    annotationPanel.setScrollOffset(apvscroll.getValue());
-    alabels.setScrollOffset(apvscroll.getValue());
+    annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+    alabels.setScrollOffset(apvscroll.getValue(), false);
   }
-  
+
   public void setWrapAlignment(boolean wrap)
   {
     av.startSeq = 0;
@@ -532,6 +571,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     fontChanged(); // This is so that the scalePanel is resized correctly
 
     validate();
+    sequenceHolderPanel.validate();
     repaint();
 
   }
@@ -596,11 +636,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     {
       width = av.getColumnSelection().findColumnPosition(width);
     }
-    if (x<0) { x = 0; };
+    if (x < 0)
+    {
+      x = 0;
+    }
+    ;
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
-    
+
     if (hextent > width)
     {
       hextent = width;
@@ -613,7 +657,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
     if ((hextent + x) > width)
     {
-      System.err.println("hextent was "+hextent+" and x was "+x);
+      System.err.println("hextent was " + hextent + " and x was " + x);
 
       x = width - hextent;
     }
@@ -630,7 +674,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
     if (x < 0)
     {
-      System.err.println("x was "+x);
+      System.err.println("x was " + x);
       x = 0;
     }
 
@@ -655,7 +699,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     }
     sendViewPosition();
 
-
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -665,8 +708,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
     if (evt == null || evt.getSource() == apvscroll)
     {
-      annotationPanel.setScrollOffset(apvscroll.getValue());
-      alabels.setScrollOffset(apvscroll.getValue());
+      annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+      alabels.setScrollOffset(apvscroll.getValue(), false);
       // annotationPanel.image=null;
       // alabels.image=null;
       // alabels.repaint();
@@ -735,9 +778,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     sendViewPosition();
 
   }
+
   private void sendViewPosition()
   {
-    StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq);
+    StructureSelectionManager.getStructureSelectionManager(av.applet)
+            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
+                    av.endSeq);
   }
 
   public void paintAlignment(boolean updateOverview)
@@ -747,7 +793,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     if (updateOverview)
     {
       jalview.structure.StructureSelectionManager
-              .getStructureSelectionManager(av.applet).sequenceColoursChanged(this);
+              .getStructureSelectionManager(av.applet)
+              .sequenceColoursChanged(this);
 
       if (overviewPanel != null)
       {
@@ -766,7 +813,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     invalidate();
     Dimension d = idPanel.idCanvas.getSize();
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-    
+
     if (av.getWrapAlignment())
     {
       int maxwidth = av.getAlignment().getWidth();
@@ -792,12 +839,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-    alabels.repaint();
-
     seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
     idPanel.idCanvas.repaint();
+    if (!av.wrapAlignment)
+    {
+      if (av.showAnnotation)
+      {
+        alabels.repaint();
+        annotationPanel.repaint();
+      }
+      scalePanel.repaint();
+    }
+
   }
 
   protected Panel sequenceHolderPanel = new Panel();
@@ -849,7 +902,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     // idPanelHolder.setPreferredSize(new Dimension(70, 10));
     this.setLayout(borderLayout7);
 
-    //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
     sequenceHolderPanel.setLayout(borderLayout3);
     seqPanelHolder.setLayout(borderLayout1);
     scalePanelHolder.setBackground(Color.white);
@@ -906,65 +959,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
-    // TODO: this should be merged with other annotation update stuff - that
-    // sits on AlignViewport
-    boolean updateCalcs = false;
-    boolean conv = av.isShowGroupConservation();
-    boolean cons = av.isShowGroupConsensus();
-    boolean showprf = av.isShowSequenceLogo();
-    boolean showConsHist = av.isShowConsensusHistogram();
-
-    boolean sortg = true;
-
-    // remove old automatic annotation
-    // add any new annotation
-
-    ; // OrderedBy(av.alignment.getSequencesArray());
-    // intersect alignment annotation with alignment groups
+    updateAnnotation(applyGlobalSettings, false);
+  }
 
-    AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
-    Hashtable oldrfs = new Hashtable();
-    if (aan != null)
-    {
-      for (int an = 0; an < aan.length; an++)
-      {
-        if (aan[an].autoCalculated && aan[an].groupRef != null)
-        {
-          oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-          av.getAlignment().deleteAnnotation(aan[an]);
-          aan[an] = null;
-        }
-      }
-    }
-    if (av.getAlignment().getGroups()!= null)
-    {
-      for (SequenceGroup sg:av.getAlignment().getGroups())
-      {
-        updateCalcs = false;
-        if (applyGlobalSettings || !oldrfs.containsKey(sg))
-        {
-          // set defaults for this group's conservation/consensus
-          sg.setshowSequenceLogo(showprf);
-          sg.setShowConsensusHistogram(showConsHist);
-        }
-        if (conv)
-        {
-          updateCalcs = true;
-          av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
-        }
-        if (cons)
-        {
-          updateCalcs = true;
-          av.getAlignment().addAnnotation(sg.getConsensus(), 0);
-        }
-        // refresh the annotation rows
-        if (updateCalcs)
-        {
-          sg.recalcConservation();
-        }
-      }
-    }
-    oldrfs.clear();
+  public void updateAnnotation(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    av.updateGroupAnnotationSettings(applyGlobalSettings,
+            preserveNewGroupSettings);
     adjustAnnotationHeight();
   }
 
@@ -973,16 +975,25 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   {
     return av.getAlignment();
   }
+
+  @Override
+  public String getViewName()
+  {
+    return getName();
+  }
+
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return StructureSelectionManager.getStructureSelectionManager(av.applet);
+    return StructureSelectionManager
+            .getStructureSelectionManager(av.applet);
   }
+
   @Override
   public void raiseOOMWarning(String string, OutOfMemoryError error)
   {
     // TODO: JAL-960
-    System.err.println("Out of memory whilst '"+string+"'");
+    System.err.println("Out of memory whilst '" + string + "'");
     error.printStackTrace();
   }