X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b7028ac1db9b1a30f4de3beda4e6451b11f2490e;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=17a24f6784db057381f7fb9a317c74d6ad9e289b;hpb=5ec1087f3f500339cbcba33e604164cb828a9cd8;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755
new mode 100644
index 17a24f6..b7028ac
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,45 +1,48 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.gui;
 
 import java.beans.*;
 import java.io.*;
+import java.util.Hashtable;
+import java.util.Vector;
 
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.161 $
  */
 public class AlignmentPanel extends GAlignmentPanel implements
-        AdjustmentListener, Printable
+        AdjustmentListener, Printable, AlignmentViewPanel
 {
   public AlignViewport av;
 
@@ -71,9 +74,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Creates a new AlignmentPanel object.
    * 
    * @param af
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
@@ -178,8 +181,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     AlignmentI al = av.getAlignment();
     int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-    int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
-            / 3));
+    int maxwidth = Math.max(20,
+            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
     int i = 0;
     int idWidth = 0;
     String id;
@@ -222,75 +225,100 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Highlight the given results on the alignment.
    * 
-   * @param results
-   *                DOCUMENT ME!
    */
   public void highlightSearchResults(SearchResults results)
   {
     scrollToPosition(results);
     seqPanel.seqCanvas.highlightSearchResults(results);
   }
+
   /**
-   * scroll the view to show the position of the highlighted
-   * region in results (if any) and redraw the overview
+   * scroll the view to show the position of the highlighted region in results
+   * (if any) and redraw the overview
+   * 
    * @param results
    */
-  public boolean scrollToPosition(SearchResults results) {
+  public boolean scrollToPosition(SearchResults results)
+  {
     return scrollToPosition(results, true);
   }
+
   /**
-   * scroll the view to show the position of the highlighted
-   * region in results (if any)
+   * scroll the view to show the position of the highlighted region in results
+   * (if any)
+   * 
    * @param results
-   * @param redrawOverview - when set, the overview will be recalculated (takes longer)
+   * @param redrawOverview
+   *          - when set, the overview will be recalculated (takes longer)
    * @return false if results were not found
    */
-  public boolean scrollToPosition(SearchResults results, boolean redrawOverview) {
-    int startv,endv,starts,ends,width;
-    // TODO: properly locate search results in view when large numbers of hidden columns exist before highlighted region
+  public boolean scrollToPosition(SearchResults results,
+          boolean redrawOverview)
+  {
+    int startv, endv, starts, ends, width;
+    // TODO: properly locate search results in view when large numbers of hidden
+    // columns exist before highlighted region
     // do we need to scroll the panel?
     // TODO: tons of nullpointereexceptions raised here.
-    if (results != null && results.getSize()>0 && av!=null && av.alignment!=null)
+    if (results != null && results.getSize() > 0 && av != null
+            && av.alignment != null)
     {
       int seqIndex = av.alignment.findIndex(results);
-      if (seqIndex==-1)
+      if (seqIndex == -1)
       {
         return false;
       }
       SequenceI seq = av.alignment.getSequenceAt(seqIndex);
       
-      int [] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq, seq.getStart(), seq.getEnd());
-      // TODO: VAMSAS: fix hidden column issue where scroll to left from C terminus is not visible
-      if (r==null)
+      int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+      if (r == null)
       {
         return false;
       }
       int start = r[0];
       int end = r[1];
-      if (start<0)
+      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+      // DEBUG
+      if (start < 0)
       {
         return false;
       }
-      if (end==seq.getEnd())
+      if (end == seq.getEnd())
       {
         return false;
       }
+      if (av.hasHiddenColumns)
+      {
+        start = av.getColumnSelection().findColumnPosition(start);
+        end = av.getColumnSelection().findColumnPosition(end);
+        if (start==end)
+        {
+          if (!av.colSel.isVisible(r[0]))
+          {
+            // don't scroll - position isn't visible
+            return false;
+          }
+        }
+      }
       if (!av.wrapAlignment)
       {
-        if ((startv=av.getStartRes()) >= start)
+        if ((startv = av.getStartRes()) >= start)
+        {
+          setScrollValues(start - 1, seqIndex);
+        }
+        else if ((endv = av.getEndRes()) <= end)
         {
-          setScrollValues(start-1, seqIndex);
-        } else if
-                ((endv=av.getEndRes()) <= end)
+          setScrollValues(startv + 1 + end - endv, seqIndex);
+        }
+        else if ((starts = av.getStartSeq()) > seqIndex)
         {
-          setScrollValues(startv+1+end-endv, seqIndex);
-        } else if ((starts=av.getStartSeq()) > seqIndex) {
           setScrollValues(av.getStartRes(), seqIndex);
-        } else if ((ends=av.getEndSeq()) <= seqIndex)
+        }
+        else if ((ends = av.getEndSeq()) <= seqIndex)
         {
-          setScrollValues(av.getStartRes(), starts+seqIndex-ends+1);
+          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
         }
       }
       else
@@ -298,11 +326,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
         scrollToWrappedVisible(start);
       }
     }
-    if (!redrawOverview && overviewPanel!=null)
+    if (redrawOverview && overviewPanel != null)
     {
       overviewPanel.setBoxPosition();
-    } 
-    paintAlignment(!redrawOverview);
+    }
+    paintAlignment(redrawOverview);
     return true;
   }
 
@@ -310,7 +338,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int cwidth = seqPanel.seqCanvas
             .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-    if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth))
+    if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
       av.startRes = vscroll.getValue() * cwidth;
@@ -332,7 +360,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param op
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setOverviewPanel(OverviewPanel op)
   {
@@ -340,10 +368,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @param b
-   *                DOCUMENT ME!
+   * @param b Hide or show annotation panel
+   *          
    */
   public void setAnnotationVisible(boolean b)
   {
@@ -355,6 +382,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
+  /**
+   * automatically adjust annotation panel height for new annotation
+   * whilst ensuring the alignment is still visible.
+   */
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary
@@ -363,9 +394,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       System.out.println("NEEDS FIXING");
     }
-
+    validateAnnotationDimensions(true);
+    addNotify();
+    paintAlignment(true);
+  }
+  /**
+   * calculate the annotation dimensions and refresh slider values accordingly.
+   * need to do repaints/notifys afterwards. 
+   */
+  protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
     int height = annotationPanel.adjustPanelHeight();
-
+    
     if (hscroll.isVisible())
     {
       height += hscroll.getPreferredSize().height;
@@ -374,23 +413,27 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       height = alignFrame.getHeight() / 2;
     }
-
+    if (!adjustPanelHeight)
+    {
+      // maintain same window layout whilst updating sliders
+      height=annotationScroller.getSize().height;
+    }
     hscroll.addNotify();
-
+    
     annotationScroller.setPreferredSize(new Dimension(annotationScroller
             .getWidth(), height));
 
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), height));
     annotationScroller.validate();// repaint();
-    repaint();
+    annotationScroller.addNotify();
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param wrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setWrapAlignment(boolean wrap)
   {
@@ -448,7 +491,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param right
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -481,17 +524,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Adjust row/column scrollers to show a visible position in the alignment.
    * 
-   * @param x
-   *                DOCUMENT ME!
-   * @param y
-   *                DOCUMENT ME!
+   * @param x visible column to scroll to
+   *          DOCUMENT ME!
+   * @param y visible row to scroll to
+   *          
    */
   public void setScrollValues(int x, int y)
   {
-//    System.err.println("Scroll to "+x+","+y);
-    if (av==null || av.alignment==null)
+    // System.err.println("Scroll to "+x+","+y);
+    if (av == null || av.alignment == null)
     {
       return;
     }
@@ -546,7 +589,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
@@ -558,9 +601,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av
-              .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
-                      .getCharWidth())) - 1);
+      av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -643,8 +684,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (updateOverview)
     {
-      jalview.structure.StructureSelectionManager
-              .getStructureSelectionManager().sequenceColoursChanged(this);
+      av.getStructureSelectionManager().sequenceColoursChanged(this);
 
       if (overviewPanel != null)
       {
@@ -657,7 +697,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void paintComponent(Graphics g)
   {
@@ -700,16 +740,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param pg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pf
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pi
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    * 
    * @throws PrinterException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public int print(Graphics pg, PageFormat pf, int pi)
           throws PrinterException
@@ -733,18 +773,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param pg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pwidth
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pheight
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pi
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    * 
    * @throws PrinterException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
           throws PrinterException
@@ -840,8 +880,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
-              .getCharHeight());
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+              av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
@@ -854,7 +894,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 - 4;
       }
 
-      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+      pg.drawString(
+              seq.getDisplayId(av.getShowJVSuffix()),
+              xPos,
               (((i - startSeq) * av.charHeight) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -880,18 +922,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * DOCUMENT ME!
    * 
    * @param pg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pwidth
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pheight
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param pi
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    * 
    * @throws PrinterException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
           int pi) throws PrinterException
@@ -1012,6 +1054,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (System.getProperty("java.awt.headless") != null
               && System.getProperty("java.awt.headless").equals("true"))
       {
+        // TODO: JAL-244
         width = alignFrame.getWidth() - vscroll.getPreferredSize().width
                 - alignFrame.getInsets().left
                 - alignFrame.getInsets().right;
@@ -1272,25 +1315,139 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * close the panel - deregisters all listeners and nulls any references to alignment data.
+   * close the panel - deregisters all listeners and nulls any references to
+   * alignment data.
    */
   public void closePanel()
   {
-    jalview.structure.StructureSelectionManager ssm = 
-      jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager();
-    ssm.removeStructureViewerListener(seqPanel, null);
-    ssm.removeSelectionListener(seqPanel);
     PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
     PaintRefresher.RemoveComponent(idPanel.idCanvas);
     PaintRefresher.RemoveComponent(this);
-    if (av!=null) {
+    if (av != null)
+    {
+      jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+      ssm.removeStructureViewerListener(seqPanel, null);
+      ssm.removeSelectionListener(seqPanel);
       av.alignment = null;
       av = null;
-    } else {
-      if (Cache.log.isDebugEnabled()) {
+    }
+    else
+    {
+      if (Cache.log.isDebugEnabled())
+      {
         Cache.log.warn("Closing alignment panel which is already closed.");
       }
     }
   }
+
+  /**
+   * hides or shows dynamic annotation rows based on groups and av state flags
+   */
+  public void updateAnnotation()
+  {
+    updateAnnotation(false);
+  }
+
+  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
+
+    Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+    // intersect alignment annotation with alignment groups
+
+    AlignmentAnnotation[] aan = av.alignment.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.alignment.deleteAnnotation(aan[an]);
+          aan[an] = null;
+        }
+      }
+    }
+    SequenceGroup sg;
+    if (gr != null)
+    {
+      for (int g = 0; g < gr.size(); g++)
+      {
+        updateCalcs = false;
+        sg = (SequenceGroup) gr.elementAt(g);
+        if (applyGlobalSettings || !oldrfs.containsKey(sg))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setshowSequenceLogo(showprf);
+          sg.setShowConsensusHistogram(showConsHist);
+        }
+        if (conv)
+        {
+          updateCalcs = true;
+          av.alignment.addAnnotation(sg.getConservationRow(), 0);
+        }
+        if (cons)
+        {
+          updateCalcs = true;
+          av.alignment.addAnnotation(sg.getConsensus(), 0);
+        }
+        // refresh the annotation rows
+        if (updateCalcs)
+        {
+          sg.recalcConservation();
+        }
+      }
+    }
+    oldrfs.clear();
+    adjustAnnotationHeight();
+  }
+
+  @Override
+  public AlignmentI getAlignment()
+  {
+    return av.alignment;
+  }
+
+  /**
+   * get the name for this view
+   * @return 
+   */
+  public String getViewName()
+  {
+    return av.viewName;
+  }
+
+  /**
+   * Make/Unmake this alignment panel the current input focus
+   * @param b
+   */
+  public void setSelected(boolean b)
+  {
+    try {
+      alignFrame.setSelected(b);
+      } catch (Exception ex) {};
+      
+    if (b)
+    {
+      alignFrame.setDisplayedView(this);
+    } 
+  }
+
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return av.getStructureSelectionManager();
+  }
 }