X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=3e91f21f52ca8748d74b69799d5292eef158b667;hb=6173092ff5cb03f039cac674bfc8bc4f969976a5;hp=de0a7b1c70d837318717a0aeb3dd5c20c1148610;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index de0a7b1..3e91f21 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,191 +1,483 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, 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 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.
-*
-* 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 - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
+ *
+ * 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
+ */
 package jalview.gui;
 
-import jalview.datamodel.*;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 
-public class ScalePanel extends JPanel
-{
+import jalview.datamodel.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScalePanel
+    extends JPanel implements MouseMotionListener, MouseListener
+{
   protected int offy = 4;
-  public    int width;
 
+  /** DOCUMENT ME!! */
+  public int width;
   protected AlignViewport av;
   AlignmentPanel ap;
-
   boolean stretchingGroup = false;
+  int min; //used by mouseDragged to see if user
+  int max; //used by mouseDragged to see if user
+  boolean mouseDragging = false;
 
+  // wants to delete columns
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
-    this.av         = av;
+    this.av = av;
     this.ap = ap;
 
-    addMouseListener(new MouseAdapter()
+    addMouseListener(this);
+    addMouseMotionListener(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    final int res;
+
+    if (av.hasHiddenColumns)
     {
-      public void mousePressed(MouseEvent evt)
+      res = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
+    else
+    {
+      res = x;
+    }
+
+    min = res;
+    max = res;
+
+    if (SwingUtilities.isRightMouseButton(evt))
+    {
+      JPopupMenu pop = new JPopupMenu();
+      if (reveal != null)
       {
-        doMousePressed(evt);
+        JMenuItem item = new JMenuItem("Reveal");
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.showColumn(reveal[0]);
+            reveal = null;
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+
+        if (av.getColumnSelection().getHiddenColumns().size() > 1)
+        {
+          item = new JMenuItem("Reveal All");
+          item.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              av.showAllHiddenColumns();
+              reveal = null;
+              ap.paintAlignment(true);
+              if (ap.overviewPanel != null)
+              {
+                ap.overviewPanel.updateOverviewImage();
+              }
+            }
+          });
+          pop.add(item);
+        }
+        pop.show(this, evt.getX(), evt.getY());
       }
-      public void mouseReleased(MouseEvent evt)
+      else if (av.getColumnSelection().contains(res))
       {
-        doMouseReleased(evt);
+        JMenuItem item = new JMenuItem("Hide Columns");
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.hideColumns(res, res);
+            if (av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() == av.alignment.getHeight())
+            {
+              av.setSelectionGroup(null);
+            }
+
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+        pop.show(this, evt.getX(), evt.getY());
       }
-
-    });
-    addMouseMotionListener(new MouseMotionAdapter()
+    }
+    else // LEFT MOUSE TO SELECT
     {
-      public void mouseDragged(MouseEvent evt)
+      if (!evt.isControlDown() && !evt.isShiftDown())
       {
-        doMouseDragged(evt);
+        av.getColumnSelection().clear();
       }
-    });
-
-  }
-
-
-  public void doMousePressed(MouseEvent evt) {
-    int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
-    SequenceGroup sg = null;
 
-    if (av.getColumnSelection().contains(res))
-      av.getColumnSelection().removeElement(res);
-    else
-    {
       av.getColumnSelection().addElement(res);
-
-      sg = new SequenceGroup();
+      SequenceGroup sg = new SequenceGroup();
       for (int i = 0; i < av.alignment.getSequences().size(); i++)
-        sg.addSequence(av.alignment.getSequenceAt(i));
+      {
+        sg.addSequence(av.alignment.getSequenceAt(i), false);
+      }
 
       sg.setStartRes(res);
       sg.setEndRes(res);
+      av.setSelectionGroup(sg);
+
+      if (evt.isShiftDown())
+      {
+        int min = Math.min(av.getColumnSelection().getMin(), res);
+        int max = Math.max(av.getColumnSelection().getMax(), res);
+        for (int i = min; i < max; i++)
+        {
+          av.getColumnSelection().addElement(i);
+        }
+        sg.setStartRes(min);
+        sg.setEndRes(max);
+      }
 
-      ap.annotationPanel.addEditableColumn(res);
     }
-    av.setSelectionGroup(sg);
-    ap.repaint();
+
+    ap.paintAlignment(false);
   }
 
-  public void doMouseReleased(MouseEvent evt)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
   {
-    if(!stretchingGroup)
-      return;
+    mouseDragging = false;
 
-    int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-   if (! av.getColumnSelection().contains(res))
-     av.getColumnSelection().addElement(res);
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
 
-   SequenceGroup sg = av.getSelectionGroup();
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
 
-   if(res>sg.getStartRes())
-     sg.setEndRes(res);
-   else if(res<sg.getStartRes())
-     sg.setStartRes(res);
+    if (!stretchingGroup)
+    {
+      ap.paintAlignment(false);
 
-   stretchingGroup = false;
-   ap.repaint();
+      return;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      if (res > sg.getStartRes())
+      {
+        sg.setEndRes(res);
+      }
+      else if (res < sg.getStartRes())
+      {
+        sg.setStartRes(res);
+      }
+    }
+    stretchingGroup = false;
+    ap.paintAlignment(false);
   }
 
-  public void doMouseDragged(MouseEvent evt)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
   {
-    int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+    mouseDragging = true;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    if (res < 0)
+    {
+      res = 0;
+    }
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (res > av.alignment.getWidth())
+    {
+      res = av.alignment.getWidth() - 1;
+    }
+
+    if (res < min)
+    {
+      min = res;
+    }
+
+    if (res > max)
+    {
+      max = res;
+    }
 
     SequenceGroup sg = av.getSelectionGroup();
-    if(sg!=null)
+
+    if (sg != null)
     {
       stretchingGroup = true;
+
+      if (!av.getColumnSelection().contains(res))
+      {
+        av.getColumnSelection().addElement(res);
+      }
+
       if (res > sg.getStartRes())
+      {
         sg.setEndRes(res);
-      else if (res < sg.getStartRes())
+      }
+      if (res < sg.getStartRes())
+      {
         sg.setStartRes(res);
+      }
 
-       ap.annotationPanel.addEditableColumn(res);
-      ap.repaint();
+      int col;
+      for (int i = min; i <= max; i++)
+      {
+        col = av.getColumnSelection().adjustForHiddenColumns(i);
+
+        if ( (col < sg.getStartRes()) || (col > sg.getEndRes()))
+        {
+          av.getColumnSelection().removeElement(col);
+        }
+        else
+        {
+          av.getColumnSelection().addElement(col);
+        }
+      }
+
+      ap.paintAlignment(false);
     }
   }
 
+  public void mouseEntered(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.seqPanel.scrollCanvas(null);
+    }
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.seqPanel.scrollCanvas(evt);
+    }
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      return;
+    }
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+    reveal = null;
+    for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+    {
+      int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
+          elementAt(i);
+      if (res + 1 == region[0] || res - 1 == region[1])
+      {
+        reveal = region;
+        ToolTipManager.sharedInstance().registerComponent(this);
+        this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");
+        break;
+      }
+      else
+      {
+        this.setToolTipText(null);
+      }
+
+    }
+
+    repaint();
+  }
+
+  int[] reveal;
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
   public void paintComponent(Graphics g)
   {
     drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
   }
 
-// scalewidth will normally be screenwidth,
-  public void drawScale(Graphics g, int startx, int endx, int width, int height)
+  // scalewidth will normally be screenwidth,
+  public void drawScale(Graphics g, int startx, int endx, int width,
+                        int height)
   {
-    Graphics2D gg = (Graphics2D)g;
+    Graphics2D gg = (Graphics2D) g;
     gg.setFont(av.getFont());
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                          RenderingHints.VALUE_ANTIALIAS_ON);
+    }
 
     //Fill in the background
     gg.setColor(Color.white);
-    gg.fillRect(0,0,width, height);
+    gg.fillRect(0, 0, width, height);
     gg.setColor(Color.black);
 
-
     //Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220,0,0));
-    for (int i=0; i<cs.size(); i++)
+    gg.setColor(new Color(220, 0, 0));
+
+    for (int i = 0; i < cs.size(); i++)
     {
-      int sel  = cs.columnAt(i);
-      if ( sel >= startx  && sel <= endx)
-        gg.fillRect((sel-startx)*av.charWidth,0,av.charWidth,getHeight());
-    }
+      int sel = cs.columnAt(i);
+      if (av.hasHiddenColumns)
+      {
+        sel = av.getColumnSelection().findColumnPosition(sel);
+      }
 
+      if ( (sel >= startx) && (sel <= endx))
+      {
+        gg.fillRect( (sel - startx) * av.charWidth, 0, av.charWidth,
+                    getHeight());
+      }
+    }
 
     // Draw the scale numbers
     gg.setColor(Color.black);
-    int scalestartx = (startx/10) * 10;
+
+    int scalestartx = (startx / 10) * 10;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = av.charHeight -fm.getDescent();
+    int y = av.charHeight - fm.getDescent();
+
+    if ( (scalestartx % 10) == 0)
+    {
+      scalestartx += 5;
+    }
 
-    if(scalestartx%10==0)
-      scalestartx+=5;
+    String string;
+    int maxX = 0;
 
-    for (int i=scalestartx;i < endx; i+= 5)
+    for (int i = scalestartx; i < endx; i += 5)
     {
-      if(i%10==0)
+      if ( (i % 10) == 0)
       {
-        gg.drawString(String.valueOf(i), (i - startx - 1) * av.charWidth, y);
-        gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                    y+2,
-                    (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                    y+fm.getDescent()*2);
+        string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(
+            i));
+        if ( (i - startx - 1) * av.charWidth > maxX)
+        {
+          gg.drawString(string,
+                        (i - startx - 1) * av.charWidth, y);
+          maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);
+        }
+
+        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
+                            (av.charWidth / 2)), y + 2,
+                    (int) ( ( (i - startx - 1) * av.charWidth) +
+                           (av.charWidth / 2)),
+                    y + (fm.getDescent() * 2));
+
       }
       else
-        gg.drawLine( (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                    y+fm.getDescent(),
-                    (int) ( (i - startx - 1) * av.charWidth + av.charWidth / 2),
-                   y+fm.getDescent()*2);
+      {
+        gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +
+                            (av.charWidth / 2)), y + fm.getDescent(),
+                    (int) ( ( (i - startx - 1) * av.charWidth) +
+                           (av.charWidth / 2)), y + (fm.getDescent() * 2));
+      }
+    }
 
+    if (av.hasHiddenColumns)
+    {
+      gg.setColor(Color.blue);
+      int res;
+      if (av.getShowHiddenMarkers())
+      {
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();
+             i++)
+        {
+
+          res = av.getColumnSelection().findHiddenRegionPosition(i) -
+              startx;
+
+          if (res < 0 || res > endx - scalestartx)
+          {
+            continue;
+          }
+
+          gg.fillPolygon(new int[]
+                         {res * av.charWidth - av.charHeight / 4,
+                         res * av.charWidth + av.charHeight / 4,
+                         res * av.charWidth},
+                         new int[]
+                         {
+                         y - av.charHeight / 2, y - av.charHeight / 2,
+                         y + 8
+          }, 3);
+
+        }
+      }
 
+      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
+      {
+        gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);
+      }
     }
-  }
-
 
+  }
 }