X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=6ef52220a4968e5a218500fb059874be8c96138b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=19b26c8217a7f710becb1868385987d8b4dcadbd;hpb=bb72a052b1308e9d6d28fc97dd458c6e11f116e8;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 19b26c8..6ef5222 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -1,283 +1,535 @@
-/*
- * 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
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ScalePanel extends JPanel
-{
-    protected int offy = 4;
-
-    /** 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
-
-    // wants to delete columns
-    public ScalePanel(AlignViewport av, AlignmentPanel ap)
-    {
-        this.av = av;
-        this.ap = ap;
-
-        addMouseListener(new MouseAdapter()
-            {
-                public void mousePressed(MouseEvent evt)
-                {
-                    doMousePressed(evt);
-                }
-
-                public void mouseReleased(MouseEvent evt)
-                {
-                    doMouseReleased(evt);
-                }
-            });
-        addMouseMotionListener(new MouseMotionAdapter()
-            {
-                public void mouseDragged(MouseEvent evt)
-                {
-                    doMouseDragged(evt);
-                }
-            });
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMousePressed(MouseEvent evt)
-    {
-        int x = evt.getX();
-        int res = (x / av.getCharWidth()) + av.getStartRes();
-        SequenceGroup sg = null;
-
-        min = res;
-        max = res;
-
-        if (av.getColumnSelection().contains(res))
-        {
-            av.getColumnSelection().removeElement(res);
-            ap.annotationPanel.removeEditableColumn(res);
-        }
-        else
-        {
-            av.getColumnSelection().addElement(res);
-            sg = new SequenceGroup();
-
-            for (int i = 0; i < av.alignment.getSequences().size(); i++)
-            {
-                sg.addSequence(av.alignment.getSequenceAt(i), false);
-            }
-
-            sg.setStartRes(res);
-            sg.setEndRes(res);
-        }
-
-        av.setSelectionGroup(sg);
-        ap.repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseReleased(MouseEvent evt)
-    {
-        int x = evt.getX();
-        int res = (x / av.getCharWidth()) + av.getStartRes();
-
-        if (av.getColumnSelection() != null)
-        {
-            for (int i = 0; i < av.getColumnSelection().size(); i++)
-            {
-                ap.annotationPanel.addEditableColumn(av.getColumnSelection()
-                                                       .columnAt(i));
-            }
-        }
-
-        if (!stretchingGroup)
-        {
-            ap.repaint();
-
-            return;
-        }
-
-        SequenceGroup sg = av.getSelectionGroup();
-
-        if (res > sg.getStartRes())
-        {
-            sg.setEndRes(res);
-        }
-        else if (res < sg.getStartRes())
-        {
-            sg.setStartRes(res);
-        }
-
-        stretchingGroup = false;
-        ap.repaint();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseDragged(MouseEvent evt)
-    {
-        int x = evt.getX();
-        int res = (x / av.getCharWidth()) + av.getStartRes();
-
-        if (res < min)
-        {
-            min = res;
-        }
-
-        if (res > max)
-        {
-            max = res;
-        }
-
-        SequenceGroup sg = av.getSelectionGroup();
-
-        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())
-            {
-                sg.setStartRes(res);
-            }
-
-            for (int i = min; i <= max; i++)
-            {
-                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
-                {
-                    av.getColumnSelection().removeElement(i);
-                    ap.annotationPanel.removeEditableColumn(res);
-                }
-                else
-                {
-                    av.getColumnSelection().addElement(i);
-                }
-            }
-
-            ap.repaint();
-        }
-    }
-
-    /**
-     * 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)
-    {
-        Graphics2D gg = (Graphics2D) g;
-        gg.setFont(av.getFont());
-
-        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.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++)
-        {
-            int sel = cs.columnAt(i);
-
-            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;
-
-        FontMetrics fm = gg.getFontMetrics(av.getFont());
-        int y = av.charHeight - fm.getDescent();
-
-        if ((scalestartx % 10) == 0)
-        {
-            scalestartx += 5;
-        }
-
-        for (int i = scalestartx; i < endx; i += 5)
-        {
-            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));
-            }
-            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));
-            }
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScalePanel extends JPanel implements MouseMotionListener,
+        MouseListener
+{
+  protected int offy = 4;
+
+  /** 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.ap = ap;
+
+    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())
+    {
+      x = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
+
+    if (x >= av.getAlignment().getWidth())
+    {
+      res = av.getAlignment().getWidth() - 1;
+    }
+    else
+    {
+      res = x;
+    }
+
+    min = res;
+    max = res;
+
+    if (SwingUtilities.isRightMouseButton(evt))
+    {
+      JPopupMenu pop = new JPopupMenu();
+      if (reveal != null)
+      {
+        JMenuItem item = new JMenuItem(
+                MessageManager.getString("label.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().hasHiddenColumns())
+        {
+          item = new JMenuItem(
+                  MessageManager.getString("action.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());
+      }
+      else if (av.getColumnSelection().contains(res))
+      {
+        JMenuItem item = new JMenuItem(
+                MessageManager.getString("label.hide_columns"));
+        item.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            av.hideColumns(res, res);
+            if (av.getSelectionGroup() != null
+                    && av.getSelectionGroup().getSize() == av
+                            .getAlignment().getHeight())
+            {
+              av.setSelectionGroup(null);
+            }
+
+            ap.paintAlignment(true);
+            if (ap.overviewPanel != null)
+            {
+              ap.overviewPanel.updateOverviewImage();
+            }
+          }
+        });
+        pop.add(item);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+    }
+    else
+    // LEFT MOUSE TO SELECT
+    {
+      if (!evt.isControlDown() && !evt.isShiftDown())
+      {
+        av.getColumnSelection().clear();
+      }
+
+      av.getColumnSelection().addElement(res);
+      SequenceGroup sg = new SequenceGroup();
+      // try to be as quick as possible
+      SequenceI[] iVec = av.getAlignment().getSequencesArray();
+      for (int i = 0; i < iVec.length; i++)
+      {
+        sg.addSequence(iVec[i], false);
+        iVec[i] = null;
+      }
+      iVec = null;
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+
+      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);
+      }
+      av.setSelectionGroup(sg);
+    }
+
+    ap.paintAlignment(false);
+    av.sendSelection();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    if (av.hasHiddenColumns())
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (res >= av.getAlignment().getWidth())
+    {
+      res = av.getAlignment().getWidth() - 1;
+    }
+
+    if (!stretchingGroup)
+    {
+      ap.paintAlignment(false);
+
+      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);
+    av.sendSelection();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    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.getAlignment().getWidth())
+    {
+      res = av.getAlignment().getWidth() - 1;
+    }
+
+    if (res < min)
+    {
+      min = res;
+    }
+
+    if (res > max)
+    {
+      max = res;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (sg != null)
+    {
+      stretchingGroup = true;
+
+      if (!av.getColumnSelection().contains(res))
+      {
+        av.getColumnSelection().addElement(res);
+      }
+
+      if (res > sg.getStartRes())
+      {
+        sg.setEndRes(res);
+      }
+      if (res < sg.getStartRes())
+      {
+        sg.setStartRes(res);
+      }
+
+      int col;
+      for (int i = min; i <= max; i++)
+      {
+        col = i; // 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.getSeqPanel().scrollCanvas(null);
+    }
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+    if (mouseDragging)
+    {
+      ap.getSeqPanel().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;
+    if (av.getColumnSelection().getHiddenColumns() != null)
+    {
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
+      {
+        if (res + 1 == region[0] || res - 1 == region[1])
+        {
+          reveal = region;
+          ToolTipManager.sharedInstance().registerComponent(this);
+          this.setToolTipText(MessageManager
+                  .getString("label.reveal_hidden_columns"));
+          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)
+  {
+    Graphics2D gg = (Graphics2D) g;
+    gg.setFont(av.getFont());
+
+    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.setColor(Color.black);
+
+    // Fill the selected columns
+    ColumnSelection cs = av.getColumnSelection();
+    int s;
+    if (cs != null)
+    {
+      gg.setColor(new Color(220, 0, 0));
+
+      for (int i = 0; i < cs.size(); i++)
+      {
+        int sel = cs.columnAt(i);
+        if (av.hasHiddenColumns())
+        {
+          if (cs.isVisible(sel))
+          {
+            sel = cs.findColumnPosition(sel);
+          }
+          else
+          {
+            continue;
+          }
+        }
+
+        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;
+
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = av.charHeight - fm.getDescent();
+
+    if ((scalestartx % 10) == 0)
+    {
+      scalestartx += 5;
+    }
+
+    String string;
+    int maxX = 0;
+
+    for (int i = scalestartx; i < endx; i += 5)
+    {
+      if ((i % 10) == 0)
+      {
+        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(
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+                y + 2,
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+                y + (fm.getDescent() * 2));
+
+      }
+      else
+      {
+        gg.drawLine(
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+                y + fm.getDescent(),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+                y + (fm.getDescent() * 2));
+      }
+    }
+
+    if (av.hasHiddenColumns())
+    {
+      gg.setColor(Color.blue);
+      int res;
+      if (av.getShowHiddenMarkers()
+              && av.getColumnSelection().getHiddenColumns() != null)
+      {
+        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(MessageManager.getString("label.reveal_columns"),
+                reveal[0] * av.charWidth, 0);
+      }
+    }
+
+  }
+}