X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FScalePanel.java;h=2445e2cdee1883e52cd838b50cfe3472c36e7b0d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=86884862a9d994a9f65e56e1ceb215d672042608;hpb=32c056ffe34e60a1fde83bf4061af6e82d41f958;p=jalview.git

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 8688486..2445e2c 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -1,239 +1,466 @@
-/*
- * 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.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class ScalePanel
-    extends Panel
-{
-
-  protected int offy = 4;
-  public int width;
-
-  protected AlignViewport av;
-  AlignmentPanel ap;
-
-  boolean stretchingGroup = false;
-
-  public ScalePanel(AlignViewport av, AlignmentPanel ap)
-  {
-    setLayout(null);
-    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);
-      }
-    });
-
-  }
-
-  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();
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
-      {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
-      }
-
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-
-      ap.annotationPanel.addEditableColumn(res);
-    }
-    av.setSelectionGroup(sg);
-    ap.repaint();
-  }
-
-  public void doMouseReleased(MouseEvent evt)
-  {
-    if (!stretchingGroup)
-    {
-      return;
-    }
-
-    int x = evt.getX();
-    int res = x / av.getCharWidth() + av.getStartRes();
-
-    if(res> av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth()-1;
-    }
-
-    if (!av.getColumnSelection().contains(res))
-    {
-      av.getColumnSelection().addElement(res);
-    }
-
-    SequenceGroup sg = av.getSelectionGroup();
-
-    if (res > sg.getStartRes())
-    {
-      sg.setEndRes(res);
-    }
-    else if (res < sg.getStartRes())
-    {
-      sg.setStartRes(res);
-    }
-
-    stretchingGroup = false;
-    ap.repaint();
-  }
-
-  public void doMouseDragged(MouseEvent evt)
-  {
-    int x = evt.getX();
-    int res = x / av.getCharWidth() + av.getStartRes();
-
-    if(res> av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth()-1;
-    }
-
-    SequenceGroup sg = av.getSelectionGroup();
-    if (sg != null)
-    {
-      stretchingGroup = true;
-      if (res > sg.getStartRes())
-      {
-        sg.setEndRes(res);
-      }
-      else if (res < sg.getStartRes())
-      {
-        sg.setStartRes(res);
-      }
-
-      ap.annotationPanel.addEditableColumn(res);
-      ap.repaint();
-    }
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
-              getSize().height);
-  }
-
-// scalewidth will normally be screenwidth,
-  public void drawScale(Graphics gg, int startx, int endx, int width,
-                        int height)
-  {
-    gg.setFont(av.getFont());
-
-    //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,
-                    getSize().height);
-      }
-    }
-
-    // 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(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);
-      }
-
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.appletgui;
+
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+public class ScalePanel extends Panel implements MouseMotionListener,
+        MouseListener
+{
+
+  protected int offy = 4;
+
+  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;
+
+  int[] reveal;
+
+  public ScalePanel(AlignViewport av, AlignmentPanel ap)
+  {
+    setLayout(null);
+    this.av = av;
+    this.ap = ap;
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    final int res;
+
+    if (av.hasHiddenColumns())
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(x);
+    }
+    else
+    {
+      res = x;
+    }
+
+    min = res;
+    max = res;
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    {
+      PopupMenu pop = new PopupMenu();
+      if (reveal != null)
+      {
+        MenuItem item = new MenuItem(
+                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().hasManyHiddenColumns())
+        {
+          item = new MenuItem(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);
+        }
+        this.add(pop);
+        pop.show(this, evt.getX(), evt.getY());
+      }
+      else if (av.getColumnSelection().contains(res))
+      {
+        MenuItem item = new MenuItem(
+                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);
+        this.add(pop);
+        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();
+      for (int i = 0; i < av.getAlignment().getSequences().size(); i++)
+      {
+        sg.addSequence(av.getAlignment().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.paintAlignment(true);
+    av.sendSelection();
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
+
+    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+    if (res > av.getAlignment().getWidth())
+    {
+      res = av.getAlignment().getWidth() - 1;
+    }
+
+    if (av.hasHiddenColumns())
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
+    if (!stretchingGroup)
+    {
+      ap.paintAlignment(false);
+
+      return;
+    }
+
+    SequenceGroup sg = av.getSelectionGroup();
+
+    if (res > sg.getStartRes())
+    {
+      sg.setEndRes(res);
+    }
+    else if (res < sg.getStartRes())
+    {
+      sg.setStartRes(res);
+    }
+
+    stretchingGroup = false;
+    ap.paintAlignment(false);
+    av.sendSelection();
+  }
+
+  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 = 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[] region : av.getColumnSelection().getHiddenColumns())
+    {
+      if (res + 1 == region[0] || res - 1 == region[1])
+      {
+        reveal = region;
+        break;
+      }
+    }
+
+    repaint();
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
+            getSize().height);
+  }
+
+  // scalewidth will normally be screenwidth,
+  public void drawScale(Graphics gg, int startx, int endx, int width,
+          int height)
+  {
+    gg.setFont(av.getFont());
+    // 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));
+    int avcharWidth = av.getCharWidth(), avcharHeight = av.getCharHeight();
+    for (int i = 0; i < cs.size(); i++)
+    {
+      int sel = cs.columnAt(i);
+      if (av.hasHiddenColumns())
+      {
+        sel = av.getColumnSelection().findColumnPosition(sel);
+      }
+
+      if ((sel >= startx) && (sel <= endx))
+      {
+        gg.fillRect((sel - startx) * avcharWidth, 0, avcharWidth,
+                getSize().height);
+      }
+    }
+
+    // Draw the scale numbers
+    gg.setColor(Color.black);
+
+    int scalestartx = (startx / 10) * 10;
+
+    FontMetrics fm = gg.getFontMetrics(av.getFont());
+    int y = avcharHeight - 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) * avcharWidth > maxX)
+        {
+          gg.drawString(string, (i - startx - 1) * avcharWidth, y);
+          maxX = (i - startx + 1) * avcharWidth + fm.stringWidth(string);
+        }
+
+        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
+                y + 2,
+                ((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
+                        + (fm.getDescent() * 2));
+
+      }
+      else
+      {
+        gg.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), y
+                + fm.getDescent(), ((i - startx - 1) * avcharWidth)
+                + (avcharWidth / 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 * avcharWidth - avcharHeight / 4,
+              res * avcharWidth + avcharHeight / 4, res * avcharWidth },
+                  new int[] { y - avcharHeight / 2, y - avcharHeight / 2,
+                      y + 8 }, 3);
+
+        }
+      }
+
+      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
+      {
+        gg.drawString(MessageManager.getString("label.reveal_columns"),
+                reveal[0] * avcharWidth, 0);
+      }
+    }
+
+  }
+
+}