-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class ScalePanel extends JPanel implements MouseMotionListener, MouseListener\r
-{\r
- protected int offy = 4;\r
-\r
- /** DOCUMENT ME!! */\r
- public int width;\r
- protected AlignViewport av;\r
- AlignmentPanel ap;\r
- boolean stretchingGroup = false;\r
- int min; //used by mouseDragged to see if user\r
- int max; //used by mouseDragged to see if user\r
- boolean mouseDragging = false;\r
-\r
- // wants to delete columns\r
- public ScalePanel(AlignViewport av, AlignmentPanel ap)\r
- {\r
- this.av = av;\r
- this.ap = ap;\r
-\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
- final int res;\r
-\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(x);\r
- else\r
- res = x;\r
-\r
- min = res;\r
- max = res;\r
-\r
- if(reveal != null && SwingUtilities.isRightMouseButton(evt))\r
- {\r
- JPopupMenu pop = new JPopupMenu();\r
- JMenuItem item = new JMenuItem("Reveal");\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- av.showColumn(reveal[0]);\r
- reveal = null;\r
- ap.repaint();\r
- if(ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- });\r
- pop.add(item);\r
-\r
- if(av.getColumnSelection().size()>1)\r
- {\r
- item = new JMenuItem("Reveal All");\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- av.showAllHiddenColumns();\r
- reveal = null;\r
- ap.repaint();\r
- if(ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- });\r
- pop.add(item);\r
- }\r
-\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- }\r
- else\r
- if (av.getColumnSelection().contains(res))\r
- {\r
- if( SwingUtilities.isRightMouseButton(evt))\r
- {\r
- JPopupMenu pop = new JPopupMenu();\r
- JMenuItem item = new JMenuItem("Hide Columns");\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- av.hideColumns(res, res);\r
- ap.repaint();\r
- if(ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- });\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- }\r
- else\r
- {\r
- av.getColumnSelection().removeElement(res);\r
- av.setSelectionGroup(null);\r
- }\r
- }\r
- else\r
- {\r
- av.getColumnSelection().addElement(res);\r
- SequenceGroup sg = new SequenceGroup();\r
-\r
- for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
- {\r
- sg.addSequence(av.alignment.getSequenceAt(i), false);\r
- }\r
-\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- av.setSelectionGroup(sg);\r
- }\r
-\r
-\r
- ap.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- mouseDragging = false;\r
-\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
-\r
- if(res> av.alignment.getWidth())\r
- {\r
- res = av.alignment.getWidth()-1;\r
- }\r
-\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
-\r
- if (!stretchingGroup)\r
- {\r
- ap.repaint();\r
-\r
- return;\r
- }\r
-\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
- if (res > sg.getStartRes())\r
- {\r
- sg.setEndRes(res);\r
- }\r
- else if (res < sg.getStartRes())\r
- {\r
- sg.setStartRes(res);\r
- }\r
-\r
- stretchingGroup = false;\r
- ap.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- mouseDragging = true;\r
-\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
- if(res<0)\r
- res = 0;\r
-\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
-\r
-\r
- if(res> av.alignment.getWidth())\r
- {\r
- res = av.alignment.getWidth()-1;\r
- }\r
-\r
- if (res < min)\r
- {\r
- min = res;\r
- }\r
-\r
- if (res > max)\r
- {\r
- max = res;\r
- }\r
-\r
-\r
-\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- stretchingGroup = true;\r
-\r
- if (!av.getColumnSelection().contains(res))\r
- {\r
- av.getColumnSelection().addElement(res);\r
- }\r
-\r
- if (res > sg.getStartRes())\r
- {\r
- sg.setEndRes(res);\r
- }\r
- if (res < sg.getStartRes())\r
- {\r
- sg.setStartRes(res);\r
- }\r
-\r
- for (int i = min; i <= max; i++)\r
- {\r
- if ((i < sg.getStartRes()) || (i > sg.getEndRes()))\r
- {\r
- av.getColumnSelection().removeElement(i);\r
- }\r
- else\r
- {\r
- av.getColumnSelection().addElement(i);\r
- }\r
- }\r
-\r
- ap.repaint();\r
- }\r
- }\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if(mouseDragging)\r
- ap.seqPanel.scrollCanvas(null);\r
- }\r
-\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if(mouseDragging)\r
- ap.seqPanel.scrollCanvas(evt);\r
- }\r
-\r
- public void mouseClicked(MouseEvent evt){}\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- if(!av.hasHiddenColumns)\r
- return;\r
-\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
-\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
-\r
- reveal = null;\r
- for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)\r
- {\r
- int [] region = (int[])av.getColumnSelection().getHiddenColumns().elementAt(i);\r
- if(res+1==region[0] || res-1==region[1])\r
- {\r
- reveal = region;\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- this.setToolTipText("Reveal Hidden Columns with Right Mouse Button");\r
- break;\r
- }\r
- else\r
- this.setToolTipText(null);\r
-\r
- }\r
-\r
- repaint();\r
- }\r
-\r
- int [] reveal;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
- {\r
- drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());\r
- }\r
-\r
- // scalewidth will normally be screenwidth,\r
- public void drawScale(Graphics g, int startx, int endx, int width,\r
- int height)\r
- {\r
- Graphics2D gg = (Graphics2D) g;\r
- gg.setFont(av.getFont());\r
-\r
- if(av.antiAlias)\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
- //Fill in the background\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, width, height);\r
- gg.setColor(Color.black);\r
-\r
- //Fill the selected columns\r
- ColumnSelection cs = av.getColumnSelection();\r
- gg.setColor(new Color(220, 0, 0));\r
-\r
- for (int i = 0; i < cs.size(); i++)\r
- {\r
- int sel = cs.columnAt(i);\r
- if(av.hasHiddenColumns)\r
- sel = av.getColumnSelection().findColumnPosition(sel);\r
-\r
- if ((sel >= startx) && (sel <= endx))\r
- {\r
- gg.fillRect((sel - startx) * av.charWidth, 0, av.charWidth,\r
- getHeight());\r
- }\r
- }\r
-\r
- // Draw the scale numbers\r
- gg.setColor(Color.black);\r
-\r
- int scalestartx = (startx / 10) * 10;\r
-\r
- FontMetrics fm = gg.getFontMetrics(av.getFont());\r
- int y = av.charHeight - fm.getDescent();\r
-\r
- if ((scalestartx % 10) == 0)\r
- {\r
- scalestartx += 5;\r
- }\r
-\r
- String string;\r
- int maxX=0;\r
-\r
- for (int i = scalestartx; i < endx; i += 5)\r
- {\r
- if ((i % 10) == 0)\r
- {\r
- string = String.valueOf(av.getColumnSelection().adjustForHiddenColumns(i));\r
- if ( (i - startx - 1) * av.charWidth > maxX)\r
- {\r
- gg.drawString(string,\r
- (i - startx - 1) * av.charWidth, y);\r
- maxX = (i - startx + 1) * av.charWidth + fm.stringWidth(string);\r
- }\r
-\r
- gg.drawLine( (int) ( ( (i - startx - 1) * av.charWidth) +\r
- (av.charWidth / 2)), y + 2,\r
- (int) ( ( (i - startx - 1) * av.charWidth) +\r
- (av.charWidth / 2)),\r
- y + (fm.getDescent() * 2));\r
-\r
- }\r
- else\r
- {\r
- gg.drawLine((int) (((i - startx - 1) * av.charWidth) +\r
- (av.charWidth / 2)), y + fm.getDescent(),\r
- (int) (((i - startx - 1) * av.charWidth) +\r
- (av.charWidth / 2)), y + (fm.getDescent() * 2));\r
- }\r
- }\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- gg.setColor(Color.blue);\r
- int res;\r
- if(av.getShowHiddenMarkers())\r
- {\r
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();\r
- i++)\r
- {\r
-\r
- res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
- startx;\r
-\r
- if(res < 0 || res > endx-scalestartx)\r
- continue;\r
-\r
- gg.fillPolygon(new int[]\r
- {res * av.charWidth - av.charHeight / 4,\r
- res * av.charWidth + av.charHeight / 4,\r
- res * av.charWidth},\r
- new int[]\r
- {\r
- y - av.charHeight / 2, y - av.charHeight / 2,\r
- y + 8\r
- }, 3);\r
-\r
- }\r
- }\r
-\r
- if (reveal != null && reveal[0] > startx && reveal[0] < endx)\r
- {\r
- gg.drawString("Reveal Columns", reveal[0] * av.charWidth, 0);\r
- }\r
- }\r
-\r
-\r
- }\r
-}\r
+/*
+ * 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.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+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 java.beans.PropertyChangeEvent;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+/**
+ * The panel containing the sequence ruler (when not in wrapped mode), and
+ * supports a range of mouse operations to select, hide or reveal columns.
+ */
+public class ScalePanel extends JPanel
+ implements MouseMotionListener, MouseListener, ViewportListenerI
+{
+ protected int offy = 4;
+
+ public int width;
+
+ protected AlignViewport av;
+
+ AlignmentPanel ap;
+
+ boolean stretchingGroup = false;
+
+ /*
+ * min, max hold the extent of a mouse drag action
+ */
+ int min;
+
+ int max;
+
+ boolean mouseDragging = false;
+
+ /*
+ * holds a hidden column range when the mouse is over an adjacent column
+ */
+ int[] reveal;
+
+ /**
+ * Constructor
+ *
+ * @param av
+ * @param ap
+ */
+ public ScalePanel(AlignViewport av, AlignmentPanel ap)
+ {
+ this.av = av;
+ this.ap = ap;
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
+ final int res;
+
+ if (av.hasHiddenColumns())
+ {
+ x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
+ }
+
+ if (x >= av.getAlignment().getWidth())
+ {
+ res = av.getAlignment().getWidth() - 1;
+ }
+ else
+ {
+ res = x;
+ }
+
+ min = res;
+ max = res;
+
+ if (evt.isPopupTrigger()) // Mac: mousePressed
+ {
+ rightMouseButtonPressed(evt, res);
+ }
+ else if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+ {
+ /*
+ * defer right-mouse click handling to mouse up on Windows
+ * (where isPopupTrigger() will answer true)
+ * but accept Cmd-click on Mac which passes isRightMouseButton
+ */
+ return;
+ }
+ else
+ {
+ leftMouseButtonPressed(evt, res);
+ }
+ }
+
+ /**
+ * Handles right mouse button press. If pressed in a selected column, opens
+ * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
+ * opens context menu for 'Reveal / Reveal All'. Else does nothing.
+ *
+ * @param evt
+ * @param res
+ */
+ protected void rightMouseButtonPressed(MouseEvent evt, final int res)
+ {
+ JPopupMenu pop = new JPopupMenu();
+ if (reveal != null)
+ {
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.reveal"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.showColumn(reveal[0]);
+ reveal = null;
+ ap.paintAlignment(true, true);
+ av.sendSelection();
+ }
+ });
+ pop.add(item);
+
+ if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
+ {
+ item = new JMenuItem(MessageManager.getString("action.reveal_all"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.showAllHiddenColumns();
+ reveal = null;
+ ap.paintAlignment(true, true);
+ av.sendSelection();
+ }
+ });
+ 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()
+ {
+ @Override
+ 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, true);
+ av.sendSelection();
+ }
+ });
+ pop.add(item);
+ pop.show(this, evt.getX(), evt.getY());
+ }
+ }
+
+ /**
+ * Handles left mouse button press
+ *
+ * @param evt
+ * @param res
+ */
+ protected void leftMouseButtonPressed(MouseEvent evt, final int res)
+ {
+ /*
+ * Ctrl-click/Cmd-click adds to the selection
+ * Shift-click extends the selection
+ */
+ // TODO Problem: right-click on Windows not reported until mouseReleased?!?
+ if (!Platform.isControlDown(evt) && !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, false);
+ av.sendSelection();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+
+ int res = (evt.getX() / av.getCharWidth())
+ + av.getRanges().getStartRes();
+
+ if (av.hasHiddenColumns())
+ {
+ res = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(res);
+ }
+
+ if (res >= av.getAlignment().getWidth())
+ {
+ res = av.getAlignment().getWidth() - 1;
+ }
+
+ if (!stretchingGroup)
+ {
+ if (evt.isPopupTrigger()) // Windows: mouseReleased
+ {
+ rightMouseButtonPressed(evt, res);
+ }
+ else
+ {
+ ap.paintAlignment(false, 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, false);
+ av.sendSelection();
+ }
+
+ /**
+ * Action on dragging the mouse in the scale panel is to expand or shrink the
+ * selection group range (including any hidden columns that it spans)
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ mouseDragging = true;
+ ColumnSelection cs = av.getColumnSelection();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
+ int res = (evt.getX() / av.getCharWidth())
+ + av.getRanges().getStartRes();
+ res = Math.max(0, res);
+ res = hidden.visibleToAbsoluteColumn(res);
+ res = Math.min(res, av.getAlignment().getWidth() - 1);
+ min = Math.min(res, min);
+ max = Math.max(res, max);
+
+ SequenceGroup sg = av.getSelectionGroup();
+ if (sg != null)
+ {
+ stretchingGroup = true;
+ cs.stretchGroup(res, sg, min, max);
+ ap.paintAlignment(false, false);
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (mouseDragging)
+ {
+ ap.getSeqPanel().scrollCanvas(null);
+ }
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ if (mouseDragging)
+ {
+ ap.getSeqPanel().scrollCanvas(evt);
+ }
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ /**
+ * Creates a tooltip when the mouse is over a hidden columns marker
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ this.setToolTipText(null);
+ reveal = null;
+ if (!av.hasHiddenColumns())
+ {
+ return;
+ }
+
+ int res = (evt.getX() / av.getCharWidth())
+ + av.getRanges().getStartRes();
+
+ reveal = av.getAlignment().getHiddenColumns()
+ .getRegionWithEdgeAtRes(res);
+
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
+
+ ToolTipManager.sharedInstance().registerComponent(this);
+ this.setToolTipText(
+ MessageManager.getString("label.reveal_hidden_columns"));
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+
+ /*
+ * shouldn't get called in wrapped mode as the scale above is
+ * drawn instead by SeqCanvas.drawNorthScale
+ */
+ if (!av.getWrapAlignment())
+ {
+ drawScale(g, av.getRanges().getStartRes(), av.getRanges().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();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ int avCharWidth = av.getCharWidth();
+ int avCharHeight = av.getCharHeight();
+
+ if (cs != null)
+ {
+ gg.setColor(new Color(220, 0, 0));
+
+ for (int sel : cs.getSelected())
+ {
+ // TODO: JAL-2001 - provide a fast method to list visible selected in a
+ // given range
+
+ if (av.hasHiddenColumns())
+ {
+ if (hidden.isVisible(sel))
+ {
+ sel = hidden.absoluteToVisibleColumn(sel);
+ }
+ else
+ {
+ continue;
+ }
+ }
+
+ if ((sel >= startx) && (sel <= endx))
+ {
+ gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
+ getHeight());
+ }
+ }
+ }
+
+ int widthx = 1 + endx - startx;
+
+ FontMetrics fm = gg.getFontMetrics(av.getFont());
+ int y = avCharHeight;
+ int yOf = fm.getDescent();
+ y -= yOf;
+ if (av.hasHiddenColumns())
+ {
+ // draw any hidden column markers
+ gg.setColor(Color.blue);
+ int res;
+
+ if (av.getShowHiddenMarkers())
+ {
+ Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+ startx + widthx + 1);
+ while (it.hasNext())
+ {
+ res = it.next() - startx;
+
+ gg.fillPolygon(
+ new int[]
+ { -1 + res * avCharWidth - avCharHeight / 4,
+ -1 + res * avCharWidth + avCharHeight / 4,
+ -1 + res * avCharWidth }, new int[]
+ { y, y, y + 2 * yOf }, 3);
+ }
+ }
+ }
+ // Draw the scale numbers
+ gg.setColor(Color.black);
+
+ int maxX = 0;
+ List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+ endx);
+
+ for (ScaleMark mark : marks)
+ {
+ boolean major = mark.major;
+ int mpos = mark.column; // (i - startx - 1)
+ String mstring = mark.text;
+ if (mstring != null)
+ {
+ if (mpos * avCharWidth > maxX)
+ {
+ gg.drawString(mstring, mpos * avCharWidth, y);
+ maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
+ }
+ }
+ if (major)
+ {
+ gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+ (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+ }
+ else
+ {
+ gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+ (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+ }
+ }
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // Respond to viewport change events (e.g. alignment panel was scrolled)
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
+ || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+ || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ // scroll event, repaint panel
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
+ }
+ }
+
+}